Pedobacter paludis sp. nov., isolated from wetland soil

  • Yuxiao Zhang
  • Jingxin Li
  • Jinling Wang
  • Gejiao Wang
Original Paper


A Gram-stain-negative, aerobic, non-motile, rod-shaped and non-spore-forming bacterium, designated YXT, was isolated from wetland soil. Compared to strain YXT, Pedobacter yonginense HMD1002T had the highest 16S rRNA gene sequence identity (97.8%), and the remaining strains had the identities below 97%. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain YXT grouped with P. yonginense HMD1002T. The values of DNA–DNA hybridization and genomic orthologous average nucleotide identity (orthoANI) between strain YXT and Pedobacter yonginense KCTC 22721T were 58.5% and 82.0%, respectively. The genome size of strain YXT was 5.0 Mb, comprising 4369 predicted genes with a DNA G+C content of 37.3 mol %. Strain YXT had menaquinone-7 as the only respiratory quinone and polar lipids of phosphatidylethanolamine, sphingolipid, aminolipid and three unidentified lipids. The predominant cellular fatty acids (> 10%) of strain YXT were summed feature 3 (iso-C15:0 2-OH and/or C16:1 ω7c), iso-C15:0 and iso-C17:0 3-OH. Strain YXT could be distinguished from the other Pedobacter members based on the data of phylogenetic distance, DNA–DNA hybridization, genomic orthoANI, RecA MLSA, core-protein comparison, and hydrolyses of l-arginine, utilization of d/l-lactate, l-alanine, 5-ketonic gluconate and glycogen. Therefore, strain YXT represents a novel species of the genus Pedobacter, for which the name Pedobacter paludis sp. nov. is proposed. The type strain is YXT (= KCTC 62520T = CCTCC AB 2018029T).


Pedobacter paludis Mining soil Polyphasic taxonomy 16S rRNA gene Genome 



We are grateful to Professor Prof. Bernhard Schink for the Latin construction of the species name. Fatty acids and polar lipid analyses were performed by Guangdong Detection Centre of Microbiology, P. R. China. This work was financially supported by the National Key Research and Development Program of China (2016YFD0800702) and National Natural Science Foundation of China (31870086).

Compliance with ethical standards

Conflict of interest

The authors declare that there are no conflicts of interest.

Supplementary material

203_2018_1605_MOESM1_ESM.pdf (480 kb)
Supplementary material 1 (PDF 480 KB)


  1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29CrossRefGoogle Scholar
  2. Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070PubMedGoogle Scholar
  3. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261CrossRefGoogle Scholar
  4. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466CrossRefGoogle Scholar
  5. Collins MD (1985) Isoprenoid quinone analysis in bacterial classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, London, pp 267–287Google Scholar
  6. Cowan ST, Steel KJ (1970) Manual for the identification of medical bacteria. Q Rev Biol 17Google Scholar
  7. Da X, Jiang F, Chang X, Ren L, Qiu X, Kan W, Zhang Y, Deng S, Fang C, Peng F (2015) Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica. Int J Syst Evol Microbiol 65:3841–3846CrossRefGoogle Scholar
  8. Dahal RH, Kim J (2016) Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 66:2205–2211CrossRefGoogle Scholar
  9. David M, Emms S, Kelly (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 16:157CrossRefGoogle Scholar
  10. De Ley J, Cattoir H, Reynaerts A (1970)) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142CrossRefGoogle Scholar
  11. Dong XZ, Cai MY (2001) Determinative manual for routine bacteriology. Scientific Press, BeijingGoogle Scholar
  12. Du J, Singh H, Ngo HT, Won KH, Kim KY, Yi TH (2015) Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 65:1241–1246CrossRefGoogle Scholar
  13. Fautz E, Reichenbach H (1980) A simple test for flexirubin-typepigments. FEMS Microbiol Lett 8:87–91CrossRefGoogle Scholar
  14. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Mol Biol Evol 17:368–376CrossRefGoogle Scholar
  15. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  16. Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ Jr (2011) Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinform 35(1):6.12.1–6.12.19Google Scholar
  17. Fitch WM (1971) Toward defining the course of evolution: minimumchange for a tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  18. Gao JL, Sun P, Mao XJ, Du YL, Liu BY, Sun JG (2017) Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 67:231–236CrossRefGoogle Scholar
  19. Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL, Holben WE, Gannon JE (2009) Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil. Int J Syst Evol Microbiol 59:1720–1726CrossRefGoogle Scholar
  20. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91CrossRefGoogle Scholar
  21. Hugh R, Leifson E (1953) The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 66:24–26PubMedPubMedCentralGoogle Scholar
  22. Hwang CY, Choi DH, Cho BC (2006) Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 56:1831–1836CrossRefGoogle Scholar
  23. Joung Y, Kim H, Joh K (2010) Pedobacter yonginense sp. nov., isolated from a mesotrophic artificial Lake in Korea. J Microbiol 48:536–540CrossRefGoogle Scholar
  24. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal-X version 2.0. Bioinformatics 23:2947–2948CrossRefGoogle Scholar
  25. 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 66:1100–1103CrossRefGoogle Scholar
  26. Li L, Stoeckert CJ Jr, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189CrossRefGoogle Scholar
  27. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B (2014) The Carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495CrossRefGoogle Scholar
  28. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39(D):225–229CrossRefGoogle Scholar
  29. Marmur J, Schildkraut CL, Doty P (1961) The reversible denaturation of DNA and its use in studies of nucleic acid homologies and the biological relatedness of microorganisms. J Chim Phys Physicochim Biol 58:945–955CrossRefGoogle Scholar
  30. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39:159–167CrossRefGoogle Scholar
  31. Moriya Y, Itoh M, Okuda S, Yoshizawa A, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:182–185CrossRefGoogle Scholar
  32. Prescott LM, Harley JP (2001) The effects of chemical agents on bacteria II: antimicrobial agents (Kirby–Bauer Method). In: Prescott LM, Harley P (eds) Laboratory exercises in microbiology. McGraw-Hill, New York, pp 257–262Google Scholar
  33. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  34. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. In: MIDI Technical Note. MIDI Inc, NewarkGoogle Scholar
  35. Sawabe T, Kita-Tsukamoto K, Thompson FL (2007) Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. J Bacteriol 189:7932–7936CrossRefGoogle Scholar
  36. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K, Joubert JJ (1998) Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. proposal of the family Sphingobact. Int J Syst Bacteriol 48:165–177CrossRefGoogle Scholar
  37. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) Mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefGoogle Scholar
  38. Tarrand JJ, Gröschel DH (1982) Rapid, modified oxidase test for oxidase-variable bacterial isolates. J Clin Microbiol 16:772–774PubMedPubMedCentralGoogle Scholar
  39. Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202CrossRefGoogle Scholar
  40. Wang B, Li X, Zheng F, Liu R, Quan J, Liang H, Guo S, Guo G, Zhang J (2007) pEGFP-T, a novel T-vector for the direct, unidirectional cloning and analysis of PCR-amplified promoters. Biotechnol Lett 29:309–312CrossRefGoogle Scholar
  41. Weisburg WG, Barns SM, Pelletier BA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703CrossRefGoogle Scholar
  42. Wu S, Zhu ZW, Fu L, Li W (2011) WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genom 12:444CrossRefGoogle Scholar
  43. Yoon JH, Kang SJ, Oh TK (2007) Pedobacter terrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 57:2462–2466CrossRefGoogle Scholar
  44. Yoon SH, Sm H, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Yuxiao Zhang
    • 1
  • Jingxin Li
    • 1
  • Jinling Wang
    • 2
  • Gejiao Wang
    • 1
  1. 1.State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanPeople’s Republic of China
  2. 2.College of Basic ScienceHuazhong Agricultural UniversityWuhanPeople’s Republic of China

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