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

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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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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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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Keywords

  • Nocardioform actinomycetes
  • gyrB
  • recN
  • Genetic distance
  • South Africa