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Paenibacillus silvestris sp. nov., Isolated from Forest Soil

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Abstract

A bacterial strain, designated 5J-6T, was isolated from soil in Cheongnyeongpo, Republic of Korea. Cells were Gram-stain-positive, strictly aerobic, and motile rods and their catalase and oxidase activities were positive. Strain 5J-6T grew at 10–30 °C, pH 6.0–9.0, and 0–0.8% (w/v) NaCl concentration, with optimum growth at 25 °C, pH 6.5, and 0.4% NaCl concentration. Anteiso-C15:0 and iso-C16:0 were detected as the predominant fatty acids and menaquinone-7 was the sole isoprenoid quinone detected. Strain 5J-6T contained phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid as major polar lipids. The peptidoglycan belonged to the type A1γ meso-diaminopimelic acid. The G+C content of the genomic DNA calculated from the whole genomic sequence was 46.1 mol%. Phylogenetic analysis of strain 5J-6T based on 16S rRNA gene sequences placed the isolate into a member of the genus Paenibacillus. Sequence similarity analysis of 16S rRNA gene sequences revealed that strain 5J-6T was most closely related to Paenibacillus aceris KUDC4121T and Paenibacillus chondroitinus DSM 5051T with 98.76% and 98.42% similarities, respectively. Average nucleotide identity and in silico DNA–DNA hybridization values between strain 5J-6T and the type strain of P. aceris were 83.97% and 28.60%, respectively. Based on the phylogenetic and phenotypic characteristics and genomic data, strain 5J-6T could be considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus silvestris sp. nov. is proposed. The type strain is 5J-6T (= KACC 21430T = JCM 33812T).

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References

  1. Ash C, Priest FG, Collins MD (1993) 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 64:253–260

    Article  CAS  Google Scholar 

  2. Huang Z, Dai W, Zhou Z, Wang G, Lin G, Yan X, Zhao F (2016) Paenibacillus terreus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 66:243–247

    Article  CAS  Google Scholar 

  3. Kong D, Zhang Q, Jiang X, Ma Q, Han X, Zhou Y, Xue H, Zhang Y, Zhang W, Ruan Z (2020) Paenibacillus solisilvae sp. nov., isolated from birch forest soil. Int J Syst Evol Microbiol 70:2690–2695

    Article  CAS  Google Scholar 

  4. Baik KS, Choe HN, Park SC, Kim EM, Seong C (2011) Paenibacillus wooponensis sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 61:2763–2768

    Article  CAS  Google Scholar 

  5. Chou JH, Chou YJ, Lin KY, Sheu SY, Sheu DS, Arun AB, Chen WM (2007) Paenibacillus fonticola sp. nov., isolated from a warm spring. Int J Syst Evol Microbiol 67:1346–1350

    Article  Google Scholar 

  6. Liu Y, Liu L, Qiu F, Schumann P, Shi Y, Zou Y, Song W (2010) Paenibacillus hunanensis sp. nov, isolated from rice seeds. Int J Syst Evol Microbiol 60:1266–1270

    Article  CAS  Google Scholar 

  7. Kong BH, Liu QF, Liu M, Liu Y, Liu L, Li CL, Li YH (2013) Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L. Int J Syst Evol Microbiol 63:1037–1044

    Article  CAS  Google Scholar 

  8. Carro L, Flores-Felix JD, Cerda-Castillo E, Ramírez-Bahena MH, Igual JM, Tejedor C, Peix A (2013) Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum. Int J Syst Evol Microbiol 63:4433–4438

    Article  CAS  Google Scholar 

  9. Velazquez E, De Miguel T, Poza M, Rivas R, Rossello-Mora R, Villa TG (2004) Paenibacillus favisporus sp. nov., a xylanolytic bacterium isolated from cow faeces. Int J Syst Evol Microbiol 54:59–64

    Article  CAS  Google Scholar 

  10. Horn MA, Ihssen J, Matthies C, Schramm A, Acker G, Drake HL (2005) Dechloromonas denitrificans sp. nov., Flavobacterium denitrificans sp. nov., Paenibacillus anaericanus sp. nov. and Paenibacillus terrae strain MH72, N2O-producing bacteria isolated from the gut of the earthworm Aporrectodea caliginosa. Int J Syst Evol Microbiol 55:1255–1265

    Article  CAS  Google Scholar 

  11. Zhou Y, Gao S, Wei DQ, Yang LL, Huang X, He J, Li WJ (2012) Paenibacillus thermophilus sp. nov., a novel bacterium isolated from a sediment of hot spring in Fujian province. China. Antonie van Leeuwenhoek 102:601–609

    Article  CAS  Google Scholar 

  12. Kim JM, Lee SH, Lee SH, Choi EJ, Jeon CO (2013) Paenibacillus hordei sp. nov., isolated from naked barley in Korea. Antonie Van Leeuwenhoek 103:3–9

    Article  Google Scholar 

  13. Roux V, Raoult D (2004) Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures. Int J Syst Evol Microbiol 54:1049–1054

    Article  CAS  Google Scholar 

  14. Kim J, Jeong SE, Khan SA, Jeon CO (2019) Hwanghaeella grinnelliae gen. nov., sp. nov., isolated from a marine red alga. Int J Syst Evol Microbiol 69:3544–3550

    Article  CAS  Google Scholar 

  15. Jeon CO, Park W, Padmanabhan P, DeRito C, Snape JR, Madsen EL (2003) Discovery of a previously undescribed bacterium with distinctive dioxygenase that is responsible for in situ biodegradation in contaminated sediment. Proc Natl Acad Sci USA 100:13591–13596

    Article  CAS  Google Scholar 

  16. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  Google Scholar 

  17. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Article  CAS  Google Scholar 

  18. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  Google Scholar 

  19. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, Tang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18

    Article  Google Scholar 

  20. Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103

    Article  CAS  Google Scholar 

  21. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  22. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, Von Mering C, Bork P (2017) Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol 34:2115–2122

    Article  CAS  Google Scholar 

  23. Chun BH, Kim KH, Jeong SE, Jeon CO (2019) Genomic and metabolic features of the Bacillus amyloliquefaciens group–B. amyloliquefaciens, B. velezensis, and B. siamensis–revealed by pan-genome analysis. Food Microbiol 77:146–157

    Article  CAS  Google Scholar 

  24. Gomori G (1955) Preparation of buffers for use in enzyme studies. Methods Enzymol 1:138–146

    Article  CAS  Google Scholar 

  25. Lányi B (1987) Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67

    Google Scholar 

  26. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P (ed) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  27. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  28. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc, Newark

    Google Scholar 

  29. Minnikin D, Patel P, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117

    Article  CAS  Google Scholar 

  30. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477

    Article  CAS  Google Scholar 

  31. Stackebrandt E, Ebers J (2006) Taxonomic parameter revisited: tarnished gold standards. Microbiol Today 33:152–155

    Google Scholar 

  32. Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    Article  CAS  Google Scholar 

  33. Rosselló-Móra R, Amann R (2015) Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 38:209–216

    Article  Google Scholar 

  34. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    Article  CAS  Google Scholar 

  35. Priest FG (2015) Paenibacillus. In: William W (ed) Bergey’s manual of systematics of archaea and bacteria. John Wiley & Sons Ltd, Hoboken

    Google Scholar 

  36. Hwang YJ, Ghim SY (2017) Paenibacillus aceris sp. nov., isolated from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea. Int J Syst Evol Microbiol 67:1039–1045

    Article  CAS  Google Scholar 

  37. Cao Y, Chen F, Li Y, Wei S, Wang G (2015) Paenibacillus ferrarius sp. nov., isolated from iron mineral soil. Int J Syst Evol Microbiol 65:165–170

    Article  CAS  Google Scholar 

  38. Priest FG, Ash P. 852VP (Effective publication: Ash, Priest and Collins 1993, 259) emend. Shida, Takagi, Kadowaki, Nakamura and Komagata 1997a, 297. John Wiley & Sons, Inc., in association with Bergey’s Manual Trust; 2015

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Acknowledgements

This work was supported by the National Research Foundation (2017M3C1B5019250) of the Ministry of Science and ICT and the National Institute of Biological Resources (NIBR202002203), funded by the Ministry of Environment (MOE) of the Republic of Korea, Republic of Korea.

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  1. Jungeun Kim and Hye Su Jung contributed equally to this study.

Authors and Affiliations

  1. Department of Life Science, Chung-Ang University, 84, HeukSeok-Ro, Dongjak-Gu, Seoul, 06974, Republic of Korea

    Jungeun Kim, Hye Su Jung, Ju Hye Baek, Byung Hee Chun, Shehzad Abid Khan & Che Ok Jeon

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  1. Jungeun Kim
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Correspondence to Che Ok Jeon.

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The GenBank accession numbers for the 16S rRNA gene and genome sequences of strain 5J-6T are MN381952 and WTUZ00000000, respectively and the GenBank accession number for the genome sequence of Paenibacillus aceris KACC 19194T is JAAOZR000000000.

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Kim, J., Jung, H.S., Baek, J.H. et al. Paenibacillus silvestris sp. nov., Isolated from Forest Soil. Curr Microbiol 78, 822–829 (2021). https://doi.org/10.1007/s00284-020-02333-4

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