Comammox Nitrospira and ammonia-oxidizing bacteria are metabolically active in a subtropical estuarine wetland

Abstract

Plant species profoundly influence soil microorganisms, yet their impact on active ammonia-oxidizing microorganisms remains largely unclear in subtropical estuarine wetlands. Here, we employed DNA stable isotope probing (DNA-SIP) technique to identify the active ammonia oxidizers under two typical plant species, Phragmites australis and Spartina alterniflora, as well as on a bare tidal flat in the Min River estuary. Our results revealed that comammox Nitrospira and ammonia-oxidizing bacteria (AOB) rather than archaea (AOA) were metabolically active in the P. australis and bare tidal flat soils. However, in S. alterniflora soils, the activity of ammonia oxidizers was inhibited, highlighting the critical role of plant species in shaping their community. The active ammonia oxidizers were primarily dominated by Nitrosomonas for AOB and clade A.1 for comammox Nitrospira. In comparison, bare tidal flat soils had a lower proportion of Nitrosospira and a higher relative abundance of comammox Nitrospira clade A.2 than those associated with P. australis. Taken together, our findings emphasize the importance of AOB and comammox Nitrospira, rather than AOA, in the nitrification processes within coastal wetlands, and underscore the critical role of plant species as a mediator.