Antonie van Leeuwenhoek

, Volume 109, Issue 2, pp 319–334 | Cite as

Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov.

  • Kanungnid Busarakam
  • Ros Brown
  • Alan T. Bull
  • Geok Yuan Annie Tan
  • Tiago D. Zucchi
  • Leonardo José da Silva
  • Wallace Rafael de Souza
  • Michael Goodfellow
Original Paper

Abstract

The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024T and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024T and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024T (=NCIMB 14972T = NRRL B-65266T).

Keywords

Amycolatopsis Polyphasic taxonomy Desert soils 

Supplementary material

10482_2015_635_MOESM1_ESM.docx (15 kb)
Supplementary material 1 (DOCX 16 kb)
10482_2015_635_MOESM2_ESM.pptx (85 kb)
Fig. S1 Neighbour-joining tree based on nearly complete 16S rRNA gene sequences (~1350 bp) showing relationships between the Amycolatopsis isolates and between them and the type strains of Amycolatopsis species. White circles indicates branches of the tree that were recovered with the maximum-likelihood and maximum-parsimony tree-making methods, the white and black diamonds indicate branches that were recovered with maximum-likelihood and maximum-parsimony tree-making algorithms, respectively. Numbers at the nodes indicate levels of bootstrap support based on a neighbour-joining analysis of 1000 resampled datasets; only values above 50 % are shown. The scale bar indicates 0.005 substitutions per nucleotide position (PPTX 86 kb)

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Kanungnid Busarakam
    • 1
    • 6
  • Ros Brown
    • 1
  • Alan T. Bull
    • 2
  • Geok Yuan Annie Tan
    • 3
  • Tiago D. Zucchi
    • 4
    • 5
  • Leonardo José da Silva
    • 4
  • Wallace Rafael de Souza
    • 4
  • Michael Goodfellow
    • 1
  1. 1.School of BiologyNewcastle UniversityNewcastle upon TyneUK
  2. 2.School of BiosciencesUniversity of KentCanterburyUK
  3. 3.Institute of Biological SciencesUniversity of MalayaKuala LumpurMalaysia
  4. 4.Laboratório de MicrobiologiaEMBRAPA Meio AmbienteJaguariúnaBrazil
  5. 5.AgrivalleSaltoBrazil
  6. 6.Department of Agricultural TechnologyThailand Institute of Scientific and Technological ResearchPathum ThaniThailand

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