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Volume 72, Issue 12

sp. nov., isolated from saline-alkali soil No Access

Abstract

A Gram-stain-negative, aerobic and rod-shaped bacterium, strain Y2R2, was isolated from a saline–alkali soil sample collected from Binhai New Area, Tianjin, PR China. Growth of strain Y2R2 was observed at 10–45 °C (optimum, 30 °C), at pH 6.0–11.0 (optimum, pH 9.0) and in the presence of 0–15 % (w/v) NaCl (optimum, 9.0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Y2R2 was affiliated with the genus and showed the highest similarity to BJGMM-B45 (99.0%) and DSM 4740 (98.4%). The digital DNA–DNA hybridization and average nucleotide identity values of 21.0–22.8 % and 73.3–75.7 % with the closely related species BJGMM-B45, DSM 4740, AL12, N12 and SYSU ZJ2214 were lower than the threshold recommended for species discrimination.

The major respiratory quinone of strain Y2R2 was Q-9 and the major cellular fatty acids consisted of C, C cyclo ω8 and summed feature 8 (C ω7 and/or C ω6). The DNA G+C content of strain Y2R2 was 57.0 mol%. On the basis of this polyphasic taxonomic study, strain Y2R2 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Y2R2 (=CGMCC 1.16974=KCTC 72578).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Halomonas binhaiensis , Proteobacteria and taxonomy
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31571790)
    • Principle Award Recipient: XiaoyanLi
  • Tianjin Agricultural University Graduate Scientific Research and Innovation Project (Award 2021XY029)
    • Principle Award Recipient: HegangLu
© 2022 The Authors
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2022-12-20
2024-05-20
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References

  1. 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]
  2. Dou G, He W, Liu H, Ma Y. Halomonas heilongjiangensis sp. nov., a novel moderately halophilic bacterium isolated from saline and alkaline soil. Antonie van Leeuwenhoek 2015; 108:403–413 [View Article] [PubMed]
     [Google Scholar]
  3. Carlson RP, Oshota O, Shipman M, Caserta JA, Hu P et al. Integrated molecular, physiological and in silico characterization of two Halomonas isolates from industrial brine. Extremophiles 2016; 20:261–274 [View Article] [PubMed]
     [Google Scholar]
  4. Soto-Ramírez N, Sánchez-Porro C, Rosas S, González W, Quiñones M et al. Halomonas avicenniae sp. nov., isolated from the salty leaves of the black mangrove Avicennia germinans in Puerto Rico. Int J Syst Evol Microbiol 2007; 57:900–905 [View Article] [PubMed]
     [Google Scholar]
  5. Xu L, Xu X-W, Meng F-X, Huo Y-Y, Oren A et al. Halomonas zincidurans sp. nov., a heavy-metal-tolerant bacterium isolated from the deep-sea environment. Int J Syst Evol Microbiol 2013; 63:4230–4236 [View Article] [PubMed]
     [Google Scholar]
  6. 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]
  7. Mormile MR, Romine MF, Garcia MT, Ventosa A, Bailey TJ et al. Halomonas campisalis sp. nov., a denitrifying, moderately haloalkaliphilic bacterium. Syst Appl Microbiol 1999; 22:551–558 [View Article] [PubMed]
     [Google Scholar]
  8. García MT, Mellado E, Ostos JC, Ventosa A. Halomonas organivorans sp. nov., a moderate halophile able to degrade aromatic compounds. Int J Syst Evol Microbiol 2004; 54:1723–1728 [View Article] [PubMed]
     [Google Scholar]
  9. Amjres H, Béjar V, Quesada E, Abrini J, Llamas I. Halomonas rifensis sp. nov., an exopolysaccharide-producing, halophilic bacterium isolated from a solar saltern. Int J Syst Evol Microbiol 2011; 61:2600–2605 [View Article] [PubMed]
     [Google Scholar]
  10. Llamas I, Béjar V, Martínez-Checa F, Martínez-Cánovas MJ, Molina I et al. Halomonas stenophila sp. nov., a halophilic bacterium that produces sulphate exopolysaccharides with biological activity. Int J Syst Evol Microbiol 2011; 61:2508–2514 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Oren A, Ventosa A. International Committee on Systematics of Prokaryotes subcommittee on the taxonomy of Halobacteriaceae and subcommittee on the taxonomy of Halomonadaceae. Minutes of the joint open meeting, 23 May 2016, San Juan, Puerto Rico. Int J Syst Evol Microbiol 2016; 66:4291–4295 [View Article]
     [Google Scholar]
  13. Ren M, Li X, Zhang Y, Jin Y, Li S et al. Massilia armeniaca sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2018; 68:2319–2324 [View Article] [PubMed]
     [Google Scholar]
  14. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
     [Google Scholar]
  15. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
     [Google Scholar]
  16. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  17. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  18. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
     [Google Scholar]
  21. Urbanczyk Y, Ogura Y, Hayashi T, Urbanczyk H. Genomic evidence that Vibrio inhibens is a heterotypic synonym of Vibrio jasicida. Int J Syst Evol Microbiol 2016; 66:3214–3218 [View Article] [PubMed]
     [Google Scholar]
  22. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  23. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article] [PubMed]
     [Google Scholar]
  24. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
     [Google Scholar]
  25. de la Haba RR, Márquez MC, Papke RT, Ventosa A. Multilocus sequence analysis of the family Halomonadaceae. Int J Syst Evol Microbiol 2012; 62:520–538 [View Article] [PubMed]
     [Google Scholar]
  26. Kämpfer P, Rekha PD, Busse H-J, 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]
  27. Yan F, Fang J, Cao J, Wei Y, Liu R et al. Halomonas piezotolerans sp. nov., a multiple-stress-tolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench. Int J Syst Evol Microbiol 2020; 70:2560–2568 [View Article] [PubMed]
     [Google Scholar]
  28. 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; 10:1207 [View Article]
     [Google Scholar]
  29. Mata JA, Martínez-Cánovas J, Quesada E, Béjar V. A detailed phenotypic characterisation of the type strains of Halomonas species. Syst Appl Microbiol 2002; 25:360–375 [View Article]
     [Google Scholar]
  30. Huang H-D, Wang W, Ma T, Li G-Q, Liang F-L et al. Sphingomonas sanxanigenens sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:719–723 [View Article] [PubMed]
     [Google Scholar]
  31. Pandiyan K, Kushwaha P, Bagul SY, Chakdar H, Madhaiyan M et al. Halomonas icarae sp. nov., a moderately halophilic bacterium isolated from beach soil in India. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  32. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  33. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids MIDI; 1990
     [Google Scholar]
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Halomonas binhaiensis sp. nov., isolated from saline-alkali soil
Int J Syst Evol Microbiol 72, 005652 (2023); https://doi.org/10.1099/ijsem.0.005652
/content/journal/ijsem/10.1099/ijsem.0.005652
/content/journal/ijsem/10.1099/ijsem.0.005652
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