Actinobacteria Isolated from an Underground Lake and Moonmilk Speleothem from the Biggest Conglomeratic Karstic Cave in Siberia as Sources of Novel Biologically Active Compounds

Abstract

Actinobacteria isolated from unstudied ecosystems are one of the most interesting and promising sources of novel biologically active compounds. Cave ecosystems are unusual and rarely studied. Here, we report the isolation and characterization of ten new actinobacteria strains isolated from an ancient underground lake and moonmilk speleothem from the biggest conglomeratic karstic cave in Siberia with a focus on the biological activity of the obtained strains and the metabolite dereplication of one active strain. Streptomyces genera isolates from moonmilk speleothem demonstrated antibacterial and antifungal activities. Some of the strains were able to inhibit the growth of pathogenic Candida albicans.

A Phenotypic and Genotypic Analysis of the Antimicrobial Potential of Cultivable Streptomyces Isolated from Cave Moonmilk Deposits

“…Finally, the trimmed alignments were concatenated into a single (MLSA) supermatrix of 10,632 nucleotides for 70 isolates using SCaFoS v1.30k ( Roure et al, 2007 ). For 16S rRNA phylogenies, the closest relatives to the moonmilk isolates were recovered by BLAST searches using full-length 16S rRNA sequences, along with the Streptomyces isolates from a moonmilk deposit in Siberia ( Axenov-Gribanov et al, 2016 ). For the eight isolates for which the genomes were not sequenced (MM9, MM32, MM39, MM55, MM73, MM88, MM90, MM93), nearly full-length 16S rRNA sequences were obtained using PCR primers and conditions as previously reported ( Maciejewska et al, 2015 ).…”

“…The geological isolation of caves from surface processes makes them a unique niche, not only to study microbial interactions and adaptations to extreme oligotrophy, but also to screen for potentially novel bioactive compounds. Although, the most common Actinobacteria reported from caves belong to Pseudonocardiaceae and Nocardiaceae families ( Stomeo et al, 2008 ; Porca et al, 2012 ; Quintana et al, 2013 ; Riquelme et al, 2015 ), many investigations have identified cultivable members of the genus Streptomyces , which are the most prolific antimicrobial producers ( Cañaveras et al, 1999 ; Groth et al, 1999 ; Cheeptham et al, 2013 ; Nimaichand et al, 2015 ; Axenov-Gribanov et al, 2016 ). The presence of Actinobacteria as dominant members of microbial ecosystems in caves is puzzling, as these bacteria, particularly Streptomyces are often presented as major protagonists in the recycling of the residual plant biomass in nutrient-rich soil environments ( Hodgson, 2000 ).…”

“…Its curative properties could be associated with the presence of the numerous filamentous Actinobacteria, particularly Streptomyces , presumably producing bioactive molecules. Indeed, isolation of Streptomyces with antimicrobial and antifungal activities has been reported for moonmilk from the Bolshaya Oreshnaya Cave in Siberia ( Axenov-Gribanov et al, 2016 ). The identification of potential novel compounds with broad-spectrum activities from Streptomyces found in this karstic secondary deposit supports the idea of moonmilk being a great target for bioactivity screening, although to date very few studies have examined cultivable moonmilk microbiome and the diversity of its metabolome as a possible reservoir of novel compounds.…”

The ‘gifted’ actinomycete Streptomyces leeuwenhoekii

“…IB 2014/I/78-8, a distantly related Streptomyces strain to S. leeuwenhoekii C34 T and isolated from a Siberian cave ecosystem (Axenov-Gibanov et al 2016). This finding suggests that these strains might share a highly similar chaxalactin PKS, which is not surprising given the number of examples of similar biosynthetic gene clusters occurring in distinct actinomycetes often isolated from different geographical locations.…”

Optimization of cytotoxic activity of Nocardia sp culture broths using a design of experiments

“…These bacteria are also well described for their interesting biotechnological applications [7]. Actinobacteria are widespread in environment making them PLOS accessible sources of novel bioactive metabolites as we can see with Streptomyces and Nocardia strains isolated from underground lake and moonmilk [8]. Microbial population associated with lichens have been recently characterized in the lichen symbiosis classically defined like a dual symbiosis between a green alga (or a cyanobacterium) and a fungus [9].…”