Cover crop functional types differentially alter the content and composition of soil organic carbon in particulate and mineral-associated fractions

Mulches assist degraded soil recovery via stimulating biogeochemical cycling: metagenomic analysis

Soil degradation of urban greening has caused soil fertility loss and soil organic carbon depletion. Organic mulches are made from natural origin materials, and represent a cost-effective and environment-friendly remediation method for urban greening. To reveal the effects of organic mulch on soil physicochemical characteristics and fertility, we selected a site that was covered with organic mulch for 6 years and a nearby lawn-covered site. The results showed that soil organic matter, total nitrogen, and available phosphorus levels were improved, especially at a depth of 0-20 cm. The activities of cellulase, invertase, and dehydrogenase in soil covered with organic mulch were 17.46%, 78.98%, and 283.19% higher than those under lawn, respectively. The marker genes of fermentation, aerobic respiration, methanogenesis, and methane oxidation were also enriched in the soil under organic mulch. Nitrogen cycling was generally repressed by the organic mulch, but the assimilatory nitrate and nitrite reduction processes were enhanced. The activity of alkaline phosphatase was 12.63% higher in the mulch-covered soil, and functional genes involved in phosphorus cycling were also enriched. This study presents a comprehensive investigation of the influence of organic mulch on soil microbes and provides a deeper insight into the recovery strategy for soil degradation following urban greening. KEY POINTS: • Long-term cover with organic mulches assists soil recovery from degradation • Soil physical and chemical properties were changed by organic mulches • Organic mulches enhanced genes involved in microbially mediated C and P cycling • Soil organic matter was derived from decomposition of organic mulch and carbon fixation • N cycling was repressed by mulches, except for assimilatory NO2- and NO3- reductions.

Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem

Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.

Green manure removal with reduced nitrogen improves saline-alkali soil organic carbon storage in a wheat-green manure cropping system

The incorporation of green manure into cropping systems is a potential strategy for sequestering soil carbon (C), especially in saline-alkali soil. Yet, there are still unknown about the substitution impacts of green manure on nitrogen (N) fertilizer in wheat-green manure multiple cropping system. Herein, a five-year field experiment was performed to determine the impact of three levels of N fertilizer inputs [i.e., N fertilizer reduced by 0 % (100N), 10 % (90 N), and 20 % (80 N)] with aboveground biomass of green manure removal (0GM) and return (100GM) on soil organic carbon (SOC) storage and its primary determinants. The results demonstrated that no significant interaction on SOC storage was detected between green manure and N fertilizer management. 80 N enhanced SOC storage in bulk soil by 7.4 and 13.2 % in 0-20 cm soil depth relative to 100 N and 90 N (p < 0.05). Regardless of N fertilizer levels, compared with 100GM, 0GM increased SOC storage in bulk soil by 14.2-34.6 % in 0-40 cm soil depth (p < 0.05). This was explained by an increase in soil macro-aggregates (>2 and 0.25-2 mm) proportion contributing to SOC physical protection. Meanwhile, the improvement of SOC storage under 0GM was due to the decrease of soil C- and N-acquisition enzyme activities, and microbial resource limitation. Alternatively, the variation partitioning analyses (VPA) results further suggested that C- and N-acquisition enzyme activities, as well as microbial resource limitation were the most important factors for SOC storage. The findings highlighted those biological factors played a dominant role in SOC accumulation compared to physical factors. The aboveground biomass of green manure removal with N fertilizer reduced by 20 % is a viable option to enhance SOC storage in a wheat-green manure multiple cropping system.

Global synthesis on the response of soil microbial necromass carbon to climate-smart agriculture

Climate-smart agriculture (CSA) supports the sustainability of crop production and food security, and benefiting soil carbon storage. Despite the critical importance of microorganisms in the carbon cycle, systematic investigations on the influence of CSA on soil microbial necromass carbon and its driving factors are still limited. We evaluated 472 observations from 73 peer-reviewed articles to show that, compared to conventional practice, CSA generally increased soil microbial necromass carbon concentrations by 18.24%. These benefits to soil microbial necromass carbon, as assessed by amino sugar biomarkers, are complex and influenced by a variety of soil, climatic, spatial, and biological factors. Changes in living microbial biomass are the most significant predictor of total, fungal, and bacterial necromass carbon affected by CSA; in 61.9%-67.3% of paired observations, the CSA measures simultaneously increased living microbial biomass and microbial necromass carbon. Land restoration and nutrient management therein largely promoted microbial necromass carbon storage, while cover crop has a minor effect. Additionally, the effects were directly influenced by elevation and mean annual temperature, and indirectly by soil texture and initial organic carbon content. In the optimal scenario, the potential global carbon accrual rate of CSA through microbial necromass is approximately 980 Mt C year-1, assuming organic amendment is included following conservation tillage and appropriate land restoration. In conclusion, our study suggests that increasing soil microbial necromass carbon through CSA provides a vital way of mitigating carbon loss. This emphasizes the invisible yet significant influence of soil microbial anabolic activity on global carbon dynamics.

Dynamics of Carbon and Soil Enzyme Activities under Arabica Coffee Intercropped with Brachiaria decumbens in the Brazilian Cerrado

The change in land use in the Brazilian Cerrado modifies the dynamics of soil organic matter (SOM) and, consequently, carbon (C) stocks and their fractions and soil enzyme activities. This study evaluated the effect of brachiaria (Brachiaria decumbens Stapf.) intercropped with Arabica coffee (Coffea arabica L.) on the stock and fractions of soil carbon and enzyme activities. The experiment was arranged in a completely randomized block design with three replications and treatments in a factorial design. The first factor consisted of coffee with or without intercropped brachiaria, the second of Arabica coffee cultivars ('I.P.R.103' and 'I.P.R.99') and the third factor of the point of soil sampling (under the canopy (UC) and in inter-rows (I)). Soil was sampled in layers of 0-10, 10-20, 20-30, 30-40, 40-60 and 60-80 cm. Soil from the 0-10 cm layer was also used to analyze enzymatic activity. Significant effects of coffee intercropped with brachiaria were confirmed for particulate organic carbon (POC), with highest contents in the 0-10 and 20-30 cm layers (9.62 and 6.48 g kg-1, respectively), and for soil enzymes (280.83 and 180.3 μg p-nitrophenol g-1 for arylsulfatase and β-glucosidase, respectively).

Changes over time in organic matter dynamics and copper solubility in a vineyard soil after incorporation of cover crop residues: Insights from a batch experiment

Cover crops (CCs) are increasingly used in viticulture because they benefit the soil and the environment in many ways. This study investigated the extent to which the incorporation of CC residues altered organic matter (OM) and Cu dynamics in a Cu-contaminated vineyard topsoil. A 92-day incubation period was used to monitor changes over time in carbon mineralization, carbon hydrolytic enzyme activity, concentration and optical properties of dissolved organic matter (DOM), and Cu solubility after the addition (or not) of two CC residues, oat or faba bean. The results revealed that adding CCs transitorily increased the concentration of DOM in soil solution, as well as the activity of C hydrolytic enzymes and C mineralization rates. DOM content was approximately two orders of magnitude higher in CC-amended soils than in the control soil on day 0, after which it gradually decreased to reach concentrations similar to those measured in the control soil on day 92. Analyses of DOM optical properties showed that its molecular weight and degree of humification increased over time with a decrease in its concentration. The close relationship between DOM and Cu concentrations in the soil solution suggests that degradation of CCs releases soluble forms of C capable of complexing and solubilizing Cu, and hence that incorporating CC residues can transitorily increase the solubility of Cu in vineyard topsoils. Despite their different C:N ratios, oat and faba bean had almost the same effect on Cu dynamics, implying that C inputs played a prominent role in explaining the interactions between OM and Cu within the timeframe of our experiment. In conclusion, this study enabled recommendations on how to mitigate the risk of Cu ecotoxicity associated with incorporating CCs in Cu-contaminated vineyard soils.

Cover cropping promotes soil carbon sequestration by enhancing microaggregate-protected and mineral-associated carbon

Cover cropping can improve soil C sequestration compared to no cover cropping, but the mechanism of C sequestration in soil aggregates and minerals needs more exploration. We explored C sequestration using C fractions in soil aggregates and minerals by cover crops in a five-year old summer cover crop - winter wheat (Triticum aestivum L.) rotation system at Changwu National Agroecology Experimental Station in the Chinese Loess Plateau. Three cover crops as soybean (Glycine max L., SB), sudangrass (Sorghum sudanense (Piper) Stapf, SG), soybean and sudangrass mixture (SS) were planted during summer fallow and incorporated into the soil two weeks prior to wheat planting each year. Soil samples at 0-10, 10-20, and 20-40 cm depths were collected at wheat harvest after 5-yr and analyzed for C fractions which were coarse particulate organic C (cPOC), intra-microaggregate fine particulate organic C (iPOC), free fine particulate organic C (fPOC), and mineral-associated organic C (MOC). The iPOC and MOC are considered as protected C against mineralization. Compared to no cover crop (CK), cover crops increased large macroaggregate proportion at 0-10 cm by 18-22 %, with SS having a greater mean-weight diameter (MWD) than other treatments. Cover crops had greater MOC, iPOC, and fPOC fractions than CK in most aggregate-size classes and the bulk soil at all depths, with SS having the greatest C fractions. The MOC was greater than any other C fractions, regardless of cover crop species. Cover cropping can enhance soil aggregation and C sequestration by increasing microaggregate-protected and mineral-associated C compared to no cover cropping, resulting in improved soil C stabilization. Cover crop mixture was more effective in promoting soil aggregate stability and C fractions than single cover crop species.

Enhancing estimation of cover crop biomass using field-based high-throughput phenotyping and machine learning models

Incorporating cover crops into cropping systems offers numerous potential benefits, including the reduction of soil erosion, suppression of weeds, decreased nitrogen requirements for subsequent crops, and increased carbon sequestration. The aboveground biomass (AGB) of cover crops strongly influences their performance in delivering these benefits. Despite the significance of AGB, a comprehensive field-based high-throughput phenotyping study to quantify AGB of multiple cover crops in the U.S. Midwest has not been found. This study presents a two-year field experiment carried out in Eastern Nebraska, USA, to estimate AGB of five different cover crop species [canola (Brassica napus L.), rye (Secale cereale L.), triticale (Triticale × Triticosecale L.), vetch (Vicia sativa L.), and wheat (Triticum aestivum L.)] using high-throughput phenotyping and Machine Learning (ML) models. Destructive AGB sampling was performed three times during each spring season in 2022 and 2023. An array of morphological, spectral, thermal, and environmental features from the sensors were utilized as feature inputs of ML models. Moderately strong linear correlations between AGB and the selected features were observed. Four ML models, namely Random Forests Regression (RFR), Support Vector Regression (SVR), Partial Least Squares Regression (PLSR), and Artificial Neural Network (ANN), were investigated. Among the four models, PLSR achieved the highest Coefficient of Determination (R2) of 0.84 and the lowest Root Mean Squared Error (RMSE) of 892 kg/ha (Normalized RMSE (NRMSE) = 8.87%), indicating that PLSR could be the most appropriate method for estimating AGB of multiple cover crop species. Feature importance analysis ranked spectral features like Normalized Difference Red Edge (NDRE), Solar-induced Fluorescence (SIF), Spectral Reflectance at 485 nm (R485), and Normalized Difference Vegetation Index (NDVI) as top model features using PLSR. When utilizing fewer feature inputs, ANN exhibited better prediction performance compared to other models. Using morphological and spectral parameters as input features alone led to a R2 of 0.80 and 0.77 for AGB prediction using ANN, respectively. This study demonstrated the feasibility of high-throughput phenotyping and ML techniques for accurately estimating AGB of multiple cover crop species. Further enhancement of model performance could be achieved through additional destructive sampling conducted across multiple locations and years.

A stoichiometric approach to estimate sources of mineral-associated soil organic matter

Mineral-associated soil organic matter (MAOM) is the largest, slowest cycling pool of carbon (C) in the terrestrial biosphere. MAOM is primarily derived from plant and microbial sources, yet the relative contributions of these two sources to MAOM remain unresolved. Resolving this issue is essential for managing and modeling soil carbon responses to environmental change. Microbial biomarkers, particularly amino sugars, are the primary method used to estimate microbial versus plant contributions to MAOM, despite systematic biases associated with these estimates. There is a clear need for independent lines of evidence to help determine the relative importance of plant versus microbial contributions to MAOM. Here, we synthesized 288 datasets of C/N ratios for MAOM, particulate organic matter (POM), and microbial biomass across the soils of forests, grasslands, and croplands. Microbial biomass is the source of microbial residues that form MAOM, whereas the POM pool is the direct precursor of plant residues that form MAOM. We then used a stoichiometric approach-based on two-pool, isotope-mixing models-to estimate the proportional contribution of plant residue (POM) versus microbial sources to the MAOM pool. Depending on the assumptions underlying our approach, microbial inputs accounted for between 34% and 47% of the MAOM pool, whereas plant residues contributed 53%-66%. Our results therefore challenge the existing hypothesis that microbial contributions are the dominant constituents of MAOM. We conclude that biogeochemical theory and models should account for multiple pathways of MAOM formation, and that multiple independent lines of evidence are required to resolve where and when plant versus microbial contributions are dominant in MAOM formation.

Soil C dynamics after deforestation and subsequent conversion of arable cropland to grassland in humid temperate areas

Land use and plant-soil management influence soil organic C stocks and soil properties. This study aimed to identify the main mechanisms by which these factors alter soil organic matter (SOM) dynamics and stocks. Changes in the organic C pools and biochemical quality in different OM compartments were assessed: a) after deforestation and intensive cultivation (SOM loss) and then, b) after the conversion of cropland to grassland (SOM replenishment) in a chronosequence of recovery (1-45 years). Topsoil samples were subjected to physical fractionation to assess the distribution of free particulate OM (POM) and mineral associated OM (MAOM). SOM quality was characterized by 13C NMR spectroscopy, thermal analysis (DSC/TG), and microbial activity was monitored by isothermal microcalorimetry. Deforestation and intensive cultivation led to the loss of 80 % of the C stored in the upper mineral soil (up to 30-35 cm). The POM was almost depleted, MAOM underwent significant losses (>40 %) and all OM compounds, including the aromatic C, were affected. The large and unexpected loss of MAOM can be attributed to the low specific surface soil area and also to the labile (biodegradable) nature of the OM in this fraction. After 45 years, conversion of cropland to grassland recovered 68 % of the C lost in the mineral soil (mainly as MAOM), at an annual rate of 1.25 Mg C ha-1. The present findings showed that the persistence of long-term OM depends on how strongly organic compounds are adsorbed onto mineral surfaces (i.e., the specific surface area) and the biochemical nature of OM compounds. Adequate plant-soil management favoured the replenishment of the MAOM under these experimental conditions, and this fraction was an active pool in terms of C storage and biochemical quality. This study served to test current theories about changes in soil C fractions due to land use changes and soil-plant management.

Cover crop root morphology rather than quality controls the fate of root and rhizodeposition C into distinct soil C pools

Cover crops increase carbon (C) inputs to agricultural soils, and thus have the potential to mitigate climate change through enhanced soil organic carbon (SOC) storage. However, few studies have explored the fate of belowground C inputs associated with varying root traits into the distinct SOC pools of mineral-associated organic carbon (MAOC) particulate organic carbon (POC). Therefore, a packed 0.5 m column trial was established with 0.25 m topsoil and 0.25 m subsoil with four cover crops species (winter rye, oilseed radish, chicory, and hairy vetch) known to differ in C:N ratio and root morphology. Cover crops were 14 CO2 -labeled for 3 months, and then, half of the columns were sampled to quantify root and rhizodeposition C. In the remaining columns, plant shoots were harvested and the undisturbed soil and roots were left for incubation. Bulk soil from both sampling times was subjected to a simple fractionation scheme, where 14 C in the <50 and >50 μm fraction was assumed to represent MAOC and POC, respectively. The fast-growing rye and radish produced the highest root C. The percentage loss of C via rhizodeposition (%ClvR) showed a distinct pattern, with 22% for the more branched roots (rye and vetch) and 6%-8% for the less branched roots (radish and chicory). This suggests that root morphology plays a key role in determining rhizodeposition C. After 1 year of incubation at room temperature, the remaining MAOC and POC were positively correlated with belowground inputs in absolute terms. However, topsoil MAOC formation efficiencies (cover crop-derived MAOC remaining as a share of belowground inputs) were higher for vetch and rye (21% and 15%, respectively) than for chicory and radish (9% and 10%, respectively), suggesting a greater importance of rhizodeposition (or indirectly, root morphology) than solely substrate C:N ratio for longer term C stabilization.

Unlocking complex soil systems as carbon sinks: multi-pool management as the key

Much research focuses on increasing carbon storage in mineral-associated organic matter (MAOM), in which carbon may persist for centuries to millennia. However, MAOM-targeted management is insufficient because the formation pathways of persistent soil organic matter are diverse and vary with environmental conditions. Effective management must also consider particulate organic matter (POM). In many soils, there is potential for enlarging POM pools, POM can persist over long time scales, and POM can be a direct precursor of MAOM. We present a framework for context-dependent management strategies that recognizes soils as complex systems in which environmental conditions constrain POM and MAOM formation.

Assessing long-term impacts of cover crops on soil organic carbon in the central US Midwestern agroecosystems

Cover crops have been reported as one of the most effective practices to increase soil organic carbon (SOC) for agroecosystems. Impacts of cover crops on SOC change vary depending on soil properties, climate, and management practices, but it remains unclear how these control factors affect SOC benefits from cover crops, as well as which management practices can maximize SOC benefits. To address these questions, we used an advanced process-based agroecosystem model, ecosys, to assess the impacts of winter cover cropping on SOC accumulation under different environmental and management conditions. We aimed to answer the following questions: (1) To what extent do cover crops benefit SOC accumulation, and how do SOC benefits from cover crops vary with different factors (i.e., initial soil properties, cover crop types, climate during the cover crop growth period, and cover crop planting and terminating time)? (2) How can we enhance SOC benefits from cover crops under different cover crop management options? Specifically, we first calibrated and validated the ecosys model at two long-term field experiment sites with SOC measurements in Illinois. We then applied the ecosys model to six cover crop field experiment sites spanning across Illinois to assess the impacts of different factors on SOC accumulation. Our modeling results revealed the following findings: (1) Growing cover crops can bring SOC benefits by 0.33 ± 0.06 MgC ha^-1  year^-1 in six cover crop field experiment sites across Illinois, and the SOC benefits are species specific to legume and non-legume cover crops. (2) Initial SOC stocks and clay contents had overall small influences on SOC benefits from cover crops. During the cover crop growth period (i.e., winter and spring in the US Midwest), high temperature increased SOC benefits from cover crops, while the impacts from larger precipitation on SOC benefits varied field by field. (3) The SOC benefits from cover crops can be maximized by optimizing cover crop management practices (e.g., selecting cover crop types and controlling cover crop growth period) for the US Midwestern maize-soybean rotation system. Finally, we discussed the economic and policy implications of adopting cover crops in the US Midwest, including that current economic incentives to grow cover crops may not be sufficient to cover costs. This study systematically assessed cover crop impacts for SOC change in the US Midwest context, while also demonstrating that the ecosys model, with rigorous validation using field experiment data, can be an effective tool to guide the adaptive management of cover crops and quantify SOC benefits from cover crops. The study thus provides practical tools and insights for practitioners and policy-makers to design cover crop related government agricultural policies and incentive programs for farmers and agri-food related industries.

Divergent accumulation of amino sugars and lignins mediated by soil functional carbon pools under tropical forest conversion

Tropical primary forests are being destroyed at an alarming rate and converted for other land uses which is expected to greatly influence soil carbon (C) cycling. However, our understanding of how tropical forest conversions affect the accumulation of compounds in soil functional C pools remains unclear. Here, we collected soils from primary forests (PF), secondary forests (SF), oil-palm (OP), and rubber plantations (RP), and assessed the accumulation of plant- and microbial-derived compounds within soil organic carbon (SOC), particulate (POC) and mineral-associated (MAOC) organic C. PF conversion to RP greatly decreased SOC, POC, and MAOC concentrations, whereas conversion to SF increased POC concentrations and decreased MAOC concentrations, and conversion to OP only increased POC concentrations. PF conversion to RP decreased lignin concentrations and increased amino sugar concentrations in SOC pools which increased the stability of SOC, whereas conversion to SF only increased the lignin concentrations in POC, and conversion to OP just increased lignin concentrations in POC and decreased it in MAOC. We observed divergent dynamics of amino sugars (decrease) and lignin (increase) in SOC with increasing SOC. Only lignin concentrations increased in POC with increasing POC and amino sugars concentrations decreased in MAOC with increasing MAOC. Conversion to RP significantly decreased soil enzyme activities and microbial biomasses. Lignin accumulation was associated with microbial properties, whereas amino sugar accumulation was mainly associated with soil nutrients and stoichiometries. These results suggest that the divergent accumulation of plant- and microbial-derived C in SOC was delivered by the distribution and original composition of functional C pools under forest conversions. Forest conversions changed the formation and stabilization processes of SOC in the long run which was associated with converted plantations and management. The important roles of soil nutrients and stoichiometry also provide a natural-based solution to enhance SOC sequestration via nutrient management in tropical forests.