Pedobacter chitinilyticus sp. nov., a chitin-degrading bacterium isolated from wheat leaf tissue Free

Abstract

A bacterium, designated strain CM134L-2, was isolated from a chitin-enriched wheat leaf microbiome in Chengdu, Sichuan province, China. It was Gram-stain-negative, strictly aerobic, non-spore-forming, motile, rod-shaped, and bright yellow in colour. Strain CM134L-2 grew at 4–35 °C, at pH 6.0–9.0 and could use chitin as the only carbon resource. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CM134L-2 was most closely related to Pedobacter nanyangensis Q-4 (97.7 %) and Pedobacter zeaxanthinifaciens TDMA-5 (97.4 %). Digital DNA–DNA hybridization (dDDH) values between strain CM134L-2 with these two type strains were 26.8  and 20.8 %, respectively, and average nucleotide identity (ANI) values were 83.2 and 76.2 %; these values are lower than the proposed and generally accepted species boundaries of 70 % for dDDH and 95–96 % for ANI, which suggests strain CM134L-2 represents a novel species. The genomic DNA G+C content of strain CM134L-2 was 39.3 mol%, menaquinone-7 was the major respiratory quinone, phosphatidylethanolamine was the major polar lipid and the major components of the cellular fatty acids were iso-C15 : 0, and C16 : 1ω7c/C16 : 1ω6c (summed feature 3); these features supported the affiliation of strain CM134L-2 to the genus Pedobacter . Overall, strain CM134L-2 belongs to the genus Pedobacter , but can be classified as a novel species, for which the name Pedobacter chitinilyticus sp. nov. is proposed. The type strain is CM134L-2 (=CGMCC 1.16520=KCTC 62643).

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2018-10-11
2024-03-29
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References

  1. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K et al. 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 Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 1998; 48:165–177 [View Article][PubMed]
    [Google Scholar]
  2. Vanparys B, Heylen K, Lebbe L, de Vos P. Pedobacter caeni sp. nov., a novel species isolated from a nitrifying inoculum. Int J Syst Evol Microbiol 2005; 55:1315–1318 [View Article][PubMed]
    [Google Scholar]
  3. Hwang CY, Choi DH, Cho BC. Pedobacter roseus sp. nov., isolated from a hypertrophic pond, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2006; 56:1831–1836 [View Article][PubMed]
    [Google Scholar]
  4. Gallego V, García MT, Ventosa A. Pedobacter aquatilis sp. nov., isolated from drinking water, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2006; 56:1853–1858 [View Article][PubMed]
    [Google Scholar]
  5. Zhou Z, Jiang F, Wang S, Peng F, Dai J et al. Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus. Int J Syst Evol Microbiol 2012; 62:1963–1969 [View Article][PubMed]
    [Google Scholar]
  6. Farfán M, Montes MJ, Marqués AM. Reclassification of Sphingobacterium antarcticum Shivaji et al. 1992 as Pedobacter antarcticus comb. nov. and Pedobacter piscium (Takeuchi and Yokota 1993) Steyn et al. 1998 as a later heterotypic synonym of Pedobacter antarcticus. Int J Syst Evol Microbiol 2014; 64:863–868 [View Article][PubMed]
    [Google Scholar]
  7. du J, Singh H, Ngo HT, Won KH, Kim KY et al. 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 2015; 65:1241–1246 [View Article][PubMed]
    [Google Scholar]
  8. Margesin R, Shivaji S. Genus II. Pedobacter Steyn, Segers, Vancanneyt, Sandra, Kersters and Joubert 1998, 171VP. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ et al. (editors) Bergey’s Manual® of Systematic Bacteriology, 2nd ed. vol. 4 New York, NY, USA: Springer Science+Business Media, LLC; 2010 pp. 339–351
    [Google Scholar]
  9. Kook M, Park Y, Yi TH. Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. Int J Syst Evol Microbiol 2014; 64:1789–1794 [View Article][PubMed]
    [Google Scholar]
  10. Rasmussen MA, Madsen SM, Stougaard P, Johnsen MG. Flavobacterium sp. strain 4221 and Pedobacter sp. strain 4236 beta-1,3-glucanases that are active at low temperatures. Appl Environ Microbiol 2008; 74:7070–7072 [View Article][PubMed]
    [Google Scholar]
  11. Zhang H, Zhang J, Song M, Cheng MG, Wu YD et al. Pedobacter nanyangensis sp. nov., isolated from herbicide-contaminated soil. Int J Syst Evol Microbiol 2015; 65:3517–3521 [View Article][PubMed]
    [Google Scholar]
  12. Margesin R, Spröer C, Schumann P, Schinner F. Pedobacter cryoconitis sp. nov., a facultative psychrophile from alpine glacier cryoconite. Int J Syst Evol Microbiol 2003; 53:1291–1296 [View Article][PubMed]
    [Google Scholar]
  13. Qiu X, Qu Z, Jiang F, Ren L, Chang X et al. Pedobacter huanghensis sp. nov. and Pedobacter glacialis sp. nov., isolated from Arctic glacier foreland. Int J Syst Evol Microbiol 2014; 64:2431–2436 [View Article][PubMed]
    [Google Scholar]
  14. Gao JL, Sun P, Mao XJ, du YL, Liu BY et al. Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2017; 67:231–236 [View Article][PubMed]
    [Google Scholar]
  15. Alvin A, Miller KI, Neilan BA. Exploring the potential of endophytes from medicinal plants as sources of antimycobacterial compounds. Microbiol Res 2014; 169:483–495 [View Article][PubMed]
    [Google Scholar]
  16. Feng Y, Shen D, Song W. Rice endophyte Pantoea agglomerans YS19 promotes host plant growth and affects allocations of host photosynthates. J Appl Microbiol 2006; 100:938–945 [View Article][PubMed]
    [Google Scholar]
  17. Swiontek Brzezinska M, Jankiewicz U, Burkowska A, Walczak M. Chitinolytic microorganisms and their possible application in environmental protection. Curr Microbiol 2014; 68:71–81 [View Article][PubMed]
    [Google Scholar]
  18. Itoh T, Hibi T, Fujii Y, Sugimoto I, Fujiwara A et al. Cooperative degradation of chitin by extracellular and cell surface-expressed chitinases from Paenibacillus sp. strain FPU-7. Appl Environ Microbiol 2013; 79:7482–7490 [View Article][PubMed]
    [Google Scholar]
  19. Li Y, Zhang LL, Liu L, Tian YQ, Liu XF et al. Paludicola psychrotolerans gen. nov., sp. nov., a novel psychrotolerant chitinolytic anaerobe of the family Ruminococcaceae. Int J Syst Evol Microbiol 2017; 67:4100–4103 [View Article][PubMed]
    [Google Scholar]
  20. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991 pp. 115–175
    [Google Scholar]
  21. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67: [View Article][PubMed]
    [Google Scholar]
  22. Jeon YS, Lee K, Park SC, Kim BS, Cho YJ et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  25. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  26. 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]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. Kim DU, Kim YJ, Shin DH, Weon HY, Kwon SW et al. Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov. J Microbiol 2013; 51:25–30 [View Article][PubMed]
    [Google Scholar]
  30. Dai YM, Zhang LL, Li Y, Li YQ, Deng XH et al. Characterization of Trichococcus paludicola sp. nov. and Trichococcus alkaliphilus sp. nov., isolated from a high-elevation wetland, by phenotypic and genomic analyses. Int J Syst Evol Microbiol 2018; 68:99–105 [View Article][PubMed]
    [Google Scholar]
  31. 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]
  32. 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]
  33. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
    [Google Scholar]
  34. Yin Y, Mao X, Yang J, Chen X, Mao F et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2012; 40:W445–W451 [View Article][PubMed]
    [Google Scholar]
  35. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  36. Mata JA, Martínez-Cánovas J, Quesada E, Béjar V. A detailed phenotypic characterisation of the type strains of Halomonas species. Syst Appl Microbiol 2002; 25:360–375 [View Article][PubMed]
    [Google Scholar]
  37. Bernardet JF. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Micr 2002; 52:1049–1070
    [Google Scholar]
  38. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 611–651
    [Google Scholar]
  39. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  40. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  41. 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]
  42. Collins MD, Goodfellow M, Minnikin DE. Fatty acid, isoprenoid quinone and polar lipid composition in the classification of Curtobacterium and related taxa. J Gen Microbiol 1980; 118:29–37 [View Article][PubMed]
    [Google Scholar]
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