• Abstract and Figures
• Public Full-text

Systematic and Applied Microbiology 41 (2018) 427–436 Contents lists available at ScienceDirect Systematic and Applied Microbiology j ournal homepage: www.elsevier.de/syapm Geodermatophilus chilensis sp. nov., from soil of the Yungay ଝ,ଝଝ core-region of the Atacama Desert, Chile a,b a c d Jean Franco Castro , Imen Nouioui , Vartul Sangal , Martha E. Trujillo , a a e b Maria del Carmen Montero-Calasanz , Tara Rahmani , Alan T. Bull , Juan A. Asenjo , b a,∗ Barbara A. Andrews , Michael Goodfellow a School of Natural and Environmental Sciences, Ridley Building, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom b Centre for Biotechnology and Bioengineering (CeBiB), Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 851, Santiago, Chile c Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, United Kingdom d Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain e School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, United Kingdom a r t i c l e i n f o a b s t r a c t Article history: A polyphasic study was undertaken to establish the taxonomic status of three representative Geoder- Received 3 November 2017 T matophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12 , Received in revised form 14 March 2018 B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the Accepted 22 March 2018 genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physio- logical features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which Keywords: they were most closely associated with the type strain of Geodermatophilus obscurus. They were distin- Geodermatophilus chilensis guished from the latter by BOX-PCR fingerprint patterns and by chemotaxonomic and other phenotypic Polyphasic taxonomy properties. Average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization Atacama Desert T T values between the whole genome sequences of isolate B12 and G. obscurus DSM 43160 were 89.28%, Whole-genome sequences 87.27% and 37.4%, respectively, metrics consistent with its classification as a separate species. On the basis of these data, it is proposed that the isolates be assigned to the genus Geodermatophilus as Geoder- T T T matophilus chilensis sp. nov. with isolate B12 (CECT 9483 = NCIMB 15089 ) as the type strain. Analysis T of the whole genome sequence of G. chilensis B12 with 5341 open reading frames and a genome size of 5.5 Mb highlighted genes and gene clusters that encode for properties relevant to its adaptation to extreme environmental conditions prevalent in extreme hyper-arid Atacama Desert soils. © 2018 Published by Elsevier GmbH. Introduction [73]. They are aerobic, Gram-stain positive actinobacteria which produce rudimentary substrate hyphae that develop into multi- The genus Geodermatophilus [50] together with the genera Blas- locular vesicles which release motile or non-motile propagules; tococcus [1], Cumulibacter [33], Klenkia [66] and Modestobacter have meso-diaminopimelic acid (meso-A2pm) as the diamino acid [54] form the family Geodermatophilaceae [71,72] of the order of the peptidoglycan, fatty acids rich in iso-branched components, Geodermatophilales [87] which belongs to the class Actinobacte- tetrahydrogenated menaquinones with nine isoprene units (MK- ria [91]. Geodermatophili are recognised by using a combination 9[H4]) as the major isoprenologue, glucose, galactose, mannose and of chemotaxonomic, morphological and physiological properties ribose as diagnostic sugars; complex polar lipid patterns that gen- erally contain diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositol and usually phos- ଝ phatidylglycerol and a genomic DNA G + C content within the range The GenBank accession numbers for the 16S rRNA gene sequences of strains T 74.0–76.0 mol% [29,30,66]. B12 , B20 and B25 are KX943328, KX943329 and KX943330, respectively. The T At the time of writing, the genus Geodermatophilus encompasses GenBank accession number for the draft genome sequence of strain B12 is NVPT0000000. 18 validly published species that form a well-supported clade in ଝଝ Subject category: New taxa: Actinobacteria. the Geodermatophilaceae 16S rRNA gene tree [29,30,63] and which ∗ Corresponding author. can be distinguished using a broad range of phenotypic properties E-mail address: [email protected] (M. Goodfellow). https://doi.org/10.1016/j.syapm.2018.03.005 0723-2020/© 2018 Published by Elsevier GmbH. 428 J.F. Castro et al. / Systematic and Applied Microbiology 41 (2018) 427–436 [29,30,64]. Nearly all of these taxa have been recognised within the in distilled water and freeze dried. In turn, biomass for the molec- last five years, as exemplified by Geodermatophilus amargosae [63], ular systematic studies was prepared from 5 ml GYM Streptomyces ◦ Geodermatophilus aquaeductus [32], Geodermatophilus bullaregien- broths which had been incubated at 28 C for 10 days prior to wash- sis [30], Geodermatophilus nigrescens [70], Geodermatophilus sabuli ing twice in distilled water and stored at room temperature. [31] and Geodermatophilus pulveris [29]. Despite the recent surge in the number of Geodermatophilus species the genus remains under- speciated [26,69,96]. Geodermatophilus strains tend to be associated Phylogenetic analyses with soils, notably desert soils [19,20,50,56,58,57,59–62,65,70] T though there is evidence that they are more widely distributed in Genomic DNA was extracted from isolates B12 , B20 and B25 fol- the environment [32,65,105]. Geodermatophili tend to be resistant lowing the procedure described by Kieser et al. [38]. PCR mediated to adverse environmental conditions such as desiccation, ioniz- amplification of 16S rRNA gene sequences was performed in a final ␮ ing radiation and UV light [28–30,32,65]. Analyses of the genome volume of 25 l using primers 27f (5 AGAGTTTGATCMTGGCTCAG- [35] and the proteome [89] of the type strain of Geodermatophilus 3 ) and 1525r (5 -AAGGAGGTGATCCAGCC-3 ) [45], 100 ng of gDNA obscurus, the type species of the genus, provide an insight into and MyFiM mix (Bioline, UK) following the protocol of the man- ◦ how geodermatophili adapt to extreme environmental conditions, ufacturer; the PCR conditions were 5 min at 95 C followed by ◦ ◦ ◦ relevant factors are considered to include pigmentation, catalase 30 cycles of 30 s at both 95 C and 55 C, and 23 s at 72 C. The production and DNA repair mechanisms. PCR products were cleaned with exonuclease I and shrimp alka- The present study was undertaken to establish the taxonomic line phosphatase (NEB, UK; #E2622S), sequenced (Geneius Ltd; ® provenance of three representative Geodermatophilus strains iso- Cramlington, UK) using Big Dye terminator v3.1 cycle sequenc- lated from an extreme hyper-arid Atacama Desert soil. The isolates, ing (ThermoFisher Scientific Inc.) on an ABI sequence model 3730.1 T strains B12 , B20 and B25, were compared with the type strains (Applied Biosystems) and assembled using Pregap 4 and Gap4 soft- of Geodermatophilus species using genotypic and phenotypic prop- ware from the Staden package version 20.069 [92]. The resultant T erties known to be of value in the delineation of species of 16S rRNA gene sequences of isolates B12 (1448 bp), B20 (1457 bp) Geodermatophilus [29,30,56] and found to form a novel species. and B25 (1443 bp) were compared against the database of 16S rRNA The name proposed for this species is Geodermatophilus chilensis sequences of Archaea and Bacteria using the Basic Local Alignment T with isolate B12 as the type strain. Analysis of the whole genome Tool (BLAST) [12] at the National Center for Biotechnology Informa- sequence generated for this strain gave an insight into how such tion (NCBI) website. The sequences of the isolates were compared strains may have adapted to the harsh environmental conditions against corresponding 16S rRNA gene sequences of the type strains prevalent in extreme hyper-arid Atacama Desert soils. of Geodermatophilus species retrieved from the EzTaxon server [104]. Phylogenetic trees were inferred using MEGA software ver- sion 7.0 [44] and the neighbour-joining [80], maximum-likelihood Materials and methods [21], and maximum-parsimony algorithms [24] with 1000 boot- strap repetitions [22]. Alignment of the nucleotide sequences was Isolation of strains achieved with MUSCLE software from MEGA [18] and evolution- ary distances calculated with the Kimura-2-parameter model [40]. Geodermatophilus strains were isolated from an extreme hyper- The resultant trees were rooted using the 16S rRNA gene sequence arid soil sample collected by one of us (ATB) in November T of Modestobacter multiseptatus DSM 44406 using FigTree version 2010 from the Yungay core-region of the Atacama Desert ◦ ◦ 1.4.2 (http://tree.bio.ed.ac.uk/software/Figtree/). This software was (24 06 18.6 S/70 01 55.6 W) at 1002 m above sea level. One gram used to visualize the phylogenetic trees. All of the figures were of the soil sample was suspended in 4.0 ml of 1/4 strength Ringer’s ◦ edited in Inkscape version 0.9 (http://linkscape.org.en/). A simi- solution (Oxoid), shaken on a tumble shaker, heated at 55 C for −2 −3 larity table was generated from the sequence alignment file using 6 min prior to preparation of 10 and 10 dilutions in Ringer’s PHYDIT version 1.0 software. solution. Aliquots (100 ␮l) of each of the tenfold dilutions were spread, in triplicate, over Geodermatophilus obscurus agar [3] sup- plemented with nalidixic acid (10 ␮g/ml) and cycloheximide and BOX typing nystatin (each at 25 ␮g/ml). The isolation plates had been dried for 15 min at room temperature before incubation, as recommended by ◦ BOX-PCR fingerprints from genomic DNA extracted from the Vickers and Williams [99]. After incubation at 28 C for 2 weeks pre- isolates were generated using the BOX A1R primer [98] and exper- sumptive Geodermatophilus isolates were counted and expressed as imental conditions described previously [94].

Load more

  10

Copy Link