1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 10

gen. nov., sp. nov., a novel bacterium of the family isolated from forest soil on Danxia Mountain No Access

Abstract

A Gram-stain-negative, aerobic, short rod-shaped, yellow bacterium, designated SYSU DXS3180, was isolated from forest soil of Danxia Mountain in PR China. Growth occurred at 15–37 °C (optimum, 28–30 °C), pH 6.0–10.0 (optimum, pH 7.0–8.0) and with 0–2.0 % NaCl (optimum, 0–0.5 %, w/v). Strain SYSU DXS3180 was positive for hydrolysis of Tween 20, Tween 60, Tween 80 and starch, but negative for urease, HS production, nitrate reduction, Tween 40 and gelatin. Phylogenetic analysis based on 16S rRNA gene and genome sequences showed that SYSU DXS3180 belonged to the family . The closely related members were YG09 (94.2 %), KCS-6 (93.9 %) and SR 2-06 (93.7 %). The genome of strain SYSU DXS3180 was 7287640 bp with 5782 protein-coding genes, and the genomic DNA G+C content was 41.4 mol%. The main respiratory quinone was MK-7 and the major fatty acids (>10 %) were iso-C, iso-C 3-OH and iso-C G. The major polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. Based on the phylogenetic, phenotypic and chemotaxonomic characteristics, strain SYSU DXS3180 is proposed to represent a novel species of a novel genus named gen. nov., sp. nov., within the family . The type strain is SYSU DXS3180 (=KCTC 92895=GDMCC 1.3825 ).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Danxia Mountain , Danxiaibacter flavus sp. nov. , Danxiaibacter gen. nov. and polyphasic taxonomy
Funding
This study was supported by the:
  • Guangdong Basic and Applied Basic Research Foundation (Award 2023A1515012020)
    • Principle Award Recipient: ShuaiLi
  • Key-Area Research and Development Program of Guangdong Province (Award 2022B0202110001)
    • Principle Award Recipient: Wen-JunLi
  • Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases (Award MB2020KF05)
    • Principle Award Recipient: LeiDong
  • Guangdong Provincial Special Research Grant for the Creation of National Parks (Award 2021GJGY034)
    • Principle Award Recipient: TingZhou
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006082
2023-10-04
2024-05-08
Loading full text...

Full text loading...

References

  1. Kämpfer P, Lodders N, Falsen E. Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 2011; 61:518–523 [View Article] [PubMed]
     [Google Scholar]
  2. Shiratori H, Tagami Y, Morishita T, Kamihara Y, Beppu T et al. Filimonas lacunae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from fresh water. Int J Syst Evol Microbiol 2009; 59:1137–1142 [View Article] [PubMed]
     [Google Scholar]
  3. Han J-H, Kim T-S, Joung Y, Kim SB. Filimonas endophytica sp. nov., isolated from surface-sterilized root of Cosmos bipinnatus. Int J Syst Evol Microbiol 2015; 65:4863–4867 [View Article] [PubMed]
     [Google Scholar]
  4. Gao J-L, Sun P, Wang X-M, Qiu T-L, Lv F-Y et al. Filimonas zeae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:2730–2734 [View Article] [PubMed]
     [Google Scholar]
  5. Lin S-Y, Hameed A, Hsu Y-H, Liu Y-C, Lai W-A et al. Filimonas aquilariae sp. nov., isolated from agarwood chips. Int J Syst Evol Microbiol 2017; 67:3219–3225 [View Article] [PubMed]
     [Google Scholar]
  6. Chen W-M, Chen T-Y, Li Z-H, Kwon S-W, Sheu S-Y. Filimonas effusa sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2020; 70:1508–1515 [View Article] [PubMed]
     [Google Scholar]
  7. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article] [PubMed]
     [Google Scholar]
  8. Albert RA, Waas NE, Pavlons SC, Pearson JL, Roecker J et al. Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas. Int J Syst Evol Microbiol 2016; 66:4027–4032 [View Article] [PubMed]
     [Google Scholar]
  9. Wang CL, Lv YY, Li AZ, Bao GG, Feng GD et al. Deminuibacter soli gen. nov., sp. nov., isolated from forest soil, and reclassification of Filimonas aurantiibacter as Arvibacter aurantiibacter comb. nov. Int J Syst Evol Microbiol 2019; 69:1650–1655
     [Google Scholar]
  10. Pu Q, Zeng GH, Wang GW, Lu LE, Li A et al. Foetidibacter luteolus gen. nov., sp. nov., isolated from the rhizosphere of Salvia miltiorrhiza. Arch Microbiol 2021; 203:2425–2430
     [Google Scholar]
  11. Li S, Dong L, Lian W-H, Lin Z-L, Lu C-Y et al. Exploring untapped potential of Streptomyces spp. in Gurbantunggut Desert by use of highly selective culture strategy. Sci Total Environ 2021; 790:148235 [View Article]
     [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  17. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
     [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  19. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article]
     [Google Scholar]
  20. 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]
  21. Shi W, Sun Q, Fan G, Hideaki S, Moriya O et al. gcType: a high-quality type strain genome database for microbial phylogenetic and functional research. Nucleic Acids Res 2021; 49:D694–D705 [View Article] [PubMed]
     [Google Scholar]
  22. Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M. KEGG: integrating viruses and cellular organisms. Nucleic Acids Res 2021; 49:D545–D551 [View Article] [PubMed]
     [Google Scholar]
  23. 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] [PubMed]
     [Google Scholar]
  24. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  25. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1–14 [View Article] [PubMed]
     [Google Scholar]
  26. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  27. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  28. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [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. Liang KYH, Orata FD, Boucher YF, Case RJ. Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the proposal for the split of the “Roseobacter Clade” into a novel family, Roseobacteraceae fam. nov. Front Microbiol 2021; 12: [View Article]
     [Google Scholar]
  31. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd. edn vol 71 Washington, DC: American Society for Microbiology Press; 2007 pp 16–22 [View Article]
     [Google Scholar]
  32. 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]
  33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI inc; 1990
     [Google Scholar]
  34. 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]
  35. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006082
Loading
Danxiaibacter flavus gen. nov., sp. nov., a novel bacterium of the family Chitinophagaceae isolated from forest soil on Danxia Mountain
Int J Syst Evol Microbiol 73, 006082 (2023); https://doi.org/10.1099/ijsem.0.006082
/content/journal/ijsem/10.1099/ijsem.0.006082
/content/journal/ijsem/10.1099/ijsem.0.006082
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