Ammonia manipulates the ammonia-oxidizing archaea and bacteria in the coastal sediment-water microcosms

Ammonia was observed as a potential significant factor to manipulate the abundance and activity of ammonia-oxidizing microorganisms (AOMs) in water environments. For the first time, this study confirmed this phenomenon by laboratory cultivation. In a series of estuarine sediment-coastal water microcosms, we investigated the AOM’s phylogenetic composition and activity change in response to ammonia concentration. Increase of ammonia concentration promoted bacterial amoA gene abundance in a linear pattern. The ratio of transcribed ammonia-oxidizing bacteria (AOB) amoA gene/ammonia-oxidizing archaea (AOA) amoA gene increased from 0.1 to 43 as NH4+-N increased from less than 0.1 to 12 mg L−1, and AOA amoA transcription was undetected under 20 mg NH4+-N L−1. The incubation of stable isotope probing (SIP) microcosms revealed a faster 13C-NaHCO3 incorporation rate of AOA amoA gene under 0.1 mg NH4+-N L−1 and a sole 13C-NaHCO3 utilization of the AOB amoA gene under 20 mg NH4+-N L−1. Our results indicate that ammonia concentration manipulates the structure of AOM. AOA prefers to live and perform higher amoA transcription activity than AOB in ammonia-limited water environments, and AOB tends to take the first contributor place in ammonia-rich ones.