Actinomycetes from the Red Sea Sponge Coscinoderma mathewsi: Isolation, Diversity, and Potential for Bioactive Compounds Discovery

Abstract

The diversity of actinomycetes associated with the marine sponge Coscinoderma mathewsi collected from Hurghada (Egypt) was studied. Twenty-three actinomycetes were separated and identified based on the 16S rDNA gene sequence analysis. Out of them, three isolates were classified as novel species of the genera Micromonospora, Nocardia, and Gordonia. Genome sequencing of actinomycete strains has revealed many silent biosynthetic gene clusters and has shown their exceptional capacity for the production of secondary metabolites, not observed under classical cultivation conditions. Therefore, the effect of mycolic-acid-containing bacteria or mycolic acid on the biosynthesis of cryptic natural products was investigated. Sponge-derived actinomycete Micromonospora sp. UA17 was co-cultured using liquid fermentation with two mycolic acid-containing actinomycetes (Gordonia sp. UA19 and Nocardia sp. UA 23), or supplemented with pure mycolic acid. LC-HRESIMS data were analyzed to compare natural production across all crude extracts. Micromonospora sp. UA17 was rich with isotetracenone, indolocarbazole, and anthracycline analogs. Some co-culture extracts showed metabolites such as a chlorocardicin, neocopiamycin A, and chicamycin B that were not found in the respective monocultures, suggesting a mycolic acid effect on the induction of cryptic natural product biosynthetic pathways. The antibacterial, antifungal, and antiparasitic activities for the different cultures extracts were also tested.

Exploration of Chemical Diversity and Antitrypanosomal Activity of Some Red Sea-Derived Actinomycetes Using the OSMAC Approach Supported by LC-MS-Based Metabolomics and Molecular Modelling

“…UR23) were subjected to fermentation under a series of altering culturing conditions, that is, solid and liquid ISP2 media along with co-fermentation with mycolic acid-containing actinobacteria, Nocardia sp. UA 27 [6] also in solid and liquid ISP2 media. Solid media fermentations were performed in a number of Petri's dishes (15 dishes for each treatment), while liquid fermentations were performed as follows: each strain was fermented in 2 L Erlenmeyer flasks each containing 1.5 L ISP2 medium.…”

“…The antitrypanosomal activity was tested following the protocol of Huber and Koella [6,25]. Briefly, 104 trypanosomes per ml of Trypanosoma brucei brucei strain TC 221 were added to complete Baltz medium.…”

“…During the last 70 years, actinomycetes from terrestrial environments have been extensively investigated and have gained great success in providing much essential therapeutics (e.g., antibiotics and anticancer agents). On the other hand, these prolific producers of specialized metabolites are still poorly explored in marine environments [4][5][6]. Additionally, the vast majority of marine-derived bioactive natural products have been reported from marine actinomycetes [7,8].…”

“…Trypanosomiasis is considered one of the fetal neglected tropical diseases and threatens more than 65 million people in sub-Saharan Africa [6], thus the enormous biosynthetic capacity of actinomycetes can provide potential drug candidates against this deadly parasite. Accordingly, we decided to extend our investigation of marine-derived actinobacteria, notably those associated with the Red Sea soft corals.…”

“…Induced metabolites(1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18) of Streptomyces sp. UR23-derived extracts: upon fermentation on the solid medium (black color, 1-4), on the liquid medium (blue color, 5-9), upon the co-fermentation on the solid medium (red color, 10-13), and upon the co-fermentation in the liquid medium (brown color, 14-18).…”