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 × 103 − 5.06 × 104 copies g−1 dry sediment) was higher than that of clade B (6.26 × 102 − 6.27 × 103 copies g−1 dry sediment), and the clade A amoA gene abundance was one order of magnitude higher than that of AOA (7.24 × 102 − 6.89 × 103 copies g−1 dry sediment) and AOB (1.44 × 102 − 1.46 × 103 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.
Comammox (CMX) Nitrospira bacteria (NB) can accomplish ammonia oxidation independently, and their niche differentiation holds promise for their ecological and survival functions. In this work, the vertical niche differentiation of CMX NB was investigated in the soils of 6 water-level fluctuation (WLF) zones (both natural and artificial) in the Three Gorges Reservoir (TGR) region. The results demonstrated that the level of clade A amoA was obviously reduced with increasing soil depth in the natural WLF zones and one of the artificial WLF zones. However, in the other two artificial WLF zones, the abundance of this gene was not dramatically reduced with depth. The level of clade B amoA did not markedly decrease with increasing soil depth in most WLF zones and remained stable in the three WLF zones. Total nitrogen (TN) had the most significant effect on the abundance of CMX NB. Clade A.1, clade A.2.1, clade A.2.2, clade A.3, and clade B of CMX NB co-occurred simultaneously in all WLF zones. The number of operational taxonomic units (OTUs) of clade A in the two types of WLF zones first increased and then decreased with increasing depth, whereas the number of OTUs of clade B continuously increased with depth in the artificial WLF zone. Total carbon (TC) and pH, as environmental factors, affected the community structure of CMX NB. This study confirmed the vertical differentiation of the abundance and diversity of CMX NB in the WLF zones of the TGR region, and the artificial restoration of the WLF zones affected the niche differentiation of CMX NB to a certain degree.
CMX NB can accomplish ammonia oxidation independently, and its niche differentiation holds a promise for its ecological and survival function. In this work, the vertical niche differentiation of comammox (CMX) Nitrospira bacteria (NB) was investigated in the soils of 6 hydro-fluctuation (HF) zones (both natural and artificial) in the Three Gorges Reservoir (TGR) Region. The results demonstrated that the level of clade A amoA was obviously reduced with the increasing soil depth in the natural HF zone and one of the artificial HF zones. However, in the other two artificial HF zones, the abundance of this gene was not dramatically reduced along the depth. The level of clade B amoA was not markedly decreased with the increasing soil depth in most HF zones, and remained stable in three HF zones. Total nitrogen had the most significant effect on the abundance of CMX NB. Clade A.1, A.2.1, A.2.2, A.3, and B of CMX NB co-occurred simultaneously in all HF zones. The number of operational taxonomic units (OTUs) of clade A in the two types of HF zones was first elevated and then reduced with the increasing depth, whereas the number of OTUs of clade B was continuously increased with depth in the artificial HF zone. pH and total carbon (TC), as environmental factors, affected the community structure of CMX NB. This study confirmed the vertical differentiation of the abundance and diversity of CMX NB in the HF zone of the TGR area, and the artificial restoration of the HF zone affected the niche differentiation of CMX NB to a certain degree.
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