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.

In tropical regions, climate conditions favor fast decomposition of soil organic matter (SOM), releasing into the soil organic composts in solid, liquid, and gaseous forms with variable compositions. Dissolved organic matter (DOM), a complex mixture of thousands of organic compounds, is only a small fraction of the decomposition products; however, it is highly mobile and reactive to the soil. Therefore, DOM play a key role in soil aggregation (formation of organometallic complexes), energy source for microorganisms, as well as C storage, cycling, and provision of plant-available nutrients. DOM multifunctionality to sustain soil functions and important ecosystem services have raised global scientific interest in studies on DOM fractions. However, previous studies were conducted predominantly under temperate soil conditions in natural ecosystems. Therefore, there is paucity of information on tropical soil conditions under agricultural systems, where DOM turnover is intensified by management practices. This review synthesized information in the literature to identify and discuss the main sources, transformations, and future of DOM in soils. We also discussed the importance of this fraction in C cycling and other soil properties and processes, emphasizing agricultural systems in tropical soils. Gaps and opportunities were identified to guide future studies on DOM in tropical soils.

Increasing demand for biofuel has intensified land-use change (LUC) for sugarcane (Saccharum officinarum) expansion in Brazil. Assessments of soil quality (SQ) response to this LUC are essential for quantifying and monitoring sustainability of sugarcane production over time. Since there is not a universal methodology for assessing SQ, we conducted a field-study at three sites within the largest sugarcane-producing region of Brazil to develop a SQ index (SQI). The most common LUC scenario (i.e., native vegetation to pasture to sugarcane) was evaluated using six SQI strategies with varying complexities. Thirty eight soil indicators were included in the total dataset. Two minimum datasets were selected: one using principal component analysis (7 indicators) and the other based on expert opinion (5 indicators). Non-linear scoring curves were used to interpret the indicator values. Weighted and non-weighted additive methods were used to combine individual indicator scores into an overall SQI. Long-term conversion from native vegetation to extensive pasture significantly decreased overall SQ. In contrast, conversion from pasture to sugarcane had no significant impact on overall SQ at the regional scale, but site-specific responses were found. In general, sugarcane production improved chemical attributes (i.e., higher macronutrient levels and lower soil acidity); however it has negative effects on physical and biological attributes (i.e., higher soil compaction and structural degradation as well as lower soil organic carbon (SOC), abundance and diversity of macrofauna and microbial activity). Overall, we found that simple, user-friendly strategies were as effective as more complex ones for identifying SQ changes. Therefore, as a protocol for SQ assessments in Brazilian sugarcane areas, we recommend using a small number of indicators (e.g., pH, P, K, Visual Evaluation of Soil Structure -VESS scores and SOC concentration) and proportional weighting to reflect chemical, physical and biological processes within the soil. Our SQ evaluations also suggest that current approaches for expanding Brazilian sugarcane production by converting degraded pasture land to cropland can be a sustainable strategy for meeting increasing biofuel demand. However, management practices that alleviate negative impacts on soil physical and biological indicators must be prioritized within sugarcane producing areas to prevent unintentional SQ degradation over time.

Exploiting native soil phosphorus (P) and the large reservoirs of residual P accumulated over decades of cultivation, namely “legacy P”, has great potential to overcome the high demand of P fertilisers in Brazilian cropping systems. Long-term field experiments have shown that a large proportion (> 70%) of the surplus P added via fertilisers remains in the soil, mainly in forms not readily available to crops. An important issue is if the amount of legacy P mobilized from soil is sufficient for the crop nutritional demand and over how long this stored soil P can be effectively ‘mined’ by crops in a profitable way. Here we mapped the spatial–temporal distribution of legacy P over the past 50 years, and discussed possible agricultural practices that could increase soil legacy P usage by plants in Brazil. Mineral fertiliser and manure applications have resulted in ~ 33.4 Tg of legacy P accumulated in the agricultural soils from 1967 to 2016, with a current annual surplus rate of 1.6 Tg. Following this same rate, soil legacy P may reach up to 106.5 Tg by 2050. Agricultural management practices to enhance soil legacy P usage by crops includes increasing soil pH by liming, crop rotation, double-cropping, inter-season cover crops, no-tillage system and use of modern fertilisers, in addition to more efficient crop varieties and inoculation with P solubilising microorganisms. The adoption of these practices could increase the use efficiency of P, substantially reducing the new input of fertilisers and thus save up to 31.8 Tg of P fertiliser use (US$ 20.8 billion) in the coming decades. Therefore, exploring soil legacy P is imperative to reduce the demand for mineral fertilisers while promoting long-term P sustainability in Brazil.

Core Ideas: The SMAF efficiently detected soil quality changes under Brazilian tropical conditions. Soil Quality Index was 0.87 (native vegetation), 0.70 (pasture), and 0.74 (sugarcane). Sugarcane expansion improves soil quality, mainly due to increasing soil chemical quality. The SMAF–Soil Quality Index was significantly correlated with soil organic C stocks. The SMAF is useful for monitoring soil quality changes in Brazilian sugarcane production. The Soil Management Assessment Framework (SMAF) was developed to evaluate impacts of land use and management practices on soil quality (SQ), but its suitability for Brazilian tropical soils was unknown. We hypothesized that SMAF would be sensitive enough to detect SQ changes associated with sugarcane ( Saccharum officinarum L.) expansion for ethanol production. Field studies were performed at three sites across the south‐central region of Brazil, aiming to quantify the impacts of a land use change sequence (i.e., native vegetation–pasture–sugarcane) on SQ. Eight soil indicators were individually scored using SMAF curves developed primarily for North American soils and integrated into an overall Soil Quality Index (SQI) and its chemical, physical, and biological sectors. The SMAF scores were correlated with two other approaches used to assess SQ changes, soil organic C (SOC) stocks and Visual Evaluation of Soil Structure (VESS) scores. Our findings showed that the SMAF was an efficient tool for assessing land use change effects on the SQ of Brazilian tropical soils. The SMAF scoring curves developed using robust algorithms allowed proper assignment of scores for the soil chemical, physical, and biological indicators assessed. The SQI scores were significantly correlated with SOC stocks and VESS scores. Long‐term transition from native vegetation to extensive pasture promoted significant decreases in soil chemical, physical, and biological indicators. Overall SQI suggested that soils under native vegetation were functioning at 87% of their potential capacity, while pasture soils were functioning at 70%. Conversions of pasture to sugarcane induced slight improvements in SQ, primarily because of improved soil fertility. Sugarcane soils are functioning at 74% of their potential capacity. Based on this study, management strategies were developed to improve SQ and the sustainability of sugarcane production in Brazil.