Genome-based reclassification of Paenibacillus dauci as a later heterotypic synonym of Paenibacillus shenyangensis Free

Abstract

Paenibacillus shenyangensis and Paenibacillus dauci are Gram-stain-positive, rod-shaped and endospore-forming bacteria originally isolated from soil and carrot samples, respectively, in China. Preliminary comparative genomic analysis showed that these bacteria could constitute a single species. Therefore, in this study, their taxonomic statuses were clarified through distinct genomic metrics and phylogenetic analyses. Paenibacillus shenyangensis A9 and P. dauci H9 presented values of average nucleotide identity (ANI) and its derivative metrics (gANI and OrthoANI) ranging from 97.88 to 98.08 %, and digital DNA–DNA hybridization equal to 89.08 %. Furthermore, the identities of 16S rRNA, gyrB, rpoB, recA and recN genes were all equal or higher than 98.7 %. Phylogenies of these marker genes and the concatenated core proteome were congruent in the sense that P. shenyangensis A9 and P. dauci H9 are the closest type-strains of the genus Paenibacillus . A review of their profiles revealed that these strains do not present pronounced differences at the phenotypic and chemotaxonomic levels. Considering phylogenetic, genomic, phenotypic and chemotaxonomic data, P. dauci should be reclassified as a later heterotypic synonym of P. shenyangensis .

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2018-11-21
2024-03-28
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References

  1. Grady EN, Macdonald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016; 15:203 [View Article][PubMed]
    [Google Scholar]
  2. Beneduzi A, Costa PB, Parma M, Melo IS, Bodanese-Zanettini MH et al. Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum. Int J Syst Evol Microbiol 2010; 60:128–133 [View Article][PubMed]
    [Google Scholar]
  3. Berge O, Guinebretière MH, Achouak W, Normand P, Heulin T. Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int J Syst Evol Microbiol 2002; 52:607–616 [View Article][PubMed]
    [Google Scholar]
  4. Ambrosini A, Stefanski T, Lisboa BB, Beneduzi A, Vargas LK et al. Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential of Bacillus mycoides B38V as biofertiliser. Ann Appl Biol 2016; 168:93–110 [View Article]
    [Google Scholar]
  5. E Y, Yuan J, Yang F, Wang L, Ma J et al. PGPR strain Paenibacillus polymyxa SQR-21 potentially benefits watermelon growth by re-shaping root protein expression. AMB Express 2017; 7:104 [View Article][PubMed]
    [Google Scholar]
  6. Goswami D, Parmar S, Vaghela H, Dhandhukia P, Thakker JN. Describing Paenibacillus mucilaginosus strain N3 as an efficient plant growth promoting rhizobacteria (PGPR). Cogent Food Agric 2015; 1:1000714 [View Article]
    [Google Scholar]
  7. Parte AC. LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article][PubMed]
    [Google Scholar]
  8. Cho H, Heo J, Ahn JH, Weon HY, Kim JS et al. Paenibacillus solanacearum sp. nov., isolated from rhizosphere soil of a tomato plant. Int J Syst Evol Microbiol 2017; 67:5046–5050 [View Article][PubMed]
    [Google Scholar]
  9. Kämpfer P, Busse HJ, Mcinroy JA, Hu CH, Kloepper JW et al. Paenibacillus nebraskensis sp. nov., isolated from the root surface of field-grown maize. Int J Syst Evol Microbiol 2017; 67:4956–4961 [View Article][PubMed]
    [Google Scholar]
  10. Sant'anna FH, Ambrosini A, de Souza R, de Carvalho Fernandes G, Bach E et al. Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome-Based Metrics Improve Bacterial Taxonomic Classification. Front Microbiol 2017; 8:1849 [View Article][PubMed]
    [Google Scholar]
  11. 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][PubMed]
    [Google Scholar]
  12. 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][PubMed]
    [Google Scholar]
  13. Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ. Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 2012; 12:302 [View Article][PubMed]
    [Google Scholar]
  14. Jiang B, Zhao X, Liu J, Fu L, Yang C et al. Paenibacillus shenyangensis sp. nov., a bioflocculant-producing species isolated from soil under a peach tree. Int J Syst Evol Microbiol 2015; 65:220–224 [View Article][PubMed]
    [Google Scholar]
  15. Zhu J, Wang W, Li SH, Song SQ, Xie YQ et al. Paenibacillus wulumuqiensis sp. nov. and Paenibacillus dauci sp. nov., two novel species of the genus Paenibacillus. Arch Microbiol 2015; 197:489–495 [View Article][PubMed]
    [Google Scholar]
  16. Liu Y, Liu L, Qiu F, Schumann P, Shi Y et al. Paenibacillus hunanensis sp. nov., isolated from rice seeds. Int J Syst Evol Microbiol 2010; 60:1266–1270 [View Article][PubMed]
    [Google Scholar]
  17. Gao C, Han J, Liu Z, Xu X, Hang F et al. Paenibacillus bovis sp. nov., isolated from raw yak (Bos grunniens) milk. Int J Syst Evol Microbiol 2016; 66:1413–1418 [View Article][PubMed]
    [Google Scholar]
  18. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2015; 65:2777–2783 [View Article]
    [Google Scholar]
  19. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  20. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  21. 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]
  22. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  23. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article][PubMed]
    [Google Scholar]
  24. Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 2006; 55:539–552 [View Article][PubMed]
    [Google Scholar]
  25. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  26. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  27. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article][PubMed]
    [Google Scholar]
  28. Logan NA, Berge O, Bishop AH, Busse HJ, de Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article][PubMed]
    [Google Scholar]
  29. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  30. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article][PubMed]
    [Google Scholar]
  31. Smith SA, Dunn CW. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 2008; 24:715–716 [View Article][PubMed]
    [Google Scholar]
  32. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  33. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015; 43:6761–6771 [View Article][PubMed]
    [Google Scholar]
  34. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
    [Google Scholar]
  35. Deloger M, El Karoui M, Petit MA. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. J Bacteriol 2009; 191:91–99 [View Article][PubMed]
    [Google Scholar]
  36. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  37. Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 2003; 13:145–158 [View Article][PubMed]
    [Google Scholar]
  38. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
    [Google Scholar]
  39. 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]
  40. Padakandla SR, Lee GW, Chae JC. Paenibacillus gelatinilyticus sp. nov. a psychrotolerant bacterium isolated from a reclaimed soil and amended description of Paenibacillus shenyangensis. Antonie van Leeuwenhoek 2015; 108:1197–1203 [View Article][PubMed]
    [Google Scholar]
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