Skip to main content
SpringerLink
Log in

Paenibacillus puerhi sp. nov., isolated from the rhizosphere soil of Pu-erh tea plants (Camellia sinensis var. assamica)

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

An aerobic, Gram-staining-positive, rod-shaped, endospore-forming and motile bacterial strain, designated SJY2T, was isolated from the rhizosphere soil of tea plants (Camellia sinensis var. assamica) collected in the organic tea garden of the Jingmai Pu-erh tea district in Pu'er city, Yunnan, southwest China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Paenibacillus. The closest phylogenetic relative was Paenibacillus filicis DSM 23916T (98.1% similarity). The major fatty acids (> 10% of the total fatty acids) were anteiso-C15:0 and isoC16:0. The major respiratory quinone was MK-7 and the major polar lipid was diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The peptidoglycan contained glutamic acid, serine, alanine and meso-diaminopimelic acid. Genome sequencing revealed a genome size of 6.71 Mbp and a G + C content of 53.1%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA–DNA hybridization (dDDH) values suggested that strain SJY2T represents a new species, for which we propose the name Paenibacillus puerhi sp. nov. with the type strain SJY2T (= CGMCC 1.17156T = KCTC 43242T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

Abbreviations

ANI:

Average nucleotide identity

dDDH:

Digital DNA–DNA hybridization

COG:

Cluster of orthologous groups of proteins

CRISPR:

Clustered regularly interspaced short palindromic repeats

RNA:

Ribonucleic acid

tRNA:

Transfer ribonucleic acid

sRNA:

Small ribonucleic acid

LTR:

Long terminal repeat

LINE:

Long interspersed nuclear elements

SINE:

Short interspersed nuclear elements

RC:

Rolling circle

TR:

Terminal repeat

References

  • Ash C, Priest FG, Collins MD (1994) Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Anton Van Leeuwenhoek 64:253–260

    Article  CAS  Google Scholar 

  • Baik KS, Lim CH, Choe HN, Kim EM, Seong CN (2011) Paenibacillus rigui sp. nov., isolated from a freshwater wetland. Int J Syst Evol Microbiol 61:529–534

    Article  CAS  PubMed  Google Scholar 

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bernardet JF, Nakagawa Y, Holmes B, Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070

    PubMed  Google Scholar 

  • 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  PubMed  Google Scholar 

  • Carro L, Flores-Félix JD, Ramírez-Bahena MH, García-Fraile P, Martínez-Hidalgo P, Igual-José M, Tejedor C, Peix A, Velázquez E (2014) Paenibacillus lupini sp. nov., isolated from nodules of Lupinus albus. Int J Syst Evol Microbiol 64:3028–3033

    Article  CAS  PubMed  Google Scholar 

  • Da Costa MS, Albuquerque L, Nobre MF, Wait R (2011a) The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Methods Microbiol 38:197–206

    Article  Google Scholar 

  • Da Costa MS, Albuquerque L, Nobre MF, Wait R (2011b) The identification of polar lipids in prokaryotes. Method Microbiol 38:165–181

    Article  Google Scholar 

  • De Vos P, Ludwig W, Schleifer KH, Whitman WB (2010) Paenibacillaceae fam. nov. In list of new names and new combinations previously effectively, but not validly, published, validation list no. 132. Int J Syst Evol Microbiol 60:469–472

    Article  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  PubMed  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Galperin MY, Makarova KS, Wolf YI, Koonin EV (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43:261–269

    Article  Google Scholar 

  • Hasegawa T, Takizaea M, Tanida S (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29:319–322

    Article  CAS  Google Scholar 

  • Judicial Commission of the International Committee for Systematics of Prokaryotes (2005) The type species of the genus Paenibacillus Ash et al. 1994 is Paenibacillus polymyxa. Opinion 77. Int J Syst Evol Microbiol 55:513

  • Kim BC, Kim MN, Lee KH, Kwon SB, Bae KS, Shin KS (2009) Paenibacillus filicis sp. nov., isolated from the rhizosphere of the fern. J Microbiol 47:524–529

    Article  CAS  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 29:170–179

    Article  CAS  PubMed  Google Scholar 

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175

    Google Scholar 

  • Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714

    Article  CAS  PubMed  Google Scholar 

  • Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2:265–272

    Article  Google Scholar 

  • Lin SH, Liao YC (2013) CISA: contig integrator for sequence assembly of bacterial genomes. PLoS ONE 8:e60843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Förster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, König A, Liss T, Lüssmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) Arb: a software environment for sequence data. Nucleic Acids Res 32:1363–1371

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Murray R, Doetsch RN, Robinow CF (1994) Determinative and cytological light microscopy. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular biology. American Society for Microbiology, Washington, DC, pp 21–41

    Google Scholar 

  • Park DS, Jeong WJ, Lee KH, Oh HW, Kim BC, Bae KS, Park HY (2009) Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis. Int J Syst Evol Microbiol 59:1342–1347

    Article  CAS  PubMed  Google Scholar 

  • Piao AL, Feng XM, Nogi Y, Han L, Li Y, Lv J (2016) Sphingomonas qilianensis sp. nov., isolated from surface soil in the permafrost region of Qilian Mountains. China Curr Microbiol 72:363–369

    Article  CAS  PubMed  Google Scholar 

  • 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  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Scheldeman P, Goossens K, Rodriguez-Diaz M, Pil A, Goris J, Herman L, De Vos P, Logan Niall A, Heyndrickx M (2004) Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk. Int J Syst Evol Microbiol 54:885–891

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K (1997) 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 47:289–298

    Article  CAS  PubMed  Google Scholar 

  • Simpson JT, Wong K, Jackman SD, Schein JE, Jones Steven JM, Birol I (2009) ABySS: a parallel assembler for short read sequence data. Genome Res 19:1117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang SK, Wang Y, Chen Y, Lou K, Cao LL, Xu LH, Li WJ (2009) Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 59:2025–2031

    Article  CAS  PubMed  Google Scholar 

  • Yarza P, Richter M, Peplies J, Euzeby J, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R (2008) The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250

    Article  CAS  PubMed  Google Scholar 

  • Yoon JH, Seo WT, Shin YK, Kho YH, Kang KH, Park YH (2002) Paenibacillus chinjuensis sp. nov., a novel exopolysaccharide-producing bacterium. Int J Syst Evol Microbiol 52:15–21

    Article  Google Scholar 

  • 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  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Gao JS, Zhang S, Ali Sheirdil R, Wang XC, Zhang XX (2015) Paenibacillus rhizoryzae sp. nov., isolated from rice rhizosphere. Int J Syst Evol Microbiol 65:3053–3059

    Article  CAS  PubMed  Google Scholar 

  • Zhao ZL, Ming H, Ji WL, Khieu TN, Chu-Ky S, Cheng LJ, Meng XL, Li WJw, Nie GX (2018) Paenibacillus esterisolvens sp. nov., isolated from soil. Int J Syst Evol Microbiol 68:2145–2150

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by Yunnan Provincial Department of Science and Technology-Major Science and Technology Special Plan (Project2018ZG011) and Yunnan Provincial Key Programs of Yunnan Eco-friendly Food International Cooperation Research Center Project under Grant (Project2019ZG00909-02). We thank Prof. Bernhard Schink and Prof. Aharon Oren for the help of guidance about naming the novel species.

Author information

Authors and Affiliations

  1. Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China

    Rui-Juan Yang, Xuan-Jun Wang & Jun Sheng

  2. College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China

    Rui-Juan Yang

  3. College of Tea (Pu′er), West Yunnan University of Applied Sciences, Pu′er, 665000, Yunnan, China

    Rui-Juan Yang, Qiao-Mei Wang, Wen-Jie Zhang, Li Zhuang & Liang Yan

  4. Puer Institute of Pu-Erh Tea, Pu′er, 665000, Yunnan, China

    Rui-Juan Yang, Qiao-Mei Wang, Wen-Jie Zhang, Li Zhuang & Liang Yan

  5. College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China

    De Zhou & Jie Lv

  6. Puer Tea Science Research Institute, Pu′er, 665000, Yunnan, China

    Xing-Hua Wang

  7. College of Science, Yunnan Agricultural University, Kunming, 650201, China

    Xuan-Jun Wang

  8. State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Kunming, 650201, China

    Xuan-Jun Wang & Jun Sheng

Authors
  1. Rui-Juan Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. De Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Qiao-Mei Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xing-Hua Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wen-Jie Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Li Zhuang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xuan-Jun Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Liang Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jie Lv
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jun Sheng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Liang Yan, Jie Lv or Jun Sheng.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethics approval

This study does not describe any experimental work related to human.

Additional information

Communicated by Erko Stackebrandt.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

The GenBank/EMBL/DDBJ accession numbers for the genome and 16S rRNA sequence of SJY2T are WUWM00000000 and MN014063

Supplementary information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 928 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yang, RJ., Zhou, D., Wang, QM. et al. Paenibacillus puerhi sp. nov., isolated from the rhizosphere soil of Pu-erh tea plants (Camellia sinensis var. assamica). Arch Microbiol 203, 1375–1382 (2021). https://doi.org/10.1007/s00203-020-02135-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-020-02135-z

Keywords

Search

Navigation