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Amycolatopsis umgeniensis sp. nov., isolated from soil from the banks of the Umgeni River in South Africa

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Abstract

A novel member of the genus Amycolatopsis was isolated from soil collected from the banks of the Umgeni River, KwaZulu Natal province, South Africa. The strain, designated UM16T, grouped with the type strains of Amycolatopsis alba, Amycolatopsis coloradensis and Amycolatopsis thailandensis by 16S rRNA gene based phylogeny. Genetic distance values, based on the gyrB and recN genes, between strain UM16T and its closest relatives were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis type strains. DNA–DNA hybridisation experiments confirmed that strain UM16T represents a unique genomic species, sharing 18.4 ± 5.1, 16.2 ± 1.8 and 45.8 ± 8.9 % DNA relatedness to the type strains of A. alba, A. coloradensis and A. thailandensis, respectively. The physiological, phylogenetic and DNA-relatedness data support the description of strain UM16T as the type strain of a novel species, for which the name Amycolatopsis umgeniensis sp. nov. is proposed (= DSM 45272T = NRRL B-24724T).

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References

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 25:3389–3402

    Article  PubMed  CAS  Google Scholar 

  • Atlas RM (2004) Handbook of microbiological media, 3rd edn. CRC Press, Boca Raton

    Book  Google Scholar 

  • Bala S, Khanna R, Dadhwal M, Prabagaran SR, Shivaji S, Cullum J, Lal R (2004) Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov. Int J Syst Evol Microbiol 54:1145–1149

    Article  PubMed  CAS  Google Scholar 

  • Camas M, Sahin N, Sazak A, Spröer C, Klenk H-P (2012) Amycolatopsis magusensis sp. nov., isolated from Northern Cyprus soil. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.042770-0

  • Chomchoei A, Pathom-aree W, Yokota A, Kanongnuch C, Lumyong S (2011) Amycolatopsis thailandensis sp. nov., a poly(l-lactic acid)-degrading actinomycete, isolated from soil. Int J Syst Evol Microbiol 61:839–843

    Article  PubMed  CAS  Google Scholar 

  • Chou S, Chedore P, Kasatiya S (1998) Use of gas chromatographic fatty acid and mycolic acid cleavage product determination to differentiate among Mycobacterium genavense, Mycobacterium fortuitum, Mycobacterium simiae and Mycobacterium tuberculosis. J Clin Microbiol 36:577–579

    PubMed  CAS  Google Scholar 

  • Cook AE, Meyers PR (2003) Rapid identification of filamentous actinomycetes to the genus level using genus-specific 16S-rRNA gene restriction fragment patterns. Int J Syst Evol Microbiol 53:1907–1915

    Article  PubMed  CAS  Google Scholar 

  • Curtis SM, Meyers PR (2012) Multilocus sequence analysis of the actinobacterial genus Kribbella. Syst Appl Microbiol. doi:10.1016/j.syapm.2012.08.001

  • De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142

    Article  PubMed  Google Scholar 

  • Euzéby JP (2012) List of prokaryotic names with standing in nomenclature. http://www.bacterio.cict.fr/a/amycolatopsis.html. Accessed August 2012

  • Everest GJ, Meyers PR (2008) Kribbella hippodromi sp. nov., isolated from soil from a racecourse in South Africa. Int J Syst Evol Microbiol 58:443–446

    Article  PubMed  CAS  Google Scholar 

  • Everest GJ, Meyers PR (2009) The use of gyrB gene sequence analysis in the phylogeny of the genus Amycolatopsis. Antonie Van Leeuwenhoek 95:1–11

    Article  PubMed  CAS  Google Scholar 

  • Everest GJ, Meyers PR (2011) Evaluation of the antibiotic biosynthetic potential of the genus Amycolatopsis and description of Amycolatopsis circi sp. nov., Amycolatopsis equina sp. nov. and Amycolatopsis hippodromi sp. nov. J Appl Microbiol 111:300–311

    Article  PubMed  CAS  Google Scholar 

  • Everest GJ, Cook AE, Kirby BM, Meyers PR (2011) Evaluation of the use of recN sequence analysis in the phylogeny of the genus Amycolatopsis. Antonie Van Leeuwenhoek 100:483–496

    Article  PubMed  Google Scholar 

  • Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid–deoxyribonucleic acid hybridization in microdilution wells 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  PubMed  CAS  Google Scholar 

  • Gevers D, Huys G, Swings J (2001) Application of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 205:31–36

    Article  PubMed  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Hasegawa T, Takizawa M, Tanida S (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29:319–322

    Article  CAS  Google Scholar 

  • Henssen A, Kothe HW, Kroppenstedt RM (1987) Transfer of Pseudonocardia azurea and “Pseudonocardia fastidiosa” to the genus Amycolatopsis, with emended species description. Int J Syst Bacteriol 37:292–295

    Article  Google Scholar 

  • Huss VAR, Festl H, Schleifer KH (1983) Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192

    Article  PubMed  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  • Komagata K, Suzuki KL (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–207

    Article  CAS  Google Scholar 

  • Labeda DP (1995) Amycolatopsis coloradensis sp. nov., the Avoparcin (LL-AV290)-producing strain. Int J Syst Bacteriol 45:124–127

    Article  Google Scholar 

  • le Roes M, Goodwin CM, Meyers PR (2008) Gordonia lacunae sp. nov., isolated from an estuary. Syst Appl Microbiol 31:17–23

    Article  PubMed  Google Scholar 

  • Lechevalier MP, Lechevalier H (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443

    Article  CAS  Google Scholar 

  • Lechevalier MP, Prauser H, Labeda DP, Ruan JS (1986) Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 36:29–37

    Article  Google Scholar 

  • Lee SD (2009) Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis. Int J Syst Evol Microbiol 59:1401–1404

    Article  PubMed  CAS  Google Scholar 

  • Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M (1980) Thin layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr 188:221–233

    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 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Sensi P, Greco AM, Ballotta R (1959) Rifomycin I. Isolation and properties of rifomycin B and rifomycin complex. Antibiot Annu 7:262–270

    PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Takahashi K, Nei M (2000) Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 17:1251–1258

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Tang SK, Wang Y, Guan TW, Lee JC, Kim CJ, Li WJ (2010) Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake. Int J Syst Evol Microbiol 60:1073–1078

    Article  PubMed  CAS  Google Scholar 

  • Thomson CJ, Power E, Ruebsamen-Waigmann H, Labischinski H (2004) Antibacterial research and development in the 21st Century: an industry perspective of the challenges. Curr Opin Microbiol 7:445–450

    Article  PubMed  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) 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, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams and Wilkins, Baltimore, pp 2452–2492

    Google Scholar 

  • Wink J, Kroppenstedt RM, Ganguli BM, Nadkarni SR, Schumann P, Seibert G, Stackebrandt E (2003) Three new antibiotic producing species of the genus Amycolatopsis, Amycolatopsis balhimycina sp. nov., A. tolypomycina sp. nov., A. vancoresmycina sp. nov., and description of Amycolatopsis keratiniphila subsp. keratiniphila subsp. nov. and A. keratiniphila subsp. nogabecina subsp. nov. System Appl Microbiol 26:38–46

    Article  CAS  Google Scholar 

  • Wood SA, Kirby BM, Goodwin CM, le Roes M, Meyers PR (2007) PCR screening reveals unexpected antibiotic biosynthetic potential in Amycolatopsis sp. strain UM16. J Appl Microbiol 102:245–253

    Article  PubMed  CAS  Google Scholar 

  • Zucchi TD, Bonda ANV, Frank S, Kim B-Y, Kshetrimayum JD, Goodfellow M (2012a) Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils. Antonie Van Leeuwenhoek 102:91–98

    Article  PubMed  CAS  Google Scholar 

  • Zucchi TD, Tan GYA, Goodfellow M (2012b) Amycolatopsis thermophila sp. nov. and Amycolatopsis viridis sp. nov., thermophilic actinomycetes isolated from arid soil. Int J Syst Evol Microbiol 62:168–172

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors would like to thank Di James for DNA sequencing and Professor J. P. Euzéby for assistance with naming the isolate. GJE held an Innovation Postdoctoral Fellowship from the National Research Foundation of South Africa (NRF) and is currently a Claude Leon Foundation Postdoctoral Fellow. This work was supported by research grants to P.R.M. from the Medical Research Council of South Africa, the NRF (Grant Number: 2073133) and the University Research Committee (UCT).

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  1. Marilize le Roes-Hill

    Present address: Biocatalysis and Technical Biology Group, Cape Peninsula University of Technology, Bellville, PO Box 1906, Cape Town, 7535, South Africa

Authors and Affiliations

  1. Department of Molecular and Cell Biology, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa

    Gareth J. Everest, Marilize le Roes-Hill, Clifford Omorogie, Shuk-Kwan Cheung, Andrew E. Cook, Candice M. Goodwin & Paul R. Meyers

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Correspondence to Paul R. Meyers.

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Everest, G.J., le Roes-Hill, M., Omorogie, C. et al. Amycolatopsis umgeniensis sp. nov., isolated from soil from the banks of the Umgeni River in South Africa. Antonie van Leeuwenhoek 103, 673–681 (2013). https://doi.org/10.1007/s10482-012-9851-7

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