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Review

A Comprehensive Review of the Effects of Organic Amendments on Soil Health and Fertility: Mechanisms, Greenhouse Gas Emissions, and Implications for Sustainable Agriculture

by
Jing Xu
1,*,
Yangyang Li
2 and
Lingling Li
1
1
State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
2
Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
*
Author to whom correspondence should be addressed.
Agronomy 2025, 15(12), 2705; https://doi.org/10.3390/agronomy15122705
Submission received: 24 October 2025 / Revised: 18 November 2025 / Accepted: 23 November 2025 / Published: 25 November 2025
(This article belongs to the Section Farming Sustainability)
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Abstract

With the escalating application of chemical fertilizers, the potential for environmental pollution has increased significantly. Currently, the degradation of soil quality due to the indiscriminate use of chemical fertilizers poses a more pressing challenge than ever before, threatening both human food production and the environment. The utilization of organic amendments not only enables the efficient recycling of organic waste resources but also reduces the reliance on chemical fertilizers. Meanwhile, organic amendments play a crucial role in soil improvement, helping to stabilize and enhance crop yields. Numerous studies have investigated the impacts of organic amendments on various aspects of crop production, including soil biology, biochemistry, heavy metal accumulation, and greenhouse gas (GHG) emissions. However, these studies have predominantly focused on isolated aspects rather than adopting a comprehensive perspective. Therefore, a comprehensive analysis of the positive and adverse effects of organic amendments is important in optimizing fertilizer use to meet crop nutrient demands and advancing carbon-neutral agriculture. This study mainly explores the intrinsic mechanism of the influence of organic amendments on soil physicochemical properties, enzyme activity and microbial diversity, heavy metal contamination and mobility, and GHG emissions in farmland. Finally, recommendations for the future development of organic amendments are proposed for promoting green and sustainable agricultural practices.

1. Introduction

Fertilizers, as an indispensable input resource for crops, play an irreplaceable role in modern agricultural activities. Since the widespread adoption of chemical fertilizers in Europe in 1800s, over the past 200 years they have completely broken through the limitations of traditional agriculture, which relies on the natural recovery of soil fertility. Chemical fertilizers improve crop yields by accurately supplying crops with essential nutrients (i.e., nitrogen, phosphorus, and potassium), making a significant contribution to maintaining stable agricultural production. Simultaneously, chemical fertilizers transform the closed soil–plant cycle into an open system, restructuring the farmland nutrient cycle, maintaining soil productivity, and supporting the intensive production characteristic of modern agriculture. Moreover, the utilization of innovative products, including slow- and controlled-release fertilizers and stable fertilizers, is facilitating the establishment of an environmentally friendly fertilizer application system. According to the Statistical Yearbook 2023, published by the Food and Agriculture Organization of the United Nations (FAO), over the past decade, worldwide, the use of pesticides and fertilizers has increased by approximately 60% and 50%, respectively, while crop yields have only increased by 50%. However, the excessive application of chemical fertilizers not only leads to serious resource waste but also has a limited positive impact on crop quality. Additionally, the long-term application of large amounts of chemical fertilizers reduces the soil organic matter (SOM) content, deteriorates soil physical and chemical properties, accelerates soil acidification, and contaminates the ecological environment of agricultural soils [1,2].
As an important category of fertilizers, organic amendments are derived from sources such as plant residues, animal manure, composted materials, and other biological sources. There are six types of organic amendments applied to soils: human and animal manure, municipal biosolids (MBSs), green manure and crop residues, food residues and waste, waste from manufacturing processes, and compost [3]. Organic amendments can replenish soil organic matter, reactivate microbial communities, improve soil structure, alleviate soil acidification, and mitigate environmental pollution. Consequently, they enable sustainable increases in crop yield without degrading farmland, while simultaneously enhancing crop quality and nutritional value. Organic amendments predominantly contain nutrients in the organic state, which cannot be directly utilized by crops. These amendments are produced by microorganisms through anaerobic and aerobic processes. During this biochemical transformation, carbon dioxide (CO2), H2O, and essential mineral nutrients such as nitrogen (N), phosphorus (P), potassium (K), and calcium (Ca) are generated, along with the formation of humic substances [4,5]. Numerous studies have reported that organic amendments, characterized by their high organic matter content, comprehensive nutrient profiles, and prolonged fertilization effect, can effectively enhance soil microbial communities, improve soil fertility, and elevate the quality of agricultural products [6,7,8]. Furthermore, organic amendments play an important role in material recycling and environmental protection, aligning well with the requirements of organic and eco-agricultural practices. In addition, modern organic amendments are extremely effective in maintaining soil ecology. Amendments such as biochar-based organic fertilizer (a C-rich substance) have garnered extensive attention and application in recent years as a new type of ecological fertilizer [9,10]. Research has shown that incorporating 10% biochar into the composting process can significantly reduce the co-emissions of ammonia (NH3) and greenhouse gases (GHSs) [11]. Therefore, applying appropriate amounts of organic amendments to farmland represents a promising approach for resource utilization and sustainable development, effectively transforming waste into valuable resources.
Nevertheless, it is essential to acknowledge that organic amendments may contain hazardous residues, posing potential risks to agricultural product safety and to agroecosystems. For instance, most organic amendments, such as animal manure, generally contain more unfriendly compounds than chemical fertilizers, including heavy metals [12], amendment residues, and even microbial pathogens [13]. Moreover, the application of organic amendments to the soil may lead to increased GHG emissions. Reports indicate that more than 80% of anthropogenic nitrous oxide (N2O) emissions and 70% of anthropogenic NH3 emissions in agriculture are primarily attributed to the application of livestock manure and inorganic fertilizers [14]. Additionally, a study by He et al. [15] showed that replacing chemical fertilizers with organic amendments significantly decreased N2O emissions but increased methane (CH4) and carbon dioxide (CO2) emissions, thereby exacerbating the global warming potential (GWP). Excessive application of organic amendments can also exceed the self-digestion capacity of the soil, resulting in secondary contamination that may hinder long-term crop production.
In contrast to fast-release nutrient fertilizers, organic amendments are highly diverse, possess complex components, and undergo intricate reactions in the soil, leading to uncertain impacts on soil ecosystems. This review aims to summarize the effects of organic amendment application on physicochemical and biological properties, soil heavy metals, and GHG emission in farmland soils, delving into the mechanisms underlying the influence of organic amendments on soil health and fertility and comparing their effects with those of chemical fertilizers, in order to provide a comprehensive understanding of the advantages and disadvantages of organic amendments. This knowledge can serve as a valuable reference for the rational application of organic amendments in agricultural practices.

2. Data Sources and Research Methods

The data in this paper were collected from the Web of Science core collection by setting the search keywords as [A = (“SOM” or “soil organic matter”) and B = (“organic fertilizer” or “organic amendments”)]. The search period covered the past five years (1 January 2020 to 30 December 2024). After eliminating irrelevant literature, 3438 research articles related to SOM and organic amendments were finally obtained. With the continuous advancement of information visualization technology, knowledge graph technology has provided new methods for data analysis and processing. Therefore, VOS viewer software (V1.6.20), (https://www.vosviewer.com/, accessed on 9 January 2025), developed by Leiden University and based on Java (V1.8.0-431), was employed to graphically analyze the keywords related to organic amendments and SOM [16].
For analysis of microbial diversity and enzyme activity under organic amendments, the data were retrieved from the Web of Science core collection by setting the keywords [A = (“SOM” or “soil organic matter”) and B = (“enzyme activity”) and C = (“microbial diversity”)]. Similarly, the search timescale was within the latest 5 years (1 January 2020 to 30 December 2024). The 1567 identified articles were filtered according to the following criteria: ① clear specification of soil type and dosage of organic amendments; ② precise quantification of microbial and enzyme activity changes; and ③ priority given to long-term field trials. Eventually, 31 articles were selected for case analysis.

3. Positive Effects of Organic Amendments on Soil Ecosystems

3.1. Effect on the Soil Physical Properties

Soil physical properties, including soil structure, soil bulk density, porosity, water-holding capacity, aeration, and mechanical resistance, serve as fundamental determinants of the ecological function and agricultural potential. Globally, the prolonged use of chemical fertilizers has exacerbated soil physical degradation [17]. While organic amendments significantly improve soil physical properties, this process unfolds over the long term. Upon soil incorporation, organic materials initially undergo mineralization, during which organic matter decomposes into CO2, H2O, and mineral nutrients (N, P, K, Ca, etc.). Subsequently, under favorable conditions of material composition, moisture, and temperature, humification processes predominate, generating humic substances (i.e., humus, humic acids, and fulvic acids). These substances enhance soil water and nutrient retention while improving the availability of soil nutrients and moisture [5,18]. Generally, soils amended with organic materials exhibit lower bulk density, increased pore volume, elevated water infiltration rate, enhanced water-holding capacity, and improved aggregate stability [19,20].
Soil aggregates are formed through the cohesion and cementation of colloids and primary soil particles. The quantity and spatial arrangement of aggregates across different grain sizes determine the distribution and continuity of soil pores, which in turn govern soil hydraulic properties and influence aeration, water permeability, water storage, and tillage capacity [21,22,23]. Studies have shown that organic amendment application promotes the formation and stabilization of macroaggregates [24]. As a primary gelling agent, organic matter not only directly increases soil organic carbon content when amendments are applied but also stimulates microbial activity during decomposition. This process releases fungal hyphae and polysaccharides, which further bind soil particles to form macroaggregates [25]. Numerous studies have shown that organic amendments can significantly enhance the proportion of macroaggregates in soil, improving aggregate structure, while also increasing microaggregates aggregation degree and optimizing aggregate size distribution. These effects collectively enhance soil water–nutrient regulation and fertility [24,26].

3.2. Effect on the Soil Chemical Properties

Soil chemical properties, including pH, organic matter content, and nitrogen–phosphorus–potassium (NPK) nutrient levels, serve as core determinants of land productivity. Soil acidification has emerged as a critical constraint on soil productive potential and a significant challenge to agricultural development. Excessive use of synthetic nitrogen (N) fertilizer is widely recognized as the primary driver of soil acidification in farmlands [27]. Processes such as NH4+ nitrification, nitrate leaching, and imbalanced crop uptake of soil cations and anions accelerate soil acidification [28]. Organic amendments play a pivotal role in ameliorating soil acidification [29]. During decomposition, organic amendments generate humic acids, which are weak acids containing numerous acidic functional groups that enhance soils’ acid–base buffering capacity through acid-group dissociation and amine protonation [18]. Numerous studies have shown that manure, crop residues, and biochar can elevate soil pH, primarily due to the release of base cations (e.g., Ca2+ and Mg2+) during their decomposition and, in the case of biochar, its inherent alkalinity and high surface area which absorbs acidic cations [30,31]. Furthermore, as soil acidification is often accompanied by base cation depletion and nutrient leaching, organic amendment application strengthens soil water and nutrient retention, reduces soil nutrient leaching, and effectively mitigates soil acidification severity [28,32].
Numerous studies have explored the effects of organic amendment application on SOM (Figure 1A). SOM, composed of various C molecular structures, serves as a critical regulator of soil organic C persistence [33]. Liang et al. [34] proposed two pathways—ex vivo modification and in vivo turnover—to jointly explain soil C dynamics driven by microbial catabolism and/or anabolism, potentially improving our understanding of how soil C dynamics contribute to the terrestrial C cycle under global change (Figure 1B). Studies indicate that long-term organic amendment application increases SOM content, enhances soil nutrient supply capacity, accelerates the activation rate of humic acid for soil nutrients, improves soil nutrient levels, maintains the balance of available nutrient supply, and significantly enhances soil fertility [1,35]. As a vital component of the soil solid phase, SOM plays a key role in nutrient supply and preventing nutrient leaching. Organic amendments significantly increase SOM content; meanwhile, organic matter decomposition produces organic acids that promote mineral weathering and nutrient release, and enhance mineral nutrient availability. Organic amendments also elevate soil activated carbon and nitrogen fractions and enhance the activities of microorganisms and enzymes involved in nutrient transformation, thereby increasing soil-available nutrients [5,36]. Haque et al. [37] confirmed, through an incubation study, that organic amendments significantly increase total soil nitrogen, available potassium, and available phosphorus. Additionally, humus, due to its huge surface area and surface energy, exhibits strong adsorption capacity for available nutrients, reducing nutrient loss. Thus, organic amendment application not only ensures sufficient available nutrients but also minimizes nutrient loss and improves fertilizer utilization efficiency [18,36]. In summary, appropriate application of organic amendments significant influences soil functioning and processes (Figure 1C).

3.3. Effect on the Soil Microbial Diversity and Soil Enzyme Activity

There are a wide variety of microorganisms in the soil, which can be symbiotic or non-symbiotic with the host plant [38]. Soil microbes have a vital function in organic matter decomposition and nutrient cycling [39]. Compared with no fertilization, organic amendments provide C and N and energy for soil microbes, as well as improve the physicochemical properties of the soil microecosystem, promote microbial reproduction and increase microbial population and activity, and thereby optimize soil microbial community structure and functions [40,41]. Also, variations in soil microbial communities have been attributed to the long-term application of organic amendments that increased SOM content and soil fertility [7]. Conversely, soil microorganisms also influence SOM, as they not only mediate the SOM cycle through decomposition processes but are also the primary source of SOM through their exudates and, predominantly, the necromass from their dead bodies [38,42]. By investigating the various soil textures during the past 5 years, we found that application of organic–inorganic mixed fertilizers, application of organic fertilizers only, or application of bio-fertilizers increased abundances of soil bacteria such as Proteobacteria (3.57–49.41%), Actinomycetes (4.94–47.88%), and Acidobacteria (−15.18–44.63%) to some extent (Table S1). Also, we found that manure and other organic amendments positively affected soil microbial activity and diversity to a much greater extent than other agronomic practices (e.g., conservation tillage) (Table S1). In particular, it has been found that residual effects on soil microbial activity are often detected after the application of organic amendments, which will further prolong plant access to nutrients [43]. Ginting et al. [44] showed that the residual effects of compost and manure resulted in increased microbial biomass C by 20–40%. Dong et al. [45] also found that replacement of chemical fertilizers with organic fertilizers increased the total microbial phospholipid fatty acid (PLFA, an essential component of microbial membranes) content by 85% compared with the non-fertilized treatment.
Soil enzymes are a group of special substances with biochemical catalytic properties, mainly derived from the microbial metabolic processes, which are one of the indicators of the soil’s properties [46]. The strength of enzyme activity reflects the soil microbial activity, the intensity of biochemical reactions, and the degree of soil fertility [47]. From Table S1, we have also found that organic amendments significantly increase the activities of soil sucrase, urease, and phosphatase. Due to soil enzymes being closely related to soil microorganisms, any factors that affect soil microorganisms will certainly affect soil enzyme activities, while some soil enzymes also derive from plant and animal residues. Soil enzymes include microbial endoenzymes and exoenzymes released by microorganisms into the soil solution and adsorbed on organic and mineral soil particles [48]. Enzymes accumulated in soil are free enzymes, which are in the sorbed state. The application of organic amendments increases the SOM content, which provides abundant binding sites or protective sites for soil enzymes, which is conducive to the improvement in soil enzyme activities [49]. A comprehensive meta-analysis of 690 independent experiments revealed that organic amendments also increased the enzyme activities of the soil microbiome in soil hydrolysis of C, N, and P, and in oxidative decomposition [8]. In addition, as soil enzymes exhibit matrix preferences, organic matter characteristics, soil properties, application amounts, and application practices, and so on, influence the effect of organic amendments on soil enzyme activities.

4. Adverse Effects of Organic Amendments on Soil Ecosystems

4.1. Heavy Metal Pollution and Mobility in Agricultural Soil

From the 20th century onwards, many countries have witnessed the accumulation and exceedance of heavy metals (densities greater than 4.5 g/cm3) in agricultural soils, which has had serious impacts on crop production, caused deterioration in agricultural land, and threatened human health via the food chain. Organic amendments, as a high-quality source of nutrient inputs to farmland, in addition to providing crops with large quantities micronutrients for growth also contain some heavy metal elements. This is especially true for livestock and poultry manure. For instance, the reported concentrations of Cd in solid and liquid pig manure range from 0.19 to 0.53 mg kg−1 and 0.06 to 1.30 mg kg−1, respectively. In contrast, Cu and Zn can accumulate to considerably higher levels: Cu concentrations have been reported between 134 and 780 mg kg−1 in solid pig manure and 1 and 1386 mg kg−1 in liquid pig manure, while Zn levels vary from 206 to 1220 mg kg−1 in solid pig manure and 5 to 5832 mg kg−1 in liquid pig manure [3]. The environmental risk arises when these concentrations exceed the limits set by national organic fertilizer standards (e.g., in China, the limits for Cd, As, Hg, Pb, and Cr are 3 mg kg−1, 15 mg kg−1, 2 mg kg−1, 50 mg kg−1, and 150 mg kg−1, respectively, according to NY 525-2021) [50]. Manure with heavy metal levels above these thresholds, if applied repeatedly, will inevitably increase heavy metal content in the soil and heavy metal accumulation risk in the crops by plant root absorption. In general, the heaviness and toxicity of heavy metals are interrelated, and metals such as As, Cd, Pb, and Hg can cause biological toxicity at low doses, [51]. However, some trace elements, such as cobalt (Co), copper (Cu), chromium (Cr), iron (Fe), manganese (Mn), molybdenum (Mo), selenium (Se), and zinc (Zn), are essential for the maintenance of a wide range of biochemical and physiological functions in human beings, plants, and animals, and are known as trace elements. They are measured in trace concentrations (ppb or ppm) and can also cause soil contamination and human health hazards when applied in excess to farmland [52,53]. Liu et al. [54] showed that raw swine waste is rich in Fe, Zn, Cu, and Mn, and that the environmental risks are spread when it is used as an organic amendment in agriculture. However, whether or not the application of organic amendments will promote the uptake of heavy metals in the soil by plants depends on two aspects, as follows:
SOM adsorption and desorption of metals affect soil mineral metabolism cycles (Figure 2). Various organic manures, like pig manure, livestock manure, plant straw, and biochar, play a key role in the mobility of metals [55,56]. Element sorption on SOM “rough” surfaces can modify the physicochemical properties of minerals and affect the transport and mobility of nutrients and contaminants in soils [57]. Typically, most of the SOM adsorbed on mineral surfaces is relatively difficult to remove, suggesting that the microaggregates formed by SOM with minerals have a relatively high stability [58]. In general, the coupling between metals and SOM in soil solution is closely related to pH and to their individual concentrations, leading to similar chemical characteristics and similar behaviors [18]. For example, free Cd2+ is clearly redistributed to the organic complex form as pH increases, thereby reducing its bioavailability and toxicity. Similarly, pH has a significant effect on the fate of free Zn2+ in the soil solution, which reforms in carbonate complexes as pH increases, also leading to reduced bioavailability. In addition, the transport of micronutrients and heavy metals in SOM through the soil can be affected by dissolved oxygen concentrations. At the same time, the complexity of the soil pore space can result in widely varying migration rates, which depend to some extent on the texture of the soil layer [59]. Therefore, organic amendments increase SOM pH and soil aeration, which decreases the availability of heavy metals.
Heavy metal exceedances caused by an increase in heavy metal ions after the application of organic amendments, especially manure, are related to their competition with mineral adsorption sites, and differ in the environmental fate of different heavy metal ions. For example, SOM in soil usually also contains other inorganic ligands like salts (Na+, Cl−, Mg2+, and Ca2+) and minerals (carbonates and phosphates), and these constituents may also have a significant impact on the species and mobility of metals [18]. Reaction with chemical speciation increases the mobility of heavy metals in soil solutions. For example, soil dissolved organic C (DOC), a class of organic mixtures with complex composition, structure, and environmental behavior, can also have an impact on metal chemistry/mobility. It was reported that high concentrations of DOC increased the formation of complexes such as Cd–DOC, Zn–DOC, Ni–DOC, and Pb–DOC, which in turn increased the mobility of metals, because the metal–DOC complexes formed in the soil solution are not as tightly bound to the soil particles as are the free metal ions [18,60,61]. Consequently, organic amendments increase SOM and DOC, which improves the mobility of heavy metals.

4.2. Soil GHG Emissions

GHGs primarily include CO2, CH4, and N2O and significantly contribute to global warming [62]. Crop production is a major GHG emissions source, accounting for approximately 12% of the total anthropogenic GHG emissions worldwide [63]. According to the Food and Agricultural Organization (FAO), agrifood systems emitted 16.2 billion tonnes of CO2 equivalent (Gt CO2eq) in 2022, a 10% increase from previous estimates (FAO, 2024). This emission process is influenced by both natural factors such as temperature; moisture; precipitation; pH; and soil texture, and agricultural practices like fertilizer application (Figure 3). While organic amendments play a positive role in enhancing soil fertility and maintaining soil health, concerns exist that they may generate soil GHGs relative to chemical fertilizers. However, conflicting evidence suggests that organic fertilizer application can reduce GHG emissions by decreasing N fertilizer use and improving N fertilizer use efficiency [64,65]. Such inconsistent results (increase, decrease, or no change in GHG emissions) indicate that GHG emissions are affected by a complex interplay of factors leading to a wide range of GHG emissions behavior, which makes it difficult to draw general conclusions on a global scale.
  • CO2 emissions. CO2 represents the most important GHG, and soil CO2 emission flux is influenced by soil physicochemical processes, and is related to soil C content, cation exchange capacity, and so on [66]. Organic fertilizers and organic–inorganic fertilizer blends can significantly increase CO2 emissions [67]. Causes of CO2 emission by the application of organic amendments may be as follows: firstly, organic amendments increase the SOM content of the soil and improve the soil DOC content, and the mineralization and decomposition of organic C also increase the emission of CO2 from the soil. Secondly, organic amendments can increase the total pore size of the soil, which promotes the CO2 spreading and flux from the soil. Thirdly, organic amendments increase the number and activity of soil microorganisms, which in turn affects the surface CO2 flux.
  • CH4 emissions. CH4 is produced/emitted by the action of methanogenic bacteria under strict anaerobic conditions, and sufficient methanogenic substrate and an appropriate growth environment for methanogenic bacteria are the prerequisites to produce CH4. The application of organic amendments can improve the soil characteristics, so that it can absorb more radiant energy and increase the soil temperature, and it can also increase the soil pH, which provides favorable conditions for the growth of methanogenic bacteria, and encourages it to produce more CH4 [68]. In addition, CH4 is easily oxidized by oxidative bacteria under aerobic conditions, which reduces CH4 emissions from the soil. Decomposition of SOM decreases the soil redox potential (Eh), which leads to an increased emission of CH4. Various kinds of organic amendments such as crop straw, animal manure, compost, and sludge could increase the CH4 emissions, and the CH4 emission from straw treatment was significantly higher than that of other organic fertilizers.
  • N2O emissions. In the N cycle, biological denitrification involves nitrification and denitrification, ultimately causing N2O emissions, and the most important source, ammonia (NH3), which is produced by microorganisms consuming peptides and amino acids from protein-rich wastes [69,70]. The warming effect of N2O is approximately 300 times stronger than that of CO2, and it can be retained in the atmosphere for a longer time, participating in many photochemical reactions in the atmosphere and destroying the ozone layer [71]. Chadwick et al. [72] showed that the production and emission of soil N2O were affected by both C and N. Furthermore, they found that N2O emission was mainly restricted by exogenous N supply when organic amendments with equal carbon content were applied; in contrast, it was primarily limited by carbon when the amendments contained equal amounts of nitrogen. In addition, organic amendments not only provide energy for microbial activity, but also influence microbial activity by altering the soil C/N ratio, which in turn influences the N2O production and emission. A meta-analysis study showed that application of animal-origin manure increased N2O emissions by 17.7%, while biochar amendments significantly reduced N2O emissions by 19.7%, which resulted from the different effects on soil C/N of animal manure and biochar [73].

5. Conclusions and Perspectives

Organic amendments exert a dual impact on soil ecosystems. On the one hand, the benefits are substantial and foundational to soil health. The application of organic fertilizers consistently enhances soil physicochemical properties, including improved aggregate stability, increased water-holding capacity, and elevated levels of SOM and essential nutrients. This creates a favorable environment for a robust soil biota. Consequently, there is a significant stimulation of soil microbial biomass, diversity, and metabolic activity, which in turn drives the activity of key soil enzymes involved in nutrient cycling. This synergy between improved soil structure and heightened biological activity is paramount for sustaining long-term soil fertility and productivity. On the other hand, organic fertilizers are a direct source of heavy metal contamination in soil. Moreover, they can affect the uptake and accumulation of these metals in plants by altering their chemical speciation in the soil [74]. Furthermore, the enhanced microbial activity that drives nutrient mineralization also intensifies the production and emission of greenhouse gases, thereby contributing to climate change.
To maintain agricultural productivity, implementing optimal nutrient management strategies that reduce chemical fertilizer application, enhance nutrient utilization, and maintain soil fertility and functionality has become an urgent imperative in agricultural production. Future research should focus on the following areas:
  • Further emphasis should be placed on the return of organic materials to farmland. Organic amendments, sourced from agricultural, livestock, industrial, and domestic waste, can be recycled as fertilizers and predominantly assimilated within the soil system. This practice significantly reduces emissions into water bodies and the atmosphere, thereby mitigating the continuous cycling of pollutants within ecosystems. Increasing the quantity of organic waste returned to the field is the most effective proactive measure for reducing and preventing organic pollution in the ecological environment. The recycling of these organic materials serves not only the purpose of fertilizing, but more importantly, the protection of the ecological environment.
  • Research and development of collection and processing systems adapted to organic waste from planting and livestock farming on different scales. Under modern agricultural production practices, the problem of spatial segregation between crop cultivation and livestock has become increasingly pronounced, posing challenges to the on-site recycling of organic fertilizer nutrients into farmland. Developing collection and processing systems suitable for organic waste from various-scale agricultural activities will enable scientific treatment of most organic matter and its subsequent return to the fields, thereby enriching the soil organic matter pool.
  • Refine the application technologies for organic amendments. In agricultural production, the management of organic amendments needs to be strengthened. Strict regulations should be imposed on the application standards of organic amendments. High-quality organic amendments with low heavy metal and persistent pollutant content should be selected. Integrated application technologies for organic amendments should be established, and the application method should be optimized through site-specific and time-appropriate application, as well as the combination of organic and inorganic fertilizers. These measures will minimize the environmental risks associated with the application of organic amendments.
Currently, the availability of organic fertilizer resources is on the rise. However, instead of blindly favoring organic fertilizers or over-applying them, it is essential to recognize the advantages and disadvantages of organic fertilizers and chemical fertilizers. Guided by the principle of modern and sustainable agricultural development, especially in the context where chemical fertilizer remains the primary source of nutrients, a new perspective on organic fertilizers should be established.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agronomy15122705/s1, Table S1: Changes in soil enzyme activity and microbial diversity under different applications of organic-like fertilizers [75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105].

Author Contributions

Conceptualization, J.X. and L.L.; methodology, J.X. and L.L.; software, J.X.; validation, J.X., Y.L., and L.L.; formal analysis, J.X.; investigation, J.X.; resources, J.X.; data curation, J.X. and Y.L.; writing—original draft preparation, J.X.; writing—review and editing, Y.L. and L.L.; visualization, J.X. and Y.L.; funding acquisition, J.X. and L.L. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Key R&D Program of China (2022YFD1900305), the Major Special Research Projects in Gansu Province (22ZD6NA009), the College Teachers’ Innovation Foundation in Gansu Province (2025A-092), and the Start-up Foundation of Gansu Agricultural University for openly-recruited Ph.D. (GAU-KYQD-2021-33).

Data Availability Statement

The original contributions presented in this study are included in this article/Supplementary Materials. Further inquiries can be directed to the corresponding author.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. SOM-related research hotspots (A), C-cycle model (B) and functions (C). (A) Keyword clustering map in the field of organic amendments and SOM during 2020–2024. The larger the yellow field, the higher the relevance of the keyword’s occurrence. (B) Schematic diagram of SOM metabolic processes involved in C cycling in soil ecosystems. Primary production inputs (organic amendments, straw residues, etc.) to the soil occur through two pathways—in vivo turnover (red lines) and ex vivo (black lines) modification. The majority of the stable C pool in soil is via the soil microbial carbon pump (MCP). The microorganisms include both fungi and bacteria. (C) Functional overview of the SOM.
Figure 1. SOM-related research hotspots (A), C-cycle model (B) and functions (C). (A) Keyword clustering map in the field of organic amendments and SOM during 2020–2024. The larger the yellow field, the higher the relevance of the keyword’s occurrence. (B) Schematic diagram of SOM metabolic processes involved in C cycling in soil ecosystems. Primary production inputs (organic amendments, straw residues, etc.) to the soil occur through two pathways—in vivo turnover (red lines) and ex vivo (black lines) modification. The majority of the stable C pool in soil is via the soil microbial carbon pump (MCP). The microorganisms include both fungi and bacteria. (C) Functional overview of the SOM.
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Figure 2. Mobility of heavy metal ions from organic amendments in soil ecosystems. Organic matter amendments such as animal manure and daily wastes are composted and applied to the soil. Then, the heavy metal ions are adsorbed on the surface in the soil particles and SOM particles, and some of them are absorbed by the plants in the soil solution, while a small number of them undergo leaching. Soil pH is also critical for the mobility of metal ions. In addition, metal ions in the soil solution also form compounds with chemical speciation (like chloride ions, etc.).
Figure 2. Mobility of heavy metal ions from organic amendments in soil ecosystems. Organic matter amendments such as animal manure and daily wastes are composted and applied to the soil. Then, the heavy metal ions are adsorbed on the surface in the soil particles and SOM particles, and some of them are absorbed by the plants in the soil solution, while a small number of them undergo leaching. Soil pH is also critical for the mobility of metal ions. In addition, metal ions in the soil solution also form compounds with chemical speciation (like chloride ions, etc.).
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Figure 3. Illustration of greenhouse gas (GHG) emissions from organic amendments. In farming practices, livestock produce large amounts of CH4, and manure/urine and fresh plant straw can be composted after anaerobic digestion. During this process, soil microorganisms use NH4+ and NO3− to release greenhouse gases such as NO, CH4, and N2 after nitrification. Some of the NO3− that passes through surface runoff or leaching produces N2O in denitrification.
Figure 3. Illustration of greenhouse gas (GHG) emissions from organic amendments. In farming practices, livestock produce large amounts of CH4, and manure/urine and fresh plant straw can be composted after anaerobic digestion. During this process, soil microorganisms use NH4+ and NO3− to release greenhouse gases such as NO, CH4, and N2 after nitrification. Some of the NO3− that passes through surface runoff or leaching produces N2O in denitrification.
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Xu, J.; Li, Y.; Li, L. A Comprehensive Review of the Effects of Organic Amendments on Soil Health and Fertility: Mechanisms, Greenhouse Gas Emissions, and Implications for Sustainable Agriculture. Agronomy 2025, 15, 2705. https://doi.org/10.3390/agronomy15122705

AMA Style

Xu J, Li Y, Li L. A Comprehensive Review of the Effects of Organic Amendments on Soil Health and Fertility: Mechanisms, Greenhouse Gas Emissions, and Implications for Sustainable Agriculture. Agronomy. 2025; 15(12):2705. https://doi.org/10.3390/agronomy15122705

Chicago/Turabian Style

Xu, Jing, Yangyang Li, and Lingling Li. 2025. "A Comprehensive Review of the Effects of Organic Amendments on Soil Health and Fertility: Mechanisms, Greenhouse Gas Emissions, and Implications for Sustainable Agriculture" Agronomy 15, no. 12: 2705. https://doi.org/10.3390/agronomy15122705

APA Style

Xu, J., Li, Y., & Li, L. (2025). A Comprehensive Review of the Effects of Organic Amendments on Soil Health and Fertility: Mechanisms, Greenhouse Gas Emissions, and Implications for Sustainable Agriculture. Agronomy, 15(12), 2705. https://doi.org/10.3390/agronomy15122705

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