Abstract
The marine ecosystem has become the hotspot for finding antibiotic-producing actinomycetes across the globe. Although marine-derived actinomycetes display strain-level genomic and chemodiversity, it is unclear whether functional traits, i.e., antibiotic activity, vary in near-identical Streptomyces species. Here, we report culture-dependent isolation, antibiotic activity, phylogeny, biodiversity, abundance, and distribution of Streptomyces isolated from marine sediments across the west-central Philippines. Out of 2212 marine sediment-derived actinomycete strains isolated from 11 geographical sites, 92 strains exhibited antibacterial activities against multidrug-resistant Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. The 16S rRNA and rpoB gene sequence analyses confirmed that antibiotic-producing strains belong to the genus Streptomyces, highlighting Streptomyces parvulus as the most dominant species and three possible new species. Antibiotic-producing Streptomyces strains were highly diverse in Southern Antique, and species diversity increase with marine sediment depth. Multiple strains with near-identical 16S rRNA and rpoB gene sequences displayed varying strength of antibiotic activities. The genotyping of PKS and NRPS genes revealed that closely related antibiotic-producing strains have similar BGC domains supported by their close phylogenetic proximity. These findings collectively suggest Streptomyces' intraspecies adaptive characteristics in distinct ecological niches that resulted in outcompeting other bacteria through differential antibiotic production.
Highlights
The marine ecosystem has become the hotspot for finding antibiotic-producing actinomycetes across the globe
Genome mining on the most extensive BGC study to date using 1110 publicly available Streptomyces genomes revealed a high diversity of BGCs and distribution pattern variation in closely related strains of Streptomyces[9]. This BGCs variation in Streptomyces species is associated with an intraand interspecies recombination as a rapid response to selective pressures in ecological niches, impacting the secondary metabolite diversity among closely related s trains[8, 13,14,15,16]. It remains unclear if functional trait varies in a population of closely related strains of Streptomyces species as previous studies were all based on genome-wide analysis and metabolite profiling of Streptomyces species available in the database
There is no consensus on the distribution, co-occurrence, and antibiotic activity variations among multiple Streptomyces species and taxonomically closely related strains isolated from the same ecological niche, i.e., marine sediments
Summary
The marine ecosystem has become the hotspot for finding antibiotic-producing actinomycetes across the globe. Genome mining on the most extensive BGC study to date using 1110 publicly available Streptomyces genomes revealed a high diversity of BGCs and distribution pattern variation in closely related strains of Streptomyces[9] This BGCs variation in Streptomyces species is associated with an intraand interspecies recombination as a rapid response to selective pressures in ecological niches, impacting the secondary metabolite diversity among closely related s trains[8, 13,14,15,16]. It remains unclear if functional trait (i.e., antibiotic activities) varies in a population of closely related strains of Streptomyces species as previous studies were all based on genome-wide analysis and metabolite profiling of Streptomyces species available in the database. The unique physical properties of marine ecosystems such as high salinity and pressure, variation in temperatures, and oxygen concentrations serve as evolutionary pressures that trigger secondary metabolites’ production different from their terrestrial counterparts[22]
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