1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 8

sp. nov., isolated from cotton field soil Free

Abstract

A Gram-negative bacterium, designated S1-65, was isolated from soil samples collected from a cotton field located in the Xinjiang region of PR China. Results of 16S rRNA gene sequence analysis revealed that strain S1-65 was affiliated to the genus with its closest phylogenetic relatives being ‘’ 35Y (98.4 %), ‘’ SA29-B (98.3 %) and KA5-B (98.3 %). 16S rRNA-directed phylogenetic analysis showed that strain S1-65 formed a unique phylogenetic subclade next to ‘’ SA29-B and KA5-B, suggesting that strain S1-65 should be identified as a member of the genus . Further, substantial differences between the genotypic properties of strain S1-65 and the members of the genus , including average nucleotide identity and digital DNA–DNA hybridization, resolved the taxonomic position of strain S1-65 and suggested its positioning as representing a novel species of the genus . The DNA G+C content of strain S1-65 was 62.5 mol%, based on its draft genome sequence. The predominant respiratory quinone was ubiquinone-8. The main fatty acids were identified as summed feature 3 (Cω6/Cω7), C and iso-C. In addition, its polar lipid profile was composed of aminophospholipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Here, we propose a novel species of the genus : sp. nov. with the type strain S1-65 (=JCM 34287=CGMCC 1.18736).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): cotton field , soil and Steroidobacter
Funding
This study was supported by the:
  • Natural Science Research of Jiangsu Higher Education Institutions of China (Award 19KJB530010)
    • Principle Award Recipient: WenzhengLiu
  • Natural Science Foundation of Jiangsu Province (Award BK20190703)
    • Principle Award Recipient: WenzhengLiu
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004935
2021-08-03
2024-12-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/8/ijsem004935.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004935&mimeType=html&fmt=ahah

References

  1. Fahrbach M, Kuever J, Remesch M, Huber BE, Kämpfer P et al. Steroidobacter denitrificans gen. nov., sp. nov., a steroidal hormone-degrading gammaproteobacterium. Int J Syst Evol Microbiol 2008; 58:2215–2223 [View Article] [PubMed]
     [Google Scholar]
  2. Sakai M, Hosoda A, Ogura K, Ikenaga M. The growth of Steroidobacter agariperforans sp. nov., a novel agar-degrading bacterium isolated from soil, is enhanced by the diffusible metabolites produced by bacteria belonging to Rhizobiales. Microbes Environ 2014; 29:89–95 [View Article] [PubMed]
     [Google Scholar]
  3. Huang J-W, Hu S-L, Cheng X-K, Chen D, Kong X-K et al. Steroidobacter soli sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2019; 69:3443–3447 [View Article]
     [Google Scholar]
  4. Gong ZL, Zhang CF, Jin R, Zhang YQ. Steroidobacter flavus sp. nov., a microcystin-degrading Gammaproteobacterium isolated from soil. Antonie van Leeuwenhoek 2016; 109:1073–1079 [View Article]
     [Google Scholar]
  5. Sharma V, Siedenburg G, Birke J, Mobeen F, Jendrossek D et al. Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium “Steroidobacter cummioxidans” sp. nov., strain 35Y. PLoS One 2018; 13:e0197448 [View Article] [PubMed]
     [Google Scholar]
  6. Ikenaga M, Kataoka M, Yin X, Murouchi A, Sakai M. Characterization and distribution of agar-degrading Steroidobacter agaridevorans sp. nov., isolated from rhizosphere soils. Microbes Environ 2021; 36: [View Article] [PubMed]
     [Google Scholar]
  7. Hopkins DW, Macnaughton SJ, O’Donnell AG. A dispersion and differential centrifugation technique for representatively sampling microorganisms from soil. Soil Biol Biochem 1991; 23:217–225 [View Article]
     [Google Scholar]
  8. Prakash O, Nimonkar Y, Shouche YS. Practice and prospects of microbial preservation. FEMS Microbiol Lett 2013; 339:1–9 [View Article] [PubMed]
     [Google Scholar]
  9. Fan H, Su C, Wang Y, Yao J, Zhao K et al. Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China. J Appl Microbiol 2008; 105:529–539 [View Article] [PubMed]
     [Google Scholar]
  10. Federhen S. The NCBI taxonomy database. Nucleic Acids Res 2012; 40:136–143 [View Article] [PubMed]
     [Google Scholar]
  11. Parte AC. LPSN - List of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:613–616 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. Sourdis J, Nei M. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol Biol Evol 1988; 11:261–277 [View Article]
     [Google Scholar]
  17. Steel M, Rodrigo A. Maximum likelihood supertrees. Syst Biol 2008; 57:243–250 [View Article] [PubMed]
     [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  19. Rhodes J, Beale MA, Fisher MC. Illuminating choices for library prep: A comparison of library preparation methods for whole genome sequencing of Cryptococcus neoformans using Illumina HiSeq. PLoS One 2014; 9:11 [View Article] [PubMed]
     [Google Scholar]
  20. Burgos G, Freire-Paspuel B, Restrepo T, Camargo M, Ibarra A et al. Magnetic beads: An alternative method to enzymatic purification for SNaPshot reactions. Forensic Science International: Genetics Supplement Series 2017; 6:368–369 [View Article]
     [Google Scholar]
  21. Panaro NJ, Yuen PK, Sakazume T, Fortina P, Kricka LJ et al. Evaluation of DNA fragment sizing and quantification by the Agilent 2100 bioanalyzer. Clin Chem 2000; 46:1851–1853 [View Article] [PubMed]
     [Google Scholar]
  22. Patnaik BB, Park SY, Kang SW, Hwang HJ, Wang TH et al. Transcriptome profile of the Asian Giant Hornet (Vespa mandarinia) using Illumina HiSeq 4000 sequencing: De novo assembly, functional annotation, and discovery of SSR markers. Int J Genomics 2016; 2016:1–15 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. 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]
  25. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM et al. ABySS: A parallel assembler for short read sequence data. Genome Res 2009; 19:1117–1123 [View Article] [PubMed]
     [Google Scholar]
  26. Lin SH, Liao YC. CISA: Contig integrator for sequence assembly of bacterial genomes. PLoS One 2013; 8:e60843 [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. Yoon S-H, Ha S-M, 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]
     [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. Koon MA, Almohammed Ali K, Speaker RM, McGrath JP, Linton EW et al. Preparation of prokaryotic and eukaryotic organisms using chemical drying for morphological analysis in scanning electron microscopy (SEM. J Vis Exp 2019143 [View Article]
     [Google Scholar]
  31. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes 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]
  32. Smibert RM, Krieg NR. Phenotypic characterization. Gerhardt P, Murray R, Wood W, Krieg N. eds In Methods for General and Molecular Bacteriology Washington: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  33. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
     [Google Scholar]
  34. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  35. Deng SK, XM Y, Chu CW, Jiang J, He J. Chryseomicrobium aureum sp. nov., a bacterium isolated from activated sludge. Int J Syst Evol Microbiol 2014; 16:313–340 [View Article]
     [Google Scholar]
  36. de Lima Procópio R, Silva da, Martins M, de Azevedo J, de Araújo J. Antibiotics produced by Streptomyces. Braz J Infect Dis 2012; 16:466–471 [View Article] [PubMed]
     [Google Scholar]
  37. Sumi C, Yang B, Yeo I, Hahm Y. Antimicrobial peptides of the genus Bacillus: A new era for antibiotics. Can J Microbiol 2015; 61:93–103 [View Article] [PubMed]
     [Google Scholar]
  38. Tindall BJ. A Comparative Study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  39. 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]
  40. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. Chem METHODS Bact Syst 1985; 20:267–287
     [Google Scholar]
  41. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004935
Loading
Steroidobacter gossypii sp. nov., isolated from cotton field soil
Int J Syst Evol Microbiol 71, 004935 (2021); https://doi.org/10.1099/ijsem.0.004935
/content/journal/ijsem/10.1099/ijsem.0.004935
/content/journal/ijsem/10.1099/ijsem.0.004935
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