1887

Abstract

A bacterial strain, designated YZJH907-2, was isolated from the stem of , collected from the southern edge of the Gurbantunggut desert, Xinjiang, PR China. Cells of strain YZJH907-2 were Gram-stain-positive, aerobic and rod-shaped. They formed white or colourless circular colonies with smooth convex surfaces. Strain YZJH907-2 grew at 4–50 °C (optimum, 28–30 °C), pH 7.0–10.0 (optimum, pH 8.0–9.0) and with 0–10 % (w/v) NaCl (optimum, 3–7 %). The genomic DNA G+C content of strain YZJH907-2 was 38.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that the strain was most closely related to DSM 485 (97.37 %), B16-24 (96.87 %) and LBB3 (96.71 %). Average nucleotide identity values between YZJH907-2 and DSM 485and LBB3 were 69.2 and 69.0 %, respectively. Digital DNA–DNA hybridization values of YZJH907-2 with DSM 485 and LBB3 were 19.6 and 20.4 %, respectively. The cell wall of strain YZJH907-2 contained -diaminopimelic acid, and the major and secondary isoprenoid quinones were MK-7 and MK-5, respectively. Results of fatty acids showed that anteiso-C, iso-C and C were the predominant cellular fatty acids. Two-dimensional thin-layer chromatography analysis indicated that the polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and two unidentified glycolipids. Based on the genomic, phylogenetic and phenotypic analyses, strain YZJH907-2 represented a novel species of the genus , and thus the name sp. nov. is proposed. The type strain is YZJH907-2 (=CGMCC 1.18763=KCTC 43335).

Funding
This study was supported by the:
  • open subject of the Key Laboratory of the Autonomous Region (Award 02017D0408)
    • Principle Award Recipient: Deng-DiAn
  • Scientific projects of colleges and universities in Xinjiang Autonomous Region (Award XJEDU2018I016)
    • Principle Award Recipient: Deng-DiAn
  • National Natural Science Foundation of China (Award 32061143043)
    • Principle Award Recipient: Wen-JunLi
  • National Natural Science Foundation of China (Award 31570109)
    • Principle Award Recipient: Deng-DiAn
  • National key R & D program young scientist project (Award 2021YFD1500300)
    • Principle Award Recipient: ShuangWang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005362
2022-05-09
2022-05-18
Loading full text...

Full text loading...

References

  1. Cohn F. Untersuchungen über bakterien. Beitr Biol Pflanz 1872; 1:127–224
    [Google Scholar]
  2. Shin B, Park C, Lee BH, Lee KE, Park W. Bacillus miscanthi sp. nov., a alkaliphilic bacterium from the rhizosphere of Miscanthus sacchariflorus. Int J Syst Evol Microbiol 2020; 70:1843–1849 [View Article] [PubMed]
    [Google Scholar]
  3. Kämpfer P. Limits and possibilities of total fatty acid analysis for classification and identification of Bacillus species. Syst Appl Microbiol 1994; 17:86–98 [View Article]
    [Google Scholar]
  4. Priest FG, Goodfellow M, Todd C. A numerical classification of the genus Bacillus. J Gen Microbiol 1988; 134:1847–1882 [View Article] [PubMed]
    [Google Scholar]
  5. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  6. Fu K, Chang Z, He S. Delectis Florae Reipublicae Popularis Sinicae Agendae Academiae Sinicae Edita Beijing: Science Press; 1979
    [Google Scholar]
  7. Commissione Redactorum Florae Xinjiangensis Flora Xinjiangensis Xinjiang Science & Technology & Hygiene Publishing House; 1994
    [Google Scholar]
  8. Zhu Z-N, Li Y-R, Li Y-Q, Xiao M, Han M-X et al. Microbacterium suaedae sp. nov., isolated from Suaeda aralocaspica. Int J Syst Evol Microbiol 2019; 69:411–416 [View Article] [PubMed]
    [Google Scholar]
  9. Liu D-F, Chen S-Q, Wang H-F, Xie Y-G, Gao R et al. Hoyosella suaedae sp. nov., a novel bacterium isolated from rhizosphere soil of Suaeda aralocaspica (Bunge) Freitag & Schütze. Int J Syst Evol Microbiol 2021; 71:11 [View Article] [PubMed]
    [Google Scholar]
  10. Lu W-N, Xu Y-Z, Xie Y-G, Gao R, Song J-Q et al. Ruania rhizosphaerae sp. nov., a novel actinobacterium isolated from rhizosphere of Suaeda aralocaspica. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  11. Ma Q, Lei R-F, Li Y-Q, Abudourousuli D, Rouzi Z et al. Sanguibacter suaedae sp. nov., isolated from the root of Suaeda aralocaspica in north-west PR China. Int J Syst Evol Microbiol 2021; 71:11 [View Article]
    [Google Scholar]
  12. Yan Z-F, Lin P, Won K-H, Yang J-E, Li C-T et al. Microbacterium hibisci sp. nov., isolated from rhizosphere of mugunghwa (Hibiscus syriacus L.). Int J Syst Evol Microbiol 2017; 67:3564–3569 [View Article] [PubMed]
    [Google Scholar]
  13. Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  14. Tang S-K, Li W-J, Dong W, Zhang Y-G, Xu L-H et al. Studies of the biological characteristics of some halophilic and halotolerant actinomycetes isolated from saline and alkaline soils. Actinomycetologica 2003; 17:6–10 [View Article]
    [Google Scholar]
  15. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
    [Google Scholar]
  16. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article] [PubMed]
    [Google Scholar]
  17. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
    [Google Scholar]
  18. Komagata K, Suzuki K-I. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  19. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 2006; 5:2359–2367 [View Article]
    [Google Scholar]
  20. Tang S-K, Wang Y, Lou K, Mao P-H, Xu L-H et al. Kocuria halotolerans sp. nov., an actinobacterium isolated from a saline soil in China. Int J Syst Evol Microbiol 2009; 59:1316–1320 [View Article] [PubMed]
    [Google Scholar]
  21. 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]
  22. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  23. 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]
  24. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [Google Scholar]
  25. Liu B, Liu G-H, Wang X-Y, Wang J-P, Chen Z et al. Bacillus urbisdiaboli sp. nov., isolated from soil sampled in Xinjiang. Int J Syst Evol Microbiol 2019; 69:1591–1596 [View Article] [PubMed]
    [Google Scholar]
  26. Mo K, Huang H, Bao S, Hu Y. Bacillus caeni sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2020; 70:1503–1507 [View Article] [PubMed]
    [Google Scholar]
  27. 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]
  28. 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]
  29. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  30. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  31. 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]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  33. Fitch WM. Toward Defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  34. 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]
  35. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  36. Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 2016; 32:3047–3048 [View Article] [PubMed]
    [Google Scholar]
  37. 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]
  38. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  39. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
    [Google Scholar]
  40. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  41. 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]
  42. 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]
  43. 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]
  44. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
    [Google Scholar]
  45. 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]
  46. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
    [Google Scholar]
  47. Aizawa T, Urai M, Iwabuchi N, Nakajima M, Sunairi M. Bacillus trypoxylicola sp. nov., xylanase-producing alkaliphilic bacteria isolated from the guts of Japanese horned beetle larvae (Trypoxylus dichotomus septentrionalis). Int J Syst Evol Microbiol 2010; 60:61–66 [View Article] [PubMed]
    [Google Scholar]
  48. Vedder A. Bacillus alcalophilus n. sp. Antonie van Leeuwenhoek 1934; 1:141–147 [View Article]
    [Google Scholar]
  49. Borsodi AK, Tóth E, Aszalós JM, Bárány Á, Schumann P et al. Bacillus kiskunsagensis sp. nov., a novel alkaliphilic and moderately halophilic bacterium isolated from soda soil. Int J Syst Evol Microbiol 2017; 67:3490–3495 [View Article] [PubMed]
    [Google Scholar]
  50. Vargas VA, Delgado OD, Hatti-Kaul R, Mattiasson B. Bacillus bogoriensis sp. nov., a novel alkaliphilic, halotolerant bacterium isolated from a Kenyan soda lake. Int J Syst Evol Microbiol 2005; 55:899–902 [View Article] [PubMed]
    [Google Scholar]
  51. Hayat S, Hayat Q, Alyemeni MN, Wani AS, Pichtel J et al. Role of proline under changing environments: a review. Plant Signal Behav 2012; 7:1456–1466 [View Article] [PubMed]
    [Google Scholar]
  52. Liu Y, Qu J, Shi Z, Zhang P, Ren M. Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum. BMC Genomics 2021; 22:821 [View Article] [PubMed]
    [Google Scholar]
  53. Ofer N, Wishkautzan M, Meijler M, Wang Y, Speer A et al. Ectoine biosynthesis in Mycobacterium smegmatis. Appl Environ Microbiol 2012; 78:7483–7486 [View Article] [PubMed]
    [Google Scholar]
  54. Wolfe AJ. Glycolysis for microbiome generation. Microbiol Spectr 2015; 3: [View Article] [PubMed]
    [Google Scholar]
  55. Hussa EA, Goodrich-Blair H. It takes a village: ecological and fitness impacts of multipartite mutualism. Annu Rev Microbiol 2013; 67:161–178 [View Article] [PubMed]
    [Google Scholar]
  56. Ancheeva E, Daletos G, Proksch P. Bioactive secondary metabolites from endophytic fungi. Curr Med Chem 2020; 27:1836–1854 [View Article] [PubMed]
    [Google Scholar]
  57. Souza R de, Ambrosini A, Passaglia LMP. Plant growth-promoting bacteria as inoculants in agricultural soils. Genet Mol Biol 2015; 38:401–419 [View Article] [PubMed]
    [Google Scholar]
  58. Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S et al. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 2015; 79:293–320 [View Article] [PubMed]
    [Google Scholar]
  59. Havaux M. Carotenoid oxidation products as stress signals in plants. Plant J 2014; 79:597–606 [View Article] [PubMed]
    [Google Scholar]
  60. Hurley TR, Smitka TA, Wilton JH, Bunge RH, Hokanson GC et al. PD 113,618 and PD 118,309, new pactamycin analogs. J Antibiot 1986; 39:1086–1091 [View Article] [PubMed]
    [Google Scholar]
  61. Manck LE, Park J, Tully BJ, Poire AM, Bundy RM et al. Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean. ISME J 2022; 16:358–369 [View Article] [PubMed]
    [Google Scholar]
  62. Zhu S, Hegemann JD, Fage CD, Zimmermann M, Xie X et al. Insights into the unique phosphorylation of the lasso peptide paeninodin. J Biol Chem 2016; 291:13662–13678 [View Article] [PubMed]
    [Google Scholar]
  63. Tran PN, Tan NEH, Lee YP, Gan HM, Polter SJ et al. Whole-genome sequence and classification of 11 endophytic bacteria from poison ivy (Toxicodendron radicans). Genome Announc 2015; 3:e01319-15 [View Article] [PubMed]
    [Google Scholar]
  64. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005362
Loading
/content/journal/ijsem/10.1099/ijsem.0.005362
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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