Even a small net increase in soil organic carbon (SOC) mineralization will cause a substantial increase in the atmospheric CO ₂ concentration. It is widely recognized that the SOC mineralization within deep critical zones (2 to 12 m depth) is slower and much less influenced by anthropogenic disturbance when compared to that of surface soil. Here, we showed that 20 years of nitrogen (N) fertilization enriched a deep critical zone with nitrate, almost doubling the SOC mineralization rate. This result was supported by corresponding increases in the expressions of functional genes typical of recalcitrant SOC degradation and enzyme activities. The CO ₂ released and the SOC had a similar ¹⁴ C age (6000 to 10,000 years before the present). Our results indicate that N fertilization of crops may enhance CO ₂ emissions from deep critical zones to the atmosphere through a previously disregarded mechanism. This provides another reason for markedly improving N management in fertilized agricultural soils.

In sub-Saharan Africa, agriculture can account for up to 66% of anthropogenic greenhouse gas (GHG) emissions. Unfortunately, due to the low number of studies in the region there is still much uncertainty on how management activities can affect these emissions. To help reduce this uncertainty, we measured GHG emissions from three maize (Zea mays) growing seasons in central Kenya. Treatments included: (1) a no N application control (C); (2) split (30% at planting and 70% 1 month after planting) mineral nitrogen (N) applications (Min—100 kg N ha⁻¹); (3) split mineral N + irrigation (equivalent to 10 mm precipitation every three days—MI); (4) split mineral N + 40 kg N ha⁻¹ added as manure (MM—total N = 140 kg ha⁻¹); and (5) split mineral + intercropping with faba beans (Phaseolus vulgaris—MB). Soil CO₂ fluxes were lower in season 1 compared to seasons 2 and 3 with fluxes highest in Min (p = 0.02) in season 2 and lowest in C (p = 0.02) in season 3. There was uptake of CH₄ in these soils that decreased from season 1 to 3 as the mean soil moisture content increased. Cumulative N₂O fluxes ranged from 0.25 to 2.45 kg N₂O-N ha⁻¹, with the highest fluxes from MI during season 3 (p = 0.01) and the lowest from C during season 1 (p = 0.03). The average fertilizer induced emission factor (0.36 ± 0.03%) was roughly one-third the default value of 1%. Soil moisture was a critical factor controlling GHG emissions in these central Kenya highlands. Under low soil moisture, the soils were CH₄ sinks and minimal N₂O sources.

An integrated modelling strategy was designed and applied to the Soil-Vegetation-Atmosphere Transfer model Daisy for simulation of crop production and nitrate leaching under pedo-climatic and agronomic environment different than that of model original parameterisation. The points of significance and caution in the strategy are: •Model preparation should include field data in detail due to the high complexity of the soil and the crop processes simulated with process-based model, and should reflect the study objectives. Inclusion of interactions between parameters in a sensitivity analysis results in better account for impacts on outputs of measured variables.•Model evaluation on several independent data sets increases robustness, at least on coarser time scales such as month or year. It produces a valuable platform for adaptation of the model to new crops or for the improvement of the existing parameters set. On daily time scale, validation for highly dynamic variables such as soil water transport remains challenging. •Model application is demonstrated with relevance for scientists and regional managers. The integrated modelling strategy is applicable for other process-based models similar to Daisy. It is envisaged that the strategy establishes model capability as a useful research/decision-making, and it increases knowledge transferability, reproducibility and traceability.