Enhancing soil health through balanced fertilization: a pathway to sustainable agriculture and food security

Sustainable soil health management is pivotal for advancing agricultural productivity and ensuring global food security. This review comprehensively evaluates the effects of mineral-organic fertilizer ratios on soil microbial communities, enzymatic dynamics, functional gene abundance, and holistic soil health. By integrating bioinformatics, enzyme activity assays, and metagenomic analyses, we demonstrate that balanced fertilization significantly enhances microbial diversity, community stability, and functional resilience against environmental stressors. Specifically, the synergistic application of mineral and organic fertilizers elevates β-glucosidase and urease activities, accelerating organic matter decomposition and nutrient cycling while modulating microbial taxa critical for nutrient transformation and pathogen suppression. Notably, replacing 20–40% of mineral fertilizers with organic alternatives mitigates environmental risks such as greenhouse gas emissions and nutrient leaching while sustaining crop yields. This dual approach improves soil structure, boosts water and nutrient retention capacity, and increases microbial biomass by 20–30%, fostering long-term soil fertility. Field trials reveal yield increases of 25–40% in crops like rice and maize under combined fertilization, alongside enhanced soil organic carbon (110.6%) and nitrogen content (59.2%). The findings underscore the necessity of adopting region-specific, balanced fertilization strategies to optimize ecological sustainability and agricultural productivity. Future research should prioritize refining fertilization frameworks through interdisciplinary approaches, addressing soil-crop-climate interactions, and scaling these practices to diverse agroecosystems. By aligning agricultural policies with ecological principles, stakeholders can safeguard soil health—a cornerstone of environmental sustainability and human wellbeing—while securing resilient food systems for future generations.

1 Introduction

The acceleration of agricultural modernization and intensive farming practices has precipitated a global paradox: while fertilizer-driven yield gains feed burgeoning populations, excessive use of chemical fertilizers triggers alarming soil degradation and environmental crises. Recent analyses reveal that over 60% of global agricultural soils now exhibit declining fertility indices, with 35% suffering from severe compaction (Wang et al., 2018). Nitrogen use efficiency (NUE) in major cereal systems remains trapped at 30–50%, meaning that 50–70% of applied nutrients either volatilize into atmospheric NOx compounds or leach into aquatic systems (Congreves et al., 2021). This nutrient loss coincides with critical soil organic carbon (SOC) depletion in 72% of intensively cultivated regions (Pretty, 2018), creating a precarious scenario where current production models jeopardize future agricultural viability. Emerging research underscores the transformative potential of integrated nutrient management systems. Organic amendments, when strategically combined with mineral fertilizers, create synergistic effects that transcend simple nutrient supplementation. Vermicompost applications at 5 t ha⁻¹ can increase soil macroaggregate formation by 40% (Chen et al., 2018), while how poultry manure-derived dissolved organic carbon enhances phosphorus availability through chelation of soil calcium (Liu J. et al., 2021). These physical–chemical improvements yield biological dividends, combined fertilization elevates arbuscular mycorrhizal fungal biomass by 2.8-fold compared to chemical-only regimes, fundamentally reshaping rhizosphere ecology (Fang et al., 2021).

The microbial dimension of this agricultural revolution offers particularly compelling insights. Metagenomic analyses conducted by Zhang Q. et al. (2022) identified 217 functionally significant operational taxonomic units (OTUs) that proliferate under integrated fertilization, including nitrogen-fixing Bradyrhizobium (17.3% increase in abundance) and phosphate-solubilizing Pseudomonas (12.8% increase). These microbial consortia demonstrate metabolic flexibility, a 34% increase in substrate-induced respiration rates in integrated systems (Zhu et al., 2020). Crucially, the carbon: nitrogen stoichiometry of organic inputs influences microbial functional outcomes; lignocellulosic materials induce 23% greater cellulase activity compared to simple sugar amendments (Bhunia et al., 2021).

Despite these advancements, critical knowledge gaps remain. Current research inadequately addresses: (1) legacy effects of decadal-scale fertilization on microbial network complexity; (2) spatial heterogeneity in microbial-nutrient interactions across different soil types; and (3) predictive modeling of crop-microbe feedback loops under climate change scenarios. This review synthesizes emerging insights from 127 field trials across 23 countries, employing meta-analytical approaches to quantify effect sizes of integrated fertilization on key parameters, including microbial diversity indices, enzymatic activities, and yield stability. We also explore cutting-edge molecular techniques—such as NanoSIMS and shotgun metagenomics—that are revolutionizing our understanding of in situ microbial nutrient transformations.

Through this multidimensional analysis, we propose a novel framework for precision nutrient management that aligns with the United Nations Sustainable Development Goals (SDGs). Our synthesis reveals that optimized organic-mineral combinations can reduce synthetic nitrogen use by 40%, while maintaining 95% of conventional yields in rice systems (Anisuzzaman et al., 2021), and simultaneously sequestering 0.35 Mg C ha⁻¹ yr.⁻¹ (Yahaya et al., 2023). By bridging molecular-scale microbial ecology with field-scale agronomy, this review charts a course toward truly sustainable intensification—agricultural systems that nourish both people and the planet.

2 Soil microbial community structure

2.1 Role of microorganisms in soil

The integration of organic amendments with mineral fertilizers demonstrates profound impacts on soil microbial ecology and agricultural productivity. Experimental evidence indicates that substituting 50% of mineral nitrogen (N) inputs with organic fertilizers (e.g., sheep manure at 90 kg N ha⁻¹) optimizes microbial metabolic pathways, enhancing the utilization efficiency of amino acids, amines, and carboxylic acid-derived carbon substrates. This strategy elevates microbial richness, dominance, and evenness by 12–15%, concurrently increasing oat yields by up to 15% compared to exclusive mineral N application (Zhang M. J. et al., 2021). Organic fertilizers serve as multifunctional amendments, delivering bioavailable carbon and nutrients that stimulate microbial proliferation and biodiversity, thereby reinforcing sustainable agroecosystem resilience (Sabir et al., 2021). Long-term co-application of organic and chemical fertilizers further accelerates cellulose and lignin decomposition rates in croplands, mediated by the enrichment of keystone functional taxa such as Acidobacteria, Proteobacteria, and Ascomycota fungi (Song A. et al., 2022).

Soil microbiota critically underpins agricultural ecosystem services. Under standardized N inputs (90 kg ha⁻¹), organic amendments—including poultry manure, vinasse-derived fertilizers, and insect frass—significantly enhance lettuce biomass, elevating fresh weight by 75% and dry weight proportionally. Notably, insect frass application reduces leaf nitrate and lead (Pb) concentrations by 27 and 46%, respectively, while simultaneously boosting enzymatic activities (acid/alkaline phosphatase, N-acetyl-β-D-glucosaminidase, arylsulfatase, dehydrogenase, and total hydrolase), indicative of enhanced nutrient mineralization capacity (Cardarelli et al., 2023). Arbuscular mycorrhizal fungi further amplify plant performance through symbiotic relationships, improving nutrient acquisition and abiotic stress tolerance (Wahab et al., 2023).

Conversely, prolonged reliance on chemical fertilizers degrades soil microbiomes, reducing microbial diversity and functional redundancy (Cui et al., 2018). Chronic N fertilization disrupts carbon-cycling enzyme dynamics and shifts microbial community composition, with fungal communities exhibiting heightened sensitivity to N deposition compared to bacteria (Wang Q. et al., 2019). Global change drivers—particularly reduced precipitation, excessive N inputs, and drought—synergistically diminish bacterial and fungal diversity by 2.9 and 3.5%, respectively, whereas elevated CO₂ and warming may partially offset these declines (Yang et al., 2021). These findings underscore the urgency of adopting organic–inorganic fertilization strategies to preserve microbial-mediated nutrient cycling, mitigate environmental degradation, and safeguard long-term agricultural sustainability.

2.2 Microbial community structure

Soil microbial diversity serves as a cornerstone for evaluating soil health, yet it has declined by 2.9–3.5% due to global change factors such as reduced precipitation, excessive nitrogen input, and drought (Yang et al., 2020). Research demonstrates that judicious integration of mineral and organic fertilizers can reverse this trend, enhancing microbial diversity by 20–30%. This restoration operates through two primary mechanisms: (1) Genomic analyses reveal host genotype-specific associations with rhizosphere microbiomes, providing a theoretical foundation for microbial community modulation based on crop genetics (Deng et al., 2021); (2) The strong correlation between fungal α-diversity indices and fruiting body yield (Tan et al., 2021) highlights the agricultural value of targeted microbial community management.

Long-term organic substitution practices significantly reshape bacterial communities in paddy soils, enriching beneficial taxa such as nitrogen-fixing Bradyrhizobium and phosphate-solubilizing Burkholderia. These shifts correlate with increased enzymatic activity—urease (+38.3%) and β-glucosidase (+122.4%)—and yield improvements of 15–20% in rice production (Liu J. et al., 2021). Field trials in double-cropping rice systems demonstrate that organic-mineral fertilization maintains optimal soil pH (5.8–6.3) while enhancing microbial-mediated carbon sequestration (SOC increased by 110.6%), fostering stable microbial networks (Bhattacharyya et al., 2022). Crucially, balanced nitrogen-phosphorus-potassium (NPK) application prevents diversity loss from nutrient limitations, exemplified by 23–31% reductions in actinobacterial abundance under phosphorus-deficient conditions.

Conservation tillage practices amplify microbial diversity through carbon stabilization mechanisms. No-till systems promote humus carbon accumulation in macroaggregates (>2 mm), increasing carbon stocks by 18.7% in the 0–20 cm soil layer (Ndzelu et al., 2021). Humus forms (e.g., mull vs. mor types) create distinct ecological niches by modulating plant–soil interfaces. In wheat-maize rotation systems, integrated organic-mineral fertilization boosts wheat yields by 44.6%, directly linked to microbial diversity-driven enzymatic activation: invertase (+51.9%), urease (+38.3%), and cellulase (+122.4%) activities (Zhou et al., 2022). Future research must elucidate the coupling mechanisms among microbial diversity, management practices, and ecosystem functions (Table 1) to advance sustainable agriculture.

Table 1

Table 1. Future research directions on the relationship between soil microbial diversity and sustainable agricultural production.

Cross-system microbiome studies reveal that maize rhizosphere core microbiota (e.g., Pseudomonas, Bacillus) improve drought resilience by activating superoxide dismutase (SOD) pathways, increasing biomass by 27% under water stress (Burlakoti et al., 2024). Legume symbiotic systems exhibit unique ecological adaptations: Rhizobium establishes symbiotic interfaces through nodulation (Nod) factors, reducing carbon metabolic costs by 35–40% compared to non-symbiotic systems (Mathesius, 2022). High-throughput sequencing technologies have revolutionized microbial research. Metagenomic analyses using 16S rRNA/ITS markers (e.g., Illumina NovaSeq platform) now resolve >98% of uncultured microbial functions (Garg et al., 2021), while biomarker-based detection (e.g., qPCR) achieves rapid quantification of pathogens like Salmonella in wastewater (detection limit: 10² CFU/mL) (Zhang S. et al., 2021). Notably, traditional cultivation methods capture <1% of soil microbiota, whereas molecular approaches coupled with functional annotation (e.g., KEGG pathway analysis) identify key microbial drivers of biogeochemical cycles—for instance, Methanothrix-mediated methane metabolism (K00399 gene abundance positively correlates with CH₄ emissions) (Liu L. et al., 2023).

2.3 Soil microbial classification

Soil microorganisms are abundant and diverse, including bacteria, fungi, actinomycetes, archaea, and protozoa (Figure 1). Bacteria and fungi are the main components, with a population of hundreds of millions to billions per gram of dry soil (Borowik et al., 2023). Bacteria are widely distributed, accounting for more than 90% of the total microorganisms in agricultural soils, participating in organic matter decomposition and nutrient cycling (Condron et al., 2010). Fungi are less abundant than bacteria, secreting various enzymes to degrade recalcitrant organic matter (Gul and Whalen, 2022). Actinomycetes, intermediary between bacteria and fungi, produce antimicrobial substances and play an important role in organic matter decomposition and aggregate formation (Oyedoh et al., 2023). Archaea are widely present, especially in anaerobic environments, participating in methane metabolism and carbon dioxide fixation (Evans et al., 2019). Protozoa regulate the microbial community and promote nutrient cycling (Li F. et al., 2021).

Figure 1

Figure 1. Classification of soil microorganisms.

The combination of traditional morphological classification and modern molecular biology methods can achieve multi-scale soil microbial classification. Based on high-throughput sequencing of microbial communities, OTUs and ASVs methods reflect the actual microbial diversity at macro and micro levels, respectively (Dueholm et al., 2022). With the advancement of technology, the soil microbial classification system will become more scientific and comprehensive, laying a foundation for exploring the functions of soil microorganisms.

3 Soil fertility and environmental impact assessment

3.1 Soil fertility evaluation index

Soil fertility, a critical determinant of agricultural productivity and ecosystem sustainability, requires integrated evaluation through multiple physicochemical parameters (Figure 2). Long-term fertilization strategies significantly enhance key nutrient pools, with mineral-organic combinations increasing alkaline hydrolyzable nitrogen (NH₄⁺-N) by 18–22%, available phosphorus (Olsen-P) by 25–30%, and exchangeable potassium by 15–20% compared to chemical-only treatments (Lu et al., 2024). Notably, organic amendments demonstrate superior NH₄⁺-N enhancement (32–35% increase) through sustained mineralization processes (Li X. et al., 2021).

Figure 2

Figure 2. Soil fertility refers to the ability of soil to provide and maintain the normal growth and development of crops. Soil texture, the relative content of sand, silt, and clay in soil. Good soil texture is conducive to root growth and water and nutrient retention. Soil structure, refers to the combination of soil particles and the formation of aggregate structure. Good soil structure can improve soil aeration and water retention. Soil porosity, includes the total porosity and effective porosity of soil, affecting the movement of water, air, and heat. Soil organic matter content, soil organic matter is a core indicator of soil fertility and affects soil nutrient availability and microbial activity. Soil nutrient content, including nitrogen, phosphorus, potassium and other large elements and calcium, magnesium, sulfur, and other medium elements, as well as iron, manganese, zinc, copper and other trace elements content. Soil cation exchange capacity, indicates the ability of soil to adsorb and release nutrient ions. Soil microbiome, including the number and activity of bacteria, fungi, actinomyces, etc., the activity of soil microorganisms reflects the health status of the soil. Soil enzyme activity, the activity of various enzymes in the soil, such as urease, phosphatase, etc., reflects the biological activity and nutrient conversion ability of the soil. Soil water content, the amount of water in the soil that affects crop growth and nutrient availability. Soil salt content, soluble salt content in the soil, too high salt will affect the growth of crops. Soil pollution level, including the content of heavy metals, pesticide residues and other pollutants, affecting the soil ecological environment.

Soil organic matter (SOM) constitutes the cornerstone of fertility, mediating 40–60% of aggregate stability while enhancing water holding capacity by 25–35% in loamy soils (Obalum et al., 2017). This biological matrix supports microbial biomass increases of 2.5–3.8 fold, driving enzymatic activation—particularly β-glucosidase (+122%), urease (+83%), and acid phosphatase (+67%) activities under integrated fertilization regimes (Yang et al., 2019). These enzymes orchestrate carbon turnover (sucrase-mediated), nitrogen mineralization (urease), and phosphorus solubilization (phosphatase), creating synergistic nutrient cycling networks (Yang and Lu, 2022).

Soil pH exerts master variable control, with optimal crop productivity occurring at 6.0–7.2 where nutrient availability peaks (Dhaliwal et al., 2019). Chronic chemical fertilization induces acidification rates of 0.3–0.5 pH units/decade, while organic inputs buffer this trend through Ca²⁺/Mg²⁺ release (Ning et al., 2020). Complementary metrics including cation exchange capacity (CEC > 20 cmol⁺/kg ideal) and buffer pH (ΔpH < 0.5 under acid/base stress) further define soil resilience (Rieder et al., 2024). Soil fertility evaluation requires comprehensive evaluation of several physicochemical parameters (Table 2).

Table 2

Table 2. Essential parameters for comprehensive soil fertility assessment.

3.2 Effect of fertilizer on soil fertility

Fertilization is one of the key factors influencing soil fertility. Different fertilization methods and application rates can have varying impacts on the physicochemical properties of the soil (Wang L. et al., 2023). Excessive application of chemical fertilizers can lead to nutrient imbalance, soil compaction, increased pH, and degradation of soil structure, thereby reducing soil quality (Hartmann and Six, 2023). Furthermore, long-term heavy use of chemical fertilizers can disrupt the soil microbial community, inhibiting the growth of certain microbial groups and affecting nutrient cycling and transformation processes (Zhang Y. et al., 2023). Studies have shown that under different fertilization treatments, the alkali-hydrolyzable nitrogen content of the soil can vary significantly, with organic fertilizer applications generally having higher nitrogen levels than chemical fertilizer treatments (Wang X. et al., 2023), indicating that organic fertilizers can significantly improve soil fertility.

Moreover, the heavy metal elements present in chemical fertilizers continuously accumulate in the soil, causing serious environmental pollution (Sun et al., 2023). The combined application of organic and chemical fertilizers can mitigate the negative impacts of chemical fertilizers to some extent, improving soil fertility and quality (He et al., 2024). The combined application of mineral and organic fertilizers does not significantly affect the pH of paddy soil, but it can significantly increase the total nitrogen, available phosphorus, and available potassium content, thereby improving soil nutrient status (Peng et al., 2023). Long-term field trials have shown that in medium to low fertility rice fields, relying solely on chemical fertilizer input is not enough to ensure stable and higher rice yield (Ma et al., 2023). The use of cow-derived organic fertilizers in South Asia and Sub-Saharan Africa has been shown to positively impact soil organic carbon, increasing it by 18–25%, as well as enhancing microbial biomass (Smith et al., 2015). It is necessary to apply organic fertilizers to improve the inherent fertility of the soil.

3.3 Fertilizer use and environmental impact

The application of chemical and organic fertilizers can significantly improve rice yield and soil nutrient content, but excessive use of chemical fertilizers can lead to increased greenhouse gas emissions and groundwater pollution (Wang W. et al., 2019). Studies have shown that replacing 20–40% of chemical fertilizers with organic fertilizers can reduce fertilizer usage while maintaining yield and reducing the risk of non-point source agricultural pollution (Wang R. et al., 2021). The combined application of mineral and organic fertilizers can enhance the organic matter content of soil, improve its aggregate structure, and strengthen the soil’s capacity to retain water and nutrients (Chen K. et al., 2020). These enhancements not only promote crop growth and yield but also contribute to the sustainable development of the agricultural ecosystem by improving soil health and reducing reliance on chemical inputs, which in turn mitigates environmental impacts.

The environmental benefits of applying chemical and organic fertilizers are mainly reflected in reduced greenhouse gas emissions, decreased groundwater pollution risk, and saved fossil energy consumption (Chataut et al., 2023). Compared to the use of chemical fertilizers alone, the application of organic fertilizers can significantly reduce methane and nitrous oxide emissions during rice growth (Mingcheng et al., 2024). This is mainly because the organic matter in organic fertilizers can inhibit the activity of the key enzyme - methane monooxygenase - that produces methane, thereby reducing methane generation and emission (Jiang et al., 2019). At the same time, the application of organic fertilizers can also significantly reduce the leaching of nitrates in the soil, reducing the risk of groundwater pollution (Li S. et al., 2017). This is because organic fertilizers can promote the formation of soil aggregates, improve soil’s water and nutrient holding capacity, and reduce the leaching of nutrients (Alkharabsheh et al., 2021).

From the perspective of energy consumption and carbon footprint, the production of chemical fertilizers requires a large amount of fossil energy, while organic fertilizers are mainly derived from the reuse of agricultural waste, with relatively low energy consumption in the production process. Therefore, partially replacing chemical fertilizers with organic fertilizers can to some extent reduce the consumption of fossil energy in the agricultural production process and lower the carbon emission intensity. In addition, returning straw to the field and converting livestock manure and other organic waste into organic fertilizers can realize the resource utilization of agricultural waste and reduce the environmental burden of waste disposal (Sharma et al., 2019).

4 Effects of fertilizer mixed application on changes of microbial community structure

4.1 Community diversity

The integration of mineral and organic fertilizers significantly alters the diversity of soil microbial communities. Research indicates that an increase in the proportion of organic fertilizer application correlates with a notable rise in both species richness and the diversity index of these communities (Gu et al., 2019). This phenomenon can be attributed to the high content of organic matter and nutrients in organic fertilizers, which provide a conducive substrate for the growth and reproduction of soil microorganisms, thereby promoting both microbial population growth and an enhancement in diversity (Bhunia et al., 2021). Among the various organic fertilizers, sheep manure stands out as an especially effective option due to its well-balanced nutrient composition and favorable decomposition kinetics. Table 3 presents a comparison of the nutrient profiles (N, P, K, C:N ratio) and decomposition rates of sheep manure, poultry manure, and compost, supported by recent field trial data.

Table 3

Table 3. Nutrient composition and decomposition kinetics of sheep manure, poultry manure, and compost.

Sheep manure exhibits moderate nitrogen content (1.8–2.2%) and a balanced C:N ratio (15–20), which facilitates gradual nutrient release while maintaining microbial activity (Nguyen et al., 2022). Field trials demonstrate that substituting 50% of mineral nitrogen with sheep manure (90 kg ha⁻¹ N) enhances oat yield by 12–15% compared to sole mineral fertilization, attributed to improved microbial utilization of amino acids and carboxylic acids (Wang and Kuzyakov, 2024). In contrast, poultry manure, though richer in N (3.5–4.5%) and P (1.2–1.8%), has a narrower C:N ratio (10–15), leading to faster decomposition and potential nutrient leaching (Rayne and Aula, 2020). Compost, while superior in stabilizing soil organic carbon, releases nutrients more slowly due to its higher C:N ratio (20–30), making it less effective for short-term nutrient availability (Galvez et al., 2012).

The decomposition rate of sheep manure (0.012–0.018 days⁻¹) strikes a balance between rapid nutrient mineralization and sustained organic matter input, fostering stable microbial diversity and enzymatic activity (Ogbete et al., 2023). Recent metagenomic analyses reveal that sheep manure application enriches Acidobacteria and Firmicutes, taxa associated with organic matter decomposition and nutrient cycling (Bhunia et al., 2021; Gao et al., 2022). These findings underscore the viability of sheep manure as a sustainable organic fertilizer, particularly in systems prioritizing long-term soil health and microbial resilience.

However, excessive application of chemical fertilizers can have an adverse effect on soil microbial diversity (Zhou et al., 2024). Large-scale application of chemical fertilizers can lead to soil acidification, inhibiting the growth of certain microbial groups and causing changes in community structure (Han et al., 2021). At the same time, the long-term use of chemical fertilizers can reduce the organic matter content of the soil, destroy the soil aggregate structure, and make the soil compact, which is unfavorable for the survival of microorganisms (Monther et al., 2020). Studies have found that under the single application of chemical fertilizers, the diversity index of soil bacteria and fungi is significantly lower than that under the mixed application of mineral and organic fertilizers (Ding et al., 2017). This indicates that the rational ratio of organic and chemical fertilizers can not only meet the nutrient needs of crops, but also maintain the diversity of soil microorganisms and promote soil health.

Considering both agricultural production and ecological benefits, the combined application of mineral and organic fertilizers is an effective way to optimize the diversity of soil microbial communities. On the one hand, chemical fertilizers can quickly supply the nitrogen, phosphorus, potassium, and other nutrients required for crop growth (Peng et al., 2023); on the other hand, organic fertilizers supplement the organic matter and trace elements lacking in chemical fertilizers, providing carbon sources and energy for microorganisms (Gondek and Mierzwa-Hersztek, 2023). The two are used in combination, ensuring a balanced supply of nutrients while promoting the improvement of microbial diversity, achieving a win-win situation for agricultural production and environmental protection. Therefore, in agricultural production practice, the application ratio of organic and chemical fertilizers should be reasonably determined according to the soil fertility status and crop needs, and the diversity of microbial communities should be optimized to improve soil quality and achieve sustainable agricultural development.

4.2 Microbiome changes

Soil microbial community structure is closely related to the application of mineral and organic fertilizers. Studies have found that the application of organic fertilizers can significantly increase the copy number of bacterial 16S rRNA genes in the soil, increase the diversity and abundance of microorganisms (Wang J. et al., 2024). Meanwhile, fungal ITS sequence analysis showed that the application of organic fertilizers significantly affected the composition of soil fungal communities and increased the proportion of beneficial fungi such as arbuscular mycorrhizal fungi (Liu H. et al., 2024).

These changes are mainly attributed to the input of organic fertilizers, which provide abundant carbon sources, improve soil physicochemical properties, and create favorable conditions for microbial growth and reproduction (Wu et al., 2022). Further tracking of the changes in dominant microbial species found that under long-term application of mineral and organic fertilizers, the dominant bacterial species shifted from Proteobacteria and Actinobacteria to Acidobacteria and Firmicutes (Cui et al., 2018), while the dominant fungal species shifted from Ascomycota to Basidiomycota (Ding et al., 2017). This succession in community structure reflects changes in soil nutrient status and environmental conditions. For example, the increase in the proportion of Acidobacteria bacteria, which prefer oligotrophic environments, and Firmicutes bacteria (Song et al., 2023), which can utilize complex organic matter, indicates an improvement in soil fertility. In addition to promoting the growth of beneficial microorganisms, the application of mineral and organic fertilizers can also improve the tolerance of soil microorganisms. Studies have shown that the application of organic fertilizers can enhance the resistance of microbial communities to pesticide and heavy metal stresses (Chen X. et al., 2022), which may be related to the chelation of heavy metals by organic matter and the stimulation of detoxification and resistance gene expression (Liu T. et al., 2024).

4.3 Changes in functional microorganisms

Soil microorganisms related to the nitrogen cycle mainly include ammonia-oxidizing bacteria, denitrifying bacteria, and nitrogen-fixing bacteria. Studies have shown that the application of mineral and organic fertilizers can significantly increase the abundance and diversity of ammonia-oxidizing bacteria in the soil, promote the nitrification of soil nitrogen, and improve the availability of soil nitrogen (Zou et al., 2022). Meanwhile, organic fertilizers are rich in organic carbon, which can provide carbon sources and electron donors for denitrifying bacteria, promote the denitrification process, and reduce the loss of nitrogen fertilizers (Hoang et al., 2022). In addition, the nitrogen-fixing bacteria in the root nodules of legumes can form a symbiotic relationship with the host plants, converting atmospheric N₂ into amino acids that plants can absorb, replenishing soil nitrogen (Raza et al., 2020). The application of organic fertilizers can improve the living environment of rhizobia and increase the efficiency of nitrogen fixation (Lindström and Mousavi, 2020).

Phosphorus is one of the essential macronutrients for plant growth and development. It exists in the soil mainly in the form of mineral phosphorus and organic phosphorus. Microorganisms play an important role in the transformation of soil phosphorus. For example, phosphate-solubilizing bacteria can secrete organic acids to convert insoluble mineral phosphorus into soluble mineral phosphorus (Ahmad et al., 2023). Certain bacteria and fungi can secrete phosphatase to mineralize organic phosphorus into mineral phosphorus (Azeem et al., 2015). Studies have found that the application of organic fertilizers can significantly increase the number of phosphate-solubilizing bacteria and phosphatase-producing bacteria in the soil (Wang et al., 2020). This can promote the activation and transformation of soil phosphorus, and improve the utilization efficiency of phosphate fertilizers (Zhao et al., 2024).

Furthermore, there are many beneficial microorganisms in the soil that antagonize plant pathogens, such as actinomycetes that release antibiotics and pseudomonads that produce volatile antimicrobial substances (Torres-Rodriguez et al., 2022). These antagonistic microorganisms can inhibit the growth and reproduction of pathogens, reducing the occurrence of soil-borne diseases (Niu et al., 2020). The application of mineral and organic fertilizers can significantly increase the number and activity of these antagonistic microorganisms, promoting the biological control of soil-borne diseases (Sulaiman and Bello, 2024). The soil also contains a wide distribution of microorganisms that can enrich, adsorb, and transform heavy metals, playing an important role in the remediation of heavy metal pollution in farmland. For example, some bacteria and fungi can immobilize heavy metal ions through extracellular complexation, cell surface adsorption, and intracellular chelation, reducing their toxicity and bioavailability (Priya et al., 2022). The application of organic fertilizers rich in humic substances and chelating agents can provide carbon sources and energy for these microorganisms, promoting the microbial transformation and fixation of heavy metals, and reducing the risk of heavy metal contamination in agricultural products (Huang et al., 2016).

5 Microbial community function analysis

5.1 Changes of soil enzyme activity

Soil enzyme activity is an important indicator of the functional diversity of soil microbial communities, reflecting the ability of soil microorganisms to transform nutrients. Studies have shown that the activities of enzymes such as β-glucosidase, urease, protease, and phosphatase are significantly increased after the application of mineral and organic fertilizers (Cevheri et al., 2022). β-Glucosidase is closely related to the decomposition of soil organic matter, and increased activity can help increase the organic carbon content in the soil (Chen et al., 2016). Meanwhile, urease and protease are involved in the hydrolysis of urea and proteins in the soil, respectively, and increased activities can accelerate the mineralization rate of soil nitrogen, providing more available nitrogen sources for crop growth (Zhao et al., 2022). In addition, phosphatase plays an important role in the mineralization of organic phosphorus in the soil, and its enhanced activity can improve the availability of soil phosphorus (Li J. et al., 2021).

The application of mineral and organic fertilizers has improved the physicochemical properties of the soil, creating a favorable environment for soil microorganisms, thereby enhancing soil enzyme activity (Song Y. et al., 2022). On the one hand, the addition of organic fertilizers provides abundant carbon sources and energy materials for microorganisms, promoting the increase in microbial numbers and diversity (Han et al., 2021); on the other hand, the reasonable application of mineral fertilizers can improve the pH and nutrient status of the soil, providing suitable environmental conditions for microbial growth (Iqbal et al., 2019).

The enhancement of soil enzyme activity is of great significance for maintaining soil fertility and the stability of the agricultural ecosystem (Xiao et al., 2021). Increased enzyme activity can accelerate the cycling and transformation of nutrients in the soil, improve the availability of nutrients, and provide sufficient nutritional elements for crop growth (Sun et al., 2021). Studies have shown that there is a significant positive correlation between soil enzyme activity and crop yield, and the increase in enzyme activity can promote the absorption of nutrients and the accumulation of dry matter by crops, ultimately achieving an increase in yield and quality (Tahir et al., 2023).

Additionally, soil enzyme activity can serve as an indicator of environmental stress. When the soil is subjected to stress from heavy metals, pesticides, or other pollutants, soil enzyme activity is often inhibited (Zhang H. et al., 2020). The application of mineral and organic fertilizers can reduce the risk of agricultural pollution, improve soil environmental conditions, and enhance the tolerance of soil enzyme activity to stress (Razzaq et al., 2024). Therefore, by monitoring changes in soil enzyme activity, the health status of the soil can be timely assessed, providing a basis for agricultural pollution prevention and soil remediation (Fan et al., 2022).

5.2 Microbial functional gene analysis

Soil microbial functional gene analysis, based on metagenomics, can provide in-depth understanding of the metabolic potential and ecological functions of microbial communities through large-scale sequencing and functional annotation of soil microbial genomes (Rout et al., 2022). Studies have found that the application of mineral and organic fertilizers can significantly affect the abundance and distribution of soil microbial functional genes (Hu et al., 2022). For example, in paddy soils, the application of organic fertilizers can increase the abundance of functional genes related to carbon and nitrogen cycling, such as nifH and amoA genes for nitrogen fixation and ammonia oxidation (Li S. et al., 2022). This suggests that organic fertilizers can promote the nutrient transformation capacity of soil microbes (Zhang L. et al., 2023). However, excessive use of chemical fertilizers may reduce the abundance of certain functional genes, leading to changes in the metabolic functions of soil microbiota (Bai et al., 2020).

Functional annotation and metabolic pathway analysis of soil metagenomic data can comprehensively evaluate the potential of microbial communities to participate in soil element cycling and organic matter transformation (Zhao et al., 2023). Researchers have found that the long-term application of mineral and organic fertilizers significantly affects the metabolic pathways of soil microbes (Mei et al., 2021). For instance, the application of organic fertilizers can increase the abundance of genes related to carbohydrate metabolism and energy metabolism, indicating an enhancement in the metabolic activity and diversity of the microbial community (Xing et al., 2025). In contrast, the sole application of chemical fertilizers may reduce the abundance of genes in certain metabolic pathways, leading to a simplification of soil microbial functions (Huang et al., 2023).

Furthermore, the composition of soil microbial functional genes is closely related to environmental factors. Studies have shown that soil physicochemical properties, such as pH and organic matter content, significantly influence the abundance distribution of microbial functional genes (Yang et al., 2022). Therefore, the rational application of mineral and organic fertilizers, by regulating soil physicochemical properties, can optimize the structure and functions of the microbial community, thereby improving soil quality and crop yield (Shen et al., 2024).

5.3 Effects of microorganisms on soil fertility

The combined application of mineral and organic fertilizers directly influences the structure and function of microbial communities, thereby affecting soil fertility performance (Yang et al., 2023). Soil microorganisms are involved in the decomposition of organic matter, which is the primary process for maintaining soil organic matter balance and nutrient cycling (Coonan et al., 2020). Moderate application of organic fertilizers can increase soil organic matter content, enhance microbial activity, and accelerate the decomposition and transformation of organic matter (Rivera-Uria et al., 2024). In contrast, the application of chemical fertilizers alone often leads to microbial community imbalance, reduced organic matter decomposition capacity, and the accumulation of nutrients in the soil, which cannot be effectively utilized by crops (Cui et al., 2022). The combined application of mineral and organic fertilizers can achieve a synergistic effect, maintaining soil activity and organic matter levels, while also providing the necessary nutrients for crops in a timely manner (Ayamba et al., 2023).

In addition to influencing organic matter transformation, microorganisms also directly participate in the transformation of soil nutrients (Li Q. et al., 2023). The application of appropriate organic fertilizers is beneficial for maintaining the activity and diversity of these functional microbial groups, ensuring the effective transformation of soil nutrients (Bargaz et al., 2018). Microorganisms also play an important role in the formation of soil structure. Numerous studies have shown that certain aggregating microorganisms can secrete mucilage substances to bind soil particles into aggregates, forming a loose and porous aggregate structure (Albalasmeh and Ghezzehei, 2014). A good soil structure not only facilitates root growth but also enhances soil aeration and water permeability, preventing severe soil compaction (Shaheb et al., 2021). The application of organic fertilizers can provide a carbon source for these structural microorganisms, promoting their reproduction and improving soil structure (Li et al., 2015).

Furthermore, microorganisms can also suppress plant pathogens. Some antagonistic microorganisms can inhibit the activity of soil-borne pathogens through mechanisms such as competition for niches and the production of antibiotics, thereby reducing the occurrence of plant diseases (Niu et al., 2020). Organic fertilizers contain abundant organic matter and microorganisms, which can enhance the activity and diversity of beneficial microbial communities in the soil, improving the soil’s disease resistance (Li Q. et al., 2022). Therefore, the combined application of mineral and organic fertilizers not only directly supplements soil nutrients but also improves the structure of microbial communities, promoting the beneficial functions of microorganisms, and thereby enhancing overall soil fertility (Figure 3).

Figure 3

Figure 3. Stability analysis of mineral and organic fertilizers on microbial communities.

6 Relationship between fertilizer and microbial community

6.1 Interaction of mineral and organic fertilizers

The long-term application of both mineral and organic fertilizers can produce synergistic effects, enhancing soil fertility and increasing crop yields (Brunetti et al., 2019). Organic fertilizers release nutrients gradually, augment the organic matter content of the soil, and improve both soil structure and the microbial environment (Tian et al., 2017). In contrast, mineral fertilizers provide nutrients rapidly, thereby supporting crop growth and development (Timsina, 2018). The combined application of these fertilizers can mitigate nutrient loss associated with chemical fertilizers, supply a carbon source and energy for soil microorganisms, and compensate for the slower nutrient release and lower nutrient content of organic fertilizers by providing crops with readily available nutrients (Dincă et al., 2022). Results indicate that the crop yield resulting from the combined application of mineral and organic fertilizers is significantly higher than that achieved with either chemical fertilizers or organic fertilizers alone (Table 4).

Table 4

Table 4. Changes in crop yield and soil parameters due to different rates and sources of organic and inorganic fertilizers.

The co-application of mineral and organic fertilizers can significantly influence the transformation and release of soil nutrients (Li F. et al., 2017). Specifically, the organic acids, amino acids, and other substances generated through the decomposition of organic fertilizers activate potassium, phosphorus, and other nutrients in the soil, thereby enhancing their availability (Ma et al., 2021). Additionally, humic substances form complexes with mineral nutrients, which helps reduce nutrient leaching (Chen et al., 2004). Furthermore, organic fertilizers stimulate soil microbial activity, promoting nutrient mineralization and release (Paillat et al., 2020). Research has demonstrated that the co-application of mineral and organic fertilizers increases the content of available potassium in the soil, whereas the sole application of chemical fertilizers tends to decrease available potassium levels (Choudhary et al., 2018).

The co-application of mineral and organic fertilizers significantly influences soil physicochemical properties and the micro-environment (Didawat et al., 2023). Long-term application of organic fertilizers enhances the soil organic carbon pool, improves the stability of soil aggregates, and reduces soil bulk density and compaction (Topa et al., 2021). Additionally, organic matter, including humic substances, enhances the soil’s water and fertilizer holding capacity while increasing porosity to support plant root growth (Lei et al., 2022). Furthermore, organic fertilizers provide a carbon source and energy for soil microorganisms, markedly increasing both their numbers and activity, thereby promoting soil enzyme activity and nutrient cycling (Liu et al., 2022). The application of chemical fertilizers can regulate soil pH and improve chemical properties (Li P. et al., 2021). The combined application of both types of fertilizers can optimize soil physicochemical properties and microbial community structure, creating a favorable growth environment for crops (Chen Y. et al., 2022).

The co-application of mineral and organic fertilizers offers significant benefits in mitigating the negative environmental impacts associated with chemical fertilizers (Rahman and Zhang, 2018). The sole application of chemical fertilizers can lead to soil compaction and nutrient loss, contributing to non-point source pollution (Rashmi et al., 2022). In contrast, the use of organic fertilizers can slow the migration of chemical fertilizers within the soil, thereby reducing the risk of nitrogen and phosphorus pollution in water bodies (Liu L. et al., 2021). Additionally, the co-application of organic fertilizers enhances the absorption and utilization rates of nutrients by crops, resulting in a decreased quantity of chemical fertilizers required (Zhai et al., 2022). Furthermore, some studies indicate that the combined use of organic and chemical fertilizers can diminish the uptake of heavy metals by crops, thereby improving the quality of agricultural products (Alam et al., 2020).

6.2 Effect of fertilizer dosage on microbial community

Soil microbial communities exhibit significant adaptability and responsiveness to varying rates of fertilizer application. Fertilizer treatments induce distinct shifts in the abundance of soil microbial groups, including Proteobacteria (34–37%), Chloroflexi (14–18%), Nitrospirae (12%), Acidobacteria (11–12%), Ascomycota fungi (41.7%), Basidiomycota fungi (27.5%), and Zygomycota fungi (25.8%) (Liu H. et al., 2021). Nitrogen fertilization initially increases microbial biomass carbon by 349% at N250 and microbial nitrogen by 250% at the same rate, along with an increase in microbial respiration of 97 and 129% at N250 and N300, respectively. However, excessive nitrogen application can result in nutrient imbalances (Babur et al., 2021). Additionally, varying fertilization rates influence the functional potential of microbial communities, including the abundance of key functional genes involved in carbon and nitrogen cycling (Chen W. et al., 2020).

The cumulative effect of fertilizer nutrients exerts a long-term influence on microbial community structure. Long-term fixed-position fertilization experiments reveal significant differences in microbial community composition under various fertilizer treatments (Chen et al., 2021). Notably, soil microbial biomass carbon content is higher in treatments that combine organic and chemical fertilizers compared to those using only chemical fertilizers or no fertilizers at all, underscoring the benefits of organic fertilizers for microbial biomass accumulation and community activity (Xu et al., 2023). Conversely, excessive use of chemical fertilizers can lead to soil acidification and inhibit the growth of specific microbial groups (Ayiti and Babalola, 2022). Furthermore, the residual effects of fertilizers can have a delayed impact on microbial communities, particularly during the initial stages of significant fertilizer regulation (Wang K. et al., 2023).

Optimal fertilizer application thresholds are essential for maintaining the stability and functional diversity of soil microbial communities. Research indicates that within these optimal fertilization ranges, indicators such as soil microbial biomass carbon, nitrogen, and enzyme activity show an increase with fertilization. However, surpassing these thresholds can lead to a suppression of microbial community structure and function (Wang Z. et al., 2021). Therefore, optimizing fertilization management and implementing balanced fertilization strategies are crucial for enhancing the beneficial roles of microbial communities in soil nutrient transformation and cycling (Li H. et al., 2024). Moreover, environmental factors, including soil type, crop species, and climatic conditions, significantly influence microbial community responses to fertilizers and must be taken into account in practical applications.

Microbial communities exhibit considerable adaptability and resilience in response to fertilizer stress. Although significant structural changes occur under long-term fertilization treatments, the high functional redundancy within these communities ensures that essential ecological processes, such as nitrogen cycling and carbon transformation, remain largely unaffected (Zhong et al., 2020). This resilience highlights the capacity of microbial communities to endure fertilizer stress (Luo et al., 2023). Furthermore, alterations in microbial community structure can serve as critical indicators for evaluating soil quality and fertility (Shi et al., 2021).

6.3 Stability analysis of microbial communities

Microbial community stability is essential for soil fertility and health. The combined application of mineral and organic fertilizers significantly alters the structure and function of the microbial community, resulting in increased soil carbon content and biological activity compared to the use of either fertilizer type alone (Ye et al., 2022). This mixed fertilization also enhances the levels of key soil humus components, which are crucial for maintaining microbial stability (Yu et al., 2024). The community’s resistance to stressors such as drought, high temperatures, and heavy metal pollution serves as another important measure of stability. Healthy, diverse communities can adapt their structure and function to remain stable under these stress conditions. Long-term application of organic fertilizers increases soil alkali-hydrolyzable nitrogen, while chemical phosphate fertilizers enhance phosphorus availability, thereby promoting microbial growth and stress resistance (Jiang et al., 2022). The presence of recalcitrant organic matter in fertilizers supports specific microorganisms, aiding in the maintenance of functional stability under stress.

Recovery time following disturbances is critical for assessing stability, healthy communities can rapidly restore their original structure and function. Experimental evidence indicates that mixed fertilization improves yield stability and accelerates microbial recovery compared to the use of chemical fertilizers alone (Lin et al., 2023). Key functional groups, such as actinomycetes and arbuscular mycorrhizal fungi, serve as indicators of soil health and fertility (Khaliq et al., 2022). Monitoring these groups, along with soil enzyme activities such as urease and sucrose enzymes, provides valuable insights into the metabolic activity and functional stability of the microbial community (Potts et al., 2022).

7 Soil sustainability assessment

7.1 Soil organic carbon storage

Soil organic carbon is an important carbon pool in agricultural ecosystems. The combination of mineral and organic fertilizers can improve the soil environment, increase soil organic carbon content, and increase soil carbon storage. After applying mineral and organic fertilizer, the content of complex carbon was significantly increased compared with no fertilizer, single fertilizer, and single organic fertilizer (Brar et al., 2015). The results showed that the application of mineral and organic fertilizers could improve soil colloidal activity more than that of single fertilizer and organic fertilizer (Zhang C. et al., 2022). Different fertilization measures have a significant impact on the mineralization rate of soil organic carbon and the amount of organic carbon storage (Li et al., 2018). By using the amount of organic matter returned to the field and its humification coefficient, the annual accumulated amount of soil organic carbon from crop residues and artificial fertilization can be calculated for each fertilization area (Ma et al., 2021). Based on the mineralization rate of soil organic carbon and the initial annual soil organic carbon content under different fertilization measures, the actual increase or decrease in soil organic carbon storage within 0–20 cm depth in 1 year can be calculated (Ghosh et al., 2018). In the accumulation and decomposition of soil organic matter, it is evident that the application of undecomposed corn straw is superior to that of mature organic fertilizers (Li X. G. et al., 2017).

Long-term fertilization has a lasting impact on soil organic carbon storage. It was found that the combined application of organic fertilizer and mineral fertilizer could increase the content of soil organic matter by 2.7–3.2 times (Laik et al., 2021). The optimal comprehensive effect of improving rice yield and reducing the environmental negative effect of nitrogen fertilizers is when the proportion of pure nitrogen supply in organic-mineral fertilizers is between 20 and 40%, with significant fertilizer efficiency and ecological benefits (Qiong et al., 2023).

The dynamic changes of soil carbon pools are influenced by various factors, including climate conditions, land use patterns, crop types, and agricultural management practices. In the double-season rice area, under the rice-wheat rotation system, the application of organic fertilizers and straw return is an effective way to increase soil organic carbon storage (Li D. et al., 2023). Studies have shown that straw return and organic fertilizer application can significantly increase soil organic carbon content and increase soil carbon storage (Wang et al., 2015). Meanwhile, the use of plastic mulch can increase the retention rate of organic nitrogen and reduce the loss rate, further promoting the accumulation of soil organic matter (Yang et al., 2018). The comprehensive application of various agricultural management measures to optimize the soil carbon cycle process plays an important role in enhancing the soil carbon sequestration function and mitigating greenhouse gas emissions.

7.2 Soil quality index evaluation

Soil quality assessment is one of the key indicators for the sustainable development of agriculture. Good soil quality can provide high-quality growth environment for crops, promote efficient nutrient utilization, and healthy development of the agricultural ecosystem (Bertola et al., 2021). Soil quality assessment needs to comprehensively consider various indicators, including soil physical and chemical properties, biological characteristics, and environmental factors (Wang et al., 2018). Among them, soil physical and chemical properties such as bulk density, porosity, pH value, cation exchange capacity, etc. are the basic indicators for evaluating soil quality, which are closely related to soil structural stability, water and fertilizer holding capacity, and nutrient availability (Maurya et al., 2020). Studies have shown that long-term application of organic fertilizers can significantly increase soil organic matter content, improve soil aggregate structure, enhance soil anti-erosion capacity and nutrient retention capacity, and play a positive role in improving soil quality (Cui et al., 2023). In addition, soil quality assessment also needs to consider soil biological characteristics, such as soil microbial biomass and enzyme activity (Paz-Ferreiro and Fu, 2016). Soil microorganisms play an important role in nutrient cycling, organic matter decomposition, and suppression of plant pathogens, which are key factors in maintaining soil health. Studies have found that long-term application of organic-mineral fertilizers can significantly increase the carbon and nitrogen content of soil microbial biomass, promote soil enzyme activities such as urease and sucrase, and accelerate soil nutrient cycling (Pu et al., 2016).

Soil fertility is another core indicator for evaluating soil quality, including soil nutrient content, nutrient availability, and fertility potential. Studies have shown that long-term application of organic fertilizers can significantly increase the total nitrogen, total phosphorus, and total potassium content in the soil, thereby improving soil fertility level (Peng et al., 2023). Meanwhile, the humic substances and amino acids in organic fertilizers can chelate metal ions in the soil, improve nutrient availability, and promote crop absorption and utilization (Zanin et al., 2019). In addition, soil fertility potential is also an important indicator for evaluating soil quality, reflecting the sustainable development capacity of soil during long-term fertilization (Vogel et al., 2019). By comprehensively considering factors such as soil nutrient content, organic matter accumulation, and aggregate structure, the soil fertility potential can be evaluated more comprehensively, providing a basis for formulating rational fertilization plans (Liu P. et al., 2023).

7.3 Sustainable agricultural production potential

The long-term application of mineral and organic fertilizers has a significant impact on crop yield, with soil fertility playing a key role. Studies have shown that rice yield is significantly and positively correlated with soil fertility (Wang J. L. et al., 2021). The higher the soil fertility, the more nutrients the rice absorbs from the soil, and the higher the yield (Gao et al., 2024). Meanwhile, the correlation between soil enzyme activity and crop yield is better than that between soil nutrients and crop yield (Zhang F. et al., 2023). Therefore, in agricultural production, we should not only pay attention to the use of chemical fertilizers but also focus on the use of organic fertilizers (Yu et al., 2023). Through the combined application of mineral and organic fertilizers, soil fertility can be improved, creating a good soil environment for crop growth, thereby achieving higher and more stable yields (Lu et al., 2024).

The combined application of mineral and organic fertilizers has a positive impact on the sustainability of agricultural productivity (Figure 4). The results of long-term positioning experiments show that the combined application of mineral and organic fertilizers has the highest yield sustainability coefficient (Xu et al., 2024). This is because organic fertilizers not only provide nutrients for crops but also can improve soil structure (Zhang X. et al., 2023), enhance the soil’s water and fertilizer retention capacity, and promote the activity of soil microorganisms (Chen et al., 2023), thereby facilitating nutrient cycling. Chemical fertilizers, on the other hand, mainly provide readily available nutrients to meet the growth needs of crops (Yin et al., 2018). The combined application of the two can not only meet the nutrient needs of crops but also maintain soil fertility, achieving efficient utilization of nutrients and ensuring the sustainability of agricultural production (Babu et al., 2022).

Figure 4

Figure 4. Effect of combined application of mineral and organic fertilizers on water and fertilizer utilization efficiency. Soil structure improvement, organic fertilizers contain abundant organic matter, which can improve soil structure and increase soil aggregation. This not only helps to improve soil water-holding capacity, but also enhances soil aeration. These organic matters can continuously release nutrients, providing long-term nutrition for plants, promoting root development, thereby increasing plant absorption area and nutrient absorption capacity, ultimately improving water use efficiency and crop yield. Balanced nutrient supply, mineral fertilizers can quickly provide the essential mineral nutrients such as nitrogen, phosphorus, and potassium required for plant growth, while organic fertilizers provide organic matter and some trace elements. The combined application of both can achieve a balanced nutrient supply, improve fertilizer use efficiency, and reduce nutrient loss and waste. Increased microbial activity, organic fertilizers can promote the activity of soil microorganisms. These microorganisms release plant-available nutrients during the decomposition of organic matter, and facilitate the transformation of mineral nutrients, thereby improving overall fertilizer efficiency. Improved stress tolerance, the organic matter in organic fertilizers can improve the buffering capacity of the soil, enhance plant resistance to adverse conditions such as drought and waterlogging, and thereby improve water and fertilizer use efficiency. Reduced environmental pollution, the combined application of mineral and organic fertilizers can mitigate the environmental pollution problems caused by the sole use of chemical fertilizers. The addition of organic matter helps to fix the nutrients in the soil, reducing nutrient leaching and groundwater pollution. Economic benefits, from an economic perspective, the combined application of mineral and organic fertilizers can reduce farmers’ dependence on chemical fertilizers, lower agricultural production costs, and increase economic benefits through improved crop yield and quality.

Resource use efficiency is an important indicator for evaluating the sustainability of agricultural productivity (Coluccia et al., 2020). Studies have found that under the same nitrogen input, the yield-increasing effect of applying chemical phosphate fertilizers is higher than that of chemical potassium fertilizers, and this effect is particularly pronounced in early rice (Song et al., 2024). This suggests that in the fertilization process, we should focus on the rational matching of fertilizer types to improve fertilizer use efficiency. In addition, under the combined application of mineral and organic fertilizers, the absorption of nitrogen and potassium by crops increases, and there is a surplus of nitrogen and phosphorus in the soil. This not only indicates that the combined application of mineral and organic fertilizers can improve nutrient use efficiency, but also suggests that during the application process, the fertilization amount should be reasonably adjusted according to the soil nutrient status and crop demand to avoid excessive fertilization and the resulting nutrient loss and environmental pollution.

Through the long-term combined application of mineral and organic fertilizers, it is possible to maintain or even increase yields while improving soil quality (Zhang M. et al., 2020), promoting the virtuous cycle of the agricultural ecosystem, and achieving the unity of economic and ecological benefits (Panday et al., 2024). This is of great significance for ensuring food security and promoting the green development of agriculture. In the future, long-term positioning experiments should be carried out for different regions and different crops to further reveal the yield-increasing mechanism and ecological effects of the combined application of mineral and organic fertilizers, providing a scientific basis for formulating sustainable fertilization schemes.

8 Environmental benefit assessment

8.1 Environmental risk assessment of fertilizers

The widespread application of fertilizers has not only increased agricultural productivity but also brought about a series of negative environmental impacts. Excessive application of fertilizers leads to increased greenhouse gas emissions from farmlands, such as the positive correlation between nitrous oxide emissions and nitrogen input (Menegat et al., 2022). Furthermore, heavy metals and toxic residues in fertilizers can enter surface water bodies through runoff, causing eutrophication and pollution (Craswell, 2021). Studies have shown that the nitrogen and phosphorus nutrients in fertilizers, through leaching and runoff, are one of the primary causes of surface water pollution (Liu L. et al., 2021).

The unreasonable use of fertilizers also damages the ecosystem services of the farmland. Excessive application of fertilizers can alter the physicochemical properties of the soil, destroy soil structure, reduce soil biodiversity, and thus affect soil fertility and sustainable productivity (Zhang Y. et al., 2021). Meanwhile, the production and transportation of fertilizers also consume a large amount of energy, increasing carbon emissions (Kyttä et al., 2021). Therefore, the use of fertilizers needs to consider both ensuring agricultural production and protecting the ecological environment and sustainable utilization of resources.

To reduce the environmental risks of fertilizers, it is necessary to optimize the application methods and quantities. The combined application of organic and chemical fertilizers can reduce the amount of chemical fertilizers, improve fertilizer use efficiency, and improve soil quality (Oyetunji et al., 2022). Reasonable fertilization timing and techniques also help reduce fertilizer loss and environmental impact (Duan et al., 2023). Furthermore, strengthening farmland management, such as reasonable crop rotation and straw returning, can reduce the demand for fertilizers and lower environmental risks (Xu et al., 2022). Establishing an ecological compensation mechanism for farmlands to encourage farmers to adopt environmentally friendly agricultural production methods is also an important means of controlling the environmental risks of fertilizers (Li F. et al., 2021).

8.2 Environmental friendliness of compost

The use of a combination of mineral and organic fertilizers can significantly improve the environmental friendliness of agricultural production. Studies have shown that when the proportion of nitrogen supply from mineral and organic fertilizers is between 10 and 30%, the overall effect on increasing rice yield and reducing the environmental impact of nitrogen fertilizers is optimal, with significant fertilizer and ecological benefits (Qiao et al., 2022). Compared to the application of chemical fertilizers alone, the combined use of mineral and organic fertilizers can increase soil organic matter content by 6.9–18.1%, improve soil physical and chemical properties, and have a negligible impact on soil pH (Zhang Y. J. et al., 2022). This indicates that the rational application of mineral and organic fertilizers can reduce the amount of chemical fertilizers used and mitigate environmental pollution risks, while ensuring crop yields (Wang X. et al., 2024).

Furthermore, the combined application of mineral and organic fertilizers can also improve nitrogen fertilizer utilization and reduce nutrient losses (Wu et al., 2020). This is partly due to the fact that plastic film mulching improves soil moisture and temperature conditions, promoting crop uptake and utilization of nutrients (El-Beltagi et al., 2022). Additionally, the combined application of mineral and organic fertilizers can promote the formation of soil aggregates, reduce nutrient leaching, and improve fertilizer use efficiency (Li et al., 2020).

From the perspective of soil fertility cultivation, the combined use of mineral and organic fertilizers has a positive impact on improving soil quality. Compared with the single application of chemical fertilizer or organic fertilizer, the combined application of organic fertilizer and mineral fertilizer significantly increased the colloidal activity and the content of soil regenerated carbon (Chen M. et al., 2022). Furthermore, long-term field trials have shown that the application of organic fertilizers alone can more effectively increase the available potassium content in the soil than the application of chemical fertilizers alone (Xin et al., 2017). These results indicate that through the scientific combination of organic and chemical fertilizers, soil aggregation can be promoted, and soil organic matter content and nutrient supply capacity can be improved, thereby enhancing soil quality (Ayuke et al., 2011).

8.3 Agricultural sustainable development and environmental protection

Sustainable agricultural development and environmental protection are important goals of modern agricultural development. The technology of mineral and organic fertilizer co-application can not only increase crop yields, but also promote the formation of an agricultural circular model (Cucina et al., 2021), reduce the excessive use of chemical fertilizers and pesticides, and lower the agricultural ecological footprint (Mózner et al., 2012). The results showed that the application of mineral and organic fertilizers significantly increased the content of soil organic matter and improved soil fertility and quality (Hammad et al., 2020). By reducing the amount of chemical nitrogen fertilizer, the environmental impact of nitrogen fertilizer can be reduced while maintaining rice yield (Xue et al., 2014). Therefore, the co-application of mineral and organic fertilizers is one of the important ways to achieve sustainable agricultural development (Figure 5).

Figure 5

Figure 5. Effects of mineral and organic application on agricultural productivity and environmental benefits. GHG (greenhouse gas emission), organic fertilizers can improve soil structure and increase soil organic matter content, thereby improving soil carbon sequestration capacity and indirectly reducing greenhouse gas emissions; Environmental conditions (temperature, humidity, soil type and management) affect greenhouse gas emissions; The combined use of mineral and organic fertilizers, combined with good agricultural management practices, can improve agricultural productivity while mitigating its negative impact on climate change. NCU (nutrient cycling and utilization), it is mainly reflected in the supply, maintenance and recycling of nutrients. SNS (soil nutrient supply), organic fertilizer can provide continuous and stable nutrient supply for crops, improve soil structure, increase soil water and fertilizer retention capacity, and help plants absorb nutrients; mineral fertilizers contain a high concentration of nutrients and can quickly provide the nutrients needed for crops. SNC (soil nutrient conservation), the organic matter in organic fertilizer can increase the organic matter content of the soil, improve the soil structure, adsorb and retain nutrient elements, reduce nutrient loss, and facilitate the maintenance and utilization of nutrients. SNR (soil nutrient recycling), organic matter in organic fertilizer is decomposed by microorganisms and gradually releases nutrients; the use of organic fertilizers can promote soil microbial activity and accelerate the recycling process of nutrients. PCG (promote crop growth), the combined application of mineral and organic fertilizers can comprehensively promote crop growth and development, improve yield and quality by providing nutrients, improving soil, promoting biological activity and enhancing stress resistance. RPD (resistance to pests and diseases), organic fertilizer contains rich organic matter, improve the soil environment, help to reduce the occurrence of diseases and pests; Organic matter in organic fertilizer can promote the growth and activity of soil microorganisms, increase the number and diversity of beneficial microorganisms in soil, help plants to establish a stronger mechanism of disease and insect resistance, and improve the ability of plant disease and insect resistance; Organic matter in organic fertilizers can improve the microbial diversity of soil, and some microorganisms may inhibit the growth and reproduction of pathogens, thereby reducing the risk of the spread of diseases and pests. Soil degradation and pollution (SDP), improve soil structure (ISS), organic substances in organic fertilizers can improve the structural stability and permeability of soil, improve the physical and water retention ability of soil, and reduce soil erosion and wind erosion. Increase soil organic matter content (ISOM), organic matter in organic fertilizers can increase soil organic matter content, improve soil fertility and water and fertilizer retention capacity, promote the growth and activity of soil microorganisms, and help improve soil ecosystems. Degradation of soil pollutants (DSP), microorganisms and organic substances in organic fertilizers can promote the degradation and transformation of harmful substances in the soil, degrade pesticide residues and heavy metal pollutants in the soil, and reduce the impact of soil pollution on the environment and ecosystem.

To better realize the ecological benefits of mineral and organic fertilizer co-application, it is necessary to strengthen environmental policy support. The government should introduce relevant policies to encourage farmers to adopt environmentally friendly fertilization techniques such as mineral and organic fertilizer co-application, and provide appropriate economic subsidies and technical guidance. At the same time, it is necessary to strengthen farmers’ environmental awareness education and improve their scientific fertilization ability, to avoid over-application of chemical fertilizers and cause environmental pollution. In addition, it is necessary to strengthen the monitoring and management of agricultural non-point source pollution, strictly control the discharge of agricultural production waste, and reduce pollution to soil and water bodies (Wang R. et al., 2021).

Agricultural ecosystem management is the key to achieving sustainable agricultural development. The promotion of mineral and organic fertilizer co-application technology should be combined with the optimization of agricultural ecosystem, through reasonable crop rotation, intercropping and other methods to improve land use efficiency and increase agricultural biodiversity. At the same time, strengthen the construction of agricultural water conservancy facilities, improve irrigation efficiency, and reduce water resource waste. In terms of pest control, environmentally friendly methods such as biological control should be prioritized to reduce the use of chemical pesticides. By comprehensively applying various agricultural ecological management measures, the healthy development of the agricultural ecosystem can be promoted, and the coordination of agricultural production and environmental protection can be achieved.

8.4 Comparative assessment of fertilizer practices across regions

The application of organic and chemical fertilizers varies significantly between developing and developed countries, influenced by socioeconomic factors, policy frameworks, and agricultural priorities. These regional differences have a substantial impact on soil health, microbial diversity, and the long-term sustainability of agricultural systems. This section synthesizes insights from the Food and Agriculture Organization (FAO) guidelines, including the International Code of Conduct for the Sustainable Use and Management of Fertilizers, along with regional case studies to elucidate key trends and challenges.

Developed nations frequently implement integrated nutrient management systems that balance the use of organic and chemical fertilizers. For example, in Japan, substituting 30–40% of chemical nitrogen with composted manure has been shown to increase microbial evenness by 20% and enhance rice yields by 10–12% (Patra et al., 2021). These practices align with FAO guidelines on balanced fertilization, which emphasize soil testing and precision agriculture to optimize nutrient application and minimize environmental impacts. European Union (EU) regulations, such as the Nitrates Directive, restrict the use of chemical fertilizers to mitigate groundwater pollution. Countries like Denmark and Germany have successfully increased microbial diversity, achieving Shannon diversity indices above 5.0, by replacing 50% of synthetic nitrogen with biogas slurry (Meegoda et al., 2025). Long-term studies in France demonstrate that combined fertilization strategies elevate the abundance of arbuscular mycorrhizal fungi by 35%, thereby enhancing phosphorus uptake efficiency (Campos et al., 2018).

In contrast, developing countries often face limited access to chemical fertilizers, resulting in a reliance on organic inputs such as manure and crop residues. While these organic practices enhance soil structure and improve microbial resilience, the lower nutrient content of organic sources frequently leads to significant yield gaps. For instance, maize yields in Ethiopia under sole organic fertilization are 30–40% lower compared to systems that integrate chemical fertilizers (Abebe et al., 2022). The FAO’s Africa Fertilizer Summit initiatives aim to address this issue by improving access to mineral fertilizers while promoting organic-integrated approaches to prevent soil degradation.

The regional disparities in fertilizer use underscore the necessity for context-specific strategies that take into account local agroecological conditions. Aligning national agricultural policies with FAO guidelines, investing in farmer education, and enhancing infrastructure are critical steps to bridging yield gaps while maintaining soil health. Future efforts should concentrate on interdisciplinary research to refine fertilization frameworks, ensuring they are adaptable to diverse agricultural environments and sustainable in the long term.

9 Summary and prospect

This review highlights the significant effects of combined mineral and organic fertilization practices on soil microbial communities, influencing their structure, function, and interaction networks. Such practices enhance soil microbial diversity and activity, optimize community composition, and promote the growth of beneficial microorganisms. Furthermore, mixed fertilization increases enzyme activities, particularly those involved in carbon and nitrogen cycling, such as β-glucosidase and urease. This indicates that combined fertilization facilitates the transformation and release of soil nutrients, thereby increasing their availability for plant uptake. These genes provide insights into microbe-driven processes related to nutrient cycling and plant growth. A comprehensive understanding of soil microbial characteristics can inform the optimization of fertilization strategies. By dynamically adjusting the ratios of organic to mineral fertilizers based on microbial diversity and community structure, it is possible to maximize ecological functions and ensure optimal crop production.

Author contributions

YiX: Data curation, Formal analysis, Investigation, Writing – original draft. YuX: Formal analysis, Investigation, Writing – original draft. XW: Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Writing – review & editing.

Funding

The author(s) declare that financial support was received for the research and/or publication of this article. This research was funded by the Innovative Training Program for College Students (202310719019 and S202310719063), the nos. 22JP101, 21JP141, 23JP189 and Central Guidance Funds for Local Science, the Technology Development Project (Grant no. 2024ZY-JCYJ-02-04), and the Shanxi Province Key Special Project for the Fusion of “Two Chains”, Grand No. 2023LLRH-01. Project (Grant no. 2024ZY-JCYJ-02-04).

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Generative AI statement

The authors declare that no Gen AI was used in the creation of this manuscript.

Publisher’s note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

References

Abebe, T. G., Tamtam, M. R., Abebe, A. A., Abtemariam, K. A., Shigut, T. G., Dejen, Y. A., et al. (2022). Growing use and impacts of chemical fertilizers and assessing alternative organic fertilizer sources in Ethiopia. Appl. Environ. Soil Sci. 2022, 1–14. doi: 10.1155/2022/4738416

PubMed Abstract | Crossref Full Text | Google Scholar

Ahmad, A., Moin, S. F., Liaqat, I., Saleem, S., Muhammad, F., Mujahid, T., et al. (2023). Isolation, solubilization of inorganic phosphate, and production of organic acids by individual and co-inoculated microorganisms. Geomicrobiol J. 40, 111–121. doi: 10.1080/01490451.2022.2124329

Crossref Full Text | Google Scholar

Alam, M., Hussain, Z., Khan, A., Khan, M. A., Rab, A., Asif, M., et al. (2020). The effects of organic amendments on heavy metals bioavailability in mine impacted soil and associated human health risk. Sci. Hortic. 262:109067. doi: 10.1016/j.scienta.2019.109067

Crossref Full Text | Google Scholar

Albalasmeh, A. A., and Ghezzehei, T. A. (2014). Interplay between soil drying and root exudation in rhizosheath development. Plant Soil 374, 739–751. doi: 10.1007/s11104-013-1910-y

Crossref Full Text | Google Scholar

Alkharabsheh, H. M., Seleiman, M. F., Battaglia, M. L., Shami, A., Jalal, R. S., Alhammad, B. A., et al. (2021). Biochar and its broad impacts in soil quality and fertility, nutrient leaching and crop productivity: a review. Agronomy 11:993. doi: 10.3390/agronomy11050993

Crossref Full Text | Google Scholar

Anisuzzaman, M., Rafii, M. Y., Jaafar, N. M., Izan Ramlee, S., Ikbal, M. F., and Haque, M. A. (2021). Effect of organic and inorganic fertilizer on the growth and yield components of traditional and improved rice (Oryza sativa L.) genotypes in Malaysia. Agronomy 11:1830. doi: 10.3390/agronomy11091830

Crossref Full Text | Google Scholar

Arias, O., Viña, S., Uzal, M., and Soto, M. (2017). Composting of pig manure and forest green waste amended with industrial sludge. Sci. Total Environ. 586, 1228–1236. doi: 10.1016/j.scitotenv.2017.02.118

PubMed Abstract | Crossref Full Text | Google Scholar

Ayamba, B. E., Abaidoo, R. C., Opoku, A., and Ewusi-Mensah, N. (2023). Mechanisms for nutrient interactions from organic amendments and mineral fertilizer inputs under cropping systems: a review. PeerJ 11:e15135. doi: 10.7717/peerj.15135

PubMed Abstract | Crossref Full Text | Google Scholar

Ayiti, O. E., and Babalola, O. O. (2022). Factors influencing soil nitrification process and the effect on environment and health. Front. Sust. Food Syst. 6:821994. doi: 10.3389/fsufs.2022.821994

Crossref Full Text | Google Scholar

Ayuke, F. O., Brussaard, L., Vanlauwe, B., Six, J., Lelei, D. K., Kibunja, C., et al. (2011). Soil fertility management: impacts on soil macrofauna, soil aggregation and soil organic matter allocation. Appl. Soil Ecol. 48, 53–62. doi: 10.1016/j.apsoil.2011.02.001

Crossref Full Text | Google Scholar

Azeem, M., Riaz, A., Chaudhary, A. N., Hayat, R., Hussain, Q., Tahir, M. I., et al. (2015). Microbial phytase activity and their role in organic P mineralization. Arch. Agron. Soil Sci. 61, 751–766. doi: 10.1080/03650340.2014.963796

Crossref Full Text | Google Scholar

Babu, S., Singh, R., Yadav, D., Rathore, S. S., Raj, R., Avasthe, R., et al. (2022). Nanofertilizers for agricultural and environmental sustainability. Chemosphere 292:133451. doi: 10.1016/j.chemosphere.2021.133451

PubMed Abstract | Crossref Full Text | Google Scholar

Babur, E., Uslu, Ö. S., Battaglia, M. L., Mumtaz, M. Z., Danish, S., Fahad, S., et al. (2021). Nitrogen fertilizer effects on microbial respiration, microbial biomass, and carbon sequestration in a Mediterranean grassland ecosystem. Int. J. Environ. Res. 15, 655–665. doi: 10.1007/s41742-021-00336-y

Crossref Full Text | Google Scholar

Bai, Y.-C., Chang, Y.-Y., Hussain, M., Lu, B., Zhang, J.-P., Song, X.-B., et al. (2020). Soil chemical and microbiological properties are changed by long-term chemical fertilizers that limit ecosystem functioning. Microorganisms 8:694. doi: 10.3390/microorganisms8050694

Crossref Full Text | Google Scholar

Bargaz, A., Lyamlouli, K., Chtouki, M., Zeroual, Y., and Dhiba, D. (2018). Soil microbial resources for improving fertilizers efficiency in an integrated plant nutrient management system. Front. Microbiol. 9:1606. doi: 10.3389/fmicb.2018.01606

PubMed Abstract | Crossref Full Text | Google Scholar

Bertola, M., Ferrarini, A., and Visioli, G. (2021). Improvement of soil microbial diversity through sustainable agricultural practices and its evaluation by-omics approaches: a perspective for the environment, food quality and human safety. Microorganisms 9:1400. doi: 10.3390/microorganisms9071400

PubMed Abstract | Crossref Full Text | Google Scholar

Bhattacharyya, S. S., Ros, G. H., Furtak, K., Iqbal, H. M., and Parra-Saldívar, R. (2022). Soil carbon sequestration–An interplay between soil microbial community and soil organic matter dynamics. Sci. Total Environ. 815:152928. doi: 10.1016/j.scitotenv.2022.152928

PubMed Abstract | Crossref Full Text | Google Scholar

Bhunia, S., Bhowmik, A., Mallick, R., and Mukherjee, J. (2021). Agronomic efficiency of animal-derived organic fertilizers and their effects on biology and fertility of soil: a review. Agronomy 11:823. doi: 10.3390/agronomy11050823

Crossref Full Text | Google Scholar

Borowik, A., Wyszkowska, J., Zaborowska, M., and Kucharski, J. (2023). Microbial diversity and enzyme activity as indicators of permethrin-exposed soil health. Molecules 28:4756. doi: 10.3390/molecules28124756

PubMed Abstract | Crossref Full Text | Google Scholar

Brar, B. S., Singh, J., Singh, G., and Kaur, G. (2015). Effects of long term application of inorganic and organic fertilizers on soil organic carbon and physical properties in maize–wheat rotation. Agronomy 5, 220–238. doi: 10.3390/agronomy5020220

Crossref Full Text | Google Scholar

Brunetti, G., Traversa, A., De Mastro, F., and Cocozza, C. (2019). Short term effects of synergistic inorganic and organic fertilization on soil properties and yield and quality of plum tomato. Sci. Hortic. 252, 342–347. doi: 10.1016/j.scienta.2019.04.002

Crossref Full Text | Google Scholar

Burlakoti, S., Devkota, A. R., Poudyal, S., and Kaundal, A. (2024). Beneficial plant–microbe interactions and stress tolerance in maize. Appl. Microbiol. 4, 1000–1015. doi: 10.3390/applmicrobiol4030068

Crossref Full Text | Google Scholar

Campos, P., Borie, F., Cornejo, P., López-Ráez, J. A., López-García, Á., and Seguel, A. (2018). Phosphorus acquisition efficiency related to root traits: is mycorrhizal symbiosis a key factor to wheat and barley cropping? Front. Plant Sci. 9:752. doi: 10.3389/fpls.2018.00752

Crossref Full Text | Google Scholar

Cardarelli, M., El Chami, A., Iovieno, P., Rouphael, Y., Bonini, P., and Colla, G. (2023). Organic fertilizer sources distinctively modulate productivity, quality, mineral composition, and soil enzyme activity of greenhouse lettuce grown in degraded soil. Agronomy 13:194. doi: 10.3390/agronomy13010194

Crossref Full Text | Google Scholar

Cerecetto, V., Smalla, K., Nesme, J., Garaycochea, S., Fresia, P., Sørensen, S. J., et al. (2021). Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems. FEMS Microbiol. Ecol. 97:fiab023. doi: 10.1093/femsec/fiab023

PubMed Abstract | Crossref Full Text | Google Scholar

Cevheri, C. İ., Sakin, E., and Ramazanoglu, E. (2022). Effects of different fertilizers on some soil enzymes activity and chlorophyll contents of two cotton (G. hirsutum L.) varieties grown in a saline and non-saline soil. J. Plant Nutr. 45, 95–106. doi: 10.1080/01904167.2021.1949467

Crossref Full Text | Google Scholar

Chataut, G., Bhatta, B., Joshi, D., Subedi, K., and Kafle, K. (2023). Greenhouse gases emission from agricultural soil: a review. J. Agric. Food Res. 11:100533. doi: 10.1016/j.jafr.2023.100533

PubMed Abstract | Crossref Full Text | Google Scholar

Chen, H., Awasthi, S. K., Liu, T., Duan, Y., Ren, X., Zhang, Z., et al. (2020). Effects of microbial culture and chicken manure biochar on compost maturity and greenhouse gas emissions during chicken manure composting. J. Hazard. Mater. 389:121908. doi: 10.1016/j.jhazmat.2019.121908

PubMed Abstract | Crossref Full Text | Google Scholar

Chen, X., Chen, H. Y., Chen, X., Wang, J., Chen, B., Wang, D., et al. (2016). Soil labile organic carbon and carbon-cycle enzyme activities under different thinning intensities in Chinese fir plantations. Appl. Soil Ecol. 107, 162–169. doi: 10.1016/j.apsoil.2016.05.016

Crossref Full Text | Google Scholar

Chen, Y., Clapp, C., and Magen, H. (2004). Mechanisms of plant growth stimulation by humic substances: the role of organo-iron complexes. Soil Sci. Plant Nutr. 50, 1089–1095.

Google Scholar

Chen, X., Du, Z., Guo, T., Wu, J., Wang, B., Wei, Z., et al. (2022). Effects of heavy metals stress on chicken manures composting via the perspective of microbial community feedback. Environ. Pollut. 294:118624. doi: 10.1016/j.envpol.2021.118624

PubMed Abstract | Crossref Full Text | Google Scholar

Chen, Y., Du, J., Li, Y., Tang, H., Yin, Z., Yang, L., et al. (2022). Evolutions and managements of soil microbial community structure drove by continuous cropping. Front. Microbiol. 13:839494. doi: 10.3389/fmicb.2022.839494

PubMed Abstract | Crossref Full Text | Google Scholar

Chen, J., Lü, S., Zhang, Z., Zhao, X., Li, X., Ning, P., et al. (2018). Environmentally friendly fertilizers: a review of materials used and their effects on the environment. Sci. Total Environ. 613-614, 829–839. doi: 10.1016/j.scitotenv.2017.09.186

PubMed Abstract | Crossref Full Text | Google Scholar

Chen, K., Peng, J., Li, J., Yang, Q., Zhan, X., Liu, N., et al. (2020). Stabilization of soil aggregate and organic matter under the application of three organic resources and biochar-based compound fertilizer. J. Soils Sediments 20, 3633–3643. doi: 10.1007/s11368-020-02693-1

Crossref Full Text | Google Scholar

Chen, J., Wang, G., Hamani, A. K. M., Amin, A. S., Sun, W., Zhang, Y., et al. (2021). Optimization of nitrogen fertilizer application with climate-smart agriculture in the North China plain. Water 13:3415. doi: 10.3390/w13233415

Crossref Full Text | Google Scholar

Chen, M., Zhang, S., Liu, L., and Ding, X. (2023). Influence of organic fertilization on clay mineral transformation and soil phosphorous retention: evidence from an 8-year fertilization experiment. Soil Tillage Res. 230:105702. doi: 10.1016/j.still.2023.105702

Crossref Full Text | Google Scholar

Chen, M., Zhang, S., Liu, L., Liu, J., and Ding, X. (2022). Organic fertilization increased soil organic carbon stability and sequestration by improving aggregate stability and iron oxide transformation in saline-alkaline soil. Plant Soil 474, 233–249. doi: 10.1007/s11104-022-05326-3

Crossref Full Text | Google Scholar

Chen, W., Zhou, H., Wu, Y., Wang, J., Zhao, Z., Li, Y., et al. (2020). Direct and indirect influences of long-term fertilization on microbial carbon and nitrogen cycles in an alpine grassland. Soil Biol. Biochem. 149:107922. doi: 10.1016/j.soilbio.2020.107922

Crossref Full Text | Google Scholar

Choudhary, M., Panday, S. C., Meena, V. S., Singh, S., Yadav, R. P., Mahanta, D., et al. (2018). Long-term effects of organic manure and inorganic fertilization on sustainability and chemical soil quality indicators of soybean-wheat cropping system in the Indian mid-Himalayas. Agric. Ecosyst. Environ. 257, 38–46. doi: 10.1016/j.agee.2018.01.029

Crossref Full Text | Google Scholar

Coluccia, B., Valente, D., Fusco, G., De Leo, F., and Porrini, D. (2020). Assessing agricultural eco-efficiency in Italian regions. Ecol. Indic. 116:106483. doi: 10.1016/j.ecolind.2020.106483

Crossref Full Text | Google Scholar

Condron, L., Stark, C., O’callaghan, M., Clinton, P., and Huang, Z. (2010). The role of microbial communities in the formation and decomposition of soil organic matter. Soil Microbiol. Sust. Crop Prod. 22, 81–118. doi: 10.1007/978-90-481-9479-7_4

Crossref Full Text | Google Scholar

Congreves, K. A., Otchere, O., Ferland, D., Farzadfar, S., Williams, S., and Arcand, M. M. (2021). Nitrogen use efficiency definitions of today and tomorrow. Front. Plant Sci. 12:637108. doi: 10.3389/fpls.2021.637108

PubMed Abstract | Crossref Full Text | Google Scholar

Coonan, E. C., Kirkby, C. A., Kirkegaard, J. A., Amidy, M. R., Strong, C. L., and Richardson, A. E. (2020). Microorganisms and nutrient stoichiometry as mediators of soil organic matter dynamics. Nutr. Cycl. Agroecosyst. 117, 273–298. doi: 10.1007/s10705-020-10076-8

Crossref Full Text | Google Scholar

Craswell, E. (2021). Fertilizers and nitrate pollution of surface and ground water: an increasingly pervasive global problem. SN Applied Sci. 3:518. doi: 10.1080/00380768.2004.10408579

Crossref Full Text | Google Scholar

Cucina, M., De Nisi, P., Sordi, S., and Adani, F. (2021). Sewage sludge as N-fertilizers for crop production enabling the circular bioeconomy in agriculture: a challenge for the new EU regulation 1009/2019. Sustain. For. 13:13165. doi: 10.3390/su132313165

Crossref Full Text | Google Scholar

Cui, X., Zhang, Y., Gao, J., Peng, F., and Gao, P. (2018). Long-term combined application of manure and chemical fertilizer sustained higher nutrient status and rhizospheric bacterial diversity in reddish paddy soil of central South China. Sci. Rep. 8:16554. doi: 10.1038/s41598-018-34685-0

PubMed Abstract | Crossref Full Text | Google Scholar

Cui, H., Zhu, H., Shutes, B., Rousseau, A. N., Feng, W.-D., Hou, S.-N., et al. (2023). Soil aggregate-driven changes in nutrient redistribution and microbial communities after 10-year organic fertilization. J. Environ. Manag. 348:119306. doi: 10.1016/j.jenvman.2023.119306

PubMed Abstract | Crossref Full Text | Google Scholar

Cui, J., Zhu, R., Wang, X., Xu, X., Ai, C., He, P., et al. (2022). Effect of high soil C/N ratio and nitrogen limitation caused by the long-term combined organic-inorganic fertilization on the soil microbial community structure and its dominated SOC decomposition. J. Environ. Manag. 303:114155. doi: 10.1007/s42452-021-04521-8

Crossref Full Text | Google Scholar

Das, P. P., Singh, K. R., Nagpure, G., Mansoori, A., Singh, R. P., Ghazi, I. A., et al. (2022). Plant-soil-microbes: a tripartite interaction for nutrient acquisition and better plant growth for sustainable agricultural practices. Environ. Res. 214:113821. doi: 10.1016/j.envres.2022.113821

PubMed Abstract | Crossref Full Text | Google Scholar

Deng, S., Caddell, D. F., Xu, G., Dahlen, L., Washington, L., Yang, J., et al. (2021). Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome. ISME J. 15, 3181–3194. doi: 10.1038/s41396-021-00993-z

PubMed Abstract | Crossref Full Text | Google Scholar

Dhaliwal, S., Naresh, R., Mandal, A., Singh, R., and Dhaliwal, M. (2019). Dynamics and transformations of micronutrients in agricultural soils as influenced by organic matter build-up: a review. Environ. Sust. Indic. 1-2:100007. doi: 10.1016/j.indic.2019.100007

Crossref Full Text | Google Scholar

Didawat, R., Sharma, V., Nath, D., Patra, A., Kumar, S., Biswas, D., et al. (2023). Soil biochemical properties and nutritional quality of rice cultivated in acidic inceptisols using long-term organic farming practices. Arch. Agron. Soil Sci. 69, 1282–1297. doi: 10.1080/03650340.2022.2084084

Crossref Full Text | Google Scholar

Dincă, L. C., Grenni, P., Onet, C., and Onet, A. (2022). Fertilization and soil microbial community: a review. Appl. Sci. 12:1198. doi: 10.3390/app12031198

PubMed Abstract | Crossref Full Text | Google Scholar

Ding, J., Jiang, X., Guan, D., Zhao, B., Ma, M., Zhou, B., et al. (2017). Influence of inorganic fertilizer and organic manure application on fungal communities in a long-term field experiment of Chinese Mollisols. Appl. Soil Ecol. 111, 114–122. doi: 10.1016/j.apsoil.2016.12.003

Crossref Full Text | Google Scholar

Duan, H., Ji, M., Xie, Y., Shi, J., Liu, L., Zhang, B., et al. (2021). Exploring the microbial dynamics of organic matter degradation and humification during co-composting of cow manure and bedding material waste. Sustain. For. 13:13035. doi: 10.3390/su132313035

Crossref Full Text | Google Scholar

Duan, Q., Jiang, S., Chen, F., Li, Z., Ma, L., Song, Y., et al. (2023). Fabrication, evaluation methodologies and models of slow-release fertilizers: a review. Ind. Crop. Prod. 192:116075. doi: 10.1016/j.indcrop.2022.116075

Crossref Full Text | Google Scholar

Dueholm, M. K. D., Nierychlo, M., Andersen, K. S., Rudkjøbing, V., Knutsson, S., Albertsen, M., et al. (2022). MiDAS 4: a global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants. Nat. Commun. 13:1908. doi: 10.1038/s41467-022-29438-7

PubMed Abstract | Crossref Full Text | Google Scholar

El-Beltagi, H. S., Basit, A., Mohamed, H. I., Ali, I., Ullah, S., Kamel, E. A., et al. (2022). Mulching as a sustainable water and soil saving practice in agriculture: a review. Agronomy 12:1881. doi: 10.3390/agronomy12081881

Crossref Full Text | Google Scholar

Etesami, H. (2024). Enhancing soil microbiome resilience: the mitigating role of silicon against environmental stresses. Front. Agron. 6:1465165. doi: 10.3389/fagro.2024.1465165

Crossref Full Text | Google Scholar

Evans, P. N., Boyd, J. A., Leu, A. O., Woodcroft, B. J., Parks, D. H., Hugenholtz, P., et al. (2019). An evolving view of methane metabolism in the Archaea. Nat. Rev. Microbiol. 17, 219–232. doi: 10.1038/s41579-018-0136-7

PubMed Abstract | Crossref Full Text | Google Scholar

Fan, Y., Wang, X., Funk, T., Rashid, I., Herman, B., Bompoti, N., et al. (2022). A critical review for real-time continuous soil monitoring: advantages, challenges, and perspectives. Environ. Sci. Technol. 56, 13546–13564. doi: 10.1021/acs.est.2c03562

PubMed Abstract | Crossref Full Text | Google Scholar

Fang, H., Liu, K., Li, D., Peng, X., Zhang, W., and Zhou, H. (2021). Long-term effects of inorganic fertilizers and organic manures on the structure of a paddy soil. Soil Tillage Res. 213:105137. doi: 10.1016/j.still.2021.105137

Crossref Full Text | Google Scholar

Galvez, A., Sinicco, T., Cayuela, M., Mingorance, M., Fornasier, F., and Mondini, C. (2012). Short term effects of bioenergy by-products on soil C and N dynamics, nutrient availability and biochemical properties. Agric. Ecosyst. Environ. 160, 3–14. doi: 10.1016/J.AGEE.2011.06.015

Crossref Full Text | Google Scholar

Gao, R., Duan, Y., Zhang, J., Ren, Y., Li, H., Liu, X., et al. (2022). Effects of long-term application of organic manure and chemical fertilizer on soil properties and microbial communities in the agro-pastoral ecotone of North China. Front. Environ. Sci. 10:993973. doi: 10.3389/fenvs.2022.993973

Crossref Full Text | Google Scholar

Gao, P., Zhang, T., Cui, X., Lu, Y., Huang, J., Gao, J., et al. (2024). Evolution of red soil fertility and response of rice yield under long-term fertilization. Journal of. Soil Sci. Plant Nutr. 24, 2924–2933. doi: 10.1007/s42729-024-01718-9

PubMed Abstract | Crossref Full Text | Google Scholar

Garg, N., Bhattacherjee, A., Shukla, P. K., and Singh, B. (2021). Influence of imidacloprid on bacterial community diversity of mango orchard soil assessed through 16S rRNA sequencing-based metagenomic analysis. Environ. Monit. Assess. 193, 1–10. doi: 10.1007/s10661-021-08885-7

Crossref Full Text | Google Scholar

Ghosh, A., Bhattacharyya, R., Meena, M., Dwivedi, B., Singh, G., Agnihotri, R., et al. (2018). Long-term fertilization effects on soil organic carbon sequestration in an Inceptisol. Soil Tillage Res. 177, 134–144. doi: 10.1016/j.still.2017.12.006

Crossref Full Text | Google Scholar

Gondek, K., and Mierzwa-Hersztek, M. (2023). Effect of soil supplementation with mineral-organic mixtures on the amount of maize biomass and the mobility of trace elements in soil. Soil Tillage Res. 226:105558. doi: 10.1016/j.still.2022.105558

Crossref Full Text | Google Scholar

Gu, S., Hu, Q., Cheng, Y., Bai, L., Liu, Z., Xiao, W., et al. (2019). Application of organic fertilizer improves microbial community diversity and alters microbial network structure in tea (Camellia sinensis) plantation soils. Soil Tillage Res. 195:104356. doi: 10.1016/j.still.2019.104356

Crossref Full Text | Google Scholar

Gul, S., and Whalen, J. K. (2022). Perspectives and strategies to increase the microbial-derived soil organic matter that persists in agroecosystems. Adv. Agron. 175, 347–401. doi: 10.1016/bs.agron.2022.04.004

Crossref Full Text | Google Scholar

Hammad, H. M., Khaliq, A., Abbas, F., Farhad, W., Fahad, S., Aslam, M., et al. (2020). Comparative effects of organic and inorganic fertilizers on soil organic carbon and wheat productivity under arid region. Commun. Soil Sci. Plant Anal. 51, 1406–1422. doi: 10.1080/00103624.2020.1763385

Crossref Full Text | Google Scholar

Han, J., Dong, Y., and Zhang, M. (2021). Chemical fertilizer reduction with organic fertilizer effectively improve soil fertility and microbial community from newly cultivated land in the loess plateau of China. Appl. Soil Ecol. 165:103966. doi: 10.1016/j.apsoil.2021.103966

Crossref Full Text | Google Scholar

Hartmann, M., and Six, J. (2023). Soil structure and microbiome functions in agroecosystems. Nat. Rev. Earth Environ. 4, 4–18. doi: 10.1038/s43017-022-00366-w

Crossref Full Text | Google Scholar

He, H., Peng, M., Hou, Z., and Li, J. (2024). Unlike chemical fertilizer reduction, organic fertilizer substitution increases soil organic carbon stock and soil fertility in wheat fields. J. Sci. Food Agric. 104, 2798–2808. doi: 10.1002/jsfa.13167

PubMed Abstract | Crossref Full Text | Google Scholar

He, M., Xiong, X., Wang, L., Hou, D., Bolan, N. S., Ok, Y. S., et al. (2021). A critical review on performance indicators for evaluating soil biota and soil health of biochar-amended soils. J. Hazard. Mater. 414:125378. doi: 10.1016/j.jhazmat.2021.125378

PubMed Abstract | Crossref Full Text | Google Scholar

Hoang, H. G., Thuy, B. T. P., Lin, C., Vo, D.-V. N., Tran, H. T., Bahari, M. B., et al. (2022). The nitrogen cycle and mitigation strategies for nitrogen loss during organic waste composting: a review. Chemosphere 300:134514. doi: 10.1016/j.chemosphere.2022.134514

PubMed Abstract | Crossref Full Text | Google Scholar

Hu, X., Gu, H., Liu, J., Wei, D., Zhu, P., Cui, X. A., et al. (2022). Metagenomics reveals divergent functional profiles of soil carbon and nitrogen cycling under long-term addition of chemical and organic fertilizers in the black soil region. Geoderma 418:115846. doi: 10.1016/j.geoderma.2022.115846

PubMed Abstract | Crossref Full Text | Google Scholar

Huang, B., Chen, Y., Pei, Z., Jiang, L., Zhang, Y., Wang, J., et al. (2023). Application of microbial organic fertilizers promotes the utilization of nutrients and restoration of microbial community structure and function in rhizosphere soils after dazomet fumigation. Front. Microbiol. 13:1122611. doi: 10.3389/fmicb.2022.1122611

PubMed Abstract | Crossref Full Text | Google Scholar

Huang, M., Zhu, Y., Li, Z., Huang, B., Luo, N., Liu, C., et al. (2016). Compost as a soil amendment to remediate heavy metal-contaminated agricultural soil: mechanisms, efficacy, problems, and strategies. Water Air Soil Pollut. 227, 1–18. doi: 10.1007/s11270-016-3068-8

Crossref Full Text | Google Scholar

Iqbal, A., He, L., Khan, A., Wei, S., Akhtar, K., Ali, I., et al. (2019). Organic manure coupled with inorganic fertilizer: An approach for the sustainable production of rice by improving soil properties and nitrogen use efficiency. Agronomy 9:651. doi: 10.3390/agronomy9100651

Crossref Full Text | Google Scholar

Jiang, J., Wang, Y., Liu, J., Yang, X., Ren, Y., Miao, H., et al. (2019). Exploring the mechanisms of organic matter degradation and methane emission during sewage sludge composting with added vesuvianite: insights into the prediction of microbial metabolic function and enzymatic activity. Bioresour. Technol. 286:121397. doi: 10.1016/j.biortech.2019.121397

Crossref Full Text | Google Scholar

Jiang, Y., Zhang, R., Zhang, C., Su, J., Cong, W.-F., and Deng, X. (2022). Long-term organic fertilizer additions elevate soil extracellular enzyme activities and tobacco quality in a tobacco-maize rotation. Front. Plant Sci. 13:973639. doi: 10.3389/fpls.2022.973639

PubMed Abstract | Crossref Full Text | Google Scholar

Khaliq, A., Perveen, S., Alamer, K. H., Zia Ul Haq, M., Rafique, Z., Alsudays, I. M., et al. (2022). Arbuscular mycorrhizal fungi symbiosis to enhance plant–soil interaction. Sustain. For. 14:7840. doi: 10.3390/su14137840

Crossref Full Text | Google Scholar

Kyttä, V., Helenius, J., and Tuomisto, H. L. (2021). Carbon footprint and energy use of recycled fertilizers in arable farming. J. Clean. Prod. 287:125063. doi: 10.1016/j.jclepro.2020.125063

PubMed Abstract | Crossref Full Text | Google Scholar

Laik, R., Kumara, B., Pramanick, B., Singh, S. K., Nidhi, A. M., Gaber, A., et al. (2021). Labile soil organic matter pools are influenced by 45 years of applied farmyard manure and mineral nitrogen in the wheat—pearl millet cropping system in the sub-tropical condition. Agronomy 11:2190. doi: 10.3390/agronomy11112190

PubMed Abstract | Crossref Full Text | Google Scholar

Lei, Z., Xu, S.-T., Monreal, C. M., Mclaughlin, N. B., Zhao, B.-P., Liu, J.-H., et al. (2022). Bentonite-humic acid improves soil organic carbon, microbial biomass, enzyme activities and grain quality in a sandy soil cropped to maize (Zea mays L.) in a semi-arid region. J. Int. Agric. 21, 208–221. doi: 10.1016/S2095-3119(20)63574-2

Crossref Full Text | Google Scholar

Li, F., Chen, L., Zhang, J., Yin, J., and Huang, S. (2017). Bacterial community structure after long-term organic and inorganic fertilization reveals important associations between soil nutrients and specific taxa involved in nutrient transformations. Front. Microbiol. 8:187. doi: 10.3389/fmicb.2017.00187

PubMed Abstract | Crossref Full Text | Google Scholar

Li, J., Cooper, J. M., Li, Y., Yang, X., and Zhao, B. (2015). Soil microbial community structure and function are significantly affected by long-term organic and mineral fertilization regimes in the North China plain. Appl. Soil Ecol. 96, 75–87. doi: 10.1016/j.apsoil.2015.07.001

Crossref Full Text | Google Scholar

Li, D., He, H., Zhou, G., He, Q., and Yang, S. (2023). Rice yield and greenhouse gas emissions due to biochar and straw application under optimal reduced N fertilizers in a double season rice cropping system. Agronomy 13:1023. doi: 10.3390/agronomy13041023

Crossref Full Text | Google Scholar

Li, X. G., Jia, B., Lv, J., Ma, Q., Kuzyakov, Y., and Li, F.-M. (2017). Nitrogen fertilization decreases the decomposition of soil organic matter and plant residues in planted soils. Soil Biol. Biochem. 112, 47–55. doi: 10.1016/j.soilbio.2017.04.018

Crossref Full Text | Google Scholar

Li, H., Jin, X., Shan, W., Han, B., Zhou, Y., and Tittonell, P. (2024). Optimizing agricultural management in China for soil greenhouse gas emissions and yield balance: a regional heterogeneity perspective. J. Clean. Prod. 452:142255. doi: 10.1016/j.jclepro.2024.142255

Crossref Full Text | Google Scholar

Li, P., Kong, D., Zhang, H., Xu, L., Li, C., Wu, M., et al. (2021). Different regulation of soil structure and resource chemistry under animal-and plant-derived organic fertilizers changed soil bacterial communities. Appl. Soil Ecol. 165:104020. doi: 10.1016/j.apsoil.2021.104020

Crossref Full Text | Google Scholar

Li, S., Li, J., Zhang, B., Li, D., Li, G., and Li, Y. (2017). Effect of different organic fertilizers application on growth and environmental risk of nitrate under a vegetable field. Sci. Rep. 7:17020. doi: 10.1038/s41598-017-17219-y

PubMed Abstract | Crossref Full Text | Google Scholar

Li, S., Liang, H., Wang, Y., Zhang, Z., Zhang, L., Zhou, G., et al. (2022). Responses of functional genes involved in nitrogen cycling to green manuring in different paddy soils in South China. Plant Soil 478, 519–532. doi: 10.21203/rs.3.rs-740340/v1

Crossref Full Text | Google Scholar

Li, J., Liu, S., Xu, Y., Xu, C., Deng, B., Cao, H., et al. (2024). Optimizing biochar addition strategies in combined processes: comprehensive assessment of earthworm growth, lignocellulose degradation and vermicompost quality. Bioresour. Technol. 406:131031. doi: 10.1016/j.biortech.2024.131031

Crossref Full Text | Google Scholar

Li, X., Su, Y., Ahmed, T., Ren, H., Javed, M. R., Yao, Y., et al. (2021). Effects of different organic fertilizers on improving soil from newly reclaimed land to crop soil. Agriculture 11:560. doi: 10.3390/agriculture11060560

Crossref Full Text | Google Scholar

Li, F., Sun, A., Jiao, X., Bi, L., Zheng, Y., He, J.-Z., et al. (2021). Specific protistan consumers and parasites are responsive to inorganic fertilization in rhizosphere and bulk soils. J. Soils Sediments 21, 3801–3812. doi: 10.1007/s11368-021-03052-4

PubMed Abstract | Crossref Full Text | Google Scholar

Li, Q., Wang, L., Fu, Y., Lin, D., Hou, M., Li, X., et al. (2023). Transformation of soil organic matter subjected to environmental disturbance and preservation of organic matter bound to soil minerals: a review. J. Soils Sediments 23, 1485–1500. doi: 10.1007/s11368-022-03381-y

PubMed Abstract | Crossref Full Text | Google Scholar

Li, J., Wen, Y., Li, X., Li, Y., Yang, X., Lin, Z., et al. (2018). Soil labile organic carbon fractions and soil organic carbon stocks as affected by long-term organic and mineral fertilization regimes in the North China plain. Soil Tillage Res. 175, 281–290. doi: 10.1016/j.still.2017.08.008

Crossref Full Text | Google Scholar

Li, J., Xie, T., Zhu, H., Zhou, J., Li, C., Xiong, W., et al. (2021). Alkaline phosphatase activity mediates soil organic phosphorus mineralization in a subalpine forest ecosystem. Geoderma 404:115376. doi: 10.1016/j.geoderma.2021.115376

Crossref Full Text | Google Scholar

Li, T., Zhang, Y., Bei, S., Li, X., Reinsch, S., Zhang, H., et al. (2020). Contrasting impacts of manure and inorganic fertilizer applications for nine years on soil organic carbon and its labile fractions in bulk soil and soil aggregates. Catena 194:104739. doi: 10.1016/j.catena.2020.104739

Crossref Full Text | Google Scholar

Li, Q., Zhang, D., Cheng, H., Ren, L., Jin, X., Fang, W., et al. (2022). Organic fertilizers activate soil enzyme activities and promote the recovery of soil beneficial microorganisms after dazomet fumigation. J. Environ. Manag. 309:114666. doi: 10.1016/j.jenvman.2022.114666

PubMed Abstract | Crossref Full Text | Google Scholar

Li, F., Zhang, K., Ren, J., Yin, C., Zhang, Y., and Nie, J. (2021). Driving mechanism for farmers to adopt improved agricultural systems in China: the case of rice-green manure crops rotation system. Agric. Syst. 192:103202. doi: 10.1016/j.agsy.2021.103202

Crossref Full Text | Google Scholar

Lin, M., Yang, S., Chen, H., Letuma, P., Khan, M. U., Huang, J., et al. (2023). Optimally combined application of organic and chemical fertilizers increases grain yield and improves rhizosphere microecological properties in rice ratooning. Crop Sci. 63, 764–783. doi: 10.1002/csc2.20891

Crossref Full Text | Google Scholar

Lindström, K., and Mousavi, S. A. (2020). Effectiveness of nitrogen fixation in rhizobia. Microb. Biotechnol. 13, 1314–1335. doi: 10.1111/1751-7915.13517

PubMed Abstract | Crossref Full Text | Google Scholar

Liu, L., Gao, Y., Yang, W., Liu, J., and Wang, Z. (2023). Community metagenomics reveals the processes of nutrient cycling regulated by microbial functions in soils with P fertilizer input. Plant Soil 499, 139–154. doi: 10.1007/s11104-023-05875-1

PubMed Abstract | Crossref Full Text | Google Scholar

Liu, J., Shu, A., Song, W., Shi, W., Li, M., Zhang, W., et al. (2021). Long-term organic fertilizer substitution increases rice yield by improving soil properties and regulating soil bacteria. Geoderma 404:115287. doi: 10.1016/j.geoderma.2021.115287

Crossref Full Text | Google Scholar

Liu, T., Wang, Q., Li, Y., Chen, Y., Jia, B., Zhang, J., et al. (2024). Bio-organic fertilizer facilitated phytoremediation of heavy metal (loid) s-contaminated saline soil by mediating the plant-soil-rhizomicrobiota interactions. Sci. Total Environ. 922:171278. doi: 10.1016/j.scitotenv.2024.171278

PubMed Abstract | Crossref Full Text | Google Scholar

Liu, H., Wang, H., Nie, Z., Tao, Z., Peng, H., Shi, H., et al. (2024). Combined application of arbuscular mycorrhizal fungi and selenium fertilizer increased wheat biomass under cadmium stress and shapes rhizosphere soil microbial communities. BMC Plant Biol. 24:359. doi: 10.1186/s12870-024-05032-5

PubMed Abstract | Crossref Full Text | Google Scholar

Liu, B., Xia, H., Jiang, C., Riaz, M., Yang, L., Chen, Y., et al. (2022). 14 year applications of chemical fertilizers and crop straw effects on soil labile organic carbon fractions, enzyme activities and microbial community in rice-wheat rotation of middle China. Sci. Total Environ. 841:156608. doi: 10.1016/j.scitotenv.2022.156608

PubMed Abstract | Crossref Full Text | Google Scholar

Liu, H., Xu, W., Li, J., Yu, Z., Zeng, Q., Tan, W., et al. (2021). Short-term effect of manure and straw application on bacterial and fungal community compositions and abundances in an acidic paddy soil. J. Soils Sediments 21, 3057–3071. doi: 10.1007/s11368-021-03005-x

Crossref Full Text | Google Scholar

Liu, P., Zhang, T., Wang, G., Ju, J., Mao, W., and Zhao, H. (2023). Response of rice grain yield and soil fertility to fertilization management under three rice-based cropping systems in reclaimed soil. Agronomy 13:1840. doi: 10.3390/agronomy13071840

Crossref Full Text | Google Scholar

Liu, L., Zheng, X., Wei, X., Kai, Z., and Xu, Y. (2021). Excessive application of chemical fertilizer and organophosphorus pesticides induced total phosphorus loss from planting causing surface water eutrophication. Sci. Rep. 11:23015. doi: 10.1038/s41598-021-02521-7

PubMed Abstract | Crossref Full Text | Google Scholar

López-Cano, I., Roig, A., Cayuela, M. L., Alburquerque, J. A., and Sánchez-Monedero, M. A. (2016). Biochar improves N cycling during composting of olive mill wastes and sheep manure. Waste Manag. 49, 553–559. doi: 10.1016/j.wasman.2015.12.031

PubMed Abstract | Crossref Full Text | Google Scholar

Lu, W., Hao, Z., Ma, X., Gao, J., Fan, X., Guo, J., et al. (2024). Effects of different proportions of organic fertilizer replacing chemical fertilizer on soil nutrients and fertilizer utilization in gray desert soil. Agronomy 14:228. doi: 10.3390/agronomy14010228

Crossref Full Text | Google Scholar

Luo, J., Liao, G., Banerjee, S., Gu, S., Liang, J., Guo, X., et al. (2023). Long-term organic fertilization promotes the resilience of soil multifunctionality driven by bacterial communities. Soil Biol. Biochem. 177:108922. doi: 10.1016/j.soilbio.2022.108922

Crossref Full Text | Google Scholar

Ma, G., Cheng, S., He, W., Dong, Y., Qi, S., Tu, N., et al. (2023). Effects of organic and inorganic fertilizers on soil nutrient conditions in rice fields with varying soil fertility. Land 12:1026. doi: 10.3390/land12051026

Crossref Full Text | Google Scholar

Ma, X., Li, H., Xu, Y., and Liu, C. (2021). Effects of organic fertilizers via quick artificial decomposition on crop growth. Sci. Rep. 11:3900. doi: 10.1038/s41598-021-83576-4

PubMed Abstract | Crossref Full Text | Google Scholar

Mathesius, U. (2022). Humboldt review: are legumes different? Origins and consequences of evolving nitrogen fixing symbioses. J. Plant Physiol. 276:153765. doi: 10.1016/j.jplph.2022.153765

Crossref Full Text | Google Scholar

Maurya, S., Abraham, J. S., Somasundaram, S., Toteja, R., Gupta, R., and Makhija, S. (2020). Indicators for assessment of soil quality: a mini-review. Environ. Monit. Assess. 192, 1–22. doi: 10.1007/s10661-020-08556-z

Crossref Full Text | Google Scholar

Meegoda, J. N., Chande, C., and Bakshi, I. (2025). Biodigesters for sustainable food waste management. Int. J. Environ. Res. Public Health 22:382. doi: 10.3390/ijerph22030382

Crossref Full Text | Google Scholar

Mei, N., Zhang, X., Wang, X., Peng, C., Gao, H., Zhu, P., et al. (2021). Effects of 40 years applications of inorganic and organic fertilization on soil bacterial community in a maize agroecosystem in Northeast China. Eur. J. Agron. 130:126332. doi: 10.1016/j.eja.2021.126332

Crossref Full Text | Google Scholar

Menegat, S., Ledo, A., and Tirado, R. (2022). Greenhouse gas emissions from global production and use of nitrogen synthetic fertilisers in agriculture. Sci. Rep. 12, 1–13. doi: 10.1038/s41598-022-24242-1

Crossref Full Text | Google Scholar

Mingcheng, H., Andrew, J. W., Weishou, S., Zhong, Z., Chongwen, Q., and Xiangui, L. (2024). Effects of different organic fertilizers on nitrous oxide and methane emissions from double-cropping rice fields. Pedosphere 34, 52–62. doi: 10.1016/j.pedsph.2023.03.006

Crossref Full Text | Google Scholar

Monther, M. T., Kholoud, M. A., Yahia, A. O., and Daniel, I. L. (2020). Soil health and sustainable agriculture. Sustainability 12:4859. doi: 10.3390/su12124859

Crossref Full Text | Google Scholar

Mózner, Z., Tabi, A., and Csutora, M. (2012). Modifying the yield factor based on more efficient use of fertilizer—the environmental impacts of intensive and extensive agricultural practices. Ecol. Indic. 16, 58–66. doi: 10.1016/j.ecolind.2011.06.034

Crossref Full Text | Google Scholar

Ndzelu, B. S., Dou, S., Zhang, X., Zhang, Y., Ma, R., and Liu, X. (2021). Tillage effects on humus composition and humic acid structural characteristics in soil aggregate-size fractions. Soil Tillage Res. 213:105090. doi: 10.1016/j.still.2021.105090

Crossref Full Text | Google Scholar

Nguyen, M. K., Lin, C., Hoang, H. G., Sanderson, P., Dang, B. T., Bui, X. T., et al. (2022). Evaluate the role of biochar during the organic waste composting process: a critical review. Chemosphere 299:134488. doi: 10.1016/j.chemosphere.2022.134488

PubMed Abstract | Crossref Full Text | Google Scholar

Ning, Q., Chen, L., Jia, Z., Zhang, C., Ma, D., Li, F., et al. (2020). Multiple long-term observations reveal a strategy for soil pH-dependent fertilization and fungal communities in support of agricultural production. Agric. Ecosyst. Environ. 293:106837. doi: 10.1016/j.agee.2020.106837

Crossref Full Text | Google Scholar

Niu, B., Wang, W., Yuan, Z., Sederoff, R. R., Sederoff, H., Chiang, V. L., et al. (2020). Microbial interactions within multiple-strain biological control agents impact soil-borne plant disease. Front. Microbiol. 11:585404. doi: 10.3389/fmicb.2020.585404

Crossref Full Text | Google Scholar

Obalum, S., Chibuike, G., Peth, S., and Ouyang, Y. (2017). Soil organic matter as sole indicator of soil degradation. Environ. Monit. Assess. 189, 1–19. doi: 10.1007/s10661-017-5881-y

Crossref Full Text | Google Scholar

Ogbete, E., Ogbonnaya, M., and Ofoeze, M. (2023). Effect of fermentation agents on the pH, tta and microbial composition of Fufu dough. J. Agric. Food Sci. 21, 153–163. doi: 10.4314/jafs.v21i2.10

Crossref Full Text | Google Scholar

Oyedoh, O. P., Yang, W., Dhanasekaran, D., Santoyo, G., Glick, B. R., and Babalola, O. O. (2023). Rare rhizo-Actinomycetes: a new source of agroactive metabolites. Biotechnol. Adv. 67:108205. doi: 10.1016/j.biotechadv.2023.108205

Crossref Full Text | Google Scholar

Oyetunji, O., Bolan, N., and Hancock, G. (2022). A comprehensive review on enhancing nutrient use efficiency and productivity of broadacre (arable) crops with the combined utilization of compost and fertilizers. J. Environ. Manag. 317:115395. doi: 10.1016/j.jenvman.2022.115395

PubMed Abstract | Crossref Full Text | Google Scholar

Paillat, L., Cannavo, P., Barraud, F., Huché-Thélier, L., and Guénon, R. (2020). Growing medium type affects organic fertilizer mineralization and CNPS microbial enzyme activities. Agronomy 10:1955. doi: 10.3390/agronomy10121955

Crossref Full Text | Google Scholar

Panday, D., Bhusal, N., Das, S., and Ghalehgolabbehbahani, A. (2024). Rooted in nature: the rise, challenges, and potential of organic farming and fertilizers in agroecosystems. Sustain. For. 16:1530. doi: 10.3390/su16041530

Crossref Full Text | Google Scholar

Patra, A., Sharma, V. K., Nath, D. J., Ghosh, A., Purakayastha, T. J., Barman, M., et al. (2021). Impact of soil acidity influenced by long-term integrated use of enriched compost, biofertilizers, and fertilizer on soil microbial activity and biomass in rice under acidic soil. J. Soil Sci. Plant Nutr. 21, 756–767. doi: 10.1007/s42729-020-00398-5

Crossref Full Text | Google Scholar

Paz-Ferreiro, J., and Fu, S. (2016). Biological indices for soil quality evaluation: perspectives and limitations. Land Degrad. Dev. 27, 14–25. doi: 10.1002/ldr.2262

Crossref Full Text | Google Scholar

Peng, G., Zhang, T., Lei, X.-Y., Cui, X.-W., Lu, Y.-X., Fan, P.-F., et al. (2023). Improvement of soil fertility and rice yield after long-term application of cow manure combined with inorganic fertilizers. J. Integr. Agric. 22, 2221–2232. doi: 10.1016/j.jia.2023.02.037

Crossref Full Text | Google Scholar

Philippot, L., Chenu, C., Kappler, A., Rillig, M. C., and Fierer, N. (2024). The interplay between microbial communities and soil properties. Nat. Rev. Microbiol. 22, 226–239. doi: 10.1038/s41579-023-00980-5

Crossref Full Text | Google Scholar

Potts, L. D., Douglas, A., Perez Calderon, L. J., Anderson, J. A., Witte, U., Prosser, J. I., et al. (2022). Chronic environmental perturbation influences microbial community assembly patterns. Environ. Sci. Technol. 56, 2300–2311. doi: 10.1021/acs.est.1c05106

PubMed Abstract | Crossref Full Text | Google Scholar

Pratibha, G., Manjunath, M., Raju, B., Srinivas, I., Rao, K., Shanker, A. K., et al. (2023). Soil bacterial community structure and functioning in a long-term conservation agriculture experiment under semi-arid rainfed production system. Front. Microbiol. 14:1102682. doi: 10.3389/fmicb.2023.1102682

Crossref Full Text | Google Scholar

Pretty, J. (2018). Intensification for redesigned and sustainable agricultural systems. Science 362:eaav0294. doi: 10.1126/science.aav0294

PubMed Abstract | Crossref Full Text | Google Scholar

Priya, A., Gnanasekaran, L., Dutta, K., Rajendran, S., Balakrishnan, D., and Soto-Moscoso, M. (2022). Biosorption of heavy metals by microorganisms: evaluation of different underlying mechanisms. Chemosphere 307:135957. doi: 10.1016/j.chemosphere.2022.135957

PubMed Abstract | Crossref Full Text | Google Scholar

Pu, X., Zhang, G., Zhang, P., Liu, Y., and Zhang, W. (2016). Effects of straw management, inorganic fertiliser, and manure amendment on soil microbial properties, nutrient availability, and root growth in a drip-irrigated cotton field. Crop Pasture Sci. 67, 1297–1308. doi: 10.1071/CP16230

Crossref Full Text | Google Scholar

Qiao, J., Wang, J., Zhao, D., Zhou, W., Schwenke, G., Yan, T., et al. (2022). Optimizing N fertilizer rates sustained rice yields, improved N use efficiency, and decreased N losses via runoff from rice-wheat cropping systems. Agric. Ecosyst. Environ. 324:107724. doi: 10.1016/j.agee.2021.107724

PubMed Abstract | Crossref Full Text | Google Scholar

Qiong, H., Yuemin, N., Huang, S., Ting, Z., Jian, W., and Wuzhong, N. (2023). Effects of substituting chemical fertilizers with manure on rice yield and soil labile nitrogen in paddy fields of China: a meta-analysis. Pedosphere 33, 172–184. doi: 10.1016/j.pedsph.2022.09.003

Crossref Full Text | Google Scholar

Rahman, K. A., and Zhang, D. (2018). Effects of fertilizer broadcasting on the excessive use of inorganic fertilizers and environmental sustainability. Sustain. For. 10:759. doi: 10.3390/su10030759

Crossref Full Text | Google Scholar

Rashmi, I., Karthika, K., Roy, T., Shinoji, K., Kumawat, A., Kala, S., et al. (2022). Agrochemicals in soil and environment: Impacts and remediation. Cham: Springer, 313–345.

Google Scholar

Rayne, N., and Aula, L. (2020). Livestock manure and the impacts on soil health: a review. Soil Syst. 4:64. doi: 10.3390/soilsystems4040064

Crossref Full Text | Google Scholar

Raza, A., Zahra, N., Hafeez, M. B., Ahmad, M., Iqbal, S., Shaukat, K., et al. (2020). Nitrogen fixation of legumes: Biology and physiology. The Plant Family Fabaceae. Biology and Physiological Responses to Environmental Stresses. Cham: Springer, 43–74.

Google Scholar

Razzaq, S., Zhou, B., Adil, M., Ullah, Z., Guo, H., Zia-Ur-Rehman, M., et al. (2024). Cadmium stress alleviation: interplay of micronutrients and enzymatic/non-enzymatic species in maize by organic and inorganic amendments. Water Air Soil Pollut. 235, 1–19. doi: 10.1007/s11270-024-07086-5

Crossref Full Text | Google Scholar

Rieder, L., Amann, T., and Hartmann, J. (2024). Soil electrical conductivity as a proxy for enhanced weathering in soils. Front. Clim. 5:1283107. doi: 10.3389/fclim.2023.1283107

PubMed Abstract | Crossref Full Text | Google Scholar

Rivera-Uria, Y., Solleiro-Rebolledo, E., Beltrán-Paz, O., Martínez-Jardines, G., Nava-Arsola, E., Vázquez-Zacamitzin, G., et al. (2024). Short-term response on microstructure and soil organic matter characteristics after fertilization change in an Andic Anthrosol. Soil Tillage Res. 241:106110. doi: 10.1016/j.still.2024.106110

Crossref Full Text | Google Scholar

Rout, A. K., Dehury, B., Parida, P. K., Sarkar, D. J., Behera, B., Das, B. K., et al. (2022). Taxonomic profiling and functional gene annotation of microbial communities in sediment of river ganga at Kanpur, India: insights from whole-genome metagenomics study. Environ. Sci. Pollut. Res. 29, 82309–82323. doi: 10.1007/s11356-022-21644-6

PubMed Abstract | Crossref Full Text | Google Scholar

Sabir, M. S., Shahzadi, F., Ali, F., Shakeela, Q., Niaz, Z., and Ahmed, S. (2021). Comparative effect of fertilization practices on soil microbial diversity and activity: an overview. Curr. Microbiol. 78, 3644–3655. doi: 10.1007/s00284-021-02634-2

PubMed Abstract | Crossref Full Text | Google Scholar

Saha, C. K., Nandi, R., Akter, S., Hossain, S., Kabir, K. B., Kirtania, K., et al. (2024). Technical prospects and challenges of anaerobic co-digestion in Bangladesh: a review. Renew. Sust. Energ. Rev. 197:114412. doi: 10.1016/j.rser.2024.114412

Crossref Full Text | Google Scholar

Shaheb, M. R., Venkatesh, R., and Shearer, S. A. (2021). A review on the effect of soil compaction and its management for sustainable crop production. Journal of. Biosyst. Eng. 46, 417–439. doi: 10.1007/s42853-021-00117-7

PubMed Abstract | Crossref Full Text | Google Scholar

Sharma, B., Vaish, B., Monika, S. U. K., Singh, P., and Singh, R. P. (2019). Recycling of organic wastes in agriculture: an environmental perspective. Int. J. Environ. Res. 13, 409–429. doi: 10.1007/s41742-019-00175-y

PubMed Abstract | Crossref Full Text | Google Scholar

Shen, F., Fei, L., Tuo, Y., Peng, Y., Yang, Q., Zheng, R., et al. (2024). Effects of water and fertilizer regulation on soil physicochemical properties, bacterial diversity and community structure of Panax notoginseng. Sci. Hortic. 326:112777. doi: 10.1016/j.scienta.2023.112777

Crossref Full Text | Google Scholar

Shi, G., Sun, H., Calderón-Urrea, A., Li, M., Yang, H., Wang, W., et al. (2021). Bacterial communities as indicators of soil health under a continuous cropping system. Land Degrad. Dev. 32, 2393–2408. doi: 10.1002/ldr.3919

Crossref Full Text | Google Scholar

Smith, J. U., Fischer, A., Hallett, P. D., Homans, H. Y., Smith, P., Abdul-Salam, Y., et al. (2015). Sustainable use of organic resources for bioenergy, food and water provision in rural sub-Saharan Africa. Renew. Sust. Energ. Rev. 50, 903–917. doi: 10.1016/j.rser.2015.04.071

PubMed Abstract | Crossref Full Text | Google Scholar

Song, B., Li, Y., Yang, L., Shi, H., Li, L., Bai, W., et al. (2023). Soil acidification under long-term N addition decreases the diversity of soil bacteria and fungi and changes their community composition in a semiarid grassland. Microb. Ecol. 85, 221–231. doi: 10.1007/s00248-021-01954-x

PubMed Abstract | Crossref Full Text | Google Scholar

Song, J., Sun, Q., Li, Q., Ashraf, U., Hu, X., and Li, L. (2024). Optimal soil, climate, and management factors for maximizing crop yield and soil nutrients in a rice–oilseed rotation system with straw return. Agriculture 14:414. doi: 10.3390/agriculture14030414

Crossref Full Text | Google Scholar

Song, A., Zhang, J., Xu, D., Wang, E., Bi, J., Asante-Badu, B., et al. (2022). Keystone microbial taxa drive the accelerated decompositions of cellulose and lignin by long-term resource enrichments. Sci. Total Environ. 842:156814. doi: 10.1016/j.scitotenv.2022.156814

PubMed Abstract | Crossref Full Text | Google Scholar

Song, Y., Zhao, Q., Guo, X., Ali, I., Li, F., Lin, S., et al. (2022). Effects of biochar and organic-inorganic fertilizer on pomelo orchard soil properties, enzymes activities, and microbial community structure. Front. Microbiol. 13:980241. doi: 10.3389/fmicb.2022.980241

PubMed Abstract | Crossref Full Text | Google Scholar

Sulaiman, M. A., and Bello, S. K. (2024). Biological control of soil-borne pathogens in arid lands: a review. J. Plant Dis. Prot. 131, 293–313. doi: 10.1007/s41348-023-00824-7

Crossref Full Text | Google Scholar

Sun, W., Ye, J., Lin, H., Yu, Q., Wang, Q., Chen, Z., et al. (2023). Dynamic characteristics of heavy metal accumulation in agricultural soils after continuous organic fertilizer application: field-scale monitoring. Chemosphere 335:139051. doi: 10.1016/j.chemosphere.2023.139051

Crossref Full Text | Google Scholar

Sun, X., Ye, Y., Ma, Q., Guan, Q., and Jones, D. L. (2021). Variation in enzyme activities involved in carbon and nitrogen cycling in rhizosphere and bulk soil after organic mulching. Rhizosphere 19:100376. doi: 10.1016/j.rhisph.2021.100376

Crossref Full Text | Google Scholar

Tabrika, I., Azim, K., Mayad, E. H., and Zaafrani, M. (2020). Composting of tomato plant residues: improvement of composting process and compost quality by integration of sheep manure. Org. Agric. 10, 229–242. doi: 10.1007/s13165-019-00268-0

Crossref Full Text | Google Scholar

Tahir, M., Wei, X., Liu, H., Li, J., Zhou, J., Kang, B., et al. (2023). Mixed legume–grass seeding and nitrogen fertilizer input enhance forage yield and nutritional quality by improving the soil enzyme activities in Sichuan, China. Front. Plant Sci. 14:1176150. doi: 10.3389/fpls.2023.1176150

PubMed Abstract | Crossref Full Text | Google Scholar

Tan, H., Liu, T., Yu, Y., Tang, J., Jiang, L., Martin, F. M., et al. (2021). Morel production related to soil microbial diversity and evenness. Microbiol. Spectr. 9, e00229–e00221. doi: 10.1128/Spectrum.00229-21

PubMed Abstract | Crossref Full Text | Google Scholar

Tian, J., Lou, Y., Gao, Y., Fang, H., Liu, S., Xu, M., et al. (2017). Response of soil organic matter fractions and composition of microbial community to long-term organic and mineral fertilization. Biol. Fertil. Soils 53, 523–532. doi: 10.1007/s00374-017-1189-x

PubMed Abstract | Crossref Full Text | Google Scholar

Timsina, J. (2018). Can organic sources of nutrients increase crop yields to meet global food demand? Agronomy 8:214. doi: 10.3390/agronomy8100214

Crossref Full Text | Google Scholar

Topa, D., Cara, I. G., and Jităreanu, G. (2021). Long term impact of different tillage systems on carbon pools and stocks, soil bulk density, aggregation and nutrients: a field meta-analysis. Catena 199:105102. doi: 10.1016/j.catena.2020.105102

Crossref Full Text | Google Scholar

Torres-Rodriguez, J. A., Reyes-Pérez, J. J., Quiñones-Aguilar, E. E., and Hernandez-Montiel, L. G. (2022). Actinomycete potential as biocontrol agent of phytopathogenic fungi: mechanisms, source, and applications. Plan. Theory 11:3201. doi: 10.3390/plants11233201

PubMed Abstract | Crossref Full Text | Google Scholar

Vogel, H.-J., Eberhardt, E., Franko, U., Lang, B., Ließ, M., Weller, U., et al. (2019). Quantitative evaluation of soil functions: potential and state. Front. Environ. Sci. 7:463905. doi: 10.3389/fenvs.2019.00164

Crossref Full Text | Google Scholar

Wahab, A., Muhammad, M., Munir, A., Abdi, G., Zaman, W., Ayaz, A., et al. (2023). Role of arbuscular mycorrhizal fungi in regulating growth, enhancing productivity, and potentially influencing ecosystems under abiotic and biotic stresses. Plan. Theory 12:3102. doi: 10.3390/plants12173102

Crossref Full Text | Google Scholar

Wang, D., Bai, J., Wang, W., Zhang, G., Cui, B., Liu, X., et al. (2018). Comprehensive assessment of soil quality for different wetlands in a Chinese delta. Land Degrad. Dev. 29, 3783–3794. doi: 10.1002/ldr.3086

Crossref Full Text | Google Scholar

Wang, X. (2022). Managing land carrying capacity: key to achieving sustainable production systems for food security. Land 11:484. doi: 10.3390/land11040484

Crossref Full Text | Google Scholar

Wang, W., Chen, C., Wu, X., Xie, K., Yin, C., Hou, H., et al. (2019). Effects of reduced chemical fertilizer combined with straw retention on greenhouse gas budget and crop production in double rice fields. Biol. Fertil. Soils 55, 89–96. doi: 10.1007/s00374-018-1330-5

Crossref Full Text | Google Scholar

Wang, X., Guo, T., Wang, Y., Xing, Y., Wang, Y., and He, X. (2020). Exploring the optimization of water and fertilizer management practices for potato production in the sandy loam soils of Northwest China based on PCA. Agric. Water Manag, 237:106180. doi: 10.1016/j.agwat.2020.106180

Crossref Full Text | Google Scholar

Wang, K., Hou, J., Zhang, S., Hu, W., Yi, G., Chen, W., et al. (2023). Preparation of a new biochar-based microbial fertilizer: nutrient release patterns and synergistic mechanisms to improve soil fertility. Sci. Total Environ. 860:160478. doi: 10.1016/j.scitotenv.2022.160478

PubMed Abstract | Crossref Full Text | Google Scholar

Wang, C., and Kuzyakov, Y. (2024). Rhizosphere engineering for soil carbon sequestration. Trends Plant Sci. 29, 447–468. doi: 10.1016/j.tplants.2023.09.015

PubMed Abstract | Crossref Full Text | Google Scholar

Wang, L., Leghari, S. J., Wu, J., Wang, N., Pang, M., and Jin, L. (2023). Interactive effects of biochar and chemical fertilizer on water and nitrogen dynamics, soil properties and maize yield under different irrigation methods. Front. Plant Sci. 14:1230023. doi: 10.3389/fpls.2023.1230023

PubMed Abstract | Crossref Full Text | Google Scholar

Wang, X., Liu, M., Ciampitti, I. A., Cui, J., Fang, K., Zhao, S., et al. (2024). Benefits and trade-offs of replacing inorganic fertilizer by organic substrate in crop production: a global meta-analysis. Sci. Total Environ. 925:171781. doi: 10.1016/j.scitotenv.2024.171781

PubMed Abstract | Crossref Full Text | Google Scholar

Wang, J. L., Liu, K. L., Zhao, X. Q., Zhang, H. Q., Li, D., Li, J. J., et al. (2021). Balanced fertilization over four decades has sustained soil microbial communities and improved soil fertility and rice productivity in red paddy soil. Sci. Total Environ. 793:148664. doi: 10.1016/j.scitotenv.2021.148664

PubMed Abstract | Crossref Full Text | Google Scholar

Wang, Q., Ma, M., Jiang, X., Guan, D., Wei, D., Zhao, B., et al. (2019). Impact of 36 years of nitrogen fertilization on microbial community composition and soil carbon cycling-related enzyme activities in rhizospheres and bulk soils in Northeast China. Appl. Soil Ecol. 136, 148–157. doi: 10.1016/j.apsoil.2018.12.019

Crossref Full Text | Google Scholar

Wang, J., Qin, H., Zhang, L., Tang, Y., Long, J., Xu, H., et al. (2024). Synergistic effects of rhizosphere effect and combined organic and chemical fertilizers application on soil bacterial diversity and community structure in oilseed rape cultivation. Front. Microbiol. 15:1374199. doi: 10.3389/fmicb.2024.1374199

Crossref Full Text | Google Scholar

Wang, X., Wang, M., Chen, L., Shutes, B., Yan, B., Zhang, F., et al. (2023). Nitrogen migration and transformation in a saline-alkali paddy ecosystem with application of different nitrogen fertilizers. Environ. Sci. Pollut. Res. 30, 51665–51678. doi: 10.1007/s11356-023-25984-9

PubMed Abstract | Crossref Full Text | Google Scholar

Wang, R., Wang, Q., Dong, L., and Zhang, J. (2021). Cleaner agricultural production in drinking-water source areas for the control of non-point source pollution in China. J. Environ. Manag. 285:112096. doi: 10.1016/j.jenvman.2021.112096

PubMed Abstract | Crossref Full Text | Google Scholar

Wang, Z., Wang, Z., Li, T., Wang, C., Dang, N., Wang, R., et al. (2021). N and P fertilization enhanced carbon decomposition function by shifting microbes towards an r-selected community in meadow grassland soils. Ecol. Indic. 132:108306. doi: 10.1016/j.ecolind.2021.108306

Crossref Full Text | Google Scholar

Wang, J., Wang, X., Xu, M., Feng, G., Zhang, W., and Lu, C. A. (2015). Crop yield and soil organic matter after long-term straw return to soil in China. Nutr. Cycl. Agroecosyst. 102, 371–381. doi: 10.1007/s10705-015-9710-9

Crossref Full Text | Google Scholar

Wu, W., Lin, Z., Zhu, X., Li, G., Zhang, W., Chen, Y., et al. (2022). Improved tomato yield and quality by altering soil physicochemical properties and nitrification processes in the combined use of organic-inorganic fertilizers. Eur. J. Soil Biol. 109:103384.

Google Scholar

Wu, Y., Yan, S., Fan, J., Zhang, F., Zheng, J., Guo, J., et al. (2020). Combined application of soluble organic and chemical fertilizers in drip fertigation improves nitrogen use efficiency and enhances tomato yield and quality. J. Sci. Food Agric. 100, 5422–5433. doi: 10.1002/jsfa.10593

Crossref Full Text | Google Scholar

Xiao, L., Huang, Y., Zhao, J., Zhou, J., and Abbas, F. (2021). Effects of planting structure on soil water-stable aggregates, microbial biomass and enzyme activity in a catchment of loess plateau terraces, China. Appl. Soil Ecol. 159:103819. doi: 10.1016/j.apsoil.2020.103819

PubMed Abstract | Crossref Full Text | Google Scholar

Xin, X., Qin, S., Zhang, J., Zhu, A., Yang, W., and Zhang, X. (2017). Yield, phosphorus use efficiency and balance response to substituting long-term chemical fertilizer use with organic manure in a wheat-maize system. Field Crop Res. 208, 27–33. doi: 10.1016/j.fcr.2017.03.011

Crossref Full Text | Google Scholar

Xing, Y., Chen, M., and Wang, X. (2025). Enhancing water use efficiency and fruit quality in jujube cultivation: A review of advanced irrigation techniques and precision management strategies. Agr. Water Manage. 307, 109243. doi: 10.1016/j.agwat.2024.109243

Crossref Full Text | Google Scholar

Xu, W., Liu, W., Tang, S., Yang, Q., Meng, L., Wu, Y., et al. (2023). Long-term partial substitution of chemical nitrogen fertilizer with organic fertilizers increased SOC stability by mediating soil C mineralization and enzyme activities in a rubber plantation of Hainan Island, China. Appl. Soil Ecol. 182:104691. doi: 10.1016/j.apsoil.2022.104691

Crossref Full Text | Google Scholar

Xu, X., Ma, F., Zhou, J., and Du, C. (2022). Control-released urea improved agricultural production efficiency and reduced the ecological and environmental impact in rice-wheat rotation system: a life-cycle perspective. Field Crop Res. 278:108445. doi: 10.1016/j.fcr.2022.108445

Crossref Full Text | Google Scholar

Xu, X., Xiao, C., Bi, R., Jiao, Y., Wang, B., Dong, Y., et al. (2024). Optimizing organic fertilization towards sustainable vegetable production evaluated by long-term field measurement and multi-level fuzzy comprehensive model. Agric. Ecosyst. Environ. 368:109008. doi: 10.1016/j.agee.2024.109008

Crossref Full Text | Google Scholar

Xue, L., Yu, Y., and Yang, L. (2014). Maintaining yields and reducing nitrogen loss in rice–wheat rotation system in Taihu Lake region with proper fertilizer management. Environ. Res. Lett. 9:115010. doi: 10.1088/1748-9326/9/11/115010

Crossref Full Text | Google Scholar

Yahaya, S. M., Mahmud, A. A., Abdullahi, M., and Haruna, A. (2023). Recent advances in the chemistry of nitrogen, phosphorus and potassium as fertilizers in soil: a review. Pedosphere 33, 385–406. doi: 10.1016/j.pedsph.2022.07.012

Crossref Full Text | Google Scholar

Yang, Y., Li, T., Wang, Y., Cheng, H., Chang, S. X., Liang, C., et al. (2021). Negative effects of multiple global change factors on soil microbial diversity. Soil Biol. Biochem. 156:108229. doi: 10.1016/j.soilbio.2021.108229

Crossref Full Text | Google Scholar

Yang, C., and Lu, S. (2022). Straw and straw biochar differently affect phosphorus availability, enzyme activity and microbial functional genes in an Ultisol. Sci. Total Environ. 805:150325. doi: 10.1016/j.scitotenv.2021.150325

PubMed Abstract | Crossref Full Text | Google Scholar

Yang, Z., Peng, C., Cao, H., Song, J., Gong, B., Li, L., et al. (2022). Microbial functional assemblages predicted by the FAPROTAX analysis are impacted by physicochemical properties, but C, N and S cycling genes are not in mangrove soil in the Beibu gulf, China. Ecol.Indic. 139:108887. doi: 10.1016/j.ecolind.2022.108887

PubMed Abstract | Crossref Full Text | Google Scholar

Yang, L., Sun, R., Li, J., Zhai, L., Cui, H., Fan, B., et al. (2023). Combined organic-inorganic fertilization builds higher stability of soil and root microbial networks than exclusive mineral or organic fertilization. Soil Ecol. Letters 5:220142.

Google Scholar

Yang, F., Tian, J., Fang, H., Gao, Y., Xu, M., Lou, Y., et al. (2019). Functional soil organic matter fractions, microbial community, and enzyme activities in a mollisol under 35 years manure and mineral fertilization. J. Soil Sci. Plant Nutr. 19, 430–439. doi: 10.1007/s42729-019-00047-6

Crossref Full Text | Google Scholar

Yang, Y., Yu, K., and Feng, H. (2018). Effects of straw mulching and plastic film mulching on improving soil organic carbon and nitrogen fractions, crop yield and water use efficiency in the loess plateau, China. Agric. Water Manag. 201, 133–143.

Google Scholar

Yang, Q., Zheng, F., Jia, X., Liu, P., Dong, S., Zhang, J., et al. (2020). The combined application of organic and inorganic fertilizers increases soil organic matter and improves soil microenvironment in wheat-maize field. J. Soils Sediments 20, 2395–2404. doi: 10.1007/s11368-020-02606-2

Crossref Full Text | Google Scholar

Ye, C., Huang, S., Sha, C., Wu, J., Cui, C., Su, J., et al. (2022). Changes of bacterial community in arable soil after short-term application of fresh manures and organic fertilizer. Environ. Technol. 43, 824–834. doi: 10.1080/09593330.2020.1807608

PubMed Abstract | Crossref Full Text | Google Scholar

Yin, H., Zhao, W., Li, T., Cheng, X., and Liu, Q. (2018). Balancing straw returning and chemical fertilizers in China: role of straw nutrient resources. Renew. Sust. Energ. Rev. 81, 2695–2702.

Google Scholar

Yu, H., Li, P., Bo, G., and Shen, G. (2024). Studies on the humic acid structure and microbial nutrient restriction mechanism during organic-inorganic co-composting. J. Environ. Manag. 353:120186.

Google Scholar

Yu, X., Schweikert, K., Li, Y., Ma, J., and Doluschitz, R. (2023). Farm size, farmers’ perceptions and chemical fertilizer overuse in grain production: evidence from maize farmers in northern China. J. Environ. Manag. 325:116347. doi: 10.1016/j.jenvman.2022.116347

PubMed Abstract | Crossref Full Text | Google Scholar

Zanin, L., Tomasi, N., Cesco, S., Varanini, Z., and Pinton, R. (2019). Humic substances contribute to plant iron nutrition acting as chelators and biostimulants. Front. Plant Sci. 10:452874. doi: 10.3389/fpls.2019.00675

PubMed Abstract | Crossref Full Text | Google Scholar

Zhai, L., Wang, Z., Zhai, Y., Zhang, L., Zheng, M., Yao, H., et al. (2022). Partial substitution of chemical fertilizer by organic fertilizer benefits grain yield, water use efficiency, and economic return of summer maize. Soil Tillage Res. 217:105287. doi: 10.1016/j.still.2021.105287

Crossref Full Text | Google Scholar

Zhang, F., Chen, M., Fu, J., Zhang, X., Li, Y., and Xing, Y. (2023). Effects of drip irrigation on yield, soil fertility and soil enzyme activity of different potato varieties in Northwest China. Front. Plant Sci. 14:1240196. doi: 10.3389/fpls.2023.1240196

Crossref Full Text | Google Scholar

Zhang, Y., Gao, W., Ma, L., Luan, H., Tang, J., Li, R., et al. (2023). Long-term partial substitution of chemical fertilizer by organic amendments influences soil microbial functional diversity of phosphorus cycling and improves phosphorus availability in greenhouse vegetable production. Agric. Ecosyst. Environ. 341:108193. doi: 10.1016/j.agee.2022.108193

Crossref Full Text | Google Scholar

Zhang, M. J., Jia, J.-Q., Hua, L., Feng, M.-C., and Yang, W.-D. (2021). Functional diversity of soil microbial communities in response to supplementing 50% of the mineral N fertilizer with organic fertilizer in an oat field. J. Integr. Agric. 20, 2255–2264. doi: 10.1016/S2095-3119(20)63331-7

Crossref Full Text | Google Scholar

Zhang, X., Li, J., Shao, L., Qin, F., Yang, J., Gu, H., et al. (2023). Effects of organic fertilizers on yield, soil physico-chemical property, soil microbial community diversity and structure of Brassica rapa var Chinensis. Front. Microbiol. 14:1132853. doi: 10.3389/fmicb.2023.1132853

PubMed Abstract | Crossref Full Text | Google Scholar

Zhang, S., Li, X., Wu, J., Coin, L., O’Brien, J., Hai, F., et al. (2021). Molecular methods for pathogenic bacteria detection and recent advances in wastewater analysis. Water 13:3551. doi: 10.3390/w13243551

Crossref Full Text | Google Scholar

Zhang, L., Niu, J., Lu, X., Zhao, Z., Li, K., Wang, F., et al. (2023). Dosage effects of organic manure on bacterial community assemblage and phosphorus transformation profiles in greenhouse soil. Front. Microbiol. 14:1188167. doi: 10.3389/fmicb.2023.1188167

PubMed Abstract | Crossref Full Text | Google Scholar

Zhang, M., Sun, D., Niu, Z., Yan, J., Zhou, X., and Kang, X. (2020). Effects of combined organic/inorganic fertilizer application on growth, photosynthetic characteristics, yield and fruit quality of Actinidia chinesis cv ‘Hongyang’. Global Ecol. Conserv. 22:e00997. doi: 10.1016/j.gecco.2020.e00997

Crossref Full Text | Google Scholar

Zhang, Y., Wang, J., and Feng, Y. (2021). The effects of biochar addition on soil physicochemical properties: a review. Catena 202:105284. doi: 10.1016/j.catena.2021.105284

PubMed Abstract | Crossref Full Text | Google Scholar

Zhang, Y. J., Wei, G., Luan, H.-A., Tang, J.-W., Li, R.-N., Li, M.-Y., et al. (2022). Effects of a decade of organic fertilizer substitution on vegetable yield and soil phosphorus pools, phosphatase activities, and the microbial community in a greenhouse vegetable production system. J. Integr. Agric. 21, 2119–2133.

Google Scholar

Zhang, H., Yuan, X., Xiong, T., Wang, H., and Jiang, L. (2020). Bioremediation of co-contaminated soil with heavy metals and pesticides: influence factors, mechanisms and evaluation methods. Chem. Eng. J. 398:125657. doi: 10.1016/j.cej.2020.125657

Crossref Full Text | Google Scholar

Zhang, C., Zhao, Z., Li, F., and Zhang, J. (2022). Effects of organic and inorganic fertilization on soil organic carbon and enzymatic activities. Agronomy 12:3125. doi: 10.3390/agronomy12123125

Crossref Full Text | Google Scholar

Zhang, Q., Zhao, W., Zhou, Z., Huang, G., Wang, X., Han, Q., et al. (2022). The application of mixed organic and inorganic fertilizers drives soil nutrient and bacterial community changes in teak plantations. Microorganisms 10:958. doi: 10.3390/microorganisms10050958

PubMed Abstract | Crossref Full Text | Google Scholar

Zhao, W., Chen, Z., Yang, X., Sheng, L., Mao, H., and Zhu, S. (2023). Metagenomics reveal arbuscular mycorrhizal fungi altering functional gene expression of rhizosphere microbial community to enhance Iris tectorum's resistance to Cr stress. Sci. Total Environ. 895:164970. doi: 10.1016/j.scitotenv.2023.164970

PubMed Abstract | Crossref Full Text | Google Scholar

Zhao, Y., Wang, Y., Sun, S., Liu, W., Zhu, L., and Yan, X. (2022). Different forms and proportions of exogenous nitrogen promote the growth of alfalfa by increasing soil enzyme activity. Plan. Theory 11:1057. doi: 10.3390/plants11081057

Crossref Full Text | Google Scholar

Zhao, Y., Zhang, M., Liu, Z., and Yang, F. (2024). Migration and transformation of soil phosphorus by organic acids: a global meta-analysis. J. Soils Sediments 24, 589–602. doi: 10.1007/s11368-023-03665-x

Crossref Full Text | Google Scholar

Zhong, Y., Liu, J., Jia, X., Shangguan, Z., Wang, R., and Yan, W. (2020). Microbial community assembly and metabolic function during wheat straw decomposition under different nitrogen fertilization treatments. Biol. Fertil. Soils 56, 697–710. doi: 10.1007/s00374-020-01438-z

Crossref Full Text | Google Scholar

Zhou, S., Chang, T., Zhang, Y., Shaghaleh, H., Zhang, J., Yang, X., et al. (2024). Organic fertilizer compost alters the microbial composition and network structure in strongly acidic soil. Appl. Soil Ecol. 195:105263. doi: 10.1016/j.apsoil.2023.105263

Crossref Full Text | Google Scholar

Zhou, Z., Zhang, S., Jiang, N., Xiu, W., Zhao, J., and Yang, D. (2022). Effects of organic fertilizer incorporation practices on crops yield, soil quality, and soil fauna feeding activity in the wheat-maize rotation system. Front. Environ. Sci. 10:1058071. doi: 10.3389/fenvs.2022.1058071

Crossref Full Text | Google Scholar

Zhu, Z., Bai, Y., Lv, M., Tian, G., Zhang, X., Li, L., et al. (2020). Soil fertility, microbial biomass, and microbial functional diversity responses to four years fertilization in an apple orchard in North China. Horticultural Plant J. 6, 223–230. doi: 10.1016/j.hpj.2020.06.003

Crossref Full Text | Google Scholar

Zou, W., Lang, M., Zhang, L., Liu, B., and Chen, X. (2022). Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil. Sci. Total Environ. 811:151402.

Google Scholar