Effects of Biofertilizer on Yield and Quality of Crops and Properties of Soil Under Field Conditions in China: A Meta-Analysis

Abstract

Biofertilizers play a crucial role in promoting sustainable agriculture in China; however, comprehensive quantification of their effects and limitations in field conditions remain unclear. In this study, a meta-analysis encompassing 1818 comparisons from 107 studies was conducted to quantify their systematic effects in field conditions in China. The results demonstrated that biofertilizers enhanced crop yields across 21 of the 23 investigated crops, with notable increases in millet (+65.42%), vegetables (e.g., Chinese cabbage +35.57%, ginger +39.18%), and legumes (kidney beans +54.03%), while cotton and rapeseed showed non-significant improvements. Nutritional quality was also improved, as evidenced by elevated levels of vitamin C (14.61%), protein (16.61%), and carotenoids (15.18%), alongside a reduction in nitrate content (21.94%). Soil health was significantly improved through increased organic matter (16.64%), enhanced enzymatic activities (urease: 57.60%; phosphatase: 43.51%), and a proliferation of beneficial microbes (bacteria: 157.10%; fungi: 30.28%), while pathogenic organisms were suppressed by 51.81%. The observed yield improvements were attributed to enhanced nutrient availability (total nitrogen: 16.67%; available phosphorus: 10.98%), optimized root growth (19.23% increase in volume), and a reduction in disease incidence (42.52%). The efficacy of biofertilizers was maximized when they were used in conjunction with organic amendments, resulting in a 29.20% increase in yield, particularly when applied prior to planting. These results show that biofertilizers boost productivity, quality, and soil functionality, depending on their production and field management practices. Their effectiveness is tied to optimizing soil properties and suppressing pathogens, providing strategies for sustainable agriculture in China.

1. Introduction

As of 2024, the global population has exceeded 8.2 billion and is anticipated to reach 10.3 billion by the mid-2080s [1]. Concurrently, approximately 9.9% of the global population, equivalent to 802 million individuals, experienced severe food insecurity in 2022 [2]. Geopolitical events, climate change, and pandemics of infectious diseases have exacerbated food shortages [3]. Chemical fertilizers, especially nitrogen fertilizers, were often improperly applied to the soil to obtain high yield in the field, resulting in resource waste, water and air pollution, soil degradation, etc. [4,5]. Consequently, sustainable agriculture presents a significant global challenge that requires increased attention.

Biofertilizers, which are developed based on living bacteria, fungi, or other microorganisms, offer potential benefits to crops and soil properties. (i) They enhance plant nutrition by facilitating nutrient availability. For instance, nitrogen-fixing bacteria associated with legumes convert atmospheric N₂ into ammonium, which is accessible to plants [6,7]. Additionally, phosphate-solubilizing bacteria (PSB) and potassium-solubilizing bacteria transform mineral nutrients from unavailable forms into accessible ones for plants, thereby improving mineral use efficiency and crop yield [8,9,10]. Furthermore, microorganisms derived from compost have the capacity to transform soil organic matter (SOM) into dissolved organic matter, which encompasses humic substances and a variety of nutrients essential for plant growth [11,12]. (ii) They stimulate plant growth and defense. They are also capable of synthesizing phytohormones, which can modulate the phytohormone networks within plants, thereby influencing their growth and defense mechanisms [13,14,15]. (iii) They suppress the pathogen and make the soil healthy. The application of biofertilizers has been demonstrated to modify the structure of microbial communities, reduce disease incidence, and enhance plant tolerance to nematodes [16,17,18]. Additionally, biofertilizers improve the physical properties of soil, such as aggregate stability, total porosity, water retention capacity, and infiltration rate, while decreasing bulk density [19]. Recent studies have shown that these alterations in soil properties due to biofertilizer application significantly impact the structure of the soil’s microbial community [20].

Furthermore, the effects of biofertilizers are contingent upon the living microbes they contain, with each microbial species or strain exhibiting distinct effects and requiring specific optimal living conditions [21,22]. For example, various strains of Bacillus amyloliquefaciens are capable of producing distinct compounds, such as indole acetic acids, cyclic lipopeptides, volatile organic compounds, phytase, and siderophores, among others, which contribute to plant growth enhancement, pathogen resistance, and iron chelation [23]. This illustrates the multifaceted impacts of biofertilizers. Furthermore, the effects of biofertilizers can exhibit greater variability depending on differences in production methods, crop types, climatic zones, field conditions, and application techniques [21,24].

China, with its extensive range of climates and landscapes—from tropical to frigid zones and from oceanic to continental climates—demonstrates significant diversity in biofertilizer effects, as evidenced by many individual studies [25,26]. A comprehensive global analysis of the impact of biofertilizers on crop yield and nutrient use efficiency has been conducted [27]. However, the diversity and complexity of the biofertilizer effect under field conditions in China were not focused on or well-illustrated. Additionally, Atieno et al. conducted an in-depth evaluation of biofertilizer application for sustainable agriculture in the Greater Mekong region [21]. However, the existing literature lacks comprehensive quantification of these effects, and there are limitations across diverse edaphic contexts and practical management. To address this gap, this study utilized the PICO research framework, identifying sustainable field production as the P (problem), biofertilizer as the I (intervention), equal inorganic and organic materials as the C (comparison), and the properties of crops and soil as the O (outcome). With this format, a comprehensive meta-analysis was carried out to elucidate the quantitative effects of biofertilizers in Chinese field conditions to optimize their use for sustainable agriculture.

2. Materials and Methods

2.1. Data Collection

Data collection and subsequent analysis were conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines (Table S5). Relevant studies were sourced from the Web of Science (https://www.webofscience.com, accessed on 1 February 2025) and the China National Knowledge Infrastructure (CNKI, https://www.cnki.net, https://www.webofscience.com, accessed on 1 February 2025) databases up to February 2025 using Boolean operators, such as (bacteria OR fungi OR micro OR biofertilizer) AND yield AND China AND field (Topic), for the search. Studies selected for further analysis were required to meet specific criteria. (1) The variable ‘microbes’ was the sole distinction between the control and treatment groups in the experiments. (2) Each experiment was replicated at least three times. (3) The experiments were conducted under field conditions. (4) The location of the experiments and the microbial species used were clearly specified. Data on the number of replications (N), means, and standard deviations (SD) for both control and treatment groups were collected. We utilized GetData Graph Digitizer 2.26 (http://www.getdata-graph-digitizer.com/, accessed on 1 February 2025, Russian Federation) to extract means and SDs from figures when available. In cases where only standard errors (SEs) were provided, the SD was calculated using the formula SE√n. Neither the SE nor the SD was available in 42 studies, so the SD was approximated as 10% of the mean [28,29]. When multiple locations, strains, crops, application methods, or time points were present within a single study, each was treated as an independent experiment. Ultimately, 1818 comparisons from 107 studies were selected for further analysis [30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136]. The classification of climate regions followed the criteria established by Li [137] (Figure 1).

2.2. Effect Size Calculation and Its Normal Distribution Test

The effect size of the biofertilizer was quantified using the natural logarithm of the response ratio (lnR), where lnR = ln(X_E/X_C). Here, X_E and X_C denote the mean values of the experimental group (with microbes) and the control group (without microbes), respectively. A positive lnR signifies beneficial effects of the biofertilizer on crop yield, quality, and soil properties, whereas a negative lnR indicates adverse effects. The normality of the lnR distributions was assessed using the Kolmogorov–Smirnov test, the Shapiro–Wilk test, and Gaussian fitting. In cases where lnR did not follow a normal distribution, bootstrap resampling was employed for further meta-analysis [138].

2.3. Heterogeneity and Publication Bias

To evaluate data heterogeneity, several statistical measures were calculated, including the Q value (a statistic indicating the degree of heterogeneity by explaining variance), degrees of freedom (df), and I² (the proportion of variation in lnR attributable to heterogeneity). When Q < df, I² < 50%, and p > 0.05, the heterogeneity among the data is considered relatively low, suggesting that the data are appropriate for further analysis. If the specified conditions are unmet, the heterogeneity is considered excessively high, warranting further actions, such as transitioning from a fixed to a random-effects meta-analysis model, stratifying the data into subgroups, or performing a sensitivity analysis to detect and exclude outliers [139,140].

To evaluate potential publication bias, Rosenthal’s fail-safe number (Nfs) and Egger’s regression test were utilized. An Nfs greater than 5N + 10 (where N denotes the number of observations in the study) indicates an absence of significant publication bias [141]. Similarly, a p-value from Egger’s regression exceeding 0.05 suggests that publication bias is not statistically significant [142].

2.4. Meta-Analysis

The meta-analysis was conducted using the MetaWin statistical software package, Version 3.0.15 [143]. The variance and weight of the effect size in each experiment were calculated following the methodology of Rosenberg and Pei et al. [29,143]. Mean effects and their 95% confidence intervals were calculated in MetaWin according to Rosenberg [143]. If the 95% confidence interval did not overlap with zero, the biofertilizer’s effect was regarded as significant compared to the control.

2.5. Statistics

The Kolmogorov–Smirnov test, the Shapiro–Wilk test, Gaussian fitting, and ordinary least squares regression (OLS regression) were conducted using SPSS 25.0 statistics software (IBM SPSS, Inc., Armonk, NY, USA). OriginPro 2022 SR1 9.9.0.225 (OriginLab Corporation, Northampton, MA, USA) was used to make the figures.

3. Results

3.1. Normal Distribution and Heterogeneity of Biofertilizer Effect Size and Publication Bias Test

To determine the optimal meta-analysis model, we first evaluated the normality of the effect sizes associated with biofertilizer applications using the Kolmogorov–Smirnov test, the Shapiro–Wilk test, and Gaussian fitting. The results indicated that the effect sizes of biofertilizers on biomass enhancement, growth promotion, quality improvement, and soil amelioration were non-normally distributed (p < 0.05; adjusted R² relatively low). Although Gaussian fitting and the Kolmogorov–Smirnov test suggested potential normality for effect sizes related to crop yield and physiological improvement, respectively, the other two methods consistently rejected normality (Figure 2). Consequently, the bootstrap resampling method was adopted for subsequent analyses.

Substantial heterogeneity was detected in the data (Q > df, I² > 50%, p < 0.05), aligning with the inherent complexity and diversity of biofertilizer production and application practices. To address this, we stratified the data into homogeneous subgroups (e.g., by crop species, application method, and geographical region) for subsequent subgroup analyses. Additionally, effect sizes were not pooled in groups exhibiting high residual heterogeneity to avoid biased estimations. Furthermore, to evaluate potential publication bias in the included studies and ensure the reliability of subsequent analyses, Egger’s regression and the Nfs were applied. Egger’s regression results revealed no significant publication bias for the effects of biofertilizers on crop yield, quality, growth promotion, physiological enhancement, or soil improvement (p > 0.05 for all outcomes,

Table 1. Publication bias test based on Rosenthal’s Nfs and Egger’s regression.

Biofertilizer Effect	N	5N + 10	Rosenthal’s Nfs	p Value of Egger’s Regression
Yield increasing	376	1890	68,727.17	0.1985
Biomass increasing	351	1765	55,749.10	0.8089
Growth promotion	341	1715	72,679.67	0.1014
Physiology enhancement	108	550	1676.32	0.1188
Quality promotion	235	1185	7015.59	0.0614
Soil property improvement	415	2085	3669.21	0.7107

N refers to the number of studies.

). Additionally, the Nfs for these effects exceeded the threshold of 5N + 10 (where N is the number of studies), corroborating the absence of substantial publication bias (Table 1).

3.2. Biofertilizer Improves Yield and Quality of Crops Under Field Conditions in China

Biofertilizer application enhanced crop yields, with responses varying markedly by crop type (Figure 3A, Table S1). Cereal crops exhibited pronounced improvements; wheat yields increased by 22.30%, followed by rice (+13.58%) and maize (+12.77%), while millet showed the highest gain (+65.42%). Vegetables responded robustly, with Chinese cabbage (+35.57%), hot pepper (+24.78%), tomato (+21.75%), cucumber (+19.99%), and ginger (+39.18%) demonstrating significant productivity boosts. Tuber crops displayed moderate to high responses, including potato (+25.01%), sweet potato (+9.91%), and taro (+39.47%). Among legumes, soybean yields increased by 8.45%, while broad bean and kidney bean yields rose sharply by 38.72% and 54.03%. Melons showed strong gains in watermelon (+31.80%) and muskmelon (+40.05%). Oilseed crops exhibited mixed results; peanut (+28.76%) and sunflower (+17.61%) responded positively, whereas rapeseed showed only marginal improvement (+7.28%, p > 0.05). Sugar crops displayed divergent trends; sugarcane yields increased by 19.43%, and sugar beet by 14.22%. Economic crops, such as cotton (+16.22%) and tobacco (+9.86%), showed moderate enhancements, although cotton’s improvement was statistically non-significant (p > 0.05). Additionally, specialty crops, such as medicinal herbs (+43.03%) and forage alfalfa (+12.49%), exhibited significant yield improvements (Figure 3A, Table S1).

Analysis results revealed that biofertilizer application significantly and differentially enhanced yields for 21 of the 23 crops investigated, with cotton and rapeseed showing non-significant improvements. Within agronomic or taxonomic groupings, yield responses varied substantially among crop species, a pattern correlated with species-specific traits (e.g., root architecture, nutrient demand) and modulated by factors including soil properties, climatic conditions, and biofertilizer type—factors further analyzed in the following section.

Furthermore, biofertilizer application improved crop quality across three primary dimensions: nutrient composition, key quality indices, and mineral nutrient profiles. Firstly, biofertilizers significantly enhanced essential nutritional components, as vitamin C (+14.61%), protein (+16.61%), soluble sugars (+16.98%), and carotenoids (+15.18%) all increased markedly, while lipid content showed no significant change (p > 0.05). Secondly, for sensory and safety-related parameters, fruit soluble solids (+13.61%, p < 0.05)—a marker of flavor intensity—and fruit firmness (+69.47%, p < 0.05)—critical for postharvest storage—improved substantially. Nitrate content decreased by 21.94% (p < 0.05), enhancing food safety, although anthocyanin levels trended upward non-significantly (+11.61%), and titratable acidity remained unchanged.

Additionally, mineral nutrient profiles also revealed systemic enrichment. The concentrations of nitrogen (N), phosphorus (P), and potassium (K) in whole plants increased following biofertilizer application. Specifically, total N and total K exhibited significant increases of 27.58% and 26.87%, respectively, while total P showed a non-significant rise of 7.92% (Figure 3B, Table S1). Organ-specific analysis revealed pronounced enhancements in N content within roots (+104.34%) and stems (+20.00%), with marginal, statistically non-significant increases in N, P, and K observed across other plant organs. Silicon (Si) dynamics displayed tissue-specific variability; stems and leaves accumulated Si by 28.42% and 19.15%, respectively, whereas panicles exhibited a slight reduction (−4.22%) (Figure 3B, Table S1).

3.3. Impact Factors of Biofertilization on Crop Yield Under Field Conditions in China

To enhance the understanding of optimizing biofertilizer application for improved crop yield, we conducted an investigation into various factors affecting the efficacy of biofertilization. These factors included microbial categories and species, the developmental stages of strains, the materials used in conjunction with biofertilizers, the timing and method of fertilization, as well as climatic, soil, and field conditions.

The results indicated that the application of biofertilizers containing bacteria, fungi, actinomycetes, or complex organisms led to different increases in crop yield, with improvements of 18.87%, 22.67%, 12.85%, and 18.02%, respectively (Figure 4A, Table S2). Moreover, the use of specific biofertilizers, such as Bacillus spp., Arbuscular mycorrhiza, Rhizobium spp., Trichoderma spp., and effective microorganisms (EM), resulted in notable yield enhancements of 19.36%, 25.21%, 20.65%, 17.97%, and 16.75%, respectively (Figure 4A, Table S2). It was further observed that commercial strains outperformed research strains (Figure 4A, Table S2). The direct application of beneficial strains increased yield by 18.91%, while combination with organic substances to create a compound product resulted in a more substantial yield improvement of 29.20%. When beneficial strains were compounded with both organic and chemical substances, the impact on yield was less pronounced compared to when only organic substances were used, with a yield increase of 24.50% (Figure 4B, Table S2). The application of biofertilizers demonstrated the most significant effect on yield when used in conjunction with organic fertilizers, resulting in a yield increase of 25.08%. Notably, the effects were less pronounced when biofertilizers were applied alongside chemical fertilizers or a combination of chemical and organic fertilizers compared to using organic fertilizers alone (Figure 4B, Table S2). Regarding the timing of biofertilizer application, pre-planting application (basal fertilization, seed or seedling treatment) proved more effective than post-planting application (additional or basal and additional application, Figure 4B, Table S2).

Furthermore, climate, soil, and field conditions influenced the yield increase associated with biofertilizer application in China. Results indicated that biofertilizers significantly enhance yield in all types of climates, land uses, SOM, soil pH, and field uses. However, the yield increase is more substantial in temperate continental regions, upland fields, areas with medium to high SOM, neutral pH, and protected fields compared to other conditions (Figure 4C, Table S2).

3.4. Effects of Biofertilizer on the Growth and Defense of Crops

The application of biofertilizers significantly promoted plant growth under field conditions in China. The treated plants demonstrated notable morphological enhancements in both aerial and subterranean structures. Aboveground, there was an increase in plant height by 10.51%, stem length by 53.82%, diameter at breast height (DBH) by 7.85%, and internode elongation by 6.64%, along with a remarkable 229.14% increase in branch number (Figure 5A, Table S3). Leaf development was also enhanced, with increases in leaf count, length, width, and total area by 22.73%, 16.59%, 19.83%, and 27.01%, respectively (Figure 5A, Table S3). Belowground, the root systems exhibited substantial expansion, with root length, surface area, and volume increasing by 23.68%, 38.03%, and 19.23%, respectively (Figure 5A, Table S3).

Moreover, the biomass of crops was significantly increased by 25.42% (Figure 5B, Table S3). Notably, the fresh and dry weight of the whole plant, root, and shoot were all increased significantly. Interestingly, following biofertilizer application, the relative increase in root biomass significantly surpassed that of aboveground biomass, with root fresh weight and dry weight increments exceeding those observed in shoots. Specifically, root fresh weight increased by 41.17% and dry weight by 26.06%, while it increased by 21.28% and 22.64% for aboveground tissues (Figure 5B, Table S3). For cereal crops, although no significant change in the tillering rate was observed, grains per panicle and thousand-grain weight increased markedly (+7.86% and +5.76%, respectively). Fruit trees exhibited enhanced productivity through an elevated fruit set rate (+6.60%), fruit number per plant (+50.02%), and individual fruit weight (+22.18%). In tuber crops, biofertilizers significantly reduced the proportion of small tubers (−16.04%), promoting uniform tuber sizing, which is also critical for its quality (Figure 5B, Table S3). These results collectively corroborate biofertilizers’ capacity to optimize yield.

The physiological and biochemical factors of crops were modified through biofertilizer, leading to a significant increase of 208.67% and 46.35% in nitrogenase activity and root vigor (Figure 5C, Table S4). Meanwhile, the chlorophyll content, photosynthetic rate, and stomatal conductance were increased insignificantly in the statistics. Additionally, based on the weighted data of the disease severity index and disease incidence from included studies, analyzed results showed that biofertilizers enhanced crops’ defense against diseases, revealing a significant decrease of 54.45% and 42.52% in the disease severity index and disease incidence, respectively (Figure 5C, Table S4).

3.5. Effects of Biofertilizer on the Properties of Soils

Biofertilizer application significantly improved soil fertility through targeted nutrient modulation. As a fundamental chemical indicator, SOM significantly increased by 16.64% without altering soil pH. This enhancement is critical for optimizing soil structure, texture, and its capacity to retain and supply nutrients. (Figure 5D, Table S4). Furthermore, total N and total p rose significantly by 16.67% and 16.71%, respectively, while total K showed a non-significant increase of 11.65%. Notably, available P and available K surged by 10.98% and 23.52%, reflecting enhanced nutrient bioavailability (Figure 5D, Table S4). Conversely, hydrolyzable N decreased significantly by 9.69%, suggesting potential microbial immobilization or altered nitrogen cycling dynamics (Figure 5D, Table S4). Results indicated that the status of soil mineral nutrients improved following biofertilizer application. Specifically, the content of mineral nutrients in available forms increased, while the nutrient loss rate decreased, thereby enhancing the supply of essential nutrients for crops. This improvement not only enriches the soil nutrient pool but also optimizes nutrient cycling, ensuring a more sustainable and efficient nutrient delivery system for plant growth.

Biofertilizer application profoundly reshaped soil biochemical and microbial dynamics, driving enhanced nutrient cycling and ecosystem functionality. Soil enzyme activities critical for nutrient transformation were markedly upregulated, including urease (+57.60%), phosphatase (+43.51%), sucrase (+22.12%), and catalase (+24.97%; Figure 5D, Table S4). Concurrently, nitrification rates surged by 73.13%, reflecting accelerated nitrogen mineralization. Nutrient use efficiency improved systemically, with ammonium N (NH₄⁺) loss decreasing significantly (−15.56%), despite no notable change in phosphorus loss. While soil pH remained stable, electrical conductivity dropped sharply (−46.90%), likely linked to organic matter accumulation (+16.64%) and ionic balance modulation (Figure 5D, Table S4). Soil microbiomes exhibited dramatic restructuring; bacterial and actinomyces abundances increased by 157.10% and 179.02%, respectively, with fungal populations rising moderately (+30.28%; Figure 5D, Table S4). Conversely, pathogenic microbes declined by 51.81%, suggesting biofertilizers’ dual role in enriching beneficial taxa while suppressing phytopathogens. Results indicated that biofertilizer application systematically enhances soil biochemical processes and restructures microbiomes—boosting beneficial bacterial/actinobacterial abundances while suppressing pathogens—thereby optimizing nutrient cycling, reducing nitrogen loss, and creating a conducive microenvironment for sustained crop growth and productivity.

3.6. Correlations of Crops’ Yield with Plant Growth, Soil Properties, and Soil-Borne Diseases

To examine the changing relationships between crops’ yield and plant growth, soil properties, and soil-borne disease under biofertilizer applications, OLS regression was conducted. Results revealed that an increase in crop yields was positively correlated with growth parameters (e.g., plant height, DBH, leaf area) and biomass metrics (e.g., total biomass, fresh weight), as well as soil nitrogen and phosphorus levels. Conversely, yield showed negative correlations with the soil-borne disease index and incidence (Figure 6). These findings indicated that biofertilizers enhanced yield by (1) improving soil nutrient availability, (2) suppressing soil-borne pathogens, and (3) optimizing plant growth efficiency. Notably, yield was also positively associated with quality indices, including protein content, vitamin C, soluble sugars, and soluble solids. This dual enhancement of yield and quality underscores biofertilizers’ potential to address both productivity and nutritional security in modern agriculture.

4. Discussion

4.1. Biofertilizer Is a Reliable Option for Sustainable Agriculture

China’s agricultural sector confronts a significant challenge: sustaining 18% of the global population with only 7% of the world’s arable land [144]. Historically, to satisfy increasing food demands, smallholder farmers have heavily depended on chemical fertilizers, which has led to soil degradation and environmental pollution [145,146]. Our meta-analysis, encompassing 1818 field trials, indicates that biofertilizers present a sustainable alternative, resulting in yield increases ranging from 7.28% to 50.25% across various crops (Figure 2A, Table S1). Notably, millet (+65.42%), and medicinal herbs (+43.03%) demonstrated the most substantial gains, likely due to their capacity to thrive in nutrient-deficient soils where biofertilizers enhance microbial-mediated nutrient solubilization [147,148].

In addition to yield improvements, biofertilizers significantly enhanced crop quality, a crucial factor for market competitiveness and farmer profitability [149]. Key quality indicators, including vitamin C (+14.61%), protein (+16.61%), and mineral nutrients (e.g., whole-plant nitrogen +27.58%), showed marked increases in biofertilizer-treated crops (Figure 2B, Table S1). These enhancements are consistent with global trends, where high-quality produce commands premium market prices, while the reduction in nitrate content (−21.94%) contributes to improved food safety [150].

The dual advantages of biofertilizers—enhanced yield stability and nutritional enrichment—establish them as a fundamental component in China’s shift towards sustainable agriculture. By substituting 20–30% of chemical inputs with biofertilizers, farmers can reduce environmental damage without compromising productivity [151,152]. This transformative approach not only addresses urgent food security issues but also aligns with the United Nations’ Sustainable Development Goals.

4.2. Biofertilizers Enhance Crop Yield and Quality via Soil Microbiome-Mediated Nutrient and Growth Optimization

Microbes in biofertilizers facilitated the decomposition and mineralization of fresh organic matter, thereby releasing mineral nutrients (e.g., NH₄⁺, NO₃⁻, H₂PO₄⁻, HPO₄²⁻, K⁺) into the soil [153]. Simultaneously, their functional traits—including nitrogen fixation, phosphate solubilization, and potassium mobilization—converted inert nutrients into forms accessible to plants [154,155]. This process corresponds with observed increases in total N (+16.67%), available P (+10.98%), and available K (+23.52%) following biofertilization (Figure 5D, Table S4). The observed paradoxical reduction in available N (−9.69%) is likely attributable to microbial immobilization, wherein microbes temporarily assimilate nitrogen into biomass, serving as a nutrient reservoir to mitigate losses [156]. Additionally, microbial processing of organic matter facilitated humification, as evidenced by a 16.64% increase in SOM, which is a critical factor in enhancing soil structure, water retention, and buffering capacity [157,158].

The application of biofertilizers significantly enhanced the microbial community structure, with notable increases in bacteria (+157.10%), fungi (+30.28%), and actinomyces (+179.02%) within the rhizosphere, while reducing pathogenic microbes by 51.8% (Figure 5D, Table S4). This microbial ‘shield’ effectively suppressed soil-borne diseases, leading to a reduction in both disease incidence (−42.52%) and severity (−54.45%) through mechanisms of competitive exclusion and induced systemic resistance [15,159].

The synergistic improvement in soil fertility and microbiome health facilitated enhanced plant growth [160,161]. Belowground, roots exhibited prioritized development, with length (+23.68%), surface area (+38.03%), and volume (+19.23%) increases adaptations to efficiently exploit enriched soil nutrients, which may be associated with the remodeling of root architecture by beneficial microorganisms in biofertilizers [162]. Aboveground, plants demonstrated substantial growth, as evidenced by increases in height (+10.51%), stem diameter (+7.85%), and leaf area (+27.01%; Figure 5A, Table S3). OLS regression analysis confirmed that yield gains were positively correlated with soil nitrogen and phosphorus levels, plant biomass, and crop quality indices and negatively correlated with disease indices. These findings illustrate that biofertilizers simultaneously enhance yield and quality, outcomes driven by improved soil nutrient availability and optimized plant growth.

4.3. Determinants of Biofertilizer Efficacy: Specific Plant–Microbe Interactions and Management Practices

The efficacy of biofertilizers in enhancing crop yields varied markedly across species and conditions, underscoring the critical influence of plant–microbe interactions and management practices (Figure 3 and Figure 4). Each crop possesses unique nutrient requirements, root structures and exudates, stress sensitivities, and limiting factors in specific growth conditions. Conversely, the microbial agents in each biofertilizer exhibit distinct advantages in nutrient transformation, hormone production, compatibility, and adaptability [163,164]. The complex interaction relationships formed by the combination of these two aspects give rise to the diversified effects of biofertilizers. Researchers aim to identify their optimal combinations, overcome limiting factors, and maximize agronomic benefits. Cereals exhibited pronounced responses, with millet achieving the highest yield gain (+65.42%), which may be attributed to biofertilizers enhancing its tolerance to drought stress [165,166]. In contrast, rice showed more modest improvements (+13.58%), potentially constrained by anaerobic soil conditions that limit microbial activity and SOM mineralization in flooded paddies [28]. In legume crops, kidney beans and broad beans exhibited higher yield increases than soybean (+54.03%, 38.72% vs. +8.45%), likely due to their better compatibility with nitrogen-fixing bacteria in biofertilizers, shorter growing periods, or nitrate inhibiting nitrogen fixation in soybean [167]. These disparities highlight the need for crop-tailored biofertilizer formulations that align with species-specific nutrient demands, root architectures, and stress tolerance mechanisms.

Furthermore, biofertilizer formulations, soil conditions, and application methods all influence their yield-enhancing effects. Results showed that the more favorable the conditions for the colonization and establishment in soil of beneficial microorganisms from biofertilizers, the greater the yield improvement achieved by biofertilizers (Figure 4). Appropriate organic carriers enable beneficial microorganisms in biofertilizers to maintain optimal physiological conditions and longer shelf life and achieve sufficient and effective delivery to the target application site—the soil surrounding plant roots [168]. Consistently, this study also found that when biofertilizers were compounded with or applied together with organic matter, their yield-increasing effects were better than when applied alone or in combination with chemical fertilizers (Figure 4). Additionally, this study also found that pre-planting applications, seed treatment, or seedling-stage inoculation resulted in better yield increases than post-planting biofertilization application. This aligns with findings from other studies, where early-stage inoculation facilitates successful colonization by beneficial microorganisms by modifying the soil environment and secreting beneficial metabolites. Concurrently, early intervention enables beneficial microorganisms to restrict competing microorganisms—including pathogens and non-beneficial microbes—via mechanisms like inducing antibody production, establishing systemic immune resistance, and forming physical barriers around root systems [169,170]. Field condition analysis further revealed optimal outcomes in temperate continental climates, protected land, and neutral-pH soils (Figure 4C), where stable temperatures and balanced ion exchange favor microbial persistence [171].

4.4. Limitations of the Study

The experiments included in this study specified experimental climates, soil conditions, and biofertilizer formulations, and they were conducted rigorously with controls. However, the real field condition—characterized by inherent variability in environmental stability and management practices—imposed numerous constraints. As such, these results cannot fully demonstrate the latent potential of biofertilizers but rather reflect their real-world efficacy under current operational conditions.

Although our analysis did not detect significant publication bias, research screening beneficial microorganisms and optimizing biofertilizer formulations with suboptimal or null effects may remain unpublished—a potential limitation that prevents this study from fully representing biofertilizer development. Additionally, factors like the diversity of crop cultivars, variability in crop-specific study numbers, and constraints on accessible data quantities introduced inherent limitations to our analytical scope.

5. Conclusions

The application of biofertilizers exhibits positive effects on enhancing crop yield, quality, and soil properties. The diverse yield-improving performances of biofertilizers arise from interactions among crop types, fertilizer formulations, and application methods. Our findings highlight the need to strengthen policy guidance and product development for specialized biofertilizers tailored to specific regions, crops, and soil conditions. Formulation optimization should prioritize incorporating organic substrates with high compatibility for beneficial functional microbes; concurrently, these organic materials should be applied alongside biofertilizers to maximize synergistic effects. Biofertilizers are most effectively applied before crop establishment—whether through pre-planting soil application or seed/seedling inoculation—to facilitate early colonization and function of beneficial microorganisms.