In order to investigate the distribution of anammox bacteria in river ecosystems, water and sediment samples were collected at 6 sites along the lower Yangtze River in spring and autumn in 2014. Clean reads of metagenomic sequencing were BLAST against self-constructed datasets of anammox bacterial marker genes hzsA, hzsB, hzsC and hdh, and valid hits were used to calculate their relative abundances. As results, average relative abundances of hzsA, hzsB, hzsC and hdh genes in water were extremely low due to the excess dissolved oxygen which was not suitable for anammox bacteria. Whereas, the average relative abundances in sediments were much higher, i.e., 4.540×10-10, 4.939×10-10, 4.333×10-10 and 2.859×10-10, respectively. Due to the temperature rise, average relative abundances of hzsA, hzsB, hzsC and hdh genes in sediment samples in autumn were higher than those in spring. From the changes alongside the river, average relative abundances of hzsA, hzsB, hzsC and hdh genes at Datong, Nanjing and Xuliujing were relatively higher, which was due to anthropogenic activity and salinity increase in the estuary. Based on the results of taxonomic identification, anammox bacteria in the lower Yangtze River mainly consisted of Candidatus Brocadia and Candidatus Jettenia at genus level. Relative abundances of hzsA, hzsB, hzsC and hdh genes were related to NO2--N, NO3--N and NH4+-N concentration, of which NO2--N concentration was the restrictive factor as it was much lower than NH4+-N concentration.
