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. NO 2 -N, NH 4 -N and PO 4 -P were found to influence bacterial populations in water but not those residing in the sediment.