Mechanistic Insights into Farmland Soil Carbon Sequestration: A Review of Substituting Green Manure for Nitrogen Fertilizer

Abstract

Sustainable agricultural intensification requires innovative approaches to simultaneously enhance productivity and mitigate environmental impacts—a challenge critical to global food security and climate change mitigation. The traditional fertilization system, with a single application of nitrogen fertilizer, while effective for crop yields, often leads to soil organic carbon (SOC) depletion, whereas green manure systems offer a dual benefit of nitrogen supply and SOC sequestration potential. However, the mechanisms by which green manure substitution enhances soil carbon sequestration (SCS) remain systematically underexplored in comparison to chemical fertilization. This review systematically examines (1) the mechanisms underlying SOC sequestration, (2) SOC losses associated with traditional fertilization practices, and (3) the theoretical foundation and practical applications of green manure as a nitrogen fertilizer substitute. We provide an in-depth analysis of the mechanisms through which green manure substitution drives SCS. Furthermore, we identify three critical areas for future investigation: (i) optimization of green manure management strategies to enhance SCS efficiency; (ii) comprehensive assessment of green manure’s ecological benefits through long-term, multi-scale studies; and (iii) evaluation of green manure’s climate change adaptation capacity and carbon sequestration potential across diverse climatic scenarios. These findings fundamentally advance our understanding of green manure’s role in sustainable agriculture by establishing its dual function as both a nitrogen source and carbon sequestration driver. In addition, these insights have immediate relevance for agricultural policy and practice, particularly in regions where soil health and carbon storage are prioritized alongside crop yield.

1. Introduction

In modern agriculture, the use of nitrogen fertilizer has greatly promoted the growth of global food production. Since the mid-20th century “Green Revolution”, its widespread application on a global scale has made important contributions to solving the food security problems caused by world population growth [1]. However, the increasing dependence on chemical nitrogen fertilizer in agricultural production in recent years has not only led to a decrease in crop yield, but also caused many environmental problems, such as greenhouse gas emissions, eutrophication of water bodies, and declining biodiversity [2,3]. In addition, excessive nitrogen application can easily cause soil erosion, degradation, and structural damage [4], affect the biota [5], and transform soil from a carbon sink to a carbon source. This forces us to re-examine the significance of rational nitrogen application in sustainable agricultural development, with the core task being the stability and enhancement of soil organic carbon (SOC) storage.

In this context, how to achieve sustainability in agricultural production, especially how to reduce chemical nitrogen fertilizer inputs while ensuring high crop yields, has become a hot topic in current agricultural scientific research. Green manure has gained widespread attention for its ability to improve soil nutrient availability and promote crop nutrient absorption and utilization, thereby achieving the effect of replacing chemical nitrogen fertilizer [6]. Numerous studies have shown that green manure not only reduces the use of chemical nitrogen fertilizer, but also plays an important role in improving the physical and chemical properties of soil and enhancing soil carbon sequestration [7]. On the one hand, planting green manure can not only expand the soil carbon/nitrogen pool, but also improve the physical structure of the soil, including enhancing the stability of soil aggregates, porosity, and water holding capacity [8]. On the other hand, planting green manure can increase the activity of beneficial microorganisms in the soil by changing the structure and abundance of soil microbial communities, thereby accelerating the decomposition and mineralization of organic matter and improving nutrient availability [9,10,11]. In addition, green manure accumulates a large amount of organic matter during its growth process. After returning green manure to the field, this organic matter can easily form a stable organic carbon pool in the soil, which helps with soil carbon sequestration [12]. This is crucial for addressing climate change, maintaining soil health, and improving agricultural productivity. An 11-year field experiment found that returning green manure to the field can effectively increase the content of microbial biomass C (MBC), dissolved organic C (DOC), and hot-water extractable C (HWC), which is beneficial for soil carbon sequestration [13]. Current research indicates that incorporating green manure into agricultural ecosystems enhances soil carbon sequestration primarily through three mechanisms: (1) The nitrogen-fixing capacity of green manure increases soil organic carbon sources, thereby promoting the formation and accumulation of soil organic carbon; (2) by influencing crop biomass production, green manure regulates the input of organic residue carbon; and (3) following incorporation, green manure improves soil physical structure while simultaneously modulating soil aggregation processes, which facilitates the accumulation of microbial biomass and its residues, ultimately enhancing soil carbon sequestration. However, although the potential of green manure as a substitute for nitrogen fertilizer has been partially confirmed, there is still no consensus on the comprehensive impact of the organic combination of the two on soil carbon sequestration in farmland, and the mechanism is unclear, which to some extent restricts the estimation and evaluation of carbon cycling in farmland ecosystems. Therefore, a systematic review and analysis of the mechanism and effect of replacing chemical nitrogen fertilizer with green manure on soil carbon sequestration can help clarify the controversies and uncertainties in current research.

Based on this, this article aims to systematically summarize the research progress on the use of green manure to replace nitrogen fertilizer in promoting soil carbon sequestration in recent years, and analyze the key mechanisms behind it. The literature collected in this study was sourced from the PubMed, Web of Science, and CNKI databases, and literature searches were conducted using keywords (subject headings) such as “green manure” and “carbon sequestration”, and the main years of the retrieved literature were concentrated between 2015 and 2024. Specifically, this article (1) elaborates on the mechanisms of soil carbon sequestration in farmland and the organic carbon losses caused by traditional nitrogen application methods; (2) introduces the types, characteristics, and current application status of green manure in agriculture, especially the scientific feasibility of moderately replacing chemical nitrogen fertilizer by green manure; (3) explores the specific mechanisms by which moderate substitution of chemical nitrogen fertilizer by green manures promotes soil organic carbon stabilization through physical, chemical, and microbial fixation pathways. In addition, this article also discusses the limitations of current research, including methodological deficiencies and the lack of long-term research, and proposes future research directions and possible improvement strategies based on reality, in order to provide scientific basis and practical guidance for agricultural practitioners and policymakers.

2. Mechanisms of Soil Carbon Sequestration

In the context of global climate change, the study of soil carbon sequestration mechanisms has received increasing attention, especially in agricultural ecosystems, where its role in reducing greenhouse gas emissions and promoting soil health cannot be ignored. The stability of soil organic carbon is influenced by various factors, including the interaction of physical, chemical, and microbial processes [14,15]. The formation and stability of soil aggregates are important processes for physical carbon sequestration [16]. Soil aggregates are structural units formed by the combination of organic matter, clay particles, and mineral particles through physical and biological processes. They can effectively seal organic carbon inside microaggregates and macroaggregates, blocking their direct contact with microorganisms and enzymes, thereby delaying carbon decomposition and mineralization [17]. Aggregates of different sizes in soil have unique physical properties, among which the SOC storage in macroaggregates >2 and 0.25–2 mm is greater than that in microaggregates [18,19]. That is to say, SOC storage related to soil aggregates is mainly distributed in macroaggregates, and its protective effect on organic carbon is also more significant. Through physical isolation, soil aggregates can effectively reduce exposure to organic matter and decrease the rate of carbon decomposition. In addition, in farmland management, reducing soil disturbance (such as reducing tillage and compaction) helps to maintain the structural integrity of aggregates and prevent the decomposition and loss of organic carbon. At the same time, increasing the input of organic matter into the soil (such as returning straw to the field, covering crops, etc.) can promote the formation of aggregates and provide a physical barrier for long-term carbon storage [20].

The stability of SOC in soil largely depends on its chemical binding with inorganic substances such as clay minerals and iron aluminum oxides [21]. In this process, organic molecules combine with mineral surfaces through various chemical forces such as hydrogen bonding, van der Waals forces, covalent bonds, etc., forming stable organic-inorganic complexes, thereby reducing carbon mineralization and loss [22]. In the mechanism of mineral protection, the surface area and charge characteristics of clay minerals play a key role [23]. The specific surface area and cation exchange capacity (CEC) of soil increases with an increase in clay content, which enables the soil to more effectively adsorb and fix organic carbon molecules. This adsorption not only increases the residence time of organic carbon, but also reduces its solubility and availability in soil solutions, making it difficult for microorganisms to degrade [24,25]. The formation of soil humus is another important chemical pathway for carbon sequestration [26]. Humus is a high-molecular-weight substance formed by complex biochemical transformations of organic matter, and its stability in soil is much higher than that of the original organic matter. The functional groups such as aromatic rings, phenolic hydroxyl groups, and carboxyl groups in the molecular structure of humus can form various types of bonds with soil minerals, further enhancing their stability [27]. In recent years, there have been many studies which have tended to believe that the role of organic carbon’s chemical structure itself in SOC stability has been seriously underestimated. Among the methods for studying the chemical structure of soil organic carbon, solid-state ¹³C nuclear magnetic resonance (NMR) spectroscopy has a unique advantage, in that it can analyze the chemical structure of soil organic carbon more closely to the real state. Studies have shown that a large amount of exogenous organic carbon put into the soil will promote the accelerated utilization of alkoxy carbon by soil microorganisms, while alkyl carbon itself is structurally stable and relatively enriched, thus increasing the humification index [28]. The humification index, which is the ratio of alkyl carbon to alkoxy carbon, can reflect the decomposition degree of soil organic carbon. Alkyl carbon is derived from biomolecules such as long-chain aliphatic compounds, waxes, keratins, and cork, which are structurally stable and more difficult to degrade than other soil organic carbon components, whereas alkoxy carbon is mainly carbohydrates, which are relatively easy to decompose [29]. Hydrophobicity is the ratio of hydrophobic carbon (alkyl carbon and aromatic carbon) to hydrophilic carbon (alkoxy carbon and carbonyl carbon), which reflects the stability of soil organic matter bound to aggregates. A large number of correlation studies have concluded that the larger the humification index, the more stable the soil organic carbon pool is [30], and the larger the value of hydrophobicity, the higher the stability of soil organic matter caused by the action of aggregates [31].

Soil microorganisms can directly affect the decomposition, transformation, and stabilization processes of organic matter, thus playing a crucial role in soil carbon sequestration [32,33]. During the process of decomposing plant residues and root exudates, soil microorganisms convert complex organic molecules into simple compounds. During this process, a portion of organic carbon is converted into microbial metabolites such as extracellular polysaccharides, amino acids, and lipids, which can combine with soil minerals to form stable organic–inorganic complexes [21], thereby promoting soil organic carbon sequestration. In addition, the structural and functional diversity of microbial communities plays a crucial role in carbon stabilization processes [34,35,36]. Research has shown that fungi and bacteria play important roles in the process of organic carbon conversion, but their functions are different. The former tends to utilize structurally complex and difficult-to-degrade carbon compounds, and soil dominated by fungi has a slow carbon turnover rate [37]; in contrast, bacteria tend to utilize easily degradable carbon compounds with simple structures. Among bacteria, Gram-negative bacteria have a stronger ability to utilize easily degradable carbon substrates, while Gram-positive bacteria have a stronger ability to decompose difficult-to-degrade carbon [38]. Therefore, when the fungal content is high in the soil microbial community, the microbial biomass carbon content will be higher, which is beneficial for the fixation of soil organic carbon [37,38,39]. Another important role of microorganisms in carbon sequestration is to regulate the rhizosphere ecosystem, promoting carbon input and organic matter accumulation between plants and soil [40]. Symbiotic microorganisms, such as rhizobia and mycorrhizal fungi, can enhance plant nutrient absorption, thereby increasing plant biomass and soil carbon input. This plant−microbe−soil interaction constructs a stable carbon cycling network, which is beneficial for long-term carbon storage.

3. Traditional Fertilization Methods Cause Loss of Soil Organic Carbon

In agricultural production, SOC is considered an important indicator of soil health and ecological function. Traditional fertilization methods, especially high or excessive application of chemical nitrogen fertilizer, can increase crop yields in the short term, but their long-term impact on soil organic carbon storage has attracted increasing attention [41]. It cannot be denied that the rational application of chemical nitrogen fertilizer is a key production measure to promote soil organic carbon storage, nutrient transport, and soil carbon sequestration. An 11-year field experiment showed that moderate nitrogen application significantly increased soil organic carbon storage, carbon sequestration rate, and carbon sequestration efficiency in the tillage layer. This can be attributed to nitrogen application reducing the soil C/N ratio, meeting microbial nitrogen requirements, reducing organic carbon decomposition, and thus improving soil carbon sequestration capacity [42]. However, this does not mean that the soil organic carbon content always increases with an increase in chemical nitrogen fertilizer application. Studies have shown that when the nitrogen application rate in wheat fields reaches 200 kg N ha⁻¹, the soil organic carbon storage in 0–20 cm soil is 34.77–40.54 Mg ha⁻¹, while when the nitrogen is reduced by 20% (160 kg N ha⁻¹), the soil organic carbon storage is 34.33–46.37 Mg ha⁻¹ [43]. Obviously, excessive nitrogen application reduces the soil carbon storage in wheat fields by 12.6%, this is mainly because high levels of exogenous nitrogen input can provide relatively more nitrogen sources for the soil, which increases the demand for C by soil microorganisms in order to maintain the stoichiometric balance of soil enzymes [44]. Therefore, microorganisms may secrete more carbon acquisition enzymes at high nitrogen levels, which exacerbates the decomposition of soil organic carbon. In addition, excessive nitrogen application can lead to significant changes in the proportion of bacteria and fungi in the soil. The relative abundance of bacteria, especially fast-growing bacteria, has increased, leading to rapid decomposition of soil organic matter, which causes the previously stable organic carbon to be rapidly converted into carbon dioxide and released into the atmosphere, thereby exacerbating the loss of SOC [37,38]. It can be seen that although exogenous nitrogen can promote soil carbon sequestration in farmland, it is necessary to find a reasonable threshold, otherwise it will be detrimental to soil carbon sequestration.

4. Background and Application of Moderate Replacement of Nitrogen Fertilizer with Green Manure

4.1. Definition and Classification of Green Manure

Using idle land in rest seasons or spaces to plant (free-range) nitrogen-fixing or specific nutrient crops, the green plant bodies of these crops are turned back into the field or covered on the surface to provide nutrients and organic matter for the farmland. These green plant bodies and roots are called green manure [45]. Common green manure crops can be divided into leguminous green manure and non-leguminous green manure according to plant type. Leguminous green manure mainly includes plants in the Fabaceae family, including various clovers, vetches, beans, and peas, etc. (

Table 1. Characteristics of major green manure types.

Type	Example Species	C:N	Key Functions	Suitable Conditions
Legumes	Chinese milk vetch, hairy vetch, clover	15–25:1	Biological N fixation, labile C source	pH 7–8, low–moderate-fertility soils [7]
Gramineae	Ryegrass, oat, rye	30–50:1	Long-term C storage, erosion control	Requires N supplementation [6]
Brassicas	Rapeseed, daikon radish, mustard	25–35:1	Activated phosphorus and potassium, biofumigation	Avoid continuous cropping [11]
Asteraceae	Jerusalem artichoke, sunflower, crown daisy	20–30:1	Deep C sequestration, drought resistance	Arid/semi-arid regions [6]

). Leguminous green manure can effectively convert nitrogen in the atmosphere into a form that can be absorbed by plants. This biological nitrogen fixation characteristic gives it a unique advantage in increasing soil nitrogen content; non-leguminous green manure includes numerous Brassicas (mustard, rape, radish, turnip), buckwheat, rye, sorghum-sudangrass, and many others (Table 1). Due to significant differences in ecological and climatic conditions as well as soil types in different agricultural regions, the available green manure germplasm resources vary. Currently, while green manures are widely used in countries and regions such as China, the United States, India, and Brazil (Figure 1), their impacts on soil properties are highly context-dependent. For instance, in sandy soils, green manures typically improve water retention but may provide less benefit for soil structure compared to clay soils. Similarly, in arid regions, the water requirements of green manure crops may limit their adoption, whereas in humid areas they excel at erosion control. Overall, reasonable planting of green manure can significantly improve soil quality, reduce soil erosion, and improve soil physical properties and water retention capacity. These ecological benefits provide a theoretical basis for the functional substitution of nitrogen fertilizer with green manure, especially for addressing environmental issues and promoting sustainable agricultural development [22,46].

However, the benefits of green manure can change due to environmental conditions. Depletion of soil moisture by growing legumes in wet areas does not affect the growth of wheat in the following season [47]. However, under low-rainfall conditions, planting green manure during the summer fallow period made the pre-sowing soil water storage of winter wheat 78–93 mm lower than that of the fallow treatment, which reduced the wheat yield by 13.8–23.4% [48]. In a study in Northwest China, green manure added to the field increased the crop yield and organic carbon content by 1.3 t/ha and 0.8 g/kg, respectively, compared with the no-green manure treatment [49]. Apparently, green manure is beneficial to high agricultural yields and environmentally friendly under conditions of sufficient rainfall or irrigation, but in areas with insufficient rainfall, green manure depletes the soil moisture, resulting in a reduction in the yields of the main planted crops.

The practical implementation of green manure systems requires tailored agronomic strategies to address regional variability. In temperate climates with nitrogen-deficient soils (e.g., Northern Europe), leguminous species such as Vicia faba or Trifolium pratense are prioritized for their nitrogen fixation capacity, with sowing in early spring (March–April) and incorporation 4–6 weeks before winter cereal planting to synchronize nutrient release. In contrast, arid regions (e.g., Mediterranean basins) benefit from drought-tolerant non-legumes like Brassica napus, sown post-rainy season to conserve soil moisture, while tropical systems (e.g., Southeast Asia) favor fast-growing species (e.g., Crotalaria juncea) planted post-monsoon for rapid biomass accumulation [7,8,9,22]. Field trials indicate that a minimum biomass input of 3–5 t/ha is typically required to measurably enhance SOC stocks, though heavier soils (e.g., clay loams) may demand higher inputs due to slower decomposition rates [6]. These thresholds, however, must be calibrated against local edaphic conditions and farmer resources to ensure feasibility.

4.2. Scientific Feasibility of Green Manure as a Partial Replacement for Chemical Nitrogen Fertilizer

Researchers at home and abroad have conducted extensive research on the functions of green manure in agricultural ecosystems, confirming that planting green manure has significant advantages in improving soil quality, enhancing soil nutrient availability, and promoting nutrient absorption and utilization by major crops. This also provides a theoretical basis for reducing the application of chemical nitrogen fertilizers after green manure is returned to the field while ensuring stable, high, and high-quality crop production. This is mainly reflected in the following three aspects (Figure 2).

(1) Crop growth promotion by planting and returning green manure to the field. Research on the effects of planting and returning green manure on the photosynthetic physiology, resource utilization, and yield performance of crops has shown that planting and returning green manure can effectively promote the growth and development of major crops such as wheat (Triticum aestivum) [50], maize (Zea mays L.) [51], and potato (Solanum tuberosum) [52], effectively increase the biomass, leaf area index (LAI), and photosynthetic physiological characteristics of major crops, and ultimately improve crop yield [53,54]. In addition, some studies have shown that planting green manure can promote the resource utilization efficiency of the main crops, and effectively improve water use efficiency and nitrogen use efficiency [55]. At present, the academic community has reached a consensus on the argument that green manure promotes crop growth and development. However, there is still no scientific answer on how to achieve a dynamic balance between the nutrient supply time and nutrient demand time of major crops through improved agronomic measures.

(2) Improving soil quality and enhancing soil fertility. Reasonable planting of green manure can increase farmland coverage, change soil porosity, and utilize the “shading effect” of green manure to reduce soil evaporation, transforming ineffective water consumption in farmland into effective water consumption, thereby improving soil moisture environment and providing better water conditions for major crops [56]. Planting green manure can effectively improve soil nutrient conditions. Previous studies have shown that planting green manure has nitrogen-fixing and carbon-increasing effects, and can also improve the nutrient status of phosphorus, potassium, and other nutrients in the soil, especially the mineralization and enrichment of trace elements such as calcium, iron, magnesium, and zinc [57]. The incorporation of green manure exerts profound effects on soil microbial communities, with particularly strong stimulation of nitrogen-fixing bacteria (e.g., Rhizobium and Bradyrhizobium), cellulolytic microorganisms (e.g., Cellulomonas and Trichoderma), and arbuscular mycorrhizal fungi (e.g., Glomus species). These microbial groups play pivotal roles in decomposing green manure residues and facilitating nutrient cycling. Unlike mineral nitrogen fertilization, which primarily stimulates nitrifying bacteria (e.g., Nitrosomonas), green manure promotes a more diverse microbial community through continuous supply of organic carbon substrates [58]. Through these changes in microbial communities, green manures not only reduce plant diseases in subsequent crops [59], but also increase soil enzyme activity and nutrient availability, promote nutrient absorption and utilization by major crops, and enhance soil ecological stability [60,61], which is crucial for crop morphogenesis and yield formation; it is worth mentioning that the developed and dense root system of green manure has a strong interpenetration effect on the soil. After returning green manure to the field, some undecomposed green manure plant residues remain in the soil, effectively increasing soil porosity, reducing soil bulk density and compactness, which provides good soil conditions for the growth and development of crop roots [8]. At the same time, the return of green manure to the field can significantly promote the formation of soil aggregate structure, increase soil organic matter content, expand soil carbon and nitrogen pools, promote nutrient availability, and increase microbial activity [22,32,62,63]. In addition, a large number of studies have shown that leguminous green manure crops have a low carbon-to-nitrogen ratio, which is beneficial for converting plant carbon into soil carbon. At the same time, green manure has an activating effect on the activities of sucrase, urease, phosphatase, arylsulfatase, and dehydrogenase in the soil. These soil enzymes promote the conversion of soil carbon, urea nutrients, and organic phosphorus, as well as the hydrolysis of organic sulfur (ester sulfur) and microbial activity [64].

(3) Environmental benefits. The widespread use of chemical nitrogen fertilizer has raised a series of environmental problems, particularly soil degradation, water pollution, and greenhouse gas emissions, while increasing agricultural production. In contrast, leguminous green manure crops fix atmospheric nitrogen as a plant-available nitrogen source through symbiosis with rhizobium, thereby increasing the effectiveness of nitrogen in the soil, while the application of green manure crops reduces nitrogen loss and lowers the risk of environmental pollution caused by nitrogen leaching [65]. In addition, root secretions and plant residues of green manure crops can increase soil organic matter content, improve soil structure, and enhance soil water retention and drought resistance, which can help to promote nutrient cycling and improve the microbial environment, thus enhancing the long-term productivity and sustainability of soils [41]. Green manure crops also offer important advantages in terms of GHG emission reduction. Although green manure crops may release a certain amount of greenhouse gases such as nitrogen oxides (NOx) during nitrogen fixation, their greenhouse gas emissions are relatively low compared to chemical nitrogen fertilizer application [66]. Moreover, it can reduce GHG emissions at source by reducing the need for chemical fertilizer for the main crops. With the global greening of agriculture, green manure crops not only provide a new way to increase agricultural productivity, but also provide important technical support for achieving sustainable agriculture and long-term ecosystem health.

5. Soil Carbon Sequestration and Mechanism Based on Moderate Substitution of Nitrogen Fertilizer with Green Manure

5.1. The Effect of Moderate Substitution of Nitrogen Fertilizer with Green Manure on Soil Carbon Sequestration

Among all terrestrial ecosystems, agricultural ecosystems have become more fragile due to structural simplification and human activity constraints, and SOC storage is also highly susceptible to human disturbance [14,67,68]. The long-term single cropping pattern, high amount of chemical nitrogen fertilizer input, and unreasonable agricultural practices such as the use of agricultural machinery have led to soil erosion, degradation, and structural damage, directly causing the dynamic balance between SOC and atmospheric carbon pools to be disrupted, which exacerbates the contribution of farmland soil to greenhouse gas emissions [69,70]. At present, CO₂ emissions from global agricultural sources account for 21–25% of anthropogenic greenhouse gas emissions [71], which forces us to re-examine the significance of soil carbon sequestration and emission reduction in agricultural sustainable development. The core task is to stabilize and enhance SOC storage.

In the development of modern agriculture, green manure is widely used due to its advantages of enhancing soil fertility, promoting nutrient supply to crops, and ensuring sustainable and stable crop yields [72,73,74]. Leguminous green manure can convert atmospheric CO₂ and N₂ into biomass. Planting green manure during the fallow period is an effective strategy to improve soil fertility and enhance soil carbon sequestration. In general, the sequestration of soil organic carbon (SOC) through green manure involves two distinct yet interconnected pathways: primary and secondary carbon sequestration. Primary sequestration refers to the direct input of plant-derived carbon through green manure biomass incorporation, which contributes to the labile SOC pool (e.g., particulate organic matter) [43,45]. This process is rapid but transient, as a significant fraction of fresh residues decomposes within months to years, releasing CO₂ back to the atmosphere. In contrast, secondary sequestration entails the stabilization of carbon via microbial transformation (e.g., fungal and bacterial necromass), physical protection within soil aggregates, and chemical association with mineral surfaces (e.g., clay–humus complexes) [22]. These mechanisms promote long-term SOC storage, often persisting for decades. Green manure influences both pathways: while high biomass production enhances primary sequestration, its residue quality (e.g., C:N ratio, lignin content) governs microbial efficiency and thus the proportion of carbon diverted to secondary sequestration. Gao et al. (2023) found, through long-term multi-point experiments, that planting green manure during the fallow period has great potential for increasing soil carbon storage in Chinese rice fields [45]. In this study, SOC concentration and storage increased at rates of 0.221 g kg⁻¹ yr⁻¹ and 0.442 Mg C ha⁻¹ yr⁻¹ under green manure treatment, respectively [45]. These growth rates were slightly higher than the carbon storage growth rates reported in previous studies based on global meta-analyses (the average change rate of SOC pool in the 0–20 cm topsoil under green manure conditions in the first few decades was 0.32–0.37 Mg C ha⁻¹ yr⁻¹). Another meta-analysis showed that the application of green manure can increase SOC storage by an average of 15.5% [75]. This may be because green manure introduces a large amount of fresh biomass from above and below the ground into the soil, increasing the activity and abundance of soil microorganisms, promoting the conversion of exogenous compounds into organic carbon. At the same time, green manure can also increase the physical grading of SOC and the C content in SOC light components [76]. In addition, flooding and anaerobic conditions in the rice system may reduce the decomposition of green manure, increase the formation of water-stable aggregates and macroaggregates, and thus increase the hydrocarbon content of soil [77]. Similar results have been obtained in previous studies. Gattinger et al. (2012) recorded that the soil CS rate under organic agriculture was approximately 0.45 Mg C ha⁻¹ yr⁻¹, significantly higher than that under non-organic management [78]. These results indicate that green manure plays an important role in improving soil CS in farmland. However, some studies have found that the input of green manure can accelerate the decomposition of soil organic carbon, mainly due to the increased activity of soil carbon/nitrogen-acquiring enzymes associated with returning green manure to the field, which often promotes carbon mineralization and the consumption of soil organic matter [79]. Based on this, many researchers have adopted the method of replacing chemical nitrogen fertilizer with green manure in moderation to alleviate the organic carbon decomposition caused by green manure and promote soil carbon sequestration. Chang et al. (2024) found that reducing nitrogen by 20% under the condition of returning green manure to the field is beneficial for promoting soil organic carbon sequestration [43], which is consistent with previous research results [33]. This can mainly be attributed to a reduction in exogenous nitrogen application, which can increase soil organic carbon storage by reducing soil carbon/nitrogen acquisition enzyme activity and microbial resource limitations. Previous research results also support this viewpoint (there is a negative correlation between soil organic carbon content and soil carbon acquisition enzyme activity) [80]. It can be seen that a single input of green manure may have adverse effects on the soil carbon pool, and the appropriate substitution of chemical nitrogen fertilizer with green manure can serve as a reasonable fertilization system to achieve the dual goals of ensuring food security and mitigating climate change.

In addition, factors such as the type of green manure and field management measures can affect soil organic carbon sequestration. The cover crop (CC) type can affect SOC changes. For example, some studies found grass CCs, including cereal rye (Secale ereal) and annual ryegrass (Lolium multiflorum), cause greater SOC increases than leguminous CCs like cowpea (Vigna unguiculate) and hairy vetch (Vicia villosa Roth) [81]. Other studies found greater SOC increases after the planting of legume CCs compared to grass CCs [82], with mixtures often causing the greatest increases of all [83]. One reason for these incongruous results may be differences in biomass and carbon–nitrogen (C:N) ratios between CC species. However, not all studies found CCs to result in SOC accumulation, with some demonstrating SOC losses after introduction of CCs [84]. Due to differences in climate and management, CCs may need to be used for decades in some systems to cause significant SOC increases [85]. Results also vary depending on soil texture and type, as some fine-textured soils can help to physically protect SOC from decomposition [86], depending on factors such as mineralogy and amount of soil aggregation.

5.2. Mechanisms for Driving Soil Carbon Sequestration by Moderate Substitution of Nitrogen Fertilizer by Green Manure

5.2.1. Physical Fixation

Soil aggregates are considered the main determining factors for promoting good soil structure and fertility in agricultural systems [87,88]. Previous studies have found that macroaggregates (>0.25 mm) are the largest component of soil aggregates and an important factor in promoting organic carbon sequestration [89]. Research has shown that moderate nitrogen reduction under the conditions of returning green manure to the field can promote the formation of soil macroaggregates, increase the average weight diameter and geometric average diameter of soil aggregates [90,91], and facilitate the formation of a good soil structure [92]. At the same time, returning green manure to the field is beneficial for the transformation of microaggregate SOC to macroaggregate SOC, and effectively protects the microaggregate carbon trapped in macroaggregates, significantly increasing the soil organic carbon content > 2 mm and 0.25–2 mm particle size aggregates. In addition, moderate nitrogen reduction enhances the size distribution and MWD of macroaggregates, which is beneficial for increasing the stability of soil aggregates [43], thereby promoting the protective effect on organic carbon. However, attention should be paid to the threshold of the nitrogen application rate. Wang et al. (2022) found that excessive nitrogen application may cause the decomposition of macroaggregates, accelerate the release of carbon in soil aggregates, and thus lead to the consumption of SOC storage [93]; on the contrary, moderate nitrogen application under the condition of returning green manure to the field can promote the binding of mineral particles into aggregates, enhance agglomeration, and thus promote soil organic carbon storage [94], indicating that the application of moderate nitrogen fertilizer under the condition of returning green manure to the field can protect organic carbon from decomposition by enhancing agglomeration (Figure 3). It can be seen that in agricultural practice, incorporating green manure into the planting system and combining it with appropriate nitrogen application is a promising way to solve the current dilemma in farmland management.

5.2.2. Chemical Fixation

The chemical fixation mechanism mainly involves chemical binding between organic carbon and soil minerals [95,96]. After applying green manure, the organic matter produced during plant growth reacts with soil minerals to form organic–inorganic complexes [97]. Research has shown that the formation of these complexes significantly improves the stability of soil organic carbon, reduces the mineralization rate of organic carbon, and enhances the soil’s carbon storage capacity [21,98]. At the same time, moderate nitrogen application can improve soil chemical properties and increase the effectiveness of nutrients in soil, and this improvement in nutritional conditions can promote the growth and metabolic activity of microorganisms [99], thereby enhancing the formation of organic–inorganic complexes. In addition, under the condition of returning green manure to the field, moderate nitrogen reduction can promote the transfer of soil light organic carbon to aggregated particle organic carbon [100], drive the enrichment of free iron and amorphous iron in the aggregated structure [101], increase the content of fatty organic carbon, carboxylic acid state, and aromatic organic carbon in various particle size aggregates of soil, increase the relative ratio of aromatic carbon/fatty carbon and carboxylic acid carbon/fatty carbon in each aggregate [27], increase clay mineral adsorption sites [102], improve soil carbon stability, and green manure can enhance the interaction between soil biota and non-biota, which is also beneficial for the formation and stability of soil organic carbon. In addition, the application of green manure can usually improve the pH value and cation-exchange capacity of soil [103], thereby creating a favorable chemical environment for long-term storage of organic carbon. It can be seen that the combination of green manure and nitrogen fertilizer should be fully considered in agricultural production to achieve the best soil carbon sequestration effect. Most notably, recent studies highlight that root architectural traits of green manure species significantly modulate SOC sequestration patterns. Deep-rooting legumes (e.g., alfalfa) exhibit greater potential for subsoil carbon storage through root-derived particulate organic matter [104], whereas shallow-rooting species (e.g., clover) predominantly enhance rhizodeposition in topsoil [105]. Particularly, the composition of root exudates (e.g., carboxylates vs. phenolics) varies across species, differentially stimulating microbial necromass accumulation—a key precursor for mineral-associated organic matter formation. This suggests that green manure selection should consider root trait characteristics to target specific soil carbon pools. Of course, there is never a single mechanism for organic carbon stabilization. For example, green manure incorporation enhances soil organic matter stabilization through interconnected physical and chemical mechanisms. The decomposition process simultaneously promotes physical encapsulation within soil aggregates and chemical binding to mineral surfaces, particularly iron/aluminum oxides and clay particles, and released organic compounds act as both binding agents for aggregate formation and substrates for mineral adsorption.

5.2.3. Microbiological Fixation

Numerous studies have shown that the diversity and biomass of microorganisms in soil significantly increase after the application of green manure. This change not only enhances the activity and conversion rate of organic carbon, but also promotes the storage of microbial biomass carbon (MBC) [35,36]. However, some studies also suggest that green manure application boosts microbial activity and biomass carbon (MBC) in the short term, but long-term soil carbon sequestration primarily occurs through the stabilization of microbial necromass (e.g., fungal cell walls and bacterial membranes) via chemical binding to soil minerals, forming persistent organo-mineral complexes [106]. Under the condition of returning green manure to the field, the application of appropriate chemical nitrogen fertilizer can enhance the utilization efficiency of organic carbon by microorganisms. This process enhances the accumulation of organic carbon in soil by promoting the metabolic activity of microorganisms [84]. At the same time, extracellular polysaccharides, mucus, and other metabolites produced by microorganisms during the decomposition of organic matter can combine with soil particles [107], forming stable organic mineral complexes. This complex plays an important role in the long-term storage of soil organic carbon. In addition, the combined application of green manure and chemical nitrogen fertilizer significantly alters microbial community structure, particularly enhancing the abundance of key functional groups including (1) cellulolytic bacteria (e.g., Cellulomonas, Bacillus), which decompose plant residues; (2) arbuscular mycorrhizal fungi (Glomus, Rhizophagus) that facilitate carbon transfer to soil aggregates; and (3) actinobacteria (Streptomyces spp.), responsible for degrading complex organic compounds. These microbial groups collectively drive organic carbon conversion through residue decomposition (bacteria), physical protection via hyphal networks (fungi), and formation of stable microbial necromass (actinobacteria), with their synergistic effects enhancing both short-term carbon cycling and long-term sequestration [9,10,108]. In summary, the combined application of green manure and chemical nitrogen fertilizer can further promote the diversity and metabolic activity of soil microorganisms, creating more favorable conditions for soil organic carbon sequestration.

In addition, the extracellular polysaccharides, mucus, and metabolites generated by microorganisms during organic matter decomposition serve dual functions in carbon stabilization: they chemically bind organic compounds to mineral surfaces (particularly iron/aluminum oxides and clay edges) while simultaneously acting as binding agents that physically bridge soil particles into aggregates. These microbial byproducts thus directly mediate both chemical stabilization (through organo-mineral complexation) and physical protection (via aggregate formation), creating a synergistic mechanism that enhances long-term soil organic carbon storage [109].

6. Challenges, Obstacles, and Limitations to Use of Green Manures

While green manures provide important benefits for soil health and sustainable agriculture, their practical implementation faces several significant challenges that must be considered.

(1)

The variable effectiveness of green manures across different environments: Their performance depends heavily on local soil conditions, climate, and management practices, making it difficult to establish universal guidelines for their use. In some cases, green manures may compete with cash crops for water and nutrients, particularly in arid regions or during drought periods.

(2)

Management complexities: Farmers must carefully time planting and termination of green manure crops to avoid interfering with main crop production cycles. This requires additional planning and labor, which can be a barrier for resource-limited operations. The decomposition rate of green manure biomass is also inconsistent, sometimes leading to temporary nitrogen immobilization that could negatively affect subsequent crops.

(3)

Economic constraints: The costs associated with seeds, establishment, and incorporation of green manure crops often outweigh the immediate economic benefits, especially for small-scale farmers. There is also typically a delay between implementing green manures and observing measurable improvements in soil quality or crop yields, which discourages short-term adoption.

(4)

Knowledge gaps and technical barriers remain significant challenges: Many farmers lack access to clear, locally relevant information about optimal green manure species selection and management techniques. Additionally, some farming systems lack the necessary equipment or infrastructure to effectively incorporate green manures into their operations.

While green manures can reduce the need for synthetic fertilizers, they cannot completely replace them in most intensive agricultural systems. Determining the appropriate balance between green manure use and supplemental fertilization requires careful monitoring and site-specific adjustments. These challenges highlight the need for continued research and extension efforts to develop more adaptable and economically viable green manure systems tailored to different agricultural contexts. Addressing these limitations will be crucial for maximizing the potential of green manures in sustainable crop production.

7. Future Research Directions and Suggestions

(1)

Improve soil carbon sequestration efficiency by optimizing green manure management strategies: Selecting unique green manure varieties for specific regions to adapt to the climate conditions and soil textures of different agricultural areas and clarifying the optimal planting window for different climate zones will help maximize the growth potential and ecological benefits of green manure. In addition, it is particularly crucial to utilize intercropping, multiple cropping, crop rotation, and other modes based on the characteristics of resources and crop biology in different regions, allocate space and time reasonably, and organically incorporate green manure into the planting system to achieve efficient resource utilization.

(2)

Evaluate the ecological benefits of green manure through long-term and multi-scale research: Conducting cross-year long-term positioning experiments will provide data support for understanding the long-term effects of the “green manure+nitrogen fertilizer” combined application strategy on soil carbon sequestration. In addition, remote sensing technology and geographic information systems (GISs) can be utilized to digitally monitor the carbon dynamics of intensive farmland, in order to provide broader spatial data for in-depth analysis of the role of green manure in diverse agricultural ecosystems. Meanwhile, utilizing machine learning and big data analysis techniques to establish precise carbon cycle prediction models can assist decision-makers or researchers in formulating more rational management strategies.

(3)

Explore the climate change adaptation capacity and carbon sequestration potential of green manure under different climate scenarios: Exploring the growth of green manure under extreme climate conditions such as drought, floods, and cold, and its impact on soil carbon sequestration, will help to understand its adaptability and resilience in the context of climate change. Encouraging interdisciplinary collaboration between climate science, soil science, and agricultural economics can provide a more comprehensive and authoritative perspective for a deeper understanding of the role of green manure in sustainable agriculture.

8. Conclusions

This review synthesizes the current knowledge on the dual role of green manure in sustainable agricultural intensification, highlighting its capacity to address the critical challenge of balancing productivity enhancement with environmental conservation. By systematically analyzing the mechanisms through which green manure substitution enhances soil carbon sequestration (SCS), we demonstrate that green manure systems not only provide nitrogen inputs comparable to conventional fertilization but also mitigate soil organic carbon (SOC) depletion through multiple pathways. This study has three key innovations: first, we developed a new framework linking the N-fixing capacity of green manure to specific carbon sequestration pathways, demonstrating the fundamental difference between biological N inputs and chemical fertilizers in terms of soil carbon impacts. Second, we explained the mechanisms of carbon sequestration under green manure with N fertilizer conditions in terms of physical, chemical, and microbial fixation pathways. Third, we pioneered the idea that future research should focus on the growth of green manure under extreme climatic conditions, such as drought, flood, and cold, in order to understand its adaptation and resilience in the context of climate change. The insights presented here provide a scientific foundation for policymakers and practitioners to promote green manure integration as part of sustainable agricultural policies, this work contributes to the development of agricultural systems that align with global climate goals without compromising food security.