Diversity and functions of bacterial communities in water and sediment from the watershed of the Tama River flowing a highly urbanized area

Bacterial communities are important factors governing changes in river ecology. We evaluated the diversity of bacterial communities in sediment and size-fractionated water samples collected from the Tama River, Tokyo, Japan, to verify their taxonomy and functional classes. Samples were collected from three river areas, namely up-, mid- and downstream, and analyzed using MiSeq shotgun metagenomic sequencing. Bacterial diversity in the river water was highest midstream for the free-living bacterial communities. Dominant bacterial classes upstream were Alphaproteobacteria and Betaproteobacteria, and there was a gradual shift to dominance by Actinobacteria mid- and downstream. Potential pathogenic genera, such as Flavobacterium, Mycobacterium and Bacteroides, also dominated mid- and downstream. Interestingly, Mycobacterium was most abundant midstream, whereas Pseudomonas was observed upstream. The gene possibly associated with sulfur metabolism, sigB, and those associated with purine metabolism, purF, purD, purN, purH, guaB and guaA, dominated in the bacterial communities found mid- and downstream and are thought to ensure survival and virulence in their environments. NO2-N, NH4-N and PO4-P were found to influence bacterial populations in water but not those residing in the sediment.