The Diversity, Metabolomics Profiling, and the Pharmacological Potential of Actinomycetes Isolated from the Estremadura Spur Pockmarks (Portugal)

Abstract

The Estremadura Spur pockmarks are a unique and unexplored ecosystem located in the North Atlantic, off the coast of Portugal. A total of 85 marine-derived actinomycetes were isolated and cultured from sediments collected from this ecosystem at a depth of 200 to 350 m. Nine genera, Streptomyces, Micromonospora, Saccharopolyspora, Actinomadura, Actinopolymorpha, Nocardiopsis, Saccharomonospora, Stackebrandtia, and Verrucosispora were identified by 16S rRNA gene sequencing analyses, from which the first two were the most predominant. Non-targeted LC-MS/MS, in combination with molecular networking, revealed high metabolite diversity, including several known metabolites, such as surugamide, antimycin, etamycin, physostigmine, desferrioxamine, ikarugamycin, piericidine, and rakicidin derivatives, as well as numerous unidentified metabolites. Taxonomy was the strongest parameter influencing the metabolite production, highlighting the different biosynthetic potentials of phylogenetically related actinomycetes; the majority of the chemical classes can be used as chemotaxonomic markers, as the metabolite distribution was mostly genera-specific. The EtOAc extracts of the actinomycete isolates demonstrated antimicrobial and antioxidant activity. Altogether, this study demonstrates that the Estremadura Spur is a source of actinomycetes with potential applications for biotechnology. It highlights the importance of investigating actinomycetes from unique ecosystems, such as pockmarks, as the metabolite production reflects their adaptation to this habitat.

Critical analysis of polycyclic tetramate macrolactam biosynthetic cluster phylogeny and functional diversity

“…Because PTM BGCs are fairly common, their products are frequently encountered in these studies, but sometimes incorrectly. For example, specific PTMs have been extrapolated from MS signals whose structures are incongruent with the BGC content (i.e., butremycin from a Group 1 BGC) (80–82). Others indicate both 5/5/6 and 5/6/5 PTMs being produced by individual strains, which is unlikely without supporting genomic evidence (83–86).…”

Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation

“…One example of the use of MS/MS Qemistree representation performed by Pinto-Almeida et al revealed similarities in fatty acids among marine-derived Micromonospora and Streptomyces strains and macrolactams and prenol lipids among Streptomyces strains [ 127 ].…”

Genus Nocardiopsis: A Prolific Producer of Natural Products

“…By mid-2021, 3% of marine actinomycetesderived natural products were produced by Nocardiopsis, and Nocardiopsis are the thirdlargest actinomycetes in terms of producing marine compounds [13]. In addition, Nocardiopsis are a prolific source of bioactive natural products in both marine and terrestrial environments [1] and are widely distributed in multiple ecosystems [12], including deserts [14], deep ocean [15], coastal wetlands [16], and saline-alkali soil [17]. Nocardiopsis species have the ability to survive under different and hostile environmental conditions, mainly benefitting from their excretion of enzymes, multipurpose genetic constitution, and their ability to produce compuponible solutes and surfactants [12,[18][19][20].…”