Assessing microbial identity, diversity, and community structure could be a valuable tool for monitoring the impact of xenobiotics and anthropogenic inputs in rivers, especially in urban and industrial settings. Here, we characterize the Nile River microbial community in water and sediments in summer and winter at five locations that span its natural flow through the Cairo metropolis. 16S rRNA gene datasets were analyzed to identify the role played by sample type (sediment versus water), season, and location in shaping the community, as well as to predict functional potential of the Nile River microbiome. Microbial communities were mostly influenced by sampling type (sediments versus water), while seasonal effects were only observed in water samples. Spatial differences did not represent a significant factor in shaping the community in either summer or winter seasons. Proteobacteria was the most abundant phylum in both water and sediment samples, with the order Betaproteobacteriales being the abundant one. Chloroflexi and Bacteroidetes were also prevalent in sediment samples, while Cyanobacteria and Actinobacteria were abundant in water samples. The linear discriminative analysis effect size (LEfSe) identified the cyanobacterial genus Cyanobium PCC-6307 as the main variable between summer and winter water. Sequences representing human and animal potential pathogens, as well as toxin-producing Cyanobacteria, were identified in low abundance within the Nile microbiome. Functionally predicted metabolic pathways predicted the presence of antibiotic biosynthesis, as well as aerobic xenobiotic degradation pathways in the river microbiome.

评估微生物特性、多样性和群落结构可能是监测河流中异生物质和人为输入影响的重要工具，尤其是在城市和工业环境中。在这里，我们描述了尼罗河在夏季和冬季在自然流经开罗大都市的五个地点的水和沉积物中的微生物群落。分析了 16S rRNA 基因数据集，以确定样本类型（沉积物与水）、季节和位置在塑造群落中的作用，以及预测尼罗河微生物群的功能潜力。微生物群落主要受采样类型（沉积物与水）的影响，而季节性影响仅在水样中观察到。无论是夏季还是冬季，空间差异都不是塑造社区的重要因素。Proteobacteria 是水和沉积物样品中最丰富的门，其中 Betaproteobacteriales 是最丰富的门。Chloroflexi 和 Bacteroidetes 在沉积物样品中也很普遍，而蓝藻和放线菌在水样中也很丰富。线性判别分析效应大小 (LEfSe) 确定了蓝藻属Cyanobium PCC-6307作为夏季和冬季水之间的主要变量。在尼罗河微生物组中鉴定出低丰度的代表人类和动物潜在病原体以及产生毒素的蓝藻的序列。功能预测的代谢途径预测了抗生素生物合成的存在，以及河流微生物群中的需氧外源降解​​途径。