Shifts of abundance and community composition of nitrifying microbes along the Changjiang Estuary to the East China Sea.

Nitrification, the oxidation of ammonium to nitrate via nitrite, links nitrogen fixation and nitrogen loss processes, playing key roles in coastal nitrogen cycle. However, few studies have simultaneously examined both ammonia-oxidizing and nitrite-oxidizing microbes. This work investigated the abundance and community structure of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) using archaeal amoA gene, bacterial amoA gene, and NOB nxrB gene, respectively, through q-PCR and Sanger sequencing along the Changjiang Estuary salinity gradient. Results showed that ammonia oxidizers were dominated by AOB and had higher abundance than NOB. AOA had a higher diversity at high-salinity stations, and AOB diversity decreased along the estuarine salinity gradient. The communities of AOA differed among freshwater, estuarine mixing and seawater zones, indicating a narrow ecological niche. AOB compositions displayed a wide niche, changing from Nitrosomonas-like sequences dominated to Nitrosospira-like sequences dominated along the salinity gradient. The RDA showed that sand and nitrate contents had significant impacts on the AOA community compositions, while the AOB communities were governed by clay and nitrate contents. This research provides insight into the understanding of the niche of ammonia oxidizers in the estuarine zones.