Skip to main content
Log in

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

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

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).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • 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 

  • 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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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 

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

    Article  CAS  Google Scholar 

  • 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 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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 

  • 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 

  • 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

    Article  CAS  Google Scholar 

  • 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 

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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • 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 

  • 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

    Article  CAS  Google Scholar 

  • 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 

  • 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 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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 

  • 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 

  • 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 

  • 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 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • 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 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Chapter  Google Scholar 

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

    Google Scholar 

  • 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 

  • 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 

  • 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

    Article  CAS  Google Scholar 

  • 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 

Download references

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).

Author information

Authors and Affiliations

Authors

Contributions

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.

Corresponding authors

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

Ethics declarations

Conflict of interest

The authors declare that they have no indirect or direct conflict of interest.

Ethical approval

This article does not contain any studies related to human participants or animals.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 313 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-018-1121-x

Keywords

Navigation