Niche adaptation strategies of different clades of comammox Nitrospira in the Yangtze Estuary

Abstract The discovery of complete ammonia oxidizers (comammox) changed the conventional view of the previously known two-step process of nitrification. Comammox Nitrospira that can independently oxidize ammonia to nitrate have been found existing in various ecosystems except the ocean. Estuary tidal flat wetlands are an important transition area between land and sea. Thus, studying the species dynamics of comammox Nitrospira across the estuarine salinity gradient can offer insights into their ecological distribution and physiological potential in this ecosystem. Comammox Nitrospira species were widely distributed in the Yangtze Estuary, yet with abundance lower than canonical ammonia oxidizers. A distinct differentiation of comammox Nitrospira groups driven by salinity was revealed by phylogenetic and community structure analyses. Comammox Nitrospira clade A1 was mainly distributed in the downstream region of the Yangtze River indicating its high adaptation to salinity, while clade A2 was mostly detected in the upstream regions where salinity was low. Within the previously defined clade A2, a new subcluster-clade A2.2 was determined. It accounted for 19.2% of the retrieved comammox Nitrospira sequences from the samples, and showed similar sources and consistent niches with clade A1. In addition to salinity, ammonia, pH and particle size were also important environmental factors affecting niche differentiation of comammox Nitrospira species. Taken together, we surveyed the diversity, abundance, and community structure of comammox Nitrospira along the Yangtze Estuary, alongside the niche separation of different subgroups. This shed light on the ecophysiology of comammox in global estuary ecosystems.