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Volume 69, Issue 5

Pradoshia eiseniae gen. nov., sp. nov., a spore-forming member of the family Bacillaceae capable of assimilating 3-nitropropionic acid, isolated from the anterior gut of the earthworm Eisenia fetida Free

Abstract

A Gram-stain-positive, spore-forming bacterium, EAG3, capable of growing on 3-nitropropionic acid as the sole source of carbon, nitrogen and energy, was isolated from the anterior gut of an earthworm (Eisenia fetida) reared at the Centre of Floriculture and Agribusiness Management of the University of North Bengal at Siliguri (26.7072° N, 88.3558° E), West Bengal, India. The DNA G+C content of strain EAG3 was 42.5 mol%. Strain EAG3 contained MK-7 and MK-8 as predominant menaquinones. The predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were 13-methyltetradecanoic acid, (9Z)−9-hexadecen-1-ol, 12-methyltetradecanoic acid and 14-methylpentadecanoic acid. The draft genome of strain EAG3, distributed in 57 contigs, was found to be 3.8 Mb. A total of 3811 potential coding sequences or genes were predicted, including 3672 protein-coding and 108 RNA-coding ones together with 31 pseudogenes. One hundred and thirty-five genes encoded hypothetical proteins with no meaningful homologies with known proteins. The EAG3 genome encompassed two nitronate monooxygenase and one methylmalonate-semialdehyde dehydrogenase (CoA acylating) homologues. 16S rRNA gene sequence-based phylogeny revealed that the closest relative of strain EAG3 was Bacillus methanolicus NCIMB 13113 (95.7 % similarity). Phylogenetic, physiological and biochemical characteristics differentiated strain EAG3 from B. methanolicus, as well as from the other close taxonomic relatives Planococcus rifietoensis M8, Bhargavaea cecembensis DSE10, Planomicrobium flavidum ISL-41and Fermentibacillus polygoni IEB3, with which strain EAG3 had 93.3–94.2 % 16S rRNA gene sequence similarities. The new isolate, therefore, was considered as representing a novel genus of family Bacillaceae , for which the name Pradoshia eiseniae gen. nov., sp. nov. is proposed, with EAG3 (=LMG 30312=JCM 32460) as the type strain.

  • Received:
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Keyword(s): Bacillaceae , Eisenia fetida , menaquinones , polar lipids , Pradoshia eiseniae and scaffolds
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2019-02-25
2024-04-24
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References

  1. Logan NA, DeVos P. Family I. Bacillaceae. In DeVos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey's Manual of Systematic Bacteriology vol. 3 The Firmicutes Dordrecht New York: Springer; 2009 pp. 20–22
     [Google Scholar]
  2. Li J, Liu J, Shen Y, Ni J. Swionibacillus sediminis gen. nov., sp. nov., a member of the family Bacillaceae isolated from ocean sediment. Int J Syst Evol Microbiol 2017; 67:3440–3445 [View Article][PubMed]
     [Google Scholar]
  3. Anderson RC, Majak W, Rassmussen MA, Callaway TR, Beier RC et al. Toxicity and metabolism of the conjugates of 3-nitropropanol and 3-nitropropionic acid in forages poisonous to livestock. J Agric Food Chem 2005; 53:2344–2350 [View Article][PubMed]
     [Google Scholar]
  4. Francis K, Smitherman C, Nishino SF, Spain JC, Gadda G. The biochemistry of the metabolic poison propionate 3-nitronate and its conjugate acid, 3-nitropropionate. IUBMB Life 2013; 65:759–768 [View Article][PubMed]
     [Google Scholar]
  5. Anderson RC, Rasmussen MA, Allison MJ. Metabolism of the plant toxins nitropropionic acid and nitropropanol by ruminal microorganisms. Appl Environ Microbiol 1993; 59:3056–3061[PubMed]
     [Google Scholar]
  6. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1 [View Article]
     [Google Scholar]
  7. Kumar A, Mukherjee S, Chakraborty R. Characterization of a novel trimethoprim resistance gene, dfrA28, in class 1 integron of an oligotrophic Acinetobacter johnsonii strain, MB52, isolated from River Mahananda, India. Microb Drug Resist 2010; 16:29–37 [View Article][PubMed]
     [Google Scholar]
  8. Pearson WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 1990; 183:63–98[PubMed]
     [Google Scholar]
  9. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  10. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article][PubMed]
     [Google Scholar]
  11. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
     [Google Scholar]
  12. 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]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  14. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  15. 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]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  17. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24:1596–1599 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
     [Google Scholar]
  20. Tatusova T, Dicuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article][PubMed]
     [Google Scholar]
  21. 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]
  22. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:81–285 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. Ankenbrand MJ, Keller A, Chain F. bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 2016; 59:783–791 [View Article][PubMed]
     [Google Scholar]
  25. Dupont CL, Rusch DB, Yooseph S, Lombardo MJ, Richter RA et al. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. Isme J 2012; 6:1186–1199 [View Article][PubMed]
     [Google Scholar]
  26. Claus D. A standardized gram staining procedure. World J Microbiol Biotechnol 1992; 8:451–452 [View Article][PubMed]
     [Google Scholar]
  27. Murray RGE, Doetsch RN, Robinow CF. Determinative and cytological light microscopy. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 21–41
     [Google Scholar]
  28. Leighton TJ, Doi RH. The stability of messenger ribonucleic acid during sporulation in Bacillus subtilis. J Biol Chem 1971; 246:3189–3195[PubMed]
     [Google Scholar]
  29. MacFaddin JF. Biochemical Tests for Identification of Medical Bacteria, 3rd ed. Baltimore, Md: Williams and Wilkins; 2000 pp. 29
     [Google Scholar]
  30. Hugh R, Leifson E. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 1953; 66:24–26[PubMed]
     [Google Scholar]
  31. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  32. Lanyi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
     [Google Scholar]
  33. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology vol. 620 Washington, DC: American Society for Microbiology; 1994 pp. 622
     [Google Scholar]
  34. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
     [Google Scholar]
  35. 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]
  36. Tindall BJ. Qualitative and quantitative distribution of diether lipids in haloalkaliphilic archaebacteria. Syst Appl Microbiol 1985; 6:243–246 [View Article]
     [Google Scholar]
  37. Kaur I, Das AP, Acharya M, Klenk HP, Sree A et al. Planococcus plakortidis sp. nov., isolated from the marine sponge Plakortis simplex (Schulze). Int J Syst Evol Microbiol 2012; 62:883–889 [View Article][PubMed]
     [Google Scholar]
  38. Arfman N, Dijkhuizen L, Kirchhof G, Ludwig W, Schleifer KH et al. Bacillus methanolicus sp. nov., a new species of thermotolerant, methanol-utilizing, endospore-forming bacteria. Int J Syst Bacteriol 1992; 42:439–445 [View Article][PubMed]
     [Google Scholar]
  39. Tiago I, Pires C, Mendes V, Morais PV, da Costa MS et al. Bacillus foraminis sp. nov., isolated from a non-saline alkaline groundwater. Int J Syst Evol Microbiol 2006; 56:2571–2574 [View Article][PubMed]
     [Google Scholar]
  40. Albert RA, Archambault J, Rosselló-Mora R, Tindall BJ, Matheny M. Bacillus acidicola sp. nov., a novel mesophilic, acidophilic species isolated from acidic Sphagnum peat bogs in Wisconsin. Int J Syst Evol Microbiol 2005; 55:2125–2130 [View Article][PubMed]
     [Google Scholar]
  41. Heyndrickx M, Logan NA, Lebbe L, Rodríguez-Díaz M, Forsyth G et al. Bacillus galactosidilyticus sp. nov., an alkali-tolerant beta-galactosidase producer. Int J Syst Evol Microbiol 2004; 54:617–621 [View Article][PubMed]
     [Google Scholar]
  42. Hirota K, Aino K, Yumoto I. Fermentibacillus polygoni gen. nov., sp. nov., an alkaliphile that reduces indigo dye. Int J Syst Evol Microbiol 2016; 66:2247–2253 [View Article][PubMed]
     [Google Scholar]
  43. Romano I, Giordano A, Lama L, Nicolaus B, Gambacorta A. Planococcus rifietensis sp. nov, isolated from algal mat collected from a sulfurous spring in Campania (Italy). Syst Appl Microbiol 2003; 26:357–366 [View Article][PubMed]
     [Google Scholar]
  44. Manorama R, Pindi PK, Reddy GS, Shivaji S. Bhargavaea cecembensis gen. nov., sp. nov., isolated from the Chagos-Laccadive ridge system in the Indian Ocean. Int J Syst Evol Microbiol 2009; 59:2618–2623 [View Article][PubMed]
     [Google Scholar]
  45. Jung YT, Kang SJ, Oh TK, Yoon JH, Kim BH. Planomicrobium flavidum sp. nov., isolated from a marine solar saltern, and transfer of Planococcus stackebrandtii Mayilraj et al. 2005 to the genus Planomicrobium as Planomicrobium stackebrandtii comb. nov. Int J Syst Evol Microbiol 2009; 59:2929–2933 [View Article][PubMed]
     [Google Scholar]
  46. 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]
  47. Moreno-Vivián C, Cabello P, Martínez-Luque M, Blasco R, Castillo F. Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J Bacteriol 1999; 181:6573–6584[PubMed]
     [Google Scholar]
  48. Nishino SF, Shin KA, Payne RB, Spain JC. Growth of bacteria on 3-nitropropionic acid as a sole source of carbon, nitrogen, and energy. Appl Environ Microbiol 2010; 76:3590–3598 [View Article][PubMed]
     [Google Scholar]
  49. Salvi F, Agniswamy J, Yuan H, Vercammen K, Pelicaen R et al. The combined structural and kinetic characterization of a bacterial nitronate monooxygenase from Pseudomonas aeruginosa PAO1 establishes NMO class I and II. J Biol Chem 2014; 289:23764–23775 [View Article][PubMed]
     [Google Scholar]
  50. Stines-Chaumeil C, Talfournier F, Branlant G. Mechanistic characterization of the MSDH (methylmalonate semialdehyde dehydrogenase) from Bacillus subtilis. Biochem J 2006; 395:107–115 [View Article][PubMed]
     [Google Scholar]
  51. 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]
  52. 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 Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
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Pradoshia eiseniae gen. nov., sp. nov., a spore-forming member of the family Bacillaceae capable of assimilating 3-nitropropionic acid, isolated from the anterior gut of the earthworm Eisenia fetida
Int J Syst Evol Microbiol 69, 1265 (2019); https://doi.org/10.1099/ijsem.0.003304
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