1887

Abstract

A Gram-stain-positive, aerobic, rod-shaped, endospore-forming and motile, by means of peritrichous flagella, bacterium, designated DT12, was isolated from a lake water sample from Datun Lake of Yunnan Province, PR China. The results of phylogenetic analysis based on 16S rRNA gene sequence and the concatenated alignment of 120 ubiquitous single-copy proteins indicated that the novel strain represented a member of the genus . The sole quinone was menaquinone-7 and the cell-wall peptidoglycan was type-A1γ. The major fatty acids (>10 %) of the novel strain were iso-C and anteiso-C, while the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The results of phylogenetic analyses combined with phylogenetic, phenotypic and chemotaxonomic features, strongly supported the hypothesis that the strain should be classified as representing a novel species of the genus , for which the name sp. nov. is proposed. The type strain is DT12 (=KCTC 33958= MCCC 1H00320). The genomic analysis revealed that DT12 has various biosynthetic gene clusters for secondary metabolites, and members of the genus may represent a promising source of new natural products. Our study also showed that members of the genus are widely distributed in a variety of habitats throughout the globe, particularly in soils, human-, animal- and plant-associated environments. Members of the genus may have an important role in the growth and health of humans, plants and animals.

Funding
This study was supported by the:
  • Natural Science Foundation of Shandong Province, China (Award ZR2023QD187)
    • Principle Award Recipient: JingZhang
  • China Postdoctoral Science Foundation (Award 2022M721923)
    • Principle Award Recipient: JingZhang
  • National Natural Science Foundation of China (Award 41876166)
    • Principle Award Recipient: Zong-JunDu
  • Science & Technology Fundamental Resources Investigation Program (Award 2019FY100700)
    • Principle Award Recipient: Zong-JunDu
  • Science & Technology Fundamental Resources Investigation Program (Award 2022FY101100)
    • Principle Award Recipient: Zong-JunDu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006153
2023-11-06
2024-12-14
Loading full text...

Full text loading...

References

  1. Steven B, Chen MQ, Greer CW, Whyte LG, Niederberger TD. Tumebacillus permanentifrigoris gen. nov., sp. nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost. Int J Syst Evol Microbiol 2008; 58:1497–1501 [View Article] [PubMed]
    [Google Scholar]
  2. Wang Q, Xie N, Qin Y, Shen N, Zhu J et al. Tumebacillus flagellatus sp. nov., an α-amylase/pullulanase-producing bacterium isolated from cassava wastewater. Int J Syst Evol Microbiol 2013; 63:3138–3142 [View Article] [PubMed]
    [Google Scholar]
  3. Wu Y-F, Zhang B, Xing P, Wu Q-L, Liu S-J. Tumebacillus algifaecis sp. nov., isolated from decomposing algal scum. Int J Syst Evol Microbiol 2015; 65:2194–2198 [View Article] [PubMed]
    [Google Scholar]
  4. Baek S-H, Cui Y, Kim S-C, Cui C-H, Yin C et al. Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2011; 61:1715–1719 [View Article] [PubMed]
    [Google Scholar]
  5. Prasad RV, Bhumika V, Anil Kumar P, Srinivas NRT. Tumebacillus lipolyticus sp. nov., isolated from river water. Int J Syst Evol Microbiol 2015; 65:4363–4368 [View Article] [PubMed]
    [Google Scholar]
  6. Sung H, Kim HS, Lee J-Y, Kang W, Kim PS et al. Tumeibacillus avium sp. nov., isolated from the gut of a cinereous vulture, Aegypius monachus. Int J Syst Evol Microbiol 2018; 68:1659–1664 [View Article] [PubMed]
    [Google Scholar]
  7. Her J, Srinivasan S, Lee S-S. Tumebacillus luteolus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:4107–4112 [View Article] [PubMed]
    [Google Scholar]
  8. Kim JH, Kim W. Tumebacillus soli sp. nov., isolated from non-rhizosphere soil. Int J Syst Evol Microbiol 2016; 66:2192–2197 [View Article] [PubMed]
    [Google Scholar]
  9. Kang M, Chhetri G, Kim J, Kim I, So Y et al. Tumebacillus amylolyticus sp. nov., isolated from garden soil in Korea. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
    [Google Scholar]
  10. Chen J, Jiang X, Tong T, Miao S, Huang J et al. Sulfadiazine degradation in soils: dynamics, functional gene, antibiotic resistance genes and microbial community. Sci Total Environ 2019; 691:1072–1081 [View Article]
    [Google Scholar]
  11. Li Z, Zheng Y, Li Y, Cheng X, Huang S et al. Genotype-specific recruitment of rhizosphere bacteria from sandy loam soil for growth promotion of Cucumis sativus var. hardwickii. Front Microbiol 2022; 13:910644 [View Article] [PubMed]
    [Google Scholar]
  12. Xueliang T, Dan X, Tingting S, Songyu Z, Ying L et al. Plant resistance and leaf chemical characteristic jointly shape phyllosphere bacterial community. World J Microbiol Biotechnol 2020; 36:139 [View Article] [PubMed]
    [Google Scholar]
  13. Hamouda T, Shih AY, Baker JR. A rapid staining technique for the detection of the initiation of germination of bacterial spores. Lett Appl Microbiol 2002; 34:86–90 [View Article] [PubMed]
    [Google Scholar]
  14. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868 [View Article] [PubMed]
    [Google Scholar]
  15. Dong XZ, Cai MY. Determination of biochemical characteristics. In Manual for the Systematic Identification of General Bacteria Beijing: Science Press (in Chinese); 2001 pp 370–398
    [Google Scholar]
  16. 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]
  17. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  18. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article] [PubMed]
    [Google Scholar]
  19. Liu Q-Q, Wang Y, Li J, Du Z-J, Chen G-J. Saccharicrinis carchari sp. nov., isolated from a shark, and emended descriptions of the genus Saccharicrinis and Saccharicrinis fermentans. Int J Syst Evol Microbiol 2014; 64:2204–2209 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. 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]
  22. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  23. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article] [PubMed]
    [Google Scholar]
  24. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
    [Google Scholar]
  25. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016; 44:D457–D462 [View Article] [PubMed]
    [Google Scholar]
  26. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
    [Google Scholar]
  27. 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]
  28. Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD et al. Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria. ISME Commun 2021; 1:16 [View Article] [PubMed]
    [Google Scholar]
  29. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  30. 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]
  31. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
    [Google Scholar]
  32. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
    [Google Scholar]
  33. Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 2017; 551:457–463 [View Article] [PubMed]
    [Google Scholar]
  34. Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 2016; 4:e2584 [View Article] [PubMed]
    [Google Scholar]
  35. Mise K, Iwasaki W. Environmental atlas of prokaryotes enables powerful and intuitive habitat-based analysis of community structures. iScience 2020; 23:101624 [View Article] [PubMed]
    [Google Scholar]
  36. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  37. 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]
  38. Kikuchi Y, Kawashima M, Iwatsuki M, Kimishima A, Tsutsumi H et al. Comprehensive analysis of biosynthetic gene clusters in bacteria and discovery of Tumebacillus as a potential producer of natural products. J Antibiot 2023; 76:316–323 [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006153
Loading
/content/journal/ijsem/10.1099/ijsem.0.006153
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL
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