Niche differentiation of comammox Nitrospira in sediments of the Three Gorges Reservoir typical tributaries, China

Complete ammonia oxidizer (Comammox) can complete the whole nitrification process independently, whose niche differentiation is important guarantee for its survival and ecological function. This study investigated the niche differentiation of comammox Nitrospira in the sediments of three typical tributaries of the Three Gorges Reservoir (TGR). Clade A and clade B of comammox Nitrospira coexisted in all sampling sites simultaneously. The amoA gene abundance of clade A and B was gradually increased or decreased along the flow path of the three tributaries with obvious spatial differentiation. The amoA gene abundance of comammox Nitrospira clade A (6.36 × 10(3) − 5.06 × 10(4) copies g(−1) dry sediment) was higher than that of clade B (6.26 × 10(2) − 6.27 × 10(3) copies g(−1) dry sediment), and the clade A amoA gene abundance was one order of magnitude higher than that of AOA (7.24 × 10(2) − 6.89 × 10(3) copies g(−1) dry sediment) and AOB (1.44 × 10(2) − 1.46 × 10(3) copies g(−1) dry sediment). A significant positive correlation was observed between comammox Nitrospira clade A amoA gene abundance and flow distance (P < 0.05). The number of operational taxonomic units (OTUs) in two sub-clades of clade A accounted for the majority in different tributaries, indicating that clade A also had population differentiation among different tributaries. This study revealed that comammox Nitrospira in the sediments of TGR tributaries have niche differentiation and clade A.2 played a more crucial role in comammox Nitrospira community.