The use of crop residues as a bioenergy feedstock is considered a potential strategy to mitigate greenhouse gas (GHG) emissions. However, indiscriminate harvesting of crop residues can induce deleterious effects on soil functioning, plant growth and other ecosystem services. Here, we have summarized the information available in the literature to identify and discuss the main trade-offs and synergisms involved in crop residue management for bioenergy production. The data consistently showed that crop residue harvest and the consequent lower input of organic matter into the soil led to C storage depletions over time, reducing cycling, supply and availability of soil nutrients, directly affecting the soil biota. Although the biota regulates key functions in the soil, crop residue can also cause proliferation of some important agricultural pests. In addition, crop residues act as physical barriers that protect the soil against raindrop impact and temperature variations. Therefore, intensive crop residue harvest can cause soil structure degradation, leading to soil compaction and increased risks of erosion. With regard to GHG emissions, there is no consensus about the potential impact of management of crop residue harvest. In general, residue harvest decreases CO₂ and N₂O emissions from the decomposition process, but it has no significant effect on CH₄ emissions. Plant growth responses to soil and microclimate changes due to crop residue harvest are site and crop specific. Adoption of the best management practices can mitigate the adverse impacts of crop residue harvest. Longterm experiments within strategic production regions are essential to understand and monitor the impact of integrated agricultural systems and propose customized solutions for sustainable crop residue management in each region or landscape. Furthermore, private and public investments/cooperations are necessary for a better understanding of the potential environmental, economic and social implications of crop residue use for bioenergy production.

The total or partial removal of sugarcane (Saccharum spp. L.) straw for bioenergy production may deplete soil quality and consequently affect negatively crop yield. Plants with lower yield potential may present lower concentration of leaf-tissue nutrients, which in turn changes light reflectance of canopy in different wavelengths. Therefore, vegetation indexes, such as the normalized difference vegetation index (NDVI) associated with concentration of leaf-tissue nutrients could be a useful tool for monitoring potential sugarcane yield changes under straw management. Two sites in São Paulo state, Brazil were utilized to evaluate the potential of NDVI for monitoring sugarcane yield changes imposed by different straw removal rates. The treatments were established with 0%, 25%, 50%, and 100% straw removal. The data used for the NDVI calculation was obtained using satellite images (CBERS-4) and hyperspectral sensor (FieldSpec Spectroradiometer, Malvern Panalytical, Almelo, Netherlands). Besides sugarcane yield, the concentration of the leaf-tissue nutrients (N, P, K, Ca, and S) were also determined. The NDVI efficiently predicted sugarcane yield under different rates of straw removal, with the highest performance achieved with NDVI derived from satellite images than hyperspectral sensor. In addition, leaf-tissue N and P concentrations were also important parameters to compose the prediction models of sugarcane yield. A prediction model approach based on data of NDVI and leaf-tissue nutrient concentrations may help the Brazilian sugarcane sector to monitor crop yield changes in areas intensively managed for bioenergy production.