The Nile River Microbiome Reveals a Remarkably Stable Community Between Wet and Dry Seasons, and Sampling Sites, in a Large Urban Metropolis (Cairo, Egypt).

World freshwater supplies are in need of microbiome diversity analyses as a first step to future ecological studies, and to monitor water safety and quality. The Nile is a major north-flowing river in Africa that displays both spatial and temporal variations in its water quality. Here, we present the first microbiome analysis of the Nile River water in two seasons: (1) summer representing the wet season, and (2) winter representing the dry season, as sampled around Cairo, the capital of Egypt. Surface river water samples were collected from selected locations along the path of river, and the microbial composition was analyzed by next-generation sequencing of the 16S rRNA gene. We found a striking stability in the Nile microbiome community structure along the examined geographical urban sites and between the wet and dry seasons as evidenced by the high proportion of shared operational taxonomic unit values among all samples. The community was dominated by the Cyanobacteria (mainly Synechococcus), Actinobacteria candidate family (ACK-M1), and Proteobacteria (mainly family Comamonadaceae). Among these dominant taxa, Synechococcus exhibited seasonal driven variation in relative abundance. Other taxa were predominantly rare across all seasons and locations, including genera members of which have been implicated as pathogens such as Acinetobacter, Aeromonas, and Legionella. In addition, comparisons with data on freshwater microbiome in other world regions suggest that surface water communities in large rivers exhibit limited variation. Our results offer the first insights on microbial composition in one of the most notable rivers near a large metropolis.