Linking Abundance and Activity of Ammonia-Oxidising Bacteria and Archaea in an Agriculturally Impacted First-Order Stream.

Lower-order streams in agricultural landscapes receive major anthropogenic nitrogen inputs. Streambed sediments host diverse microbial communities that can influence nitrogen (N) fluxes and water chemistry. Both bacterial and archaeal ammonia oxidizers inhabit streambeds, but their respective contributions to nitrification are often unresolved. We investigated a first-order stream in southern Germany to assess the contribution of distinct ammonia-oxidising populations to streambed nitrification. We combined in situ geochemical data, 16S rRNA and functional-gene amplicon sequencing, quantitative PCR and microcosm incubations with selective chemical inhibitors. A process-based reaction model quantified total nitrification rates and inferred contributions of ammonia-oxidising archaea (AOA) and bacteria (AOB), while population-specific kinetic parameters were estimated using Bayesian inference. We found that AOB dominated nitrification and responded more strongly to ammonium inputs than AOA despite being less abundant. Among them, populations of Nitrosomonas and Nitrosospira spp. were most important. Differences in ammonia-oxidation rates and ammonia-oxidising communities between sediment depths and successive stream segments suggest a hydrological influence on streambed nitrification. Our study demonstrates the strength of combining field data, microcosm incubations and modelling to better understand microbial N-cycling in the environment. It also mandates caution when interpreting functional-gene abundance as a proxy for in situ reactive potential.