Ecological distribution of ammonia oxidizers in Yellow River sediments and their influencing factors

Ammonia oxidation, the first and rate-limiting step of nitrification, is a crucial step in nitrogen cycling. The distribution patterns of key ammonia oxidizers, including ammonia-oxidizing archaea (AOA) and bacteria (AOB), and comammox (complete ammonia oxidation) Nitrospira, provide vital insights for nitrogen cycling in natural ecosystems. Currently, the distribution and contribution of AOA, AOB and comammox Nitrospira in freshwater ecosystems remain largely underexplored. This study explored the abundances, diversity, phylogenetic characteristics, and community structures of AOA, AOB and comammox Nitrospira in the Yellow River sediments using high-throughput sequencing and qPCR. Comammox Nitrospira displayed the highest amoA gene abundance in sediments from all sampling sites compared to that of AOA and AOB. The diversity of AOA shown no significant correlations with physicochemical properties, while the diversity of AOB negatively correlated with pH (p < 0.05), and the diversity of comammox Nitrospira positively correlated with NH₄⁺ content and TC content (p < 0.05), respectively. Phylogenetic analysis identified Nitrososphaera, Nitrosospira, and cladeA1 as the most dominant clusters of AOA, AOB and comammox Nitrospira, respectively. The community composition of AOA, AOB, and comammox Nitrospira exhibited distinct spatial patterns, varying across the upper, middle and lower reaches. pH was the key factor shaping the community structure of AOB and comammox Nitrospira (p < 0.05), while organic carbon was the key determinant of the AOA community structure (p < 0.05). The results of this study advance our understanding of N cycling in freshwater ecosystems.