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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 10

sp. nov., isolated from the South China Sea No Access

Abstract

A Gram-positive, rod-shaped, motile, spore-forming bacterium, designated strain IB182496, was isolated from coastal sand of the South China Sea. The strain grew optimally at pH 7.0–9.0, 20–30 °C, and with NaCl 3.0–5.0 %. The predominant menaquinone was MK-7 and the major cellular fatty acids were anteiso-C, iso-C and C. The polar lipids in the cell wall included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and one unidentified lipid. The comparison of 16S rRNA gene sequences indicated that strain IB182496 was most closely related to ‘’ SMB1 and SA-7-6 with similarities of 95.7 and 95.5 %, respectively. The whole-genome average nucleotide identity values between strain IB182496 and the two reference strains were 70.8 and 70.5%, and the digital DNA–DNA hybridization values were 18.7 and 18.0 %, respectively. Genomic analyses showed that strain IB182496 presented a genome of 6.22 Mbp with chromosomal G+C content of 60.3 %, and a total of 5261 genes were predicted. The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain IB182496 should be considered as representing a novel species of the genus , for which we propose the name sp. nov. with the type strain IB182496 (=MCCC 1K04627=JCM 34216).

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  • Accepted:
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Keyword(s): 16S rRNA gene , coastal sand , Paenibacillus sabuli sp. nov. and polyphasic taxonomy
© 2022 The Authors
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2022-10-20
2024-05-18
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References

  1. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek 1993; 64:253–260 [View Article]
     [Google Scholar]
  2. Chen Y, Ye L, Huang H, Jiang M, Hu Y et al. Paenibacillus oceani sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  3. Niu L, Tang T, Ma Z, Song L, Zhang K et al. Paenibacillus yunnanensis sp. nov., isolated from Pu’er tea. Int J Syst Evol Microbiol 2015; 65:3806–3811 [View Article]
     [Google Scholar]
  4. Priest FG. Genus I. Paenibacillus. In De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W et al. eds The Firmicutes, Bergey’s Manual of Systematic Bacteriology, 2nd. edition. vol 2 New York, US: Springer; 2009 pp 269–296
     [Google Scholar]
  5. De Vos P, Ludwig W. eds The Firmicutes, Bergey’s Manual of Systematic Bacteriology, 2nd edn. New York: Springer; 2009 p 269
     [Google Scholar]
  6. Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 1997; 47:289–298 [View Article]
     [Google Scholar]
  7. Grady EN, MacDonald J, Liu L, Richman A, Yuan Z-C. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016; 15:203–221 [View Article]
     [Google Scholar]
  8. Wang M, Yang M, Zhou G, Luo X, Zhang L et al. Paenibacillus tarimensis sp. nov., isolated from sand in Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:2081–2085 [View Article]
     [Google Scholar]
  9. Cha I-T, Cho E-S, Yoo Y, Seok YJ, Park I et al. Paenibacillus arcticus sp. nov., isolated from Arctic soil. Int J Syst Evol Microbiol 2017; 67:4385–4389 [View Article]
     [Google Scholar]
  10. Trinh NH, Kim J. Paenibacillus piri sp. nov., isolated from urban soil. Int J Syst Evol Microbiol 2020; 70:656–661 [View Article]
     [Google Scholar]
  11. Yoon JH, Kang SJ, Yeo SH, Oh TK. Paenibacillus alkaliterrae sp. nov., isolated from an alkaline soil in Korea. Int J Syst Evol Microbiol 2005; 55:2339–2344 [View Article]
     [Google Scholar]
  12. Yoon JH, Lee ST, Park YH. Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int J Syst Bacteriol 1998; 48 Pt 1:187–194 [View Article]
     [Google Scholar]
  13. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article]
     [Google Scholar]
  14. Mo K, Wang L, Wu Q, Ye L, Liu X et al. Pontibacter mangrovi sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2020; 70:4245–4249 [View Article]
     [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]
     [Google Scholar]
  16. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  17. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article]
     [Google Scholar]
  18. 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]
     [Google Scholar]
  19. 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]
     [Google Scholar]
  20. Singh H, Kaur M, Jangra M, Mishra S, Nandanwar H et al. Antimicrobial properties of the novel bacterial isolate Paenibacilllus sp. SMB1 from a halo-alkaline lake in India. Sci Rep 2019; 9:11561–11573 [View Article]
     [Google Scholar]
  21. Wang M, Yang M, Zhou G, Luo X, Zhang L et al. Paenibacillus tarimensis sp. nov., isolated from sand in Xinjiang, China. Int J Syst Evol Microbiol 2008; 58:2081–2085 [View Article]
     [Google Scholar]
  22. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article]
     [Google Scholar]
  23. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [View Article]
     [Google Scholar]
  24. 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]
     [Google Scholar]
  25. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article]
     [Google Scholar]
  26. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365–8370 [View Article]
     [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]
     [Google Scholar]
  28. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie vVan Leeuwenhoek 2017; 110:1281–1286 [View Article]
     [Google Scholar]
  29. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–73 [View Article]
     [Google Scholar]
  30. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182–2191 [View Article]
     [Google Scholar]
  31. 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:D457–62 [View Article] [PubMed]
     [Google Scholar]
  32. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003; 4:41–55 [View Article]
     [Google Scholar]
  33. 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]
     [Google Scholar]
  34. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 1994; 44:846–849 [View Article]
     [Google Scholar]
  35. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics. Int J Syst Bacteriol 1987; 37:463–464 [View Article]
     [Google Scholar]
  36. Vaz-Moreira I, Faria C, Nobre MF, Schumann P, Nunes OC et al. Paenibacillus humicus sp. nov., isolated from poultry litter compost. Int J Syst Evol Microbiol 2007; 57:2267–2271 [View Article]
     [Google Scholar]
  37. Thorat V, Kirdat K, Tiwarekar B, Dhanavade P, Karodi P et al. Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup. Arch Microbiol 2022; 204:127 [View Article]
     [Google Scholar]
  38. Dsouza M, Taylor MW, Ryan J, MacKenzie A, Lagutin K et al. Paenibacillus darwinianus sp. nov., isolated from gamma-irradiated Antarctic soil. Int J Syst Evol Microbiol 2014; 64:1406–1411 [View Article]
     [Google Scholar]
  39. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  40. 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]
     [Google Scholar]
  41. Murray TS, Ledizet M, Kazmierczak BI. Swarming motility, secretion of type 3 effectors and biofilm formation phenotypes exhibited within a large cohort of Pseudomonas aeruginosa clinical isolates. J Med Microbiol 2010; 59:511–520 [View Article]
     [Google Scholar]
  42. Bhatt HB, Azmatunnisa Begum M, Chintalapati S, Chintalapati VR, Singh SP. Desertibacillus haloalkaliphilus gen. nov., sp. nov., isolated from a saline desert. Int J Syst Evol Microbiol 2017; 67:4435–4442 [View Article]
     [Google Scholar]
  43. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  44. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids. MIDI; 2001
  45. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
     [Google Scholar]
  46. 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]
  47. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
     [Google Scholar]
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Paenibacillus sabuli sp. nov., isolated from the South China Sea
Int J Syst Evol Microbiol 72, 005568 (2022); https://doi.org/10.1099/ijsem.0.005568
/content/journal/ijsem/10.1099/ijsem.0.005568
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