Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 71, Issue 11

sp. nov., isolated from the root of in north-west PR China Free

Abstract

A bacterial strain, designated YZGR15, was isolated from the root of an annual halophyte , collected from the southern edge of the Gurbantunggut desert, north-west PR China. Cells of the isolate were Gram-stain-positive, facultatively anaerobic, irregular rods. Growth occurred at 4–42 °C (optimum, 30–37 °C), at pH 6.0–9.0 (optimum, pH 7.0–7.5) and in the presence of 0–9 % (w/v) NaCl (optimum, 2–5 %). Phylogenetic analysis using 16S rRNA gene sequences indicated that strain YZGR15 showed the highest sequence similarity to (98.27 %) (98.20 %) and (98.06 %). Results of genome analyses of strain YZGR15 indicated that the genome size was 3.16 Mb, with a genomic DNA G+C content of 71.9 mol%. Average nucleotide identity and digital DNA–DNA hybridization values between strain YZGR15and three type strains were in the range of 76.5–77.8 % and 20.0–22.2 %, respectively. Analysis of the cellular component of strain YZGR15 revealed that the primary fatty acids were anteiso-C, C, C and iso-C and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and two unidentified glycolipids. The cell-wall characteristic amino acids were glutamic acid, alanine and an unknown amino acid. The whole-cell sugars for the strain were mannose, ribose, rhamnose, glucose and an unidentified sugar. The predominant respiratory quinone was MK-9(H). Based on the results of genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain YZGR15 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YZGR15 (=CGMCC 1.18691=KCTC 49659)

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): facultative anaerobe , genome , Gurbantunggut desert , haloalkaline ecosystem , halophyte , Sanguibacter suaedae and Suaeda aralocaspica
Funding
This study was supported by the:
  • 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
© 2021 Sun Yat-Sen University
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005108
2021-11-19
2025-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/11/ijsem005108.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005108&mimeType=html&fmt=ahah

References

  1. Fernández-Garayzábal JF, Dominguez L, Pascual C, Jones D, Collins MD. Phenotypic and phylogenetic characterization of some unknown coryneform bacteria isolated from bovine blood and milk: description of Sanguibacter gen. nov. Lett Appl Microbiol 1995; 20:69–75 [View Article] [PubMed]
     [Google Scholar]
  2. Pikuta EV, Lyu Z, Williams MD, Patel NB, Liu Y. Sanguibacter gelidistatuariae sp. nov., a novel psychrotolerant anaerobe from an ice sculpture in Antarctica, and emendation of descriptions of the family Sanguibacteraceae, the genus Sanguibacter and species S. antarcticus, S. inulinus, S. kedieii, S. marinus, S. soli and S. suarezii. Int J Syst Evol Microbiol 2017; 67:1442–1450 [View Article] [PubMed]
     [Google Scholar]
  3. Hong SG, Lee YK, Yim JH, Chun J, Lee HK. Sanguibacter antarcticus sp. nov., isolated from Antarctic sea sand. Int J Syst Evol Microbiol 2008; 58:50–52 [View Article] [PubMed]
     [Google Scholar]
  4. Pascual C, Collins MD, Grimont PA, Dominguez L, Fernandez-Garayzabal JF. Sanguibacter inulinus sp. nov. Int J Syst Bacteriol 1996; 46:811–813 [View Article] [PubMed]
     [Google Scholar]
  5. Huang Y, Dai X, He L, Wang YN, Wang BJ. Sanguibacter marinus sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2005; 55:1755–1758 [View Article] [PubMed]
     [Google Scholar]
  6. Kim MK, Pulla RK, Kim SY, Yi TH, Soung NK. Sanguibacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2008; 58:538–541 [View Article] [PubMed]
     [Google Scholar]
  7. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article] [PubMed]
     [Google Scholar]
  8. Delectis Florae Reipublicae Popularis Sinicae Agendae Academiae Sinicae Edita Flora reipublicae popularis sinicae Beijing: Science Press; 1979
     [Google Scholar]
  9. Commissione Redactorum Florae Xinjiangensis Flora Xinjiangensis Urumchi: Xinjiang Science & Technology & Hygiene Publishing House; 1994
     [Google Scholar]
  10. Mingma R, Duangmal K, Trakulnaleamsai S, Thamchaipenet A, Matsumoto A. Sphaerisporangium rufum sp. nov., an endophytic actinomycete from roots of Oryza sativa L. Int J Syst Evol Microbiol 2014; 64:1077–1082 [View Article] [PubMed]
     [Google Scholar]
  11. Smibert RM, Krieg NR. Phenotypic characterization. Gerhardt P. eds In Methods for General and Molecular Bacteriology American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  12. Kämpfer P, Irgang R, Poblete-Morales M, Glaeser SP, Cortez-San Martín M. Psychromonas aquatilis sp. nov., isolated from seawater samples obtained in the Chilean Antarctica. Int J Syst Evol Microbiol 2017; 67:1306–1311 [View Article] [PubMed]
     [Google Scholar]
  13. 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]
  14. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. Yoon SH, Ha SM, 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. 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]
  18. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M. 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]
  26. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, 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]
  27. 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]
  28. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST serverServer: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  29. 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:W87W81
     [Google Scholar]
  30. Na S-I, Kim Y-O, Yoon S-H, Ha S-M, Baek I. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
     [Google Scholar]
  31. Lee I, Ouk Kim Y, Park SC, 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]
  32. 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]
  33. 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]
  34. Gouda S, Das G, Sen SK, Shin HS, Patra JK. Endophytes: a treasure house of bioactive compounds of medicinal importance. Front Microbiol 2016; 7:1538 [View Article] [PubMed]
     [Google Scholar]
  35. Souza R, Ambrosini A, Passaglia LM. Plant growth-promoting bacteria as inoculants in agricultural soils. Genet Mol Biol 2015; 38:401–419 [View Article] [PubMed]
     [Google Scholar]
  36. Tran PN, Tan NE, Lee YP, Gan HM, Polter SJ et al. Whole-genome sequence and classification of 11 endophytic bacteria from poGenome Sequence and Classification of 11 Endophytic Bacteria from Poison Ivy (Toxicodendron radicans). Genome Announc 2015; 3:e01319-15 [View Article] [PubMed]
     [Google Scholar]
  37. 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]
  38. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:16
     [Google Scholar]
  39. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  40. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  41. 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]
  42. 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]
  43. Tang SK, Wang Y, Lou K, Mao PH, Xu LH. 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]
  44. 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]
  45. 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]
/content/journal/ijsem/10.1099/ijsem.0.005108
Loading
Sanguibacter suaedae sp. nov., isolated from the root of Suaeda aralocaspica in north-west PR China
Int J Syst Evol Microbiol 71, 005108 (2021); https://doi.org/10.1099/ijsem.0.005108
/content/journal/ijsem/10.1099/ijsem.0.005108
/content/journal/ijsem/10.1099/ijsem.0.005108
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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