Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile

Abstract

A polyphasic study was undertaken to establish the taxonomic status of three representative Geodermatophilus strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates B12, B20 and B25, were found to have chemotaxonomic and morphological properties characteristic of the genus Geodermatophilus. The isolates shared a broad range of chemotaxonomic, cultural and physiological features, formed a well-supported branch in the Geodermatophilus 16S rRNA gene tree in which they were most closely associated with the type strain of Geodermatophilus obscurus. They were distinguished from the latter by BOX-PCR fingerprint patterns and by chemotaxonomic and other phenotypic properties. Average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between the whole genome sequences of isolate B12 and G. obscurus DSM 43160 were 89.28%, 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 Geodermatophilus chilensis sp. nov. with isolate B12 (CECT 9483=NCIMB 15089) as the type strain. Analysis of the whole genome sequence of G. chilensis B12 with 5341 open reading frames and a genome size of 5.5Mb 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.

Extreme environments: microbiology leading to specialized metabolites

“…Members of the family Geodermatophilaceae have received the most attention, notably the genera Blastococcus, Geodermatophilus and Modestobacter ; members of these taxa are known to be resistant to desiccation, ionizing radiation, UV‐light and heavy metals (Sghaier et al ). Dereplicated Geodermatophilaceae strains from Atacama Desert habitats have been validly named as Blastococcus atacamensis (Castro et al ), Geodermatophilus chilensis (Castro et al ) and Modestobacter caceresii (Busarakam et al ) and shown to have moderately large genomes (3·9–5·9 Mb). Representatives of these taxa not only contain NP‐BGCs but also stress‐related genes that encode for properties such as carbon starvation, temperature fluxes, osmotic stress and UV‐light.…”

“…Another important development is the realization that in some actinobacterial taxa, such as the genera Amycolatopsis , Frankia and Micromonospora , there is a link between the distribution of NP‐BGCs and phylogeny (Adamek et al ; Carro et al ; Nouioui et al ). In addition, information drawn from whole‐genome sequences is providing fascinating insights into how micro‐organisms adapt to extreme habitats, as witnessed by the ability of members of the actinobacterial family Geodermatophilaceae to withstand extreme environmental conditions that prevail in hyperarid desert habitats (Castro et al , b).…”

Modestobacter altitudinis sp. nov., a novel actinobacterium isolated from Atacama Desert soil

“…In turn, many of the stress related genes were shown to be linked with carbon starvation, oxidative and osmotic stress, resistance to UV radiation and temperature fluxes, as exemplified by genes encoding for carbon starvation protein A (CstA), which promotes peptide uptake [72][73][74]; sox genes associated with responses to oxidative stress [75,76]; KatE and uvrD genes linked to protection against reactive oxygen and UV-radiation [77]; dnaK and dnaJ, hrcA, grpE and Hsp genes related to responses to heat shock [78]; a family of proteins associated with cold shock responses [79] and coxE, coxD and coxG genes along with a coxSML cluster coding for utilisation of carbon monoxide indicating that the isolate may have a chemolithoautotrophic lifestyle [80]. Similar patterns of stress-related genes have been detected in the genomes of the type strains of the B. atacamensis [16], G. chilensis [17], M. caceresii [10] and 'M. excelsi' [3].…”

“…excelsi' are rich in stress genes that provide an insight into how these organisms have adapted to the prevailing environmental conditions in hyper-arid Atacama Desert soils [3,10]. Moreover, genomes of representative type strains of the family Geodermatophilaceae revealed many biosynthetic gene clusters (BGCs) related to the biosynthesis of secondary metabolites, as exemplified by the genomes of the type strains of Blastococcus atacamensis [16], Geodermatophilus chilensis [17], M. caceresii [10] and 'M. excelsi' [3].…”

Plant growth promoting rhizobacteria from Juan Fernández archipelago improve germination rate of endangered plant Solanum fernandezianum Phil.

“…The sequences of the nearest type species for each isolate were retrieved from GenBank (Benson et al, 2017). Phylogenetic analyses were carried out after Castro et al (2018); phylogenetic trees were inferred with MEGA software version 7.0 (Kumar et al, 2016). The bacterial strains were deposited in the Chilean Collection of Microbial Genetic Resources (http://www.cchrgm.cl) with the following access codes RGM 2525, RGM 2526 and RGM 2607.…”