Current trends in bioenergy production pinpoint agricultural residues as a potential source of low-cost abundant biomass. However, harvesting crop residues or manures with energetic aims will certainly have an impact on soil, where they would be no longer disposed. Several soil scientists caution that the continuous removal of crop residues from soil for bioenergy production will create a negative nutrient budget, decreasing soil fertility and carbon stocks and accelerating soil erosion. On the other hand, the production of energy from biomass yields large quantities of by-products which could be disposed of as soil amendments as they are produced on a progressively larger scale. In two independent laboratory incubation studies we followed carbon (C) and nitrogen (N) dynamics and greenhouse gas emissions after soil amendment with (1) ¹⁵N labelled manure compared to its successive bioenergy by-products: ¹⁵N digestate and ¹⁵N biochar, and (2) doubly labelled (¹³C, ¹⁵N) wheat straw compared to its by-product after enzymatic hydrolysis for second-generation bioethanol production.

The first experiment revealed that the release of N in soil derived from residue was highest with manure and it decreased after anaerobic digestion and significantly more after pyrolysis, which has important parallel effects such as the reduction of N₂O emissions. In the second experiment, the proportion of C emitted as CO₂ originating from the residue was higher for the wheat straw than for its correspondent by-product. However, the bioenergy by-product promoted native soil C mineralization which lead to similar or even higher total C losses. We conclude that replacing residue with by-products fundamentally alters N and C processes in the soil. These changes need to be studied further before a full life-cycle assessment of biofuel production chains can be made.