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

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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).

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Acknowledgments

Kanungnid Busarakam is grateful for a scholarship from the Thai Royal Government, Michael Goodfellow for an Emeritus Fellowship from the Leverhulme Trust and Tiago Zucchi for financial support (grants 2011/14333-6 and 2011/50243-1) from Fundação de Amparo à Pesquisa do Estado de São Paulo. We are grateful to Dr. Wen-Jun Li (Yunnan Institute of Microbiology) for providing the type strain of Amycolatopsis endophytica.

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  1. Kanungnid Busarakam

    Present address: Department of Agricultural Technology, Thailand Institute of Scientific and Technological Research, Pathum Thani, 12120, Thailand

Authors and Affiliations

  1. School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK

    Kanungnid Busarakam, Ros Brown & Michael Goodfellow

  2. School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK

    Alan T. Bull

  3. Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia

    Geok Yuan Annie Tan

  4. Laboratório de Microbiologia, EMBRAPA Meio Ambiente, Rod SP 340-Km 127, PO Box 69, Jaguariúna, 13820-000, Brazil

    Tiago D. Zucchi, Leonardo José da Silva & Wallace Rafael de Souza

  5. Agrivalle, Av. Tranquillo Giannini, 1050, Salto, 13329-600, Brazil

    Tiago D. Zucchi

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  1. Kanungnid Busarakam
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10482_2015_635_MOESM2_ESM.pptx

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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Busarakam, K., Brown, R., Bull, A.T. et al. Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov.. Antonie van Leeuwenhoek 109, 319–334 (2016). https://doi.org/10.1007/s10482-015-0635-8

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