1887

Abstract

A novel Gram-stain-positive, non-motile, rod-shaped bacterial strain designated LIP-1 was isolated from the contaminated soil of a pesticide factory in Xinyi, China, was investigated for its taxonomic allocation by a polyphasic approach. Cell growth occurred at 16–37 °C (optimum, 30 °C), in the presence of 0–2.0 % (w/v) NaCl (optimum, 0 %) and at pH 6.0–9.0 (optimum, pH 7.0). The major fatty acids of strain LIP-1 were anteiso-C (50.8 %), iso-C (17.6 %) and anteiso-C (17.4 %). The cell-wall peptidoglycan type was B2δ with 2,4-diaminobutyric acid as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and two unidentified glycolipids. The major menaquinones were MK-12 and MK-11. The genomic DNA G+C content was approximately 63.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LIP-1 formed a distinct clade within the radiation of the family and had the highest sequence similarity with Gsoil 259 (96.01 %) followed by SK1 (94.94 %). On the basis of the phylogenetic analyses and distinct phenotypic characteristics, a new genus, namely gen. nov., is proposed, harbouring the novel species gen. nov., sp. nov. with the type strain LIP-1 (=CCTCC AB 2015422=KCTC 39698).

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2016-12-01
2021-10-26
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References

  1. An S. Y., Xiao T., Yokota A. 2008; Schumannella luteola gen. nov., sp. nov., a novel genus of the family Microbacteriaceae . J Gen Appl Microbiol 54:253–258 [View Article][PubMed]
    [Google Scholar]
  2. Baik K. S., Park S. C., Kim H. J., Lee K. H., Seong C. N. 2010; Chryseoglobus frigidaquae gen. nov., sp. nov., a novel member of the family Microbacteriaceae . Int J Syst Evol Microbiol 60:1311–1316 [View Article][PubMed]
    [Google Scholar]
  3. Behrendt U., Ulrich A., Schumann P. 2001; Description of Microbacterium foliorum sp. nov. and Microbacterium phyllosphaerae sp. nov., isolated from the phyllosphere of grasses and the surface litter after mulching the sward, and reclassification of Aureobacterium resistens (Funke et al. 1998) as Microbacterium resistens comb. nov. Int J Syst Evol Microbiol 51:1267–1276 [View Article][PubMed]
    [Google Scholar]
  4. Beveridge T. J., Lawrence J. R., Murray R. G. E. 2007; Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology, 3rd edn. pp. 19–33 Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G. A., Schmidt T. M., Snyder L. R. Washington, DC: American Society of Microbiology;
    [Google Scholar]
  5. Cook D. M., Henriksen E. D., Rogers T. E., Peterson J. D. 2008; Klugiella xanthotipulae gen. nov., sp. nov., a novel member of the family Microbacteriaceae . Int J Syst Evol Microbiol 58:2779–2782 [View Article][PubMed]
    [Google Scholar]
  6. Dastager S. G., Lee J. C., Ju Y. J., Park D. J., Kim C. J. 2008; Cryobacterium mesophilum sp. nov., a novel mesophilic bacterium. Int J Syst Evol Microbiol 58:1241–1244 [View Article][PubMed]
    [Google Scholar]
  7. Evtushenko L. I., Dorofeeva L. V., Subbotin S. A., Cole J. R., Tiedje J. M. 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., 251 nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov. Int J Syst Evol Microbiol 50:371–380 [View Article]
    [Google Scholar]
  8. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [View Article][PubMed]
    [Google Scholar]
  9. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  10. Groth I., Schumann P., Weiss N., Martin K., Rainey F. A. 1996; Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 46:234–239 [View Article][PubMed]
    [Google Scholar]
  11. Han S. K., Nedashkovskaya O. I., Mikhailov V. V., Kim S. B., Bae K. S. 2003; Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. Int J Syst Evol Microbiol 53:2061–2066 [View Article][PubMed]
    [Google Scholar]
  12. Jang Y. H., Kim S. J., Hamada M., Tamura T., Ahn J. H., Weon H. Y., Suzuki K., Kwon S. W. 2012; Diaminobutyricimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. J Microbiol 50:1047–1052 [View Article][PubMed]
    [Google Scholar]
  13. Jang Y. H., Kim S. J., Tamura T., Hamada M., Weon H. Y., Suzuki K., Kwon S. W., Kim W. G. 2013; Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of Leifsonia kribbensis Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov. Int J Syst Evol Microbiol 63:1403–1410 [View Article][PubMed]
    [Google Scholar]
  14. Kämpfer P., Rainey F. A., Andersson M. A., Nurmiaho Lassila E. L., Ulrych U., Busse H. J., 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 50:355–363 [View Article][PubMed]
    [Google Scholar]
  15. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012a; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
    [Google Scholar]
  16. Kim S.-J., Jang Y.-H., Hamada M., Tamura T., Ahn J.-H., Weon H.-Y., Suzuki K., Kwon S.-W., Suzuki K. 2012b; Homoserinimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. J Microbiol 50:673–679 [View Article]
    [Google Scholar]
  17. Kim S. J., Tamura T., Hamada M., Ahn J. H., Weon H. Y., Park I. C., Suzuki K., Kwon S. W. 2012c; Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost. Int J Syst Evol Microbiol 62:2410–2416 [View Article][PubMed]
    [Google Scholar]
  18. Kim S. J., Moon J. Y., Hamada M., Tamura T., Weon H. Y., Suzuki K., Kwon S. W. 2013; Rudaibacter terrae gen. nov., sp. nov., isolated from greenhouse soil. Int J Syst Evol Microbiol 63:4052–4057 [View Article][PubMed]
    [Google Scholar]
  19. Kim S. J., Ahn J. H., Weon H. Y., Hamada M., Suzuki K., Kwon S. W. 2014; Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae . J Microbiol 52:527–533 [View Article][PubMed]
    [Google Scholar]
  20. Kluge A. G., Farris J. S. 1969; Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32 [View Article]
    [Google Scholar]
  21. Kuykendall L. D., Roy M. A., O'Neill J. J., Devine T. E. 1988; Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 38:358–361 [View Article]
    [Google Scholar]
  22. Lane D. L. 1991; 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics pp. 115–175 Edited by Stackebrandt E. R., Goodfellow M. Chichester: Wiley;
    [Google Scholar]
  23. Lee S. D. 2007; Labedella gwakjiensis gen. nov., sp. nov., a novel actinomycete of the family Microbacteriaceae . Int J Syst Evol Microbiol 57:2498–2502 [View Article][PubMed]
    [Google Scholar]
  24. Lee J. S., Lee K. C., Park Y. H. 2006; Microbacterium koreense sp. nov., from sea water in the South Sea of Korea. Int J Syst Evol Microbiol 56:423–427 [View Article][PubMed]
    [Google Scholar]
  25. Li H. R., Yu Y., Luo W., Zeng Y. X. 2010; Marisediminicola antarctica gen. nov., sp. nov., an actinobacterium isolated from the Antarctic. Int J Syst Evol Microbiol 60:2535–2539 [View Article][PubMed]
    [Google Scholar]
  26. Liu X. M., Chen K., Meng C., Zhang L., Zhu J. C., Huang X., Li S. P., Jiang J. D. 2014; Pseudoxanthobacter liyangensis sp. nov., isolated from dichlorodiphenyltrichloroethane-contaminated soil. Int J Syst Evol Microbiol 64:3390–3394 [View Article][PubMed]
    [Google Scholar]
  27. MacKenzie S. L. 1987; Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem 70:151–160[PubMed]
    [Google Scholar]
  28. Männistö M. K., Schumann P., Rainey F. A., Kämpfer P., Tsitko I., Tiirola M. A., Salkinoja-Salonen M. S. 2000; Subtercola boreus gen. nov., sp. nov. and Subtercola frigoramans sp. nov., two new psychrophilic actinobacteria isolated from boreal groundwater. Int J Syst Evol Microbiol 50:1731–1739 [View Article][PubMed]
    [Google Scholar]
  29. Mesbah M., Premachandran U., Whitman W. B. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167 [View Article]
    [Google Scholar]
  30. Miller L. T. 1982; Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxyacids. J Clin Microbiol 16:584–586[PubMed]
    [Google Scholar]
  31. Park Y. H., Suzuki K., Yim D. G., Lee K. C., Kim E., Yoon J., Kim S., Kho Y. H., Goodfellow M., Komagata K. 1993; Suprageneric classification of peptidoglycan group B actinomycetes by nucleotide sequencing of 5S ribosomal RNA. Antonie Van Leeuwenhoek 64:307–313 [View Article][PubMed]
    [Google Scholar]
  32. Park M. J., Kim M. K., Kim H. B., Im W. T., Yi T. H., Kim S. Y., Soung N. K., Yang D. C. 2008; Microbacterium ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol 58:429–433 [View Article][PubMed]
    [Google Scholar]
  33. Reddy G. S., Pradhan S., Manorama R., Shivaji S. 2010; Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil. Int J Syst Evol Microbiol 60:866–870 [View Article][PubMed]
    [Google Scholar]
  34. Robinson K. 1966; Some observations on the taxonomy of the genus Microbacterium. I. cultural and physiological reactions and heat resistance. J Appl Bacteriol 29:607–615 [View Article][PubMed]
    [Google Scholar]
  35. Saddler G. S., Tavecchia P., Lociuro S., Zanol M., Colombo L., Selva E. 1991; Analysis of madurose and other actinomycete whole cell sugars by gas chromatography. J Microbiol Methods 14:185–191 [View Article]
    [Google Scholar]
  36. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  37. Schleifer K. H. 1985; Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156 [CrossRef]
    [Google Scholar]
  38. Schleifer K. H., Kandler O. 1972; Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477[PubMed]
    [Google Scholar]
  39. Sheridan P. P., Loveland-Curtze J., Miteva V. I., Brenchley J. E. 2003; Rhodoglobus vestalii gen. nov., sp. nov., a novel psychrophilic organism isolated from an Antarctic Dry Valley lake. Int J Syst Evol Microbiol 53:985–994 [View Article][PubMed]
    [Google Scholar]
  40. Smibert R. M., Krieg N. R. 1994; Phenotypic characterization. In Methods for General and Molecular Bacteriology pp. 607–654 Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  41. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. 1997; Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491 [View Article]
    [Google Scholar]
  42. 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 47:474–478 [View Article][PubMed]
    [Google Scholar]
  43. Takeuchi M., Hatano K. 1998; Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium . Int J Syst Bacteriol 48 Pt 3:739–747 [View Article][PubMed]
    [Google Scholar]
  44. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. 2011; mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  45. Tel-Zur N., Abbo S., Myslabodski D., Mizrahi Y. 1999; Modified CTAB procedure for DNA isolation from epiphytic cacti of the genera Hylocereus and Selenicereus (Cactaceae). Plant Mol Biol Rep 17:249–254 [View Article]
    [Google Scholar]
  46. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [View Article][PubMed]
    [Google Scholar]
  47. Tiago I., Pires C., Mendes V., Morais P. V., da Costa M., Veríssimo A. 2005; Microcella putealis gen. nov., sp. nov., a gram-positive alkaliphilic bacterium isolated from a nonsaline alkaline groundwater. Syst Appl Microbiol 28:479–487 [View Article][PubMed]
    [Google Scholar]
  48. Tiago I., Morais P. V., da Costa M. S., Veríssimo A. 2006; Microcella alkaliphila sp. nov., a novel member of the family Microbacteriaceae isolated from a non-saline alkaline groundwater, and emended description of the genus Microcella . Int J Syst Evol Microbiol 56:2313–2316 [View Article][PubMed]
    [Google Scholar]
  49. Tindall B. J. 1990a; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [View Article]
    [Google Scholar]
  50. Tindall B. J. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  51. Tindall B. J., Sikorski J., Smibert R. M., Kreig N. R. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn. pp. 330–393 Edited by Reddy C. A., Beveridge T. J., Marzluf J. A., Schmidt T. M., Snyder L. R. Washington, DC: American Society of Microbiology;
    [Google Scholar]
  52. Vaz-Moreira I., Nobre M. F., Ferreira A. C., Schumann P., Nunes O. C., Manaia C. M. 2008; Humibacter albus gen. nov., sp. nov., isolated from sewage sludge compost. Int J Syst Evol Microbiol 58:1014–1018 [View Article][PubMed]
    [Google Scholar]
  53. Weon H.-Y., Kim S.-J., Jang Y.-H., Hamada M., Tamura T., Ahn J.-H., Suzuki K., Kwon S.-W. 2013; Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air. Int J Syst Evol Microbiol 63:2436–2441 [View Article][PubMed]
    [Google Scholar]
  54. Yokota A., Takeuchi M., Weiss N. 1993; Proposal of two new species in the genus Microbacterium: Microbacterium dextranolyticum sp. nov. and Microbacterium aurum sp. nov. Int J Syst Bacteriol 43:549–554 [View Article]
    [Google Scholar]
  55. Yoon J. H., Kang S. J., Schumann P., Oh T. K. 2006; Yonghaparkia alkaliphila gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an alkaline soil. Int J Syst Evol Microbiol 56:2415–2420 [View Article][PubMed]
    [Google Scholar]
  56. Zhang L., Song M., Cao Q., Wu S., Zhao Y., Huang J. W., Chen K., Li S. P., Xia Z. Y., Jiang J. D. 2015a; Camelimonas fluminis sp. nov., a cyhalothrin-degrading bacterium isolated from river water. Int J Syst Evol Microbiol 65:3109–3114 [View Article][PubMed]
    [Google Scholar]
  57. Zhang L., Zhou Q. X., Song M., Chen X. L., Xu X. H., Chen K., Li S. P., Jiang J. D. 2015b; Qingshengfania soli gen. nov., sp. nov., a member of the order Rhizobiales isolated from the soil of a pesticide factory. Int J Syst Evol Microbiol 65:4608–4614 [View Article][PubMed]
    [Google Scholar]
  58. Zhi X. Y., Li W. J., Stackebrandt E. 2009; An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59:589–608 [View Article][PubMed]
    [Google Scholar]
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