Amycolatopsis vastitatis sp. nov., an isolate from a high altitude subsurface soil on Cerro Chajnantor, northern Chile

Abstract

The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina, its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5 (= NCIMB 14970 = NRRL B-65279).

Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns

“…Such discontinuous distribution of natural product bioclusters within a target taxon underlines the importance of rigorous classification in bioprospecting. Within the strain library used in this study was the high BGC containing, newly described A. vastitatis isolated from Cerro Chajnantor soil at 4000 m [89]. Similar conclusions can be drawn from phylogenomic studies on representatives of the genus Micromonospora [90].…”

Biodiversity of Culturable Endophytic Actinobacteria Isolated from High Yield Camellia oleifera and Their Plant Growth Promotion Potential

“…Considering that XL27 grows in the most acidic soil and XL210 in the most nutritionally impoverished soil, we expect that Amycolatopsis may have a helpful role to XL27 and XL210 in the harsh condition. Moreover, Amycolatopsis strains are also known as a rich source of novel secondary metabolites [55]; hence, endophytic Streptomyces and Amycolatopsis, especially the ones with PGP traits, will be paid extreme attention to assess their potential as PGP agents in greenhouse/field conditions, and to better understand their interactions with C. oleifera and the environment.…”

Extreme environments: microbiology leading to specialized metabolites

“…Recently, presumptively gifted isolates from a high‐altitude Cerro Chajnantor gravel soil in northern Chile have been validly named as Micromonospora acroterricola (Carro et al ), Micromonospora arida and Micromonospora inaquosa (Carro et al ). Similarly, novel dereplicated isolates belonging to less well‐known genera have been validly named, as exemplified by Amycolatopsis vastitatis (Idris et al ), Lentzea chajnantorensis (Idris et al ) and Pseudonocardia nigra (Trujillo et al ). The genomes of some of these isolates have the capacity to synthesize many novel specialized metabolites and contain stress‐related genes that provide an insight into how actinobacteria adapt to the extreme environmental conditions found in Atacama Desert habitats (Idris et al ; Carro et al ).…”