Actinoplanes deserti sp. nov., isolated from a desert soil sample

Abstract

A novel actinomycete, designated strain YIM CF22T, was isolated from a desert soil sample collected from Turpan in Xinjiang Uyghur Autonomous Region, north-western China. The taxonomic position of the strain YIM CF22T is described based on a polyphasic approach. Strain YIM CF22T was found to form irregular sporangia on agar media. It contains meso-diaminopimelic acid in the cell wall peptidoglycan. The major menaquinone was identified as MK-9(H4); the polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified phospholipids and two unidentified glycolipids. The whole cell sugars were found to be ribose, mannose, galactose, glucose and xylose. The major cellular fatty acids were found to be (> 5%) iso-C16:0 (43.5%), anteiso-C17:0 (10.2%), iso-C15:0 (7.1%), C17:1 ω8c (6.3%) and iso H-C16:1 (5.9%). The G+C content was determined to be 70.8%. 16S rRNA gene sequence analysis of strain YIM CF22T showed high similarity (97.0%) to Actinoplanes rishiriensis NBRC 108556T. The strain also showed high 16S rRNA gene sequence similarities to Verrucosispora sediminis CGMCC 4.3550T (96.9%) and Micromonospora tulbaghiae DSM 45142T (96.8%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM CF22T clusters with A. rishiriensis NBRC 108556T, Actinoplanes globisporus JCM 3186T and Actinoplanes rhizophilus NEAU-A-2T. Based on the differential phenotypic characteristics and the results of DNA–DNA relatedness and phylogenetic analysis, it is proposed that strain YIM CF22T represents a novel species of the genus Actinoplanes, for which the name Actinoplanes deserti sp. nov. is proposed. The type strain is YIM CF22T (= KCTC 39543T = CCTCC AB2018113T).

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References

  1. Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz MDC, Sahin N, Smith DL, Kim KE, Peluso P, Deshpande S, Woyke T, Shapiro N, Kyrpides NC, Klenk HP, Göker M, Goodfellow M (2018) Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 8:1–23

    Article  Google Scholar 

  2. Cerny G (1978) Studies on the aminopeptidase test for the distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5:113–122

    CAS  Article  Google Scholar 

  3. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    CAS  Article  Google Scholar 

  4. Couch JN (1950) Actinoplanes, a new genus of the Actinomycetales. J Elisha Mitchell Sci 66:87–92

    Google Scholar 

  5. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP, Xu LH, Jiang CL (2001) Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51:357–363

    CAS  Article  Google Scholar 

  6. Dai HQ, Wang J, Xin YH, Pei G, Tang SK, Ren B, Ward A, Ruan JS, Li WJ, Zhang LX (2010) Verrucosispora sediminis sp nov., a cyclodipeptide-producing actinomycete from deep-sea sediment. Int J Syst Evol Microbiol 60:1807–1812

    CAS  Article  Google Scholar 

  7. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution well as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

    Article  Google Scholar 

  8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    CAS  Article  Google Scholar 

  9. Gordon RE, Barnett DA, Handerhan JE, Pang CHN (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63

    Article  Google Scholar 

  10. He H, Xing J, Liu C, Li C, Ma Z, Li J, Xiang W, Wang X (2015) Actinoplanes rhizophilus sp. nov., an actinomycete isolated from the rhizosphere of Sansevieria trifasciata Prain. Int J Syst Evol Microbiol 65:4763–4768

    CAS  Article  Google Scholar 

  11. Hu HY, Lim BR, Goto N, Fujie K (2001) Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples. J Microbiol Methods 47:17–24

    CAS  Article  Google Scholar 

  12. Kaewkla O, Thamchaipenet A, Franco CM (2017) Micromonospora terminaliae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of the medicinal plant Terminalia mucronata. Int J Syst Evol Microbiol 67:225–230

    Article  Google Scholar 

  13. Kelly KL (1964) Inter-society color council-national bureau of standards color name charts illustrated with centroid colors. US Government Printing Office, Washington, DC

    Google Scholar 

  14. Kirby BM, Meyers PR (2010) Micromonospora tulbaghiae sp. nov., isolated from the leaves of wild garlic, Tulbaghia violacea. Int J Syst Evol Microbiol 60:1328–1333

    CAS  Article  Google Scholar 

  15. Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. In: Colwell RR, Grigorova R (eds) Methods in microbiology. Academic Press, Orlando

    Google Scholar 

  16. Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703–704

    CAS  Article  Google Scholar 

  17. Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367

    CAS  Article  Google Scholar 

  18. Larkin MA, Blackshields G, Brown N, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948

    CAS  Article  Google Scholar 

  19. Lechevalier MP, Bievre CD, Lechevalier H (1977) Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260

    CAS  Article  Google Scholar 

  20. Li WJ, Xu P, Schuman P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China) and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    Article  Google Scholar 

  21. Li SH, Yu XY, Park DJ, Hozzein WN, Kim CJ, Shu WS, Wadaan MA, Ding LX, Li WJ (2015) Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique. Antonie Van Leeuwenhoek 107:357–366

    CAS  Article  Google Scholar 

  22. Locci R (1989) Streptomyces and related genera. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2451–2508

    Google Scholar 

  23. Marcone GL, Binda E, Reguzzoni M, Gastaldo L, Dalmastri C, Marinelli F (2017) Classification of Actinoplanes sp. ATCC 33076, an actinomycete that produces the glycolipodepsipeptide antibiotic ramoplanin, as Actinoplanes ramoplaninifer sp. nov. Int J Syst Evol Microbiol 67:4181–4188

    Article  Google Scholar 

  24. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    CAS  Article  Google Scholar 

  25. Minnikin DE, O’donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinines and polar lipids. J Microbiol Methods 2:233–241

    CAS  Article  Google Scholar 

  26. Ngaemthao W, Chunhametha S, Suriyachadkun C (2016) Actinoplanes subglobosus sp. nov., isolated from mixed deciduous forest soil. Int J Syst Evol Microbiol 66:4850–4855

    Article  Google Scholar 

  27. Qu Z, Bao XD, Xie QY, Zhao YX, Yan B, Dai HF, Chen HQ (2018) Actinoplanes sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 68:71–75

    Article  Google Scholar 

  28. 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 110:455–456

    Article  Google Scholar 

  29. 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 

  30. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:16

    Google Scholar 

  31. Sazak A, Sahin N, Camas M (2012) Actinoplanes abujensis sp. nov., isolated from Nigerian arid soil. Int J Syst Evol Microbiol 62:960–965

    CAS  Article  Google Scholar 

  32. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  33. Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Tamura T, Hatano K (2001) Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al.1986 and ‘Actinoplanes aurantiacus’ to Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov. Int J Syst Evol Microbiol 51:2119–2125

    CAS  Article  Google Scholar 

  35. 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

    CAS  Article  Google Scholar 

  36. 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

    CAS  Article  Google Scholar 

  37. Uchida K, Aida KO (1984) An improved method for the glycolate test for simple identification of the acyl type of bacterial cell walls. J Gen Appl Microbiol 30:131–134

    CAS  Article  Google Scholar 

  38. Vobis G (2006) The genus Actinoplanes and related genera. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) In the prokaryotes: a handbook on the biology of bacteria, vol 3, 3rd edn. Springer, New York, pp 623–653

    Google Scholar 

  39. Waksman SA (1961) The actinomycetes, vol 2. Williams & Wilkins, Baltimore

    Google Scholar 

  40. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  41. Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Williams ST, Sharpe ME, HoltBergey’s JG (eds) Manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2452–2492

    Google Scholar 

  42. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    CAS  Article  Google Scholar 

  43. 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  Google Scholar 

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Acknowledgements

The authors are grateful to Prof. Wensheng Xiang (Northeast Agricultural University, China) and Dr. Tamura Tomohiko (NBRC, Japan) for their kind providing the reference type strains. This research was supported by Xinjiang Uygur Autonomous Region regional coordinated innovation project (Shanghai cooperation organization science and technology partnership program) (No. 2017E01031) and China Biodiversity Observation Networks (Sino BON). W-J Li is supported by project funded by Guangdong Province Higher Vocational Colleges & Schools Pearl River Scholar Funded Scheme (2014).

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NH, IUK, XC and WJL conducted this study. NH, IUK, XC and MX performed the experiments. XYZ and WJL supervised the experiments. NH, IUK, SL and BZF wrote the manuscript. All of the authors assisted in writing the manuscript, discussed the results and commented on the manuscript.

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Correspondence to Xiao-Yang Zhi or Wen-Jun Li.

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Habib, N., Khan, I.U., Chu, X. et al. Actinoplanes deserti sp. nov., isolated from a desert soil sample. Antonie van Leeuwenhoek 111, 2303–2310 (2018). https://doi.org/10.1007/s10482-018-1121-x

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Keywords

  • Actinoplanes deserti sp. nov.
  • Desert soil
  • Turpan desert Xinjiang
  • Polyphasic taxonomy