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Streptomyces Asenjonii Sp. Nov., Isolated from Hyper-Arid Atacama Desert Soils and Emended Description of Streptomyces Viridosporus Pridham Et Al

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Streptomyces Asenjonii Sp. Nov., Isolated from Hyper-Arid Atacama Desert Soils and Emended Description of Streptomyces Viridosporus Pridham Et Al Goodfellow M, Busarakam K, Idris H, Labeda DP, Nouioui I, Brown R, Kim B-Y, Montero-Calasanz MDC, Andrews BA, Bull AT. Streptomyces asenjonii sp. nov., isolated from hyper-arid Atacama Desert soils and emended description of Streptomyces viridosporus Pridham et al. 1958. Antonie van Leeuwenhoek (2017) DOI: https://doi.org/10.1007/s10482-017-0886-7 Copyright: © The Author(s) 2017. This article is an open access publication. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. DOI link to article: https://doi.org/10.1007/s10482-017-0886-7 Date deposited: 28/06/2017 This work is licensed under a Creative Commons Attribution 4.0 International License Newcastle University ePrints - eprint.ncl.ac.uk Antonie van Leeuwenhoek DOI 10.1007/s10482-017-0886-7 ORIGINAL PAPER Streptomyces asenjonii sp. nov., isolated from hyper-arid Atacama Desert soils and emended description of Streptomyces viridosporus Pridham et al. 1958 Michael Goodfellow . Kanungnid Busarakam . Hamidah Idris . David P. Labeda . Imen Nouioui . Roselyn Brown . Byung-Yong Kim . Maria del Carmen Montero-Calasanz . Barbara A. Andrews . Alan T. Bull Received: 10 February 2017 / Accepted: 5 May 2017 Ó The Author(s) 2017. This article is an open access publication Abstract A polyphasic study was undertaken to distinguish them from S. ghanaensis NRRL B-12104T, establish the taxonomic status of Streptomyces strains their near phylogenetic neighbour. On the basis of isolated from hyper-arid Atacama Desert soils. Anal- these genotypic and phenotypic data it is proposed that ysis of the 16S rRNA gene sequences of the isolates the isolates be recognised as a new species within the showed that they formed a well-defined lineage that genus Streptomyces, named Streptomyces asenjonii was loosely associated with the type strains of several sp. nov. The type strain of the species is KNN35.1bT Streptomyces species. Multi-locus sequence analysis (NCIMB 15082T = NRRL B-65050T). Some of the based on five housekeeping gene alleles showed that isolates, including the type strain, showed antibacte- the strains form a homogeneous taxon that is closely rial activity in standard plug assays. In addition, related to the type strains of Streptomyces ghanaensis MLSA, average nucleotide identity and phenotypic and Streptomyces viridosporus. Representative iso- data show that the type strains of S. ghanaensis and S. lates were shown to have chemotaxonomic and viridosporus belong to the same species. Conse- morphological properties consistent with their classi- quently, it is proposed that the former be recognised fication in the genus Streptomyces. The isolates have as a heterotypic synonym of the latter and an emended many phenotypic features in common, some of which description is given for S. viridosporus. Keywords Streptomyces Polyphasic taxonomy Electronic supplementary material The online version of Á Á this article (doi:10.1007/s10482-017-0886-7) contains supple- Hyper-arid Á Atacama Desert mentary material, which is available to authorized users. M. Goodfellow (&) Á K. Busarakam Á A. T. Bull H. Idris Á I. Nouioui Á R. Brown Á School of Biosciences, University of Kent, Canterbury, M. del Carmen Montero-Calasanz Kent CT2 7NJ, UK School of Biology, Newcastle University, Ridley Building 2, Newcastle upon Tyne NE1 7RU, UK B. A. Andrews e-mail: [email protected] Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, D. P. Labeda University of Chile, Beauchef, 851 Santiago, Chile National Centre for Agricultural Utilization Research, USDA ARS, Peoria, IL 61614, USA B.-Y. Kim Chunlab Inc., Seoul Natural University, Gwanak-ro, Gwanak-gu, Seoul 151-742, Republic of Korea 123 Antonie van Leeuwenhoek Introduction Tocana˜o (23°1703300S, 68°1009900W at 2219 m above sea level), using the dilution plate procedure described The prospect of isolating novel filamentous actinobac- by Okoro et al. (2009). The strains were isolated on teria that synthesise new specialised metabolites is Gauze’s No.1 agar (KNN6.11a) (Zakharova et al. enhanced when bioprospecting strategies are focused 2003), humic acid-vitamin agar (KNN35.1bT, on neglected and unexplored habitats (Hong et al. KNN35.2b) (Hayakawa and Nonomura 1987) and 2009; Tiwari and Gupta 2012; Guo et al. 2015), SM1 agar (KNN48.3e, KNN83.e) (Tan et al. 2006) including desert soils (Meklat et al. 2011; Boubetra following incubation for 14 days at 28 °C. Similarly, et al. 2013). The most extensive surveys of culturable the final strain, KNN42.f, was isolated from a starch- actinobacterial diversity in desert biomes have been casein agar plate (Ku¨ster and Williams 1964) follow- concentrated on sites in the Atacama Desert in ing inoculation with a suspension of an extreme hyper- northern Chile, the driest non-polar desert on the arid soil collected by ATB in 2010 from the Yungay planet (Bull and Asenjo 2013; Bull et al. 2016). The core region of the Atacama Desert (24°06018.600S, application of a taxonomic approach to drug discovery 70°01055.600W at 1016 m asl). These strains, together (Goodfellow and Fiedler 2010) has been effective in with Streptomyces ghanaensis NRRL B12104T (Wall- the isolation of putatively novel filamentous acti- ha¨user et al. 1965), were maintained on yeast extract— nobacteria from Atacama Desert habitats, some of malt extract agar (International Streptomyces Project which produce novel natural products (Bull et al. [ISP2] medium., Shirling and Gottlieb 1966) and as 2016; Wichner et al. 2016). Indeed, polyphasic suspensions of spores and hyphal fragments in 20%, taxonomic studies on dereplicated actinobacteria iso- v/v glycerol at -20 and -80 °C. Biomass samples for lated from hyper-arid and extreme hyper-arid Ata- most of the chemotaxonomic analyses and for the 16S cama Desert soils have led to the description of novel rRNA gene sequencing studies were prepared in shake species of Lechevalieria (Okoro et al. 2010), Lentzea flasks (180 revolutions per minute) of ISP 2 broth after (Idris et al. 2017a) and Modestobacter (Busarakam incubation at 28 °C for 14 days and washed twice in et al. 2016a) and to the detection of rare thermophilic distilled water. Cells for the chemotaxonomic analyses Amycolatopsis species (Busarakam et al. 2016b). In were freeze-dried and those for the sequencing studies addition, several new Streptomyces species have been stored at room temperature. Biomass preparations for described (Santhanam et al. 2012a, b, 2013; Idris et al. the fatty acid analyses were harvested from shake 2017b), one of which, Streptomyces leeuwenhoekii flasks of Tryptic Soy broth (Difco) following incuba- (Busarakam et al. 2014), encompasses strains that tion at 28 °C for 7 days. synthesise novel antibiotics (Nachtigall et al. 2011; Rateb et al. 2011a, b) and chaxapeptin, a new lasso Phylogenetic analysis peptide (Elsayed et al. 2015). The present study was designed to establish the 16S rRNA gene sequencing. Genomic DNA extrac- taxonomic position of several closely related Atacama tion, PCR-mediated amplification of 16S rRNA genes Desert streptomycetes. These strains were the subject and purification of the resultant products were carried of a polyphasic taxonomic study which showed that out on all of the isolates using the procedures they belong to a new species, Streptomyces asenjonii described by Kim and Goodfellow (2002). Identifica- sp. nov. tion of phylogenetic neighbours and calculation of pairwise 16S rRNA gene sequence similarities were achieved using the EzTaxon-e server (http://www. Materials and methods ezbiocloud.net/taxonomy; Yoon et al. 2017) and the resultant sequences aligned using the CLUSTAL W Isolation, maintenance and cultivation of strains algorithm from the MEGA 6 software package (Ta- mura et al. 2013). Phylogenetic analyses using the Isolates KNN6.11a, KNN35.1bT, KNN35.2b, maximum-likelihood (ML) (Felsenstein 1981) and KNN48.3e and KNN83.e were recovered from a maximum-parsimony (MP) algorithms (Fitch 1971) hyper-arid soil collected in 2012 by one of us (ATB) were also realised using the GGDC web server (Meier- from the Chaxa de Laguna, Salar de Atacama near Kolthoff et al. 2013a) of the DSMZ phylogenomics 123 Antonie van Leeuwenhoek pipeline (Meier-Kolthoff et al. 2014) adapted to single Draft genome preparation and ANI calculations genes available at http://ggdc.dsmz.de/. ML and MP trees were inferred from the alignment with RAxML The draft genome sequence of Streptomyces viri- (Stamatakis 2014) and TNT (Goloboff et al. 2008), dosporus NRRL 2414T was prepared following the respectively. The topologies of the resultant trees were protocol outlined in Labeda et al. (2016) with the evaluated by bootstrap analyses (Felsenstein 1985) exception that CLCbio Genomic Workbench Version based on 1000 replicates used in conjunction with tree- 9.5.3 (CLCbio; Boston, MA) was used for contig bisection-and-reconnection branch swapping and ten trimming and de novo assembly. This Whole Genome additional random sequence replicates for MP and Shotgun project has been deposited at DDBJ/EMBL/ rapid bootstrapping in conjunction with the auto MRE GenBank under the accession MSGP00000000. bootstopping criterion (Pattengale et al. 2010) for ML. The draft genome sequence of NRRL 2414T was The trees were rooted using the 16S rRNA gene compared with the draft genomes sequences of S. sequence of Streptomyces albus subspecies albus viridosporus T7A (Genbank accession number DSM 40317T (GenBank accession number AJFD00000000), S. ghanaensis ATCC 14672T (Gen- AJ621602). The V2 test implemented in PAUP* Bank accession number ABYA00000000), Strepto- (Swofford 2002) was used to check for compositional myces hirsutus NRRL B-3713T (GenBank accession bias. Pairwise sequence similarities were calculated number LIQT00000000), and Streptomyces cyanoalbus using the method recommended by Meier-Kolthoff NRRL B-3040T (GenBank accession number LIPS0000 et al.
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