Seasonal distribution of nitrifiers and denitrifiers in urban river sediments affected by agricultural activities

Highlights: • Nitrifiers and denitrifiers in river sediments showed seasonal and depth variability. • amoA and nosZ gene were similar between river sediments and nearby agricultural soils. • Runoff from agricultural soils affects microbial community in nearby river sediments. Nitrifiers and denitrifiers play a critical role in nitrogen removal in urban river sediments that are also affected by agricultural activities. However, the seasonal variations and vertical profile of these organisms in these river sediments are not well understood. In this study, the seasonal and depth (0 to 30 cm) distributions of the abundance and activity of nitrifiers and denitrifiers in sediments of the Pearl River in Guangzhou city were quantifying via qPCR and RT-qPCR according to various nitrifying and denitrifying functional genes, and their diversities were analyzed via high-throughput sequencing on an Illumina MiSeq platform. Results show that the distribution of nitrifiers and denitrifiers in these urban sediments were more abundant and active during the summer than winter; had distinct vertical distributions in the bacterial numbers and activity, with higher activity of the nirS gene (yearly averaged RNA:DNA 2.5% at 18 to 22 cm, vs. a yearly-depth average of 0.65%) but with lower overall numbers (yearly averaged 2.1 × 10⁶ copies g⁻¹ at 18 to 22 cm, vs. a yearly-depth average of 12.5 × 10⁶ copies g⁻¹); and their amoA and nosZ gene diversities in the sediments exhibited a correlation with the communities in nearby agricultural soils.