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Molecular-based approaches were used to characterize the coastal microbiota and to elucidate the trophic state of Red Sea. Nutrient content and enterococci numbers were monitored, and used to correlate with the abundance of microbial markers. Microbial source tracking revealed the presence of >1 human-associated  Bacteroides  spp. at some of the near-shore sampling sites and at a heavily frequented beach. Water samples collected from the beaches had occasional exceedances in enterococci numbers, higher total organic carbon (TOC, 1.48–2.18 mg/L) and nitrogen (TN, 0.15–0.27 mg/L) than that detected in the near-shore waters. Enterococci abundances obtained from next-generation sequencing did not correlate well with the cultured enterococci numbers. The abundance of certain genera, for example  Arcobacter ,  Pseudomonas  and unclassified  Campylobacterales , was observed to exhibit slight correlation with TOC and TN. Low abundance of functional genes accounting for up to 41 copies/L of each  Pseudomonas aeruginosa  and  Campylobacter coli  were detected.  Arcobacter butzleri  was also detected in abundance ranging from 111 to 238 copies/L. Operational taxonomic units (OTUs) associated with cyanobacteria,  Prochlorococcus,   Ostreococcus  spp. and  Gramella  were more prevalent in waters that were likely impacted by urban runoffs and recreational activities. These OTUs could potentially serve as quantifiable markers indicative of the water quality.

Molecular-based approaches to characterize coastal microbial community and their potential relation to the trophic state of Red Sea