1887

Abstract

A Gram-stain-positive, aerobic, endospore-forming and rod-shaped bacterium (KQ-3), which grew at 10–45 °C (optimum 35 °C), pH 8.0–10.5 (optimum pH 9.0) and in the presence of 0–16 % (w/v) NaCl (optimum 3.0 %), was isolated from a soda lake and identified as representing a novel species using a polyphasic taxonomic approach. Strain KQ-3 was catalase-positive, oxidase-negative and non-motile. Phylogenetic analysis based on 16S rRNA gene sequence affiliated KQ-3 to the genus and showed the highest similarities to M30 (97.90 %), K1-5 (97.84 %) and FJAT-45347 (97.22 %). Digital DNA–DNA hybridization and average nucleotide identity analyses revealed that KQ-3 displayed 21.4 and 72.81% genomic DNA relatedness with the most closely related strain, M30, respectively. KQ-3 contained all of the conserved signature indels that are specific for members of the genus . The DNA G+C content was 45.03 mol%. The cell-wall peptidoglycan contained -diaminopimelic acid and the polar lipids consisted of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid. The predominant menaquinone was MK-7 (100%) and the major fatty acids (>10 %) comprised anteiso-C, iso-C and iso-C. Based on the data from the current polyphasic studies, KQ-3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is KQ-3 (=ACCC 61799=KCTC 33933).

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 41877061)
    • Principle Award Recipient: YananWang
  • Fundamental Research Funds for Central Non-profit Scientific Institution (Award 1610042018005)
    • Principle Award Recipient: HaishengWang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005351
2022-05-03
2024-05-02
Loading full text...

Full text loading...

References

  1. Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753–5798 [View Article] [PubMed]
    [Google Scholar]
  2. Borsodi AK, Márialigeti K, Szabó G, Palatinszky M, Pollák B et al. Bacillus aurantiacus sp. nov., an alkaliphilic and moderately halophilic bacterium isolated from Hungarian soda lakes. Int J Syst Evol Microbiol 2008; 58:845–851 [View Article] [PubMed]
    [Google Scholar]
  3. Menes RJ, Machin EV, Iriarte A, Langleib M. Bacillus natronophilus sp. nov., an alkaliphilic bacterium isolated from a soda lake. Int J Syst Evol Microbiol 2020; 70:562–568 [View Article] [PubMed]
    [Google Scholar]
  4. Liu B, Liu G-H, Wang X-Y, Wang J-P, Zhu Y-J et al. Bacillus populi sp. nov. isolated from Populus euphratica rhizosphere soil of the Taklamakan desert. Int J Syst Evol Microbiol 2018; 68:155–159 [View Article] [PubMed]
    [Google Scholar]
  5. Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Biol 2010; 11:R116 [View Article] [PubMed]
    [Google Scholar]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967 [View Article]
    [Google Scholar]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  12. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  14. Yoon SH, Ha SM, 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] [PubMed]
    [Google Scholar]
  15. 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]
  16. 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]
  17. Banciu HL, Muntyan MS. Adaptive strategies in the double extremophilic prokaryotes inhabiting soda lakes. Curr Opin Microbiol 2015; 25:73–79 [View Article] [PubMed]
    [Google Scholar]
  18. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  19. Dong L, Wang S, Cao H, Zhao B, Zhang X et al. Bacillus lacisalsi sp. nov., a moderately haloalkaliphilic bacterium isolated from a saline-alkaline lake. Antonie van Leeuwenhoek 2020; 113:127–136 [View Article] [PubMed]
    [Google Scholar]
  20. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  21. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Zentralbl Bakteriol Mikrobiol Hyg A 1988; 268:433–434 [View Article]
    [Google Scholar]
  22. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. eds Methods for General and Molecular Microbiology, 3rd edn. Washington, DC: American Society for Microbiology; 2007 pp 330–393
    [Google Scholar]
  23. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
    [Google Scholar]
  24. Kelly KL. Inter-Society Color Council–National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  25. Wang S, Dong L, Zhao B, Zhang X, Xu S et al. Salipaludibacillus keqinensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkaline lake. Antonie van Leeuwenhoek 2019; 112:897–903 [View Article] [PubMed]
    [Google Scholar]
  26. Zhang S, Li Z, Yan Y, Zhang C, Li J et al. Bacillus urumqiensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:2305–2312 [View Article] [PubMed]
    [Google Scholar]
  27. Ohta H, Hattori T. Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium. Antonie van Leeuwenhoek 1983; 49:429–446 [View Article] [PubMed]
    [Google Scholar]
  28. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 6th ed. San Francisco: Benjamin Cummings Pearson Education; 2002
    [Google Scholar]
  29. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for Identification of Medical Bacteria Cambridge: Cambridge University Press; 2003
    [Google Scholar]
  30. Pettersson B, Lembke F, Hammer P, Stackebrandt E, Priest FG. Bacillus sporothermodurans, a new species producing highly heat-resistant endospores. Int J Syst Bacteriol 1996; 46:759–764 [View Article] [PubMed]
    [Google Scholar]
  31. 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]
  32. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  33. 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]
  34. Groth I, Schumann P, Rainey FA, Martin K, Schuetze B et al. Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil. Int J Syst Bacteriol 1997; 47:1129–1133 [View Article]
    [Google Scholar]
  35. 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]
  36. Wang H, Zhang X, Wang S, Zhao B, Lou K et al. Massilia violaceinigra sp. nov., a novel purple-pigmented bacterium isolated from glacier permafrost. Int J Syst Evol Microbiol 2018; 68:2271–2278 [View Article]
    [Google Scholar]
  37. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005351
Loading
/content/journal/ijsem/10.1099/ijsem.0.005351
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error