Cryobacterium tepidiphilum sp. nov., isolated from rhizosphere soil of lettuce (var. ramosa Hort.)

  • Ying Wang
  • Peng Cao
  • Peng Sun
  • Junwei Zhao
  • Xiujun Sun
  • Ji Zhang
  • Chenxu Li
  • Wensheng XiangEmail author
  • Xiangjing WangEmail author
Original Paper


A Gram-stain positive, aerobic, rod-shaped bacterium, designated strain NEAU-85T, was isolated from rhizosphere soil of lettuce and characterised using a polyphasic approach. Strain NEAU-85T was found to be catalase positive, motile and able to grow at between 10 and 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NEAU-85T belongs to the genus Cryobacterium and is closely related to the type strain Cryobacterium psychrotolerans JCM 13925T (98.5%) and also to Leifsonia kafniensis NCCB 100216T (97.6%). Multilocus sequence analysis using the concatenated gene sequences of the atpD, dnaK, recA, rpoB, sevY and ychF genes showed that strain NEAU-85T belongs to the genus Cryobacterium. The digital DNA–DNA hybridization values revealed that strain NEAU-85T is distinct from its close phylogenetic neighbour C. psychrotolerans. The menaquinones were identified as MK-10 and MK-11. The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylglycerol, phospholipid, an unidentified glycolipid and an unidentified lipid. The major fatty acids were identified as anteiso-C15:0, anteiso-C15:1 and iso-C16:0. The genomic DNA G + C content of strain NEAU-85T was determined to be 68.9 mol%. The DNA–DNA hybridization value between them was less than 70%. On the basis of phenotypic, genotypic and phylogenetic data, strain NEAU-85T can be concluded to represent a novel species of the genus Cryobacterium, for which the name Cryobacterium tepidiphilum sp. nov. is proposed. The type strain is NEAU-85T (= CCTCC AA 2018035T = JCM 32545T).


Cryobacterium tepidiphilum sp. nov. Polyphasic analysis 16S rRNA gene Rhizosphere soil of lettuce 



Multilocus sequence analysis


ATP synthase, beta subunit


Chaperone protein DnaK


Homologous recombination factor


RNA polymerase, beta subunit


Protein translocase subunit


GTP-binding and nucleic acid-binding protein


International Streptomyces Project






Unidentified phospholipid


Unidentified glycolipid


Unidentified lipids


Inter-society color council-national bureau of standards


Saline-sodium citrate


Gas chromatography–mass spectrometer


Molecular evolutionary genetics analysis


China center for type culture collection


Japan collection of microorganisms



This work was supported in part by grants from the National Natural Science Foundation of China (No. 31772240). We are grateful to Prof. Aharon Oren for helpful advice on the specific epithet.

Author Contributions

YW performed the laboratory experiments, analysed the data, and drafted the manuscript with PC. PS contributed to the biochemical characterisation. XS contributed to the polyphasic taxonomy. CL contributed to the morphological analyses. JZ contributed to the fatty acids determination. JZ participated in the discussions of each section of experiments. XW and WX designed the experiments and revised the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

This article does not contain any studies with human participants and/or animals performed by any of the authors. The formal consent is not required in this study.

Supplementary material

10482_2019_1287_MOESM1_ESM.docx (1.9 mb)
Supplementary material 1 (DOCX 1989 kb)


  1. Bajerski F, Ganzert L, Mangelsdorf K, Lipski A, Wagner D (2011) Cryobacterium arcticum sp. nov., a novel psychrotolerant species from an Arctic soil. Int J Syst Evol Microbiol 61:1849–1853CrossRefGoogle Scholar
  2. Chun J, Rainey FA (2014) Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 64:316–324CrossRefGoogle Scholar
  3. Collins MD (1985) Chemical methods in bacterial systematics. In: Goodfellow M, Minnikin DE (eds) Isoprenoid quinone analyses in bacterial classification and identification. Academic Press, London, pp 267–284Google Scholar
  4. Collins MD, Jones D, Kroppenstedt RM (1983) Reclassification of Brevibacterium imperiale (Steinhaus) and “Corynebacterium laevaniformans” (Dias and Bhat) in a redefined genus Microbacterium (Orla-Jensen), as Microbacterium imperiale comb. nov. and Microbacterium laevaniformans nom. rev.; comb. nov. Syst Appl Microbiol 4:65–78CrossRefGoogle Scholar
  5. Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ (2008) Cryobacterium mesophilum sp. nov., a novel mesophilic bacterium. Int J Syst Evol Microbiol 58:1241–1244CrossRefGoogle Scholar
  6. Dhotre DP, Rajabal V, Sharma A, Kulkarni GJ, Prakash O, Vemuluri VR, Joseph N, Rahi P, Shouche YS (2017) Reclassification of Phycicola gilvus (Lee et al. 2008) and Leifsonia pindariensis (Reddy et al. 2008) as Microterricola gilva comb. nov. and Microterricola pindariensis comb. nov. and emended description of the genus Microterricola. Int J Syst Evol Microbiol 67:2766–2772CrossRefGoogle Scholar
  7. Evtushenko LI, Dorofeeva LV, Subbotin SA, Cole JR, Tiedje JM (2000) Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of ‘Corynebacterium aquaticum’ Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov. Int J Syst Evol Microbiol 50:371–380CrossRefGoogle Scholar
  8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefGoogle Scholar
  9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:83–791CrossRefGoogle Scholar
  10. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  11. Fu Y, Yan R, Liu D, Jiang S, Cui L (2019) Trinickia diaoshuihuensis sp. nov., a plant growth promoting bacterium isolated from soil. Int J Syst Evol Microbiol 69:291–296CrossRefGoogle Scholar
  12. Gao RX, Liu CX, Zhao JW, Jia FY, Yu C, Yang LY, Wang XJ, Xiang WS (2014) Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora. Antonie Van Leeuwenhoek 105:307–315CrossRefGoogle Scholar
  13. Gordon RE, Barnett DA, Handerhan JE, Pang C (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63CrossRefGoogle Scholar
  14. Groth I, Schumann P, Weiss N, Martin K, Rainey FA (1996) Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 46:234–239CrossRefGoogle Scholar
  15. Inoue K (1976) Quantitative ecology of microorganisms of Showa Station in Antarctica and isolation of psychrophiles. J Gen Appl Microbiol 22:143–150CrossRefGoogle Scholar
  16. Jones KL (1949) Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 57:141–145Google Scholar
  17. Kämpfer P, Rainey FA, Andersson MA, Nurmiaho Lassila EL, Ulrych U, Busse HJ, Weiss N, Mikkola R, Salkinoja-Salonen M (2000) Frigoribacterium faeni gen. nov., sp. nov., a novel psychrophilic genus of the family Microbacteriaceae. Int J Syst Evol Microbiol 50:355–363CrossRefGoogle Scholar
  18. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow M (2000) Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 50:2031–2036CrossRefGoogle Scholar
  19. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefGoogle Scholar
  20. Komagata K, Suzuki K (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207CrossRefGoogle Scholar
  21. Kumar S, Stecher G, Tamura K (2016) Mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  22. Lechevalier MP, Lechevalier HA (1980) The chemotaxonomy of actinomycetes. In: Dietz A, Thayer DW (eds) Actinomycete taxonomy special publication, vol 6. Society of Industrial Microbiology, Arlington, pp 227–291Google Scholar
  23. Lee SD (2007) Labedella gwakjiensis gen. nov., sp. nov., a novel actinomycete of the family Microbacteriaceae. Int J Syst Evol Microbiol 57:2498–2502CrossRefGoogle Scholar
  24. Leifson E (1960) Atlas of bacterial flagellation. Academic Press, LondonCrossRefGoogle Scholar
  25. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714CrossRefGoogle Scholar
  26. Li R, Zhu H, Ruan J, Qian W, Fang X (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272CrossRefGoogle Scholar
  27. Liu Q, Liu HC, Wen Y, Zhou YG, Xin YH (2012) Cryobacterium flavum sp. nov. and Cryobacterium luteum sp. nov., isolated from glacier ice. Int J Syst Evol Microbiol 62:1296–1299CrossRefGoogle Scholar
  28. Liu Q, Liu H, Zhang J, Zhou Y, Xin Y (2013) Cryobacterium levicorallinum sp. nov. a psychrophilic bacterium isolated from glacier ice. Int J Syst Evol Microbiol 63:2819CrossRefGoogle Scholar
  29. Liu Q, Xin YH, Chen XL, Liu HC, Zhou YG, Chen WX (2018) Cryobacterium aureum sp. nov. a psychrophilic bacterium isolated from glacier ice collected from the ice tongue surface. Int J Syst Evol Microbiol 68:1173–1176CrossRefGoogle Scholar
  30. Liu Q, Liu HC, Zhou YG, Xin YH (2019) Genetic diversity of glacier-inhabiting Cryobacterium bacteria in China and description of Cryobacterium zongtaii sp. nov. and Arthrobacter glacialis sp. nov. Syst Appl Microbiol 42:168–177CrossRefGoogle Scholar
  31. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal K, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
  32. Piao CY, Zheng WW, Li Y, Liu CX, Jin LY, Song W, Yan K, Wang XJ, Xiang WS (2017) Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr. Arch Microbiol 199(7):963–970CrossRefGoogle Scholar
  33. Pindi Pavan Kumar, Hara Kishore K, Reddy GSN, Shivaji S (2009) Description of Leifsonia kafniensis sp. nov. and Leifsonia antarctica sp. nov. Int J Syst Evol Microbiol 59:1348–1352CrossRefGoogle Scholar
  34. Reddy GSN, Pradhan S, Manorama R, Shivaji S (2010) Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil. Int J Syst Evol Microbiol 60:866–870CrossRefGoogle Scholar
  35. Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131CrossRefGoogle Scholar
  36. Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and Bacteria. Antonie Van Leeuwenhoek 110:455–456CrossRefGoogle Scholar
  37. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  38. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340CrossRefGoogle Scholar
  39. Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams and Wilkins, BaltimoreGoogle Scholar
  40. Smibert RM, Krieg NR (1994) Phenotypic characterisation. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, New York, pp 607–654Google Scholar
  41. Suzuki K, Sasaki J, Uramoto M, Nakase T, Komagata K (1997) Cryobacterium psychrophilum gen. nov., sp. nov., nom. rev., comb. nov., an obligately psychrophilic actinomycete to accommodate ‘Curtobacterium psychrophilum’ Inoue and Komagata 1976. Int J Syst Bacteriol 47:474–478CrossRefGoogle Scholar
  42. Waksman SA (1961) The actinomycetes, vol. 2, classification, identification and descriptions of genera and species. Williams and Wilkins, BaltimoreGoogle Scholar
  43. Waksman SA (1967) The actinomycetes a summary of current knowledge. Ronald Press, New YorkGoogle Scholar
  44. Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams and Wilkins, Baltimore, pp 2452–2492Google Scholar
  45. Wu C, Lu X, Qin M, Wang Y, Ruan J (1989) Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing)] 16:176–178Google Scholar
  46. Xiang WS, Liu CX, Wang XJ, Du J, Xi LJ, Huang Y (2011) Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 61:1165–1169CrossRefGoogle Scholar
  47. Yokota A, Tamura T, Hasegawa T, Huang LH (1993) Catenuloplanes japonicas gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 43:805–812CrossRefGoogle Scholar
  48. 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 67:1613–1617CrossRefGoogle Scholar
  49. Zhang DC, Wang HX, Cui HL, Yang Y, Liu HC, Dong XZ, Zhou PJ (2007a) Cryobacterium psychrotolerans sp. nov., a novel psychrotolerant bacterium isolated from the China No. 1 glacier. Int J Syst Evol Microbiol 57:866–869CrossRefGoogle Scholar
  50. Zhang L, Xu Z, Patel BK (2007b) Frondicola australicus gen. nov., sp. nov., isolated from decaying leaf litter from a pine forest. Int J Syst Evol Microbiol 57:1177–1182CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Ying Wang
    • 1
  • Peng Cao
    • 1
  • Peng Sun
    • 1
  • Junwei Zhao
    • 1
  • Xiujun Sun
    • 1
  • Ji Zhang
    • 1
  • Chenxu Li
    • 1
  • Wensheng Xiang
    • 1
    • 2
    Email author
  • Xiangjing Wang
    • 1
    Email author
  1. 1.Key Laboratory of Agricultural Microbiology of Heilongjiang ProvinceNortheast Agricultural UniversityHarbinPeople’s Republic of China
  2. 2.State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China

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