Water and sediment microbiota diversity in response to temporal variation at the outlet of the Ibrahim River (Lebanon)

Bacterial diversity is an important factor controlling the functioning of aquatic ecosystems. With the critical sensitivity of the microbial community towards chemical and/or physical factors, this study aims to identify for the first time the microbiota of the Lebanese coastal Ibrahim River. Water and sediment samples were collected at the outlet of the river, between May 2016 and April 2017, covering a hydrological year. The main microbiological parameters were tested: total germs, total coliforms, fecal coliforms, Escherichia coli, and Enterococcus. A DNA extraction followed by NGS analysis was applied on both water and sediment samples, in order to investigate the bacterial diversity and the habitat specificity. The link between this microbial composition and seasonal variations was then investigated. Results showed fourteen different bacterial phyla, among which were major microorganisms, including a wide variety of pathogenic and commensal ones, frequently available in the aquatic ecosystem. Most of the detected water microbiota were mostly correlated to other freshwater samples, with the main dominance of 5 common phyla: Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Acidobacteria with the average of 43%, 13%, 16%, 10%, and 4% respectively. Despite this overall similarity, multiple patterns were visible, confirming the influence of the temporal variations and the discharge influence on taxonomic diversity. Sediment samples contained the highest relative abundance of Proteobacteria, Firmicutes, and Bacteroidetes: with an average of 31%, 44%, and 22% respectively. Our study showed that the Ibrahim River outlet has a specific habitat clustering. The among-compartment bacterial community variation, which responded to changing environmental factors, approved the existence of a meaningful temporal heterogeneity.