"Red and Black" of Organic Fertilizer: The Hidden Cost of Fertile Soil

Organic Fertilizers are rich in organic matter, which plays a crucial role in soil fertility levels, soil heavy metal availability, and greenhouse gas emissions. Organic fertilizers can significantly improve soil physical properties, alleviate soil acidification, increase nutrient availability, maintain soil nutrient balance, enhance soil chemical and biological characteristics, and optimize soil microbial community structure.
It is generally believed that the application of organic fertilizers can improve soil fertility. However, due to the wide variety and complex composition of organic fertilizers, their transformation process in soil is very complex and takes a long time, which poses uncertain impacts on soil fertility and soil environmental quality.
In recent years, quality issues have emerged in organic fertilizer raw materials and production processes, posing potential negative impacts on agricultural product safety and farmland ecological environment. Therefore, efforts should be made to minimize the environmental risks associated with the application of organic fertilizers in agricultural production.

01 The positive effects of applying organic fertilizer
The impact of organic fertilizer on soil physical properties
Applying organic fertilizer significantly improves soil physical properties. After being applied to the soil, organic fertilizer undergoes a mineralization process, completely decomposing organic matter into CO2, H2O, and mineral nutrients (N, P, K, Ca, etc.). After a certain period of time, if conditions such as material, water, and heat are suitable, the humification process gradually develops, producing humic substances (humus, humic acid, fulvic acid, etc.) that improve soil physicochemical properties. This, in turn, enhances the soil's ability to retain water and nutrients, improving the availability of soil nutrients and water. Relevant experiments have shown that both decomposed pig manure and crushed straw can reduce the bulk density of dryland plough layer soil, increase total porosity, and physical clay content. The application of organic fertilizer increases the number of large and medium-sized pores in the soil. The number of large and medium-sized pores in organic fertilizer treatments is 1.45~1.68 and 1.22~1.43 times that of chemical fertilizer treatments and no-fertilizer treatments, respectively. Additionally, the application of organic fertilizer increases the pH, EC value, and CEC content of tobacco-planting soil.
Soil aggregates are formed through the coagulation and cementation of colloids and primary soil particles. The quantity and spatial arrangement of aggregates of different sizes determine the distribution and continuity of soil pores, which in turn determine the hydraulic properties of soil, affecting soil aeration, water permeability, water retention, and tillability. Applying organic fertilizer is beneficial for the formation and maintenance of large aggregates. Organic matter is the main cementing agent for soil aggregates. In addition to increasing organic matter, the decomposition of organic fertilizer residues stimulates microbial activity, forming fungal hyphae and increasing soluble sugar content. These substances can cement soil particles to form large aggregates.
Through three consecutive years of field experiments, it was found that different application rates of organic fertilizer can significantly increase the proportion of large aggregates in the soil and improve the structure of aggregates in the soil. The appropriate fertilization rate is around 60 t·hm-2. Research has shown that organic fertilizer is conducive to increasing the aggregation degree of soil microaggregates, making the proportion of aggregates of different particle sizes more reasonable, and thereby improving the soil's water and nutrient regulation capacity and fertility level.
Soil acidification has become a key factor limiting soil production potential and a challenge affecting agricultural development. Organic fertilizers play a positive role in ameliorating soil acidification. Important factors accelerating soil acidification include NH₄+ nitrification, nitrate leaching, and the imbalance in cation and anion absorption by crops in the soil. Humic acid produced during the decomposition of organic fertilizers is a weak acid containing many acidic functional groups, which can enhance soil acid-base buffering capacity through acid base dissociation and amine protonation. A 26-year fertilizer location experiment found that applying urea alone reduces soil pH and acid-base buffering capacity. Although increasing the application of organic fertilizer also reduces soil pH, it maintains or even enhances soil acid-base buffering capacity. Additionally, since soil acidification often accompanies the depletion of base ions and nutrient leaching, applying organic fertilizer can strengthen the soil's ability to retain water and nutrients, reduce soil nutrient leaching, and effectively alleviate the degree of soil and groundwater acidification.

The impact of organic fertilizer on soil nutrients
Research indicates that long-term application of organic fertilizer can increase the soil's nutrient supply capacity, accelerate the activation of soil nutrients by humic acid, enhance soil nutrient content, maintain a balanced supply of available nutrients, and significantly improve and enrich soil fertility.
Under the same fertilization conditions, organic fertilizer plays an extremely significant role in increasing soil nutrition and improving soil organic matter quality.
Soil organic matter is an important component of the solid phase of soil, playing a crucial role in nutrient supply and preventing nutrient leaching. The application of organic fertilizer introduces a large amount of organic matter into the soil, and the decomposition of organic matter produces organic acids. These acids can promote the weathering and nutrient release of minerals through acid dissolution, and enhance the availability of mineral nutrients through complexation (chelation). Organic fertilizer also increases soil active carbon and active nitrogen components, enhancing the activity of microorganisms and enzymes related to nutrient transformation, thereby improving soil available nutrients. Relevant experiments have confirmed that applying chemical fertilizer, organic fertilizer, or a combination of organic and inorganic fertilizers can significantly increase the total nitrogen content in soil, and with the increase in the proportion of organic fertilizer input, the total nitrogen content in soil shows an increasing trend. Hartl et al. (2003) found through a 5-year field experiment that the available potassium content in soil treated with compost increased by an average of 26% compared to soil without compost.
Research indicates that in soils treated with a combination of organic and inorganic fertilizers, the higher-activity organic phosphorus components (both active and moderately active organic phosphorus) are more abundant than those in soils without fertilizer treatment or treated with chemical fertilizer alone, which is beneficial for the stable supply of available phosphorus in the soil. After being applied to the soil, phosphorus fertilizer is easily adsorbed, forming insoluble phosphates, which affects the release of phosphorus. Increasing the application of organic fertilizer can facilitate the conversion of organic phosphorus to inorganic phosphorus, and by coating oxides such as Fe, Al, and Ca with humus, it can reduce the adsorption of phosphorus, thereby enhancing the availability of phosphorus. Additionally, the adsorption of organic matter on available nutrients can reduce their loss. Therefore, the combination of organic and inorganic fertilizers not only ensures a sufficient amount of available nutrients but also reduces nutrient loss and improves fertilizer utilization efficiency.
Organic fertilizers not only contain macronutrients such as N, P, and K essential for crop growth but also contain micronutrients like S, Mg, Cu, Zn, Fe, Mn, Mo, and B. The input of trace elements from organic fertilizers into farmland is significantly higher than that from chemical fertilizers, and their effective content is much greater than that in the soil. Organic fertilizers provide the majority of trace element supplementation in farmland, and soils treated with long-term organic fertilization generally do not lack trace elements. The impact of organic fertilizers on soil trace elements varies depending on the type of organic fertilizer. Related studies have found that the application of chemical fertilizers alone reduces the content of available B, Fe, Zn, and Cu in the soil, while the combination of chemical fertilizers with cow manure or crop straw mitigates the decline in trace elements, especially when cow manure is used in combination, which significantly increases the content of available Zn, B, and Mn. Research indicates that the application of sheep manure has the greatest effect on increasing soil Fe and Mn content, while cow manure has the most pronounced effect on increasing soil Zn and Cu content. Organic fertilizers can also affect the availability of soil trace elements by altering soil physicochemical properties, such as pH, other elements, and organic matter.

The impact of organic fertilizer on soil microbial characteristics
Organic fertilizer not only directly increases soil available nutrients and improves soil physicochemical properties, but also has a significant impact on soil biological and biochemical characteristics, which are more sensitive and rapid in response to soil environmental changes and fertilization management.  
Soil microorganisms play a crucial role in the decomposition of organic matter and nutrient cycling. The quantity and activity of soil microorganisms are significant indicators of soil fertility and quality. Organic fertilizers provide the carbon, nitrogen, and energy sources required for soil microbial activities, improve the physicochemical properties of the soil microecological environment, promote microbial growth and reproduction, increase microbial quantity and activity, and optimize the structure and function of soil microbial communities. Some scholars attribute changes in soil microbial communities to the long-term application of organic fertilizers, which increases soil organic matter content and soil fertility. Organic matter is considered a major factor affecting soil microbial dynamics. Studies have found that replacing part of chemical fertilizers with organic fertilizers can significantly increase the number of bacteria, actinomycetes, and pseudomonads in cotton field soils, but inhibit fungal growth and alter the structural composition of soil microbial communities. Research indicates that organic fertilizers can significantly increase the diversity of soil bacterial communities, with soil pH being a key factor. Additionally, organic fertilizers positively promote the mineralization of soil microbial biomass C and N, as well as soil respiration, and show a highly significant positive correlation with soil organic matter levels.
Soil enzymes are a special class of substances with biochemical catalytic properties, participating in many important biochemical processes in soil. Soil enzymes are important indicators of soil fertility and crucial factors in the transformation of soil organic nutrients. Soil enzymes are closely related to soil microorganisms, and factors that affect soil microorganisms inevitably affect soil enzyme activity.  
The application of organic fertilizer brings a large number of microorganisms and enzymes into the soil, and increases the content of soil organic matter and microbial biomass C and N, providing a large amount of nutrients and enzymatic substrates for soil microorganisms, promoting their growth and reproduction, and enhancing enzyme activity. In addition, most soil enzymes are in an adsorbed state, physically and chemically adsorbed on soil organic matter and mineral particles, or coexisted with humic substances in a complexed form. The application of organic fertilizer increases the content of organic matter and humus in the soil, providing abundant binding sites or protective sites for soil enzymes, which is conducive to enhancing soil enzyme activity. Studies have found that the activities of soil invertase, urease, and neutral phosphatase in long-term organic fertilizer treatments are significantly higher than those in chemical fertilizer treatments; another study found that under the condition of combined application with chemical fertilizers and other nutrients, the urease activity in soil treated with organic fertilizer increased by 6.2% to 22.1%, phosphatase activity increased by 7.9% to 27.9%, and catalase activity increased by 45.1% to 65.2%.

02 Potential environmental risks of applying organic fertilizer
The impact of organic fertilizer on soil heavy metals
Since the 20th century, many countries have successively encountered issues of heavy metal accumulation and exceeding standards in farmland soil, severely impacting crop production and posing threats to human health through the food chain. When the content of heavy metals in soil exceeds the background value, excessive deposition leads to soil heavy metal pollution, which has become increasingly severe in recent years.
Organic fertilizers, as high-quality sources of nutrient input for farmland, not only provide crops with essential macronutrients and micronutrients for growth, but also contain varying levels of heavy metal elements. Especially organic fertilizers made from livestock manure, when applied, inevitably increase soil heavy metal content and the risk of crop absorption and accumulation of heavy metals.  
Sampling and testing of different organic fertilizers from 14 provinces (cities) across the country revealed that the heavy metal content in sludge and pig manure is higher than that in Organic Waste from other sources. Specifically, the average content of Cr, Pb, Ni, and Hg in sludge is relatively high, while the average content of Zn, Cu, Cd, and As in pig manure is relatively high. Chicken manure generally contains higher levels of Cr. Related research has found that the application of crop straw, green manure, and pig manure significantly increases the total and available contents of Cu, Zn, and Cd in soil, with pig manure having the most significant impact. Some scholars have discovered through long-term location experiments in rice paddies that long-term application of organic fertilizers increases the risk of heavy metal pollution in paddy soil. Medium and high-level organic fertilizer treatments significantly increase the total, available, and activated contents of Zn, Cu, Cd, and Pb. Similar research has found that as the years pass, the content of Cu, Zn, Pb, and Cd in soil treated with chemical fertilizers and organic fertilizers shows an increasing trend, with the most significant impact observed in soils treated solely with organic fertilizers and in soils treated with a combination of organic and chemical fertilizers.
Total heavy metal content is a commonly used indicator for evaluating the degree of soil heavy metal pollution, whereas the availability of heavy metals is primarily related to their chemical forms. Organic fertilizers are one of the most important organic substances that affect the chemical behavior of heavy metals in soil, by altering factors such as pH, Eh, and organic matter, which in turn influence the chemical forms of heavy metals in soil.
However, opinions vary on the impact of applying organic fertilizer on the availability of heavy metals in soil. On one hand, the application of organic fertilizer can enhance the availability of heavy metals in soil. This is because organic fertilizers themselves carry heavy metals with strong bioavailability, and the organic acids released during the decomposition of organic matter have an activating effect on strongly bound heavy metals in soil, thereby increasing the availability of heavy metals. On the other hand, organic matter contains a large number of functional groups, which have strong adsorption capabilities for heavy metal ions. The humic acid produced through the decomposition of humus can form complexes (chelates) with heavy metal ions, immobilizing the heavy metals, reducing their availability, and mitigating their toxicity to crops. Studies have shown that the complexes formed between humic acid and metal ions in humic acid are insoluble, which can significantly inhibit plants from absorbing heavy metal elements from the soil. When the ratio of fulvic acid to metal ions is greater than 2, it is conducive to the formation of water-soluble complexes, while a ratio less than 2 tends to form insoluble complexes. Therefore, whether the application of organic fertilizer promotes plant absorption of heavy metals from the soil depends on the above two aspects.
In addition, the impact of organic fertilizers on soil heavy metal availability is also related to the type of organic fertilizer and soil type. For soils contaminated with heavy metals, long-term application of organic fertilizers can cause heavy metals in the soil to complex with organic matter and accumulate on the soil surface, reducing the availability of heavy metals and decreasing crop absorption of heavy metals. Some scholars have studied the effects of different organic fertilizers on the forms of cadmium in cadmium-contaminated soils and found that the application of organic fertilizers promotes the transformation of cadmium in the soil from exchangeable and carbonate-bound forms to iron-manganese oxide-bound, organic-bound, and residual forms, that is, from bioavailability to non-bioavailability.

The impact of organic fertilizer on soil greenhouse gases
Soil greenhouse gases primarily consist of CO2, CH4, N2O, etc., and they exert a significant impact on global warming. Farmland stands as one of the primary sources of greenhouse gas emissions. The emission of greenhouse gases from farmland is influenced not only by natural factors such as temperature, precipitation, light, and soil texture, but also by agricultural management practices like fertilization. Investigating the effects of fertilization on soil greenhouse gases has emerged as a focal point in recent years.
Although organic fertilizers play a positive role in enhancing soil fertility and maintaining soil health, they tend to promote the emission of greenhouse gases from the soil compared to chemical fertilizers.
CO2 is the most important greenhouse gas. Soil CO2 emission flux is influenced by soil physical, chemical, and biological processes, and is related to soil carbon content, nitrogen content, cation exchange capacity, etc. Numerous studies have shown that organic fertilizer and organic-inorganic fertilizer combination can significantly increase CO2 emissions. Firstly, the application of organic fertilizer increases soil organic matter content, enhances the content of soil water-soluble organic carbon and hot water-soluble organic carbon, promotes the production of CO2, and the mineralization and decomposition of active organic carbon also increase soil CO2 emissions. Secondly, the application of organic fertilizer can increase soil total porosity, promoting the diffusion and release of CO2 in the soil. In addition, organic fertilizer increases the number and activity of soil microorganisms, enhancing soil respiration, which in turn affects surface CO2 flux.
The production and emission of CH4 are the result of methanogenic bacteria acting under strict anaerobic conditions. Adequate methanogenic substrates and a suitable growth environment for methanogenic bacteria are prerequisites for CH4 production. CH4 is mainly emitted from paddy fields. The application of organic fertilizer in paddy fields not only directly increases the carbon sink of the soil but also alters the availability of carbon and nitrogen sources for methanogenic bacteria in the soil, making them easier to be utilized by methanogenic bacteria. The activity of methanogenic bacteria is closely related to environmental conditions such as soil temperature and pH. Most methanogenic bacteria prefer to live in neutral or weakly alkaline environments, with an optimal temperature range of 35~37°C. The application of organic fertilizer can improve the thermal characteristics of the soil, allowing it to absorb more radiant energy and increase soil temperature. For acidic soil, it can also increase soil pH, providing favorable growth conditions for methanogenic bacteria and promoting the production of more CH4. Additionally, CH4 is easily oxidized by oxidizing bacteria under aerobic conditions, reducing the emission of CH4 from the soil. The decomposition of organic matter lowers the soil redox potential (Eh), leading to an increase in CH4 emissions.
The warming effect of N2O is 296 to 310 times that of CO2, and it can remain in the atmosphere for a long time, participating in many photochemical reactions and damaging the ozone layer. The nitrification and denitrification processes involving soil microorganisms are the main pathways for generating N2O. Studies have shown that the generation and emission of soil N2O are influenced by both carbon and nitrogen substrates. When organic fertilizers are applied at a carbon equivalent rate, N2O emissions are mainly constrained by the level of exogenous nitrogen supply; when applied at a nitrogen equivalent rate, N2O emissions are mainly constrained by the level of exogenous carbon supply. Therefore, organic fertilizers not only provide the energy required for microbial activities but also affect microbial activities by altering the soil C/N ratio, thereby influencing the generation and emission of N2O, a product of nitrification and denitrification reactions. Generally, the optimal C/N ratio for soil microorganisms is (25~30)/1. If the C/N ratio exceeds (25~30)/1, organic matter decomposition slows down, microbial activity weakens, and N2O emissions are suppressed; conversely, it promotes N2O emissions.
Therefore, different types of organic fertilizers have varying impacts on soil N2O emissions. Studies have found that, under the same nitrogen input, the N2O emission flux from soil with wheat straw returned to the field is higher than that from soil treated with chemical fertilizer alone. Compared to chemical fertilizer, the application of straw and pig manure significantly reduces N2O emissions. Currently, there is no unified conclusion on the impact of organic fertilizer application on soil N2O emissions, and the mechanism of its impact requires further in-depth research.

03 Conclusion and Outlook
In summary, organic fertilizers possess unparalleled advantages over chemical fertilizers in enhancing soil physicochemical properties, maintaining soil nutrient balance, and boosting soil microbial activity. However, the application of organic fertilizers (primarily sourced from livestock manure) entails risks of increasing soil heavy metal content and crop absorption and accumulation of heavy metals. Additionally, it can lead to an increase in greenhouse gas emissions (such as CO₂ and CH₄) from the soil, exacerbating the greenhouse effect. Therefore, it is recommended to strengthen the management of organic fertilizers in agricultural production, strictly regulate the production standards of organic fertilizers, select high-quality organic fertilizers (with low levels of heavy metals and persistent pollutants), and establish supporting technologies for organic fertilizer application. Optimize fertilization methods by applying fertilizer at appropriate times and locations, such as combining organic and inorganic fertilizers, to minimize the environmental risks associated with organic fertilizer application.
At present, organic fertilizer resources are showing a continuous growth trend. However, we should not blindly pursue "organic" or excessively apply organic fertilizer. We should face up to the advantages and disadvantages of organic and chemical fertilizers, adhere to the principles of agricultural modernization and sustainable development, and especially establish new understandings and concepts of organic fertilizer in the context of chemical fertilizer being the mainstay.