1887

Abstract

We carried out a polyphasic taxonomic study on a new halophilic strain designated 3(2), isolated from Meighan wetland, Iran. Cells of the novel strain were Gram-stain-negative, non-hemolytic, catalase- and oxidase-positive, rod-shaped, non-endospore-forming and motile. Cell growth occurred at 3–15 % NaCl (w/v; optimum, 5 %), pH 7.0–9.0 (optimum, pH 7.5–8.0) and 15–35 °C (optimum, 30 °C). 16S rRNA gene sequence comparisons confirmed the affiliation of strain 3(2) to the class and the genus with highest similarity to YCSA28 (98.4 %) and Al12 (97.9 %). Experimental and DNA–DNA hybridization values were 42.7 and 35.1% with IBRC-M 10931 and 48 and 35.2% with IBRC-M 10566, respectively, and indicated that they are different members of the same genus. The genome of the type strain was characterized by a size of 3.83 Mbp with 63 scaffolds and a G+C content of 64.8 mol%. Moreover, the average nucleotide identity values against Al12 and YCSA28 were 88.8 and 88.5 %, respectively. The predominant respiratory quinone was Q-9 (92 %) with Q-8 (8 %) as a minor component. Major fatty acids were C cyclo, C ω8, C ω7 and/or iso-C2-OH, C 3-OH and C ω7. The polar lipid profile of the strain contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoaminoglycolipid and four unidentified phospholipids. According to our results, strain 3(2) could be classified as a novel species in the genus for which the name sp. nov. is proposed. The type strain is 3(2) (=IBRC M 10929=LMG 29450=CIP 111708).

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2020-10-14
2024-11-07
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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
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  3. 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]
  4. 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]
  5. Franzmann PD, Burton HR, Mcmeekin TA. Halomonas subglaciescola, a new species of halotolerant bacteria isolated from Antarctica. Int J Syst Bacteriol 1987; 37:27–34
    [Google Scholar]
  6. Krieg N J, Padgett P. Phenotypic and physiological characterization methods. In Rainey F, Oren A. (editors) Methods in microbiology, Taxonomy of prokaryotes 38 Academic press. Elsevier; 2011 pp 15–61
    [Google Scholar]
  7. Qu L, Lai Q, Zhu F, Hong X, Zhang J et al. Halomonas daqiaonensis sp. nov., a moderately halophilic, denitrifying bacterium isolated from a littoral saltern. Int J Syst Evol Microbiol 2011; 61:1612–1616 [View Article][PubMed]
    [Google Scholar]
  8. 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]
  9. Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ et al. Preparation of chromosomal, plasmid and phage DNA. In Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ et al. (editors) Genetic Manipulation of Streptomyces: a Laboratory Manual Norwich: F. Crowe and Sons; 1985 pp 79–80
    [Google Scholar]
  10. Moshtaghi Nikou M, Ramezani M, Ali Amoozegar M, Rasouli M, Abolhassan Shahzadeh Fazeli S et al. Salininema proteolyticum gen. nov., sp. nov., a halophilic rare actinomycete isolated from wetland soil, and emended description of the family Glycomycetaceae . Int J Syst Evol Microbiol 2015; 65:3727–3733 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  14. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
    [Google Scholar]
  15. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol 2020
    [Google Scholar]
  16. Cashion P, Holder-Franklin MA, McCully J, Franklin M. A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 1977; 81:461–466 [View Article][PubMed]
    [Google Scholar]
  17. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article][PubMed]
    [Google Scholar]
  18. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4:184–192 [View Article][PubMed]
    [Google Scholar]
  19. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  20. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  23. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article][PubMed]
    [Google Scholar]
  24. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article][PubMed]
    [Google Scholar]
  25. 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][PubMed]
    [Google Scholar]
  26. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of isoprenoid quinones and polar-lipids. J Microbiol Methods 1984; 2:233–241
    [Google Scholar]
  27. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
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