Challenges of accounting nitrous oxide emissions from agricultural crop residues.

Crop residues are important inputs of carbon (C) and nitrogen (N) to soils and thus directly and indirectly affect nitrous oxide (N2 O) emissions. As the current inventory methodology considers N inputs by crop residues as the sole determining factor for N2 O emissions, it fails to consider other underlying factors and processes. There is compelling evidence that emissions vary greatly between residues with different biochemical and physical characteristics, with the concentrations of mineralizable N and decomposable C in the residue biomass both enhancing the soil N2 O production potential. High concentrations of these components are associated with immature residues (e.g., cover crops, grass, legumes, and vegetables) as opposed to mature residues (e.g., straw). A more accurate estimation of the short-term (months) effects of the crop residues on N2 O could involve distinguishing mature and immature crop residues with distinctly different emission factors. The medium-term (years) and long-term (decades) effects relate to the effects of residue management on soil N fertility and soil physical and chemical properties, considering that these are affected by local climatic and soil conditions as well as land use and management. More targeted mitigation efforts for N2 O emissions, after addition of crop residues to the soil, are urgently needed and require an improved methodology for emission accounting. This work needs to be underpinned by research to (1) develop and validate N2 O emission factors for mature and immature crop residues, (2) assess emissions from belowground residues of terminated crops, (3) improve activity data on management of different residue types, in particular immature residues, and (4) evaluate long-term effects of residue addition on N2 O emissions.

Current controversies on mechanisms controlling soil carbon storage: implications for interactions with practitioners and policy-makers. A review.

There is currently an intense debate about the potential for additional organic carbon storage in soil, the strategies by which it may be accomplished and what the actual benefits might be for agriculture and the climate. Controversy forms an essential part of the scientific process, but on the topic of soil carbon storage, it may confuse the agricultural community and the general public and may delay actions to fight climate change. In an attempt to shed light on this topic, the originality of this article lies in its intention to provide a balanced description of contradictory scientific opinions on soil carbon storage and to examine how the scientific community can support decision-making despite the controversy. In the first part, we review and attempt to reconcile conflicting views on the mechanisms controlling organic carbon dynamics in soil. We discuss the divergent opinions about chemical recalcitrance, the microbial or plant origin of persistent soil organic matter, the contribution of particulate organic matter to additional organic carbon storage in soil, and the spatial and energetic inaccessibility of soil organic matter to decomposers. In the second part, we examine the advantages and limitations of big data management and modeling, which are essential tools to link the latest scientific theories with the actions taken by stakeholders. Finally, we show how the analysis and discussion of controversies can guide scientists in supporting stakeholders for the design of (i) appropriate trade-offs for biomass use in agriculture and forestry and (ii) climate-smart management practices, keeping in mind their still unresolved effects on soil carbon storage.

Effects of crop residue incorporation and properties on combined soil gaseous N2O, NO, and NH3 emissions-A laboratory-based measurement approach.

Crop residues may serve as a significant source of soil emissions of N2O and other trace gases. According to the emission factors (EFs) set by the Intergovernmental Panel on Climate Change (IPCC), N2O emission is proportional to the amount of N added by residues to the soil. However, the effects of crop residues on the source and sink strength of agroecosystems for trace gases are regulated by their properties, such as the C and N content; C/N ratio; lignin, cellulose, and soluble fractions; and residue humidity. In the present study, an automated dynamic chamber method was used in combination with soil mesocosms to simultaneously measure the effects of nine different crop residues (oilseed rape, winter wheat, field pea, maize, potato, mustard, red clover, sugar beet, and ryegrass) on soil respiration (CO2) and reactive N fluxes (N2O, NO, and NH3) at a high temporal resolution. Specifically, crop residues were incorporated in the 0-4 cm topsoil layer and incubated for 60 days at a constant temperature (15 °C) and water-filled pore space (60% WFPS). Residue incorporation immediately and sharply increased soil N2O and CO2 emissions, but these were short-lived and returned to background levels within respectively 10 and 30 days. The magnitude of increase in soil NO flux following residue incorporation was lower than that in CO2 and N2O fluxes, with peak emissions observed around day 20. Overall, the N content or C/N ratio of the applied residue could not sufficiently explain the variation in soil N2O and NO emissions. The range of the calculated N2O EFs over a 60-day period was -0.17 to +4.5, being wider than that proposed by the IPCC (+0.01 to +1.1). Therefore, the residue maturity stage may be used as a simple proxy to estimate the N2O + NO emissions from incorporated residue.

N2O emissions from decomposing crop residues are strongly linked to their initial soluble fraction and early C mineralization.

The emission of nitrous oxide (N2O), a strong greenhouse gas, during crop residue decomposition in the soil can offset the benefits of residue recycling. The IPCC inventory considers agricultural N2O emissions proportional to the amount of nitrogen (N) added by residues to soils. However, N2O involves several emission pathways driven directly by the form of N returned and indirectly by changes in the soil induced by decomposition. We investigated the decomposition factors related to N2O emissions under controlled conditions. Residues of sugar beet (SUB), wheat (WHT), rape seed (RAS), potato (POT), pea (PEA), mustard (MUS), red clover (RC), alfalfa (ALF), and miscanthus (MIS), varying by maturity at the time of collection, were incubated in two soils (GRI and SLU) at 15 °C with a water-filled pore space of 60%. The residues contained a wide proportion range of water-soluble components, components soluble in neutral detergent (SOL-NDS), hemicellulose, cellulose, and lignin. Their composition drastically influenced the dynamics of C mineralization and soil ammonium and nitrate and was correlated with N2O flux dynamics. The net cumulative N2O emitted after 60 days originated mostly from MUS (4828 ± 892 g N-N2O ha-1), SUB (2818 ± 314 g N-N2O ha-1) and RC (2567 ± 1245 g N-N2O ha-1); the other residue treatments had much lower emissions (<200 g N-N2O ha-1). For the first time N2O emissions could be explained only by the residue content in the SOL-NDS, according to an exponential relationship. Residues with a high SOL-NDS (>25% DM) were also non-senescent and promoted high N2O emissions (representing 1-5% of applied N), likely directly by nitrification and indirectly by denitrification in microbial hotspots. Crop residue quality appears to be valuable information for accurately predicting N2O emissions and objectively weighing their other potential benefits to agriculture and the environment.

Multiscale modeling of microbial degradation of outer tissues of fiber-crop stems during the dew retting process.

Dew retting of fiber crops, such as hemp or flax, in the field after harvest promotes the microbial biodegradation of the tissues surrounding cellulosic fibers, which helps preserve the quality of fibers during their extraction and valorization for industry. This bioprocess is currently the bottleneck for plant fiber valorization because it is empirically managed and its controlling factors have not been properly quantified. A novel multiscale model representing tissue and polymer biodegradation was developed to simulate microbial growth on the stem during retting. The model was evaluated against experimental hemp retting data. It consistently simulated the mass loss of eight plant polymers belonging to two tissues of the stem outer layer, i.e., parenchyma and fiber bundles. Microbial growth was modeled by Monod equations and modulated by the functions of temperature and moisture. This work provides a tool for gaining more insights into microorganism behavior during retting under local climate conditions.

Enzymatic Strategies and Carbon Use Efficiency of a Litter-Decomposing Fungus Grown on Maize Leaves, Stems, and Roots.

Soil microorganisms can control the soil cycles of carbon (C), and depending on their C-use efficiency (CUE), these microorganisms either contribute to C stabilization in soil or produce CO2 when decomposing organic matter. However, little is known regarding the enzyme investment of microbial decomposers and the effects on their CUE. Our objective was to elucidate the strategies of litter-decomposing fungi as a function of litter quality. Fungal biosynthesis and respiration were accounted for by quantifying the investment in enzyme synthesis and enzyme efficiency. The basidiomycete Phanerochaete chrysosporium was grown on the leaves, stems, and roots of maize over 126 days in controlled conditions. We periodically measured the fungal biomass, enzyme activity, and chemical composition of the remaining litter and continuously measured the evolved C-CO2. The CUE observed for the maize litter was highest in the leaves (0.63), intermediate in the roots (0.40), and lowest in the stems (0.38). However, the enzyme efficiency and investment in enzyme synthesis did not follow the same pattern. The amount of litter C decomposed per mole of C-acquiring hydrolase activity was 354 µg C in the leaves, 246 µg C in the roots, and 1541 µg C in the stems (enzyme efficiency: stems > leaves > roots). The fungus exhibited the highest investment in C-acquiring enzyme when grown on the roots and produced 40-80% less enzyme activity when grown on the stems and leaves (investment in enzymes: roots > leaves > stems). The CUE was dependent on the initial availability and replenishment of the soluble substrate fraction with the degradation products. The production of these compounds was either limited because of the low enzyme efficiency, which occurred in the roots, or because of the low investments in enzyme synthesis, which occurred in the stems. Fungal biosynthesis relied on the ability of the fungus to invest in enzyme synthesis and the efficient interactions between the enzymes and the substrate. The investment decreased when N was limited, whereas the efficiency of the C-acquiring enzymes was primarily explained by the hemicellulose content and its embedment in recalcitrant lignin linkages. Our results are crucial for modeling microbial allocation strategies.

Modeling the release of organic contaminants during compost decomposition in soil.

Composts, incorporated in soils as amendments, may release organic contaminants during their decomposition. COP-Soil is presented here as a new model to simulate the interaction between organic contaminants and compost, using one module for organic matter and one for organic pollutants, with these modules being linked by several assumptions. Published results of laboratory soil incubations using labeled carbon pollutants from compost were used to test the model for one polycyclic aromatic hydrocarbon (PAH), two surfactants and one herbicide. Several simulation scenarios were tested using (i) the organic pollutant module either alone or coupled to the organic matter module, (ii) various methods to estimate the adsorption coefficients (Kd) of contaminants on organic matter and (iii) different degrading biomasses. The simulations were improved if the organic pollutant module was coupled with the organic matter module. Multiple linear regression model for Kd as a function of organic matter quality yielded the most accurate simulation results. The inclusion of specific biomass in the model made it possible to successfully predict the PAH mineralization.

Interacting microbe and litter quality controls on litter decomposition: a modeling analysis.

The decomposition of plant litter in soil is a dynamic process during which substrate chemistry and microbial controls interact. We more clearly quantify these controls with a revised version of the Guild-based Decomposition Model (GDM) in which we used a reverse Michaelis-Menten approach to simulate short-term (112 days) decomposition of roots from four genotypes of Zea mays that differed primarily in lignin chemistry. A co-metabolic relationship between the degradation of lignin and holocellulose (cellulose+hemicellulose) fractions of litter showed that the reduction in decay rate with increasing lignin concentration (LCI) was related to the level of arabinan substitutions in arabinoxylan chains (i.e., arabinan to xylan or A∶X ratio) and the extent to which hemicellulose chains are cross-linked with lignin in plant cell walls. This pattern was consistent between genotypes and during progressive decomposition within each genotype. Moreover, decay rates were controlled by these cross-linkages from the start of decomposition. We also discovered it necessary to divide the Van Soest soluble (labile) fraction of litter C into two pools: one that rapidly decomposed and a second that was more persistent. Simulated microbial production was consistent with recent studies suggesting that more rapidly decomposing materials can generate greater amounts of potentially recalcitrant microbial products despite the rapid loss of litter mass. Sensitivity analyses failed to identify any model parameter that consistently explained a large proportion of model variation, suggesting that feedback controls between litter quality and microbial activity in the reverse Michaelis-Menten approach resulted in stable model behavior. Model extrapolations to an independent set of data, derived from the decomposition of 12 different genotypes of maize roots, averaged within <3% of observed respiration rates and total CO2 efflux over 112 days.

Fate of (14)C-organic pollutant residues in composted sludge after application to soil.

Organic micropollutants may be present in biosolids, leading to soil contamination when they are recycled in agriculture. A sludge spiked with (14)C-labelled glyphosate (GLY), sodium linear dodecylbenzene sulphonate (LAS), fluoranthene (FLT) or 4-n-nonylphenol (NP) was composted with green waste and the fate of the (14)C-micropollutant residues remaining after composting was assessed after the compost application to the soil. (14)C-residues were mineralised in the soil and represented after 140d 20-32% of the initial activity for LAS, 16-25% for GLY, 6-9% for FLT and 4-7% for NP. The (14)C-residues at the end of composting that could not be extracted with methanol or ammonia were minimally remobilised or even increased for FLT. After 140d, non-extractable residues represented 38-52% of all of the (14)C-residues remaining in the soil for FLT, 50-67% for GLY, 91-92% for NP and 94-97% for LAS and in most cases, less than 1% of the (14)C-residues were water soluble, suggesting a low direct availability for leaching and microbial or plant assimilation. FLT was identified as the main compound among the methanol-extractable (14)C-residues that may be potentially available. The fate of the (14)C-organic pollutant residues in composts after application to soil could be assessed through a sequential chemical extraction scheme and depended on the chemical nature of the pollutant.

Dissipation pathways of organic pollutants during the composting of organic wastes.

The organic pollutants (OPs) present in compostable organic residues can be recovered in the final composts leading to environmental impacts related to their use in agriculture. However, the composting process may contribute to their partial dissipation that is classically evaluated through the concentration decrease in extractable OPs, without identification of the responsible mechanisms as mineralization or stabilization of OP as non-extractable residues (NER) or bound residues. The dissipation of four (14)C-labeled OPs (fluoranthene; 4-n-nonylphenol, NP; sodium linear dodecylbenzene sulfonate, LAS; glyphosate) was assessed during composting of sewage sludge and green waste. The dissipation of LAS largely resulted from its mineralization (51% of initial LAS), whereas mineralization was intermediate for NP (29%) and glyphosate (24%), and negligible for fluoranthene. The NER pathway mostly concerned NP and glyphosate, with 45% and 37% of the recovered (14)C being found as NER at the end of composting, respectively. In the final composts, the proportions of water soluble residues of OPs considered as readily available were <11% of recovered (14)C-OPs. However, most fluoranthene remained solvent extractable (72%) and potentially available, whereas only 18% of glyphosate and less than 7% of both NP and LAS remained solvent extractable in the final compost.