Effects of Dam Building on Niche Differentiation of Comammox Nitrospira in the Main Stream of the Three Gorges Reservoir Area

Complete ammonia oxidizers (comammox) can completely oxidize ammonia to nitrate, and the various habitats of comammox Nitrospira are an important guarantee for their survival. The construction of the Three Gorges Dam, China, made it easier for nitrogen to stay in the reservoir area, which may have caused the niche differentiation of comammox, thereby affecting the natural transformation process of nitrogen in the reservoir area. This study investigated comammox in river sediments in the Three Gorges Reservoir area. Comammox clade A and comammox clade B were detected in all samples, and comammox clade A was dominant. The number of dominant OTUs (Operational Taxonomic Unit) in comammox clade A.1 accounted for 18.69% of the total number of OTUs, followed by comammox clade A.2 (18.58%) and clade B (14.30%). The indicated abundance of comammox Nitrospira clade A and clade B amoA genes in the main stream of the Three Gorges Reservoir increased along the length of the river and reached the maximum in the middle part of the reservoir area. The highest abundance of ammonia-oxidizing archaea (AOA) amoA genes appeared in the upper stream section of the reservoir area. Comammox Nitrospira clade A exhibited the highest abundance (3.00 × 104 ± 8782.37 copies/g), followed by comammox Nitrospira clade B (1.83 × 103 ± 1019.82 copies/g), ammonia-oxidizing bacteria (AOB) (1.28 × 103 ± 574.69 copies/g), and AOA (1.73 × 102 ± 48.05 copies/g). The abundances of both comammox clades A and B were positively correlated with sediment pH, indicating that pH is an important environmental factor affecting the growth of comammox bacteria. Additionally, the relative abundances of both comammox clade A.2 and clade B were significantly correlated with overlying water dissolved oxygen (DO) in the reservoir area. This study thus indicated that there exists a niche differentiation of comammox Nitrospira in the main stream of the Three Gorges Reservoir area. The potential changes in the ammoxidation process and the environmental effects caused by this niche differentiation need further attention.