Temporal variability in the abundance of ammonia- oxidizing bacteria vs. archaea in sandy sediments of the Douro River estuary, Portugal

Abstract

We studied the relative abundance of betaproteobacterial ammonia-oxidizing bacteria (Betaproteobacteria AOB) vs. ammonia-oxidizing archaea (AOA) in the intertidal sediments of the Douro estuary by quantifying Betaproteobacteria AOB and AOA amoA genes over 12 mo. We also evaluated the diversity of AOA in the sandy intertidal sediments of the estuary. Real-time PCR analysis showed that the abundance of Betaproteobacteria AOB amoA genes ranged from 0.8 x 10 6 to 7.5 × 10 6 copies cm ―3 of sediment, corresponding to 0.8 to 8.4 % of the total bacterial 16S rRNA gene copies, while that of AOA amoA genes ranged from 0.9 x 10 5 to 8.6 × 10 5 gene copies cm ―3 of sediment, corresponding to 0.8 to 25.9 % of the total archaeal copies. Results revealed that bacteria dominated the ammonia-oxidizing community almost over the entire survey period, with Betaproteobacteria AOB:AOA ratios ranging from 1 to 39. Nitrification activity estimations based on the numerical abundance of Betaproteobacteria AOB and AOA amoA, and comparison with measured nitrification rates indicated that Betaproteobacteria AOB were the major contributors to the nitrification process. Phylogenetic analysis of AOA revealed that archaeal amoA sequences retrieved from Douro estuarine sediments were closely related to sequences previously found in the water column, in soils and sediments.