Diversity of culturable actinomycetes in hyper-arid soils of the Atacama Desert, Chile

Abstract

The Atacama Desert presents one of the most extreme environments on Earth and we report here the first extensive isolations of actinomycetes from soils at various locations within the Desert. The use of selective isolation procedures enabled actinomycetes to be recovered from arid, hyper-arid and even extreme hyper-arid environments in significant numbers and diversity. In some cases actinomycetes were the only culturable bacteria to be isolated under the conditions of this study. Phylogenetic analysis and some phenotypic characterisation revealed that the majority of isolates belonged to members of the genera Amycolatopsis, Lechevalieria and Streptomyces, a high proportion of which represent novel centres of taxonomic variation. The results of this study support the view that arid desert soils constitute a largely unexplored repository of novel bacteria, while the high incidence of non-ribosomal peptide synthase genes in our isolates recommend them as promising material in screening for new bioactive natural products.

Isolation and anti-HIV-1 integrase activity of lentzeosides A–F from extremotolerant lentzea sp. H45, a strain isolated from a high-altitude Atacama Desert soil

“…The strain was isolated on Gauze's No. 1 agar 31 supplemented with the antifungal antibiotics cycloheximide and nystatin (each at 25 μg ml − 1 ) using the procedure described by Okoro et al 8 The strain has phenotypic properties consistent with its classification in the genus Lentzea and forms a distinct phyletic line in the Lentzea 16S rRNA gene tree. The Lentzea isolate has been deposited in the NCIMB and NRRL public service collections under the accession numbers 14966 and B-65282, respectively, the GenBank accession number of the 16S rRNA gene sequence of the strain is LT009512.…”

“…5 However, recent research has revealed extraordinary bacterial diversity across a range of Atacama environments, 6,7 and many novel actinomycetes have been isolated from hyper-and extreme hyper-arid soils. 8,9 Biological and genome-guided screening of some of these actinomycetes has led to the isolation and characterization of new natural products belonging to diverse structural classes and exhibiting various biological activities, as exemplified by the antimicrobial chaxamycins and chaxalactins isolated from Streptomyces leeuwenhoekii C34 T , the abenquines from Streptomyces sp. DB634, the antitumor atacamycins from Streptomyces sp.…”

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

“…The water contents of Atacama desert soils are subject to day-night variations (e.g., mediated by fog) and that even the most arid regions of the Atacama receive intermittent rainfall; moreover, as may be the case at our low altitude sites, these soils will be subject to variable moisture contents as a result of high water tables controlled by precipitation in the Andes [23]. What is clear, however, is that members of novel taxa can be isolated from these soils using both traditional and not traditional methods, representing promising biotechnology opportunities.…”

The ‘gifted’ actinomycete Streptomyces leeuwenhoekii

“…Since 2004, the Atacama Desert, considered the driest and oldest desert on Earth, has been the subject of extensive culture-dependent microbial surveys in soils of hyper-aridity (Salar de Atacama and Cerro Chajnantor), extreme hyper-aridity (Yungay) and the most extreme hyper-aridity (Lomas Bayas) with the conclusion that it is, surprisingly, an abundant source of soil-dwelling microorganisms (Okoro et al 2009;Idris 2016;Bull et al 2018). A group of streptomycetes isolated from a soil sample collected from Chaxa Lagoon in the Salar de Atacama stands out for its ability to synthesise a variety of new specialised metabolites with potentially useful biological activities.…”

“…In October 2004, a soil sample collected from the Chaxa Lagoon area, with low moisture content (0.007%) and scarce total organic matter (0.03%), was subjected to selective isolation of actinomycetes, resulting in the isolation of strains of the genus Streptomyces (Okoro et al 2009). The majority of these isolates, including strains C34, C38, C58 and C79, formed a distinct subclade in the phylogenetic tree of 16S rRNA genes of the genus Streptomyces, sharing 99.5-99.9% nucleotide sequence identity Okoro et al 2009). The S. leeuwenhoekii strains grouped together in a clade well-supported by maximum likelihood and maximum parsimony tree-making algorithms ( Fig.…”