Metagenomic analysis using 16S ribosomal RNA genes of a bacterial community in an urban stream, the Tama River, Tokyo.

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. <italic>Flavobacterium</italic> (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for ~ 16% of assigned 16S reads, followed by <italic>Mycobacterium</italic>. Other dominant bacterial genera including <italic>Zoogloea</italic>, <italic>Sediminibacterium</italic>, <italic>Hyphomicrobium</italic>, <italic>Sphingopyxis</italic>, <italic>Thiothrix</italic> and <italic>Lysobacter</italic>, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, <italic>Flavobacterium</italic> was positively correlated with temperature, while <italic>Polaromonas</italic>, <italic>Pseudomonas</italic> and <italic>Bradyrhizobium</italic> were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors. [ABSTRACT FROM AUTHOR]