sp. nov., a moderately halophilic bacterium isolated from wetsalted hides Free

Abstract

A Gram-stain-negative, moderately halophilic strain, designated strain L5, was isolated from wetsalted hides collected from Chengdu, south-west PR China. The cells were motile, facultative aerobic, short rod-shaped and non-endospore-forming. Growth of strain L5 occurred at pH 6–10 (optimum, pH 8), 10–45 °C (optimum, 30 °C) and in the presence of 1–17 % (w/v) NaCl (optimum, 10 %). Results of phylogenetic analyses based on 16S rRNA, and gene sequences and its genome revealed that strain L5 belonged to the genus . Strain L5 was found to be most closely related to the type strains of , , , and (98.8, 98.6, 98.3, 97.9 and 97.4 % 16S rRNA gene sequence similarity, respectively). The draft genome was approximately 4.2 Mb in size with a G+C content of 63.5 mol%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization values among strain L5 and the selected species were 83.3–88.9 % (ANIm), 71.1–87.3 % (ANIb) and 20.2–34.6 %, which are below the recommended cutoff values. Major fatty acids were C, C 7, C 7 and C cyclo 8 and the predominant ubiquinone was Q-9, with minor ubiquinone Q-8 also present. The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, four unidentified aminophospholipids and three unidentified phospholipids. Based on the mentioned polyphasic taxonomic evidence, strain L5 represents a novel species within the genus , for which sp. nov. is proposed. The type strain is L5 (=CGMCC 1.17335=KCTC 72573).

Funding
This study was supported by the:
  • the National Key Research and Development Program of (Award 2017YFB0308401)
    • Principle Award Recipient: Yongqiang Tian
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004426
2020-09-04
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/10/5417.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004426&mimeType=html&fmt=ahah

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. Dobson SJ, Franzmann PD. Unification of the genera Deleya (Baumann et al. 1983), Halomonas (Vreeland et al. 1980), and Halovibrio (Fendrich 1988) and the species Paracoccus halodenitrificans (Robinson and gibbons 1952) into a single genus, Halomonas, and placement of the genus Zymobacter in the family Halomonadaceae . Int J Syst Bacteriol 1996; 46:550–558 [View Article]
    [Google Scholar]
  4. 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]
  5. Lu H, Xing P, Zhai L, Li H, Wu Q. Halomonas montanilacus sp. nov., isolated from hypersaline Lake Pengyanco on the Tibetan Plateau. Int J Syst Evol Microbiol 2020; 70:2859–2866 [View Article][PubMed]
    [Google Scholar]
  6. Ming H, Ji W-L, Li M, Zhao Z-L, Cheng L-J et al. Halomonas lactosivorans sp. nov., isolated from salt-lake sediment. Int J Syst Evol Microbiol 2020; 70:3504–3512 [View Article][PubMed]
    [Google Scholar]
  7. Yoon JH, Choi SH, Lee KC, Kho YH, Kang KH et al. Halomonas marisflavae sp. nov., a halophilic bacterium isolated from the Yellow Sea in Korea. Int J Syst Evol Microbiol 2001; 51:1171–1177 [View Article][PubMed]
    [Google Scholar]
  8. Kaye JZ, Márquez MC, Ventosa A, Baross JA. Halomonas neptunia sp. nov., Halomonas sulfidaeris sp. nov., Halomonas axialensis sp. nov. and Halomonas hydrothermalis sp. nov.: halophilic bacteria isolated from deep-sea hydrothermal-vent environments. Int J Syst Evol Microbiol 2004; 54:499–511 [View Article][PubMed]
    [Google Scholar]
  9. Jiang J, Pan Y, Hu S, Zhang X, Hu B et al. Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils. Int J Syst Evol Microbiol 2014; 64:1662–1669 [View Article][PubMed]
    [Google Scholar]
  10. Li H-B, Zhang L-P, Chen S-F. Halomonas korlensis sp. nov., a moderately halophilic, denitrifying bacterium isolated from saline and alkaline soil. Int J Syst Evol Microbiol 2008; 58:2582–2588 [View Article][PubMed]
    [Google Scholar]
  11. Navarro-Torre S, Carro L, Rodríguez-Llorente ID, Pajuelo E, Caviedes et al. Halomonas radicis sp. nov., isolated from Arthrocnemum macrostachyum growing in the Odiel marshes (Spain) and emended descriptions of Halomonas xinjiangensis and Halomonas zincidurans . Int J Syst Evol Microbiol 2020; 70:220–227 [View Article][PubMed]
    [Google Scholar]
  12. Chen Y-G, Zhang Y-Q, Huang H-Y, Klenk H-P, Tang S-K et al. Halomonas zhanjiangensis sp. nov., a halophilic bacterium isolated from a sea urchin. Int J Syst Evol Microbiol 2009; 59:2888–2893 [View Article][PubMed]
    [Google Scholar]
  13. Cabrera A, Aguilera M, Fuentes S, Incerti C, Russell NJ et al. Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de GATA, Almeria, southern Spain. Int J Syst Evol Microbiol 2007; 57:376–380 [View Article][PubMed]
    [Google Scholar]
  14. Lee J-C, Jeon CO, Lim J-M, Lee S-M, Lee J-M et al. Halomonas taeanensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea. Int J Syst Evol Microbiol 2005; 55:2027–2032 [View Article][PubMed]
    [Google Scholar]
  15. Jiang W, Li C, Xu B, Dong X, Ma N et al. Halomonas shantousis sp. nov., a novel biogenic amines degrading bacterium isolated from Chinese fermented fish sauce. Antonie van Leeuwenhoek 2014; 106:1073–1080 [View Article][PubMed]
    [Google Scholar]
  16. Jeong SH, Lee JH, Jung JY, Lee SH, Park MS et al. Halomonas cibimaris sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Antonie van Leeuwenhoek 2013; 103:503–512 [View Article][PubMed]
    [Google Scholar]
  17. Arahal DR, Ventosa A. The Family Halomonadaceae . In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E. (editors) The Prokaryotes: Volume 6: Proteobacteria: Gamma Subclass New York, NY: Springer New York; 2006 pp 811–835
    [Google Scholar]
  18. Gan L, Long X, Zhang H, Hou Y, Tian J et al. Halomonas saliphila sp. nov., a moderately halophilic bacterium isolated from a saline soil. Int J Syst Evol Microbiol 2018; 68:1153–1159 [View Article][PubMed]
    [Google Scholar]
  19. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [View Article][PubMed]
    [Google Scholar]
  20. Li X, Wang Z, Lu F, Zhang H, Tian J et al. Actinocorallia populi sp. nov., an endophytic actinomycete isolated from a root of Populus adenopoda (Maxim.). Int J Syst Evol Microbiol 2018; 68:2325–2330 [View Article][PubMed]
    [Google Scholar]
  21. 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]
  22. 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]
  23. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  27. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article][PubMed]
    [Google Scholar]
  28. Lin S-H, Liao Y-C, Shin-Hung L, Yu-Chieh L, Michael W. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One 2013; 8:e60843 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk H-P, 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, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article][PubMed]
    [Google Scholar]
  33. Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 2012; 40:D115–D122 [View Article][PubMed]
    [Google Scholar]
  34. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article][PubMed]
    [Google Scholar]
  35. 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]
  36. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology. Report of the ad hoc committee on the reconciliation of approaches to bacterial systematic. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  37. Li X, Wang Z, Gan L, Tian Y. Draftt genome sequence of Actinocorallia populi A251T, an actinomycetes producing polyketides and nonribosomal polypeptides. 3 Biotech 2020; 10:79 [View Article][PubMed]
    [Google Scholar]
  38. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article][PubMed]
    [Google Scholar]
  39. Ventosa A, Nieto JJ, Oren A. Biology of moderately halophilic aerobic bacteria. Microbiol Mol Biol Rev 1998; 62:504–544 [View Article][PubMed]
    [Google Scholar]
  40. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  41. Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al. Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp 25–29
    [Google Scholar]
  42. Poli A, Nicolaus B, Denizci AA, Yavuzturk B, Kazan D. Halomonas smyrnensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium. Int J Syst Evol Microbiol 2013; 63:10–18 [View Article][PubMed]
    [Google Scholar]
  43. 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]
  44. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic gram-negative rods. Microbiology 1982; 128:1959–1968 [View Article]
    [Google Scholar]
  45. 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]
  46. Quesada E, Ventosa A, Rodriguez-Valera F, Megias L, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic Gram-negative bacteria from hypersaline soils. Microbiology 1983; 129:2649–2657 [View Article]
    [Google Scholar]
  47. Menes RJ, Viera CE, Farías ME, Seufferheld MJ. Halomonas vilamensis sp. nov., isolated from high-altitude Andean lakes. Int J Syst Evol Microbiol 2011; 61:1211–1217 [View Article][PubMed]
    [Google Scholar]
  48. Kushner DJ. Life in high salt and solute concentrations: halophilic bacteria. In Microbial Life in Extreme Environments London Academic Press; 1978 pp 317–368
    [Google Scholar]
  49. Xu LH, Li WJ, Liu ZH, Jiang CL. Actinomycete Systematic—Principle, Methods and Practice Beijing: Science Press; 2007 pp 80–87
    [Google Scholar]
  50. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  51. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematic. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  52. Boltyanskaya YV, Kevbrin VV, Lysenko AM, Kolganova TV, Tourova TP et al. Halomonas mongoliensis sp. nov. and Halomonas kenyensis sp. nov., new haloalkaliphilic denitrifiers capable of N2O reduction, isolated from soda lakes. Microbiology 2007; 76:739–747 [View Article]
    [Google Scholar]
  53. Berendes F, Gottschalk G, Heine-Dobbernack E, Moore ERB, Tindall BJ. Halomonas desiderata sp. nov, a new alkaliphilic, halotolerant and denitrifying bacterium isolated from a municipal sewage works. Syst Appl Microbiol 1996; 19:158–167 [View Article]
    [Google Scholar]
  54. Wu G, Wu X-Q, Wang Y-N, Chi C-Q, Tang Y-Q et al. Halomonas daqingensis sp. nov., a moderately halophilic bacterium isolated from an oilfield soil. Int J Syst Evol Microbiol 2008; 58:2859–2865 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004426
Loading
/content/journal/ijsem/10.1099/ijsem.0.004426
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed