Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge

Nitrate (NO3 (-)) leaching is a serioushealth and ecological concern in global agroecosystems, particularlythose under the application of agricultural-managed aquifer recharge(Ag-MAR); however, there is an absence of information on microbialcontrols affecting NO3 (-) leaching outcomes.We combine natural dual isotopes of NO3 (-) (N-15/N-14 and O-18/O-16)with metagenomics, quantitative polymerase chain reaction (PCR), anda threshold indicator taxa analysis (TITAN) to investigate the activities,taxon profiles, and environmental controls of soil microbiome associatedwith NO3 (-) leaching at different depthsfrom Californian vineyards under Ag-MAR application. The isotopicsignatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil(0-10 cm), with a 12-25-fold increase of N-15-NO3 (-) and O-18-NO3 (-) after the first 24 h of flooding, followedby a sharp decrease in the enrichment of both isotopes with & SIM;80%decline in denitrification activities thereafter. In contrast, deepersoils (60-100 cm) showed minimal or no denitrification activitiesover the course of Ag-MAR application, thus resulting in 10-20-foldof residual NO3 (-) being leached. Metagenomicprofiling and laboratory microcosm demonstrated that both nitrifyingand denitrifying groups, responsible for controlling NO3 (-) leaching, decreased in abundance and potentialactivity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier anddenitrifier, had the highest and lowest tipping points with regardto the NO3 (-) changes (P < 0.05), respectively. Overall, our study provides new insightinto specific depth limitations of microbial controls on soil NO3 (-) leaching in agroecosystems. Conducting groundwater recharge in agriculturalsystemsrequires understanding of the biological controls of nitrate leachingand nitrogen cycling processes.

Automated summary

Nitrate (NO3(-)) leaching, a significant concern in global agroecosystems, is influenced by microbial activities and environmental factors. This study investigates the microbial controls on NO3(-) leaching using isotopic signatures, metagenomics, PCR, and TITAN analysis in Californian vineyards under agricultural-managed aquifer recharge (Ag-MAR) application. Results show that denitrification activities are significantly stimulated in the topsoil (0-10 cm) under Ag-MAR, while minimal denitrification occurs in deeper soils (60-100 cm), leading to substantial NO3(-) leaching. Metagenomic profiling indicates a decrease in nitrifying and denitrifying groups with soil depth. This study highlights the importance of understanding microbial controls for nitrate leaching in agricultural systems.