1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 11

sp. nov., isolated from rhizosphere soil of banana No Access

Abstract

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated as strain B61, was isolated from rhizosphere soil of banana collected from Dongguan, Guangdong Province, PR China. Growth occurred at 15–40 °C, within a pH range of pH 6.0–9.0. Results of 16S rRNA gene sequence similarity and phylogenetic analyses showed that strain B61 was most closely related to ‘’ KACC 21303 (98.9 %) and DSM 2588 (98.8 %). The genome size was 7.6 Mb with a G+C content of 45.2 mol%. The genome-inferred average nucleotide identity values between strain B61 and two closely related strains were 79.2 and 79.3 %, respectively, with corresponding digital DNA–DNA hybridization values of 22.3 and 22.6 %. The major fatty acids of the novel strain were iso-C, C 5 and iso-C 3-OH and the sole respiratory quinone was menaquinone 7 (MK-7). The polar lipids consisted of phosphatidylethanolamine, five unidentified aminolipids, four unidentified glycolipids and six unidentified lipids. The phenotypic and phylogenetic results clearly supported that strain B61 represents a novel species of the genus , for which the name , sp. nov. is proposed, with the type strain B61 (=GDMCC 1.2608=KCTC 82856).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Chitinophaga , phylogeny , rhizosphere and taxonomy
Funding
This study was supported by the:
  • the Science and Technology Project of Guangdong Province dong Province (Award 2019B030316010)
    • Principle Award Recipient: Xian-JiaoZhang
  • Natural Science Foundation of Tianjin Municipal Science and Technology Commission (Award 32000007)
    • Principle Award Recipient: Xian-JiaoZhang
  • the GDAS’ Project of Science and Technology Development (Award 2021GDASYL-20210103020)
    • Principle Award Recipient: Xian-JiaoZhang
  • the Key Realm R&D Program of Guangdong Province (Award 2018B020205001)
    • Principle Award Recipient: HonghuiZhu
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005118
2021-11-30
2024-05-14
Loading full text...

Full text loading...

References

  1. Sangkhobol V, Skerman VBD. Chitinophaga, a new genus of chitinolytic myxobacteria. Int J Syst Evol Microbiol 1981; 31:285–293
     [Google Scholar]
  2. Zou Y, Zhang X, Song H, Liu Y, Cheng Q. Chitinophaga alhagiae sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia. Int J Syst Evol Microbiol 2019; 69:1179–1184 [View Article] [PubMed]
     [Google Scholar]
  3. Dahal RH, Chaudhary DK, Kim DU, Kim J. Chitinophaga fulva sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2021 [View Article]
     [Google Scholar]
  4. Goh CBS, Wong LW, Parimannan S, Rajandas H, Loke S. Chitinophaga extrema sp. nov., isolated from subsurface soil and leaf litter in a tropical peat swamp forest. Int J Syst Evol Microbiol 2020; 70:6355–6363 [View Article] [PubMed]
     [Google Scholar]
  5. Ping W, Zhang Y, Pang H, Zhang J, Li D. Chitinophaga solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2020; 70:4808–4815 [View Article] [PubMed]
     [Google Scholar]
  6. Chaudhary DK, Kim J. Chitinophaga humicola sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:751–757 [View Article] [PubMed]
     [Google Scholar]
  7. Proença DN, Nobre MF, Morais PV. Chitinophaga costaii sp. nov., an endophyte of Pinus pinaster, and emended description of Chitinophaga niabensis. Int J Syst Evol Microbiol 2014; 64:1237–1243 [View Article] [PubMed]
     [Google Scholar]
  8. Li L, Sun L, Shi N, Liu L, Guo H. Chitinophaga cymbidii sp. nov., isolated from Cymbidium goeringii roots. Int J Syst Evol Microbiol 2013; 63:1800–1804 [View Article] [PubMed]
     [Google Scholar]
  9. Gao S, Zhang WB, Sheng XF, He LY, Huang Z. Chitinophaga longshanensis sp. nov., a mineral-weathering bacterium isolated from weathered rock. Int J Syst Evol Microbiol 2015; 65:418–423 [View Article] [PubMed]
     [Google Scholar]
  10. Tran TLQ, Anani H, Trinh HT, Pham TPT, Dang VK. Chitinophaga vietnamensis sp. nov., a multi-drug resistant bacterium infecting humans. Int J Syst Evol Microbiol 2020; 70:1758–1768 [View Article] [PubMed]
     [Google Scholar]
  11. Jin D, Kong X, Wang J, Sun JJ, Yu XY. Chitinophaga caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2018; 68:2209–2213 [View Article] [PubMed]
     [Google Scholar]
  12. Li N, Chen T, Cheng D, Yu XJ, He J. Chitinophaga sediment sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2017; 67:3485–3489 [View Article] [PubMed]
     [Google Scholar]
  13. Reichenbach H, Dworkin M. The myxobacteria. Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH. eds In The Prokaryotes, 2nd. edn New York: Springer; 1992 pp 3416–3487
     [Google Scholar]
  14. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  15. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y. 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]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. 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]
  20. 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]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  24. Zhang H, Yohe T, Huang L, Entwistle S et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:95–101
     [Google Scholar]
  25. Na SI, Kim YO, Yoon SH, SM H, 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]
  26. 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]
  27. 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]
  28. Richter M, Rossellò-mòra 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]
  29. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Letters 1980; 8:87–91 [View Article]
     [Google Scholar]
  30. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article] [PubMed]
     [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note #101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  32. 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]
  33. Tindall BJ, Sikorski J, Smibert RA, Krieg NR et al. Phenotypic characterization and the principles of comparative systematics. Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. eds In Methods for General and Molecular Microbiology, 3rd ed. edn Washington, DC: ASM Press; 2007 pp 330–393
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005118
Loading
Chitinophaga rhizophila sp. nov., isolated from rhizosphere soil of banana
Int J Syst Evol Microbiol 71, 005118 (2021); https://doi.org/10.1099/ijsem.0.005118
/content/journal/ijsem/10.1099/ijsem.0.005118
/content/journal/ijsem/10.1099/ijsem.0.005118
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