Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential

Abstract

Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.

Isolation, diversity, and biotechnological potential of rhizo- and endophytic bacteria associated with mangrove plants from Saudi Arabia

“…However, it was not a functional study, unlike the present study. Another study from the same region reported the presence and antimicrobial properties of bacterial communities in Red Sea sediments (Al-Amoudi et al, 2016). In the present study, isolates of γ-Proteobacteria were prevalent and demonstrated immense biotechnological potential.…”

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

“…The resulting tree (Fig. 2 ) shows the phylogenetic proximity of Bac48 and Bac84 to B. paralicheniformis strains and reveals them to be more distantly related to B. licheniformis than previously reported [ 30 ].…”

“…Herewith allowing strains to adapt/survive in different ecosystems (in this instance, mangrove mud as opposed to microbial mat) [ 53 – 55 ]. This makes the discovery interesting as we previously reported [ 30 ] that these strains exhibit different antimicrobial activity; specifically, B. paralicheniformis Bac84 has stronger antimicrobial potential against three-indicator pathogens: Staphylococcus aureus , Salmonella typhimurium , and Pseudomonas syringae . Thus, the disparity associated with the antimicrobial activity could be a consequence of the foreign genes providing a novel product with antimicrobial activity.…”

“…In this study, we sequenced and assembled genomes of two Bacillus strains, B. paralicheniformis Bac48 and B. paralicheniformis Bac84, both isolated from the Rabigh Harbor Lagoon of the Red Sea in Saudi Arabia. The reason for this selection has been that we previously reported that antimicrobial activity exhibited by B. paralicheniformis Bac84 is more pronounced than B. paralicheniformis Bac48, against three-indicator pathogens: Staphylococcus aureus , Salmonella typhimurium , and Pseudomonas syringae [ 30 ] . In the current study we aimed at studying the relevant differences between these two species in more details.…”

Genome sequence analysis of Zooshikella ganghwensis strain VG4 and its potential for the synthesis of antimicrobial metabolites

“…The emergence and spread of resistance against known antimicrobials has renewed interest in the discovery of microbial natural products with antimicrobial properties. Recent studies have revealed that microbes found in the Red Sea can produce a variety of antimicrobial compounds [ [1] , [2] , [3] , [4] ]. The sequencing of microbial genomes has revealed the immense genetic potential of microbes to synthesize bioactive secondary metabolites [ 5 ]; however, the vast majority of secondary metabolites has remained unidentified [ 6 ].…”