Coastal upwelling causes variations in temperature, salinity and inorganic nutrients in the 
water column, consequently leading to the shift of microbial populations and their metabolic activ ities. Impacts of the eastern Hainan upwelling (EHU) on the ammonia-oxidizing archaea (AOA) 
were investigated based on the amoA gene using pyrosequencing and quantitative PCR at both DNA 
and cDNA levels, together with the determination of the ammonia oxidation (AO) rate measured 
with 15N-labelled ammonium. By comparing stations with and without upwelling influence, we 
found that coastal upwelling correlated with an increase in amoA gene abundance, the dominance 
of distinct clades for AOA communities at the respective gene and transcript levels, and a large 
increase in the proportion of the SCM1-like (Nitrosopumilus maritimus-like) cluster as well. The AO 
rates were generally higher in the deeper water (~25 m), which was in significant positive correla tion with the proportion of cluster Water Column A (WCA) at the transcript level, indicating the 
potential contribution of this cluster to in situ ammonia oxidization. Our study demonstrated that 
coastal upwelling had a significant impact on the AOA community and ammonia oxidization rate; 
therefore, this physical forcing should be considered in the future assessment of the global nitrogen 
budgets and biogeochemical nitrogen cycles.