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Review

Effects of Microbial Agents on Soil Improvement—A Review and Bibliometric Analysis

by
Mengdi Tan
1,2,
Tianjiao Feng
1,2,3,*,
Cong Wang
4,
Xiaozhen Hao
1,2 and
Hang Yu
1,2
1
School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, China
2
Jixian National Forest Ecosystem Observation and Research Station, Linfen 042200, China
3
Engineering Technology Innovation Center for Ecological Protection and Restoration in the Middle Yellow River, Ministry of Natural Resources, Taiyuan 030006, China
4
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
*
Author to whom correspondence should be addressed.
Agronomy 2025, 15(5), 1223; https://doi.org/10.3390/agronomy15051223 (registering DOI)
Submission received: 1 April 2025 / Revised: 4 May 2025 / Accepted: 15 May 2025 / Published: 17 May 2025
(This article belongs to the Special Issue Innovations and Obstacles: Microbial Communities in the Journey of Soil Remediation)
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Versions Notes

Abstract

:
Microbial agents play a crucial role in improving soil quality, increasing soil fertility, enhancing crop yields, and reducing the incidence of diseases. The ecological benefits of these products contribute to environmental protection and to the promotion of sustainable agricultural development. Since the beginning of the 21st century, research in the academic community on the use of microbial agents for soil improvement has increased, yet a systematic summary of the progress in this field is lacking. In this paper, we review trends in microbial agent applications, focusing on their classification, mechanisms of action, and practical implementations. To achieve this, we conduct a bibliometric analysis based on the SCI-EXPANDED database of the Web of Science, using tools such as VOSviewer for visualization. We focus on microbial agents for soil improvement and analyze publication trends, research hotspots, and annual variations in relevant studies published between 2003 and 2024. The results show that (1) the number of publications on microbial soil improvement has steadily increased over the years, indicating that the academic community has maintained a high level of interest in this field. Keywords such as “soil”, “diversity”, “carbon”, and “nitrogen” have been central research hotspots in the past 20 years. The research has been highly concentrated in a few countries, including China and the United States, as well as in key institutions such as the Chinese Academy of Sciences and the United States Department of Agriculture. (2) We further analyze the principles governing microbial agent efficacy, address limitations in their application, and propose strategies to advance research in this field. Finally, several suggestions are proposed to promote the further development of research on microbial agents for soil improvement.

1. Introduction

Soil, essential for human survival, is a critical component of Earth’s environment, influencing plant, animal, and human health while serving as a key resource for food security [1,2]. Its condition is interconnected with air, water quality, and microbial activity. However, population growth, climate change, industrial expansion, and unsustainable land use have exacerbated soil pollution and degradation, threatening ecosystem stability and societal development [3]. Globally, 33% of soils face degradation from urbanization, erosion, nutrient depletion, salinization, desertification, and pollution. In China, degradation is concentrated in 13 provinces across the northwest, north, and northeast, positioning the country among those most severely impacted [4,5]. Addressing soil degradation through improved physicochemical properties and sustainable management remains a priority for soil science research [6].
Historically, agricultural reliance on chemical fertilizers boosted crop yields and organic matter content but led to soil acidification, organic loss, and environmental pollution [7]. This environmental toll has accelerated the search for eco-friendly alternatives, with microbial remediation emerging as a promising strategy due to its potential to enhance soil health through nutrient cycling, aggregate stabilization, and pollutant degradation [8,9]. To counter degradation, research focuses on understanding soil ecosystem dynamics and developing eco-friendly solutions. Current remediation strategies include biological, chemical, and physical methods. Biological approaches, leveraging plant, animal, and microbial activities to enhance soil health, have gained prominence due to their sustainability, cost-effectiveness, and environmental benefits.
Among biological technologies, phytoremediation is the most established, while soil amendments target desertification. Microbial remediation, a newer approach, employs industrially produced microbial inoculants to regulate nutrient cycles, stabilize soil aggregates, and degrade pollutants [8]. Soil microbes, integral to soil formation and nutrient cycling, act as nutrient transformers, pollutant purifiers, and ecosystem stabilizers [9,10]. Microbial agents are defined as formulated products containing live microorganisms (e.g., Bacillus, Pseudomonas, arbuscular mycorrhizal fungi) or their bioactive metabolites, specifically designed to enhance soil functions such as organic matter decomposition, nutrient cycling (C, N, P), and pollutant degradation [10,11]. These agents directly contribute to ecosystem services including soil carbon sequestration, crop yield stability, and heavy metal immobilization. Microbial agents improve fertility, reduce chemical inputs, suppress pathogens, and enhance crop yields. Their integration with phytoremediation and other techniques offers a pathway to sustainable agriculture [11,12].
Advances in microbial agent development stem from methodological innovations. Early isolation and cultivation techniques in the 19th century gave rise to microbial studies, while 1970s biomass quantification methods spurred progress in nutrient turnover analysis [13,14]. Late 20th-century molecular biology revolutionized soil microbiology, expanding microbial agent diversity, functionality, and global application [15,16]. Current research focuses on agent development, microbial interactions, biocrusts, plant–microbe synergy, and hybrid remediation technologies [17].
Despite these advancements, a critical gap persists—the existing literature either focuses on mechanistic reviews of microbial functions or bibliometric analyses of global trends, rarely integrating both to identify how research hotspots align with on-the-ground challenges in soil improvement [17,18,19]. Traditional literature analysis struggles to track trends in this vast field. Bibliometrics, combined with tools like VOSviewer, enables quantitative analysis and visualization of research progress [18]. This study uses Web of Science (WoS) and China National Knowledge Infrastructure (CNKI) data to conduct a bibliometric review of microbial soil improvement over the two decades, identifying hotspots, gaps, and future directions to guide researchers and deepen understanding of microbial agents’ ecological significance.

2. Materials and Methods

2.1. Data Sources

In this paper, we establish a database using the Science Citation Index (WoS TM Core Collection) as the source of international bibliographic information. A search query of TS = (“microbial agent” OR “microbe” OR “bacterial agent”) AND TS = (“improve” OR “restoration” OR “amendment”) AND TS = (“soil” OR “soil fertility” OR “crop yield” OR “soil-borne pathogen”) was applied, excluding review articles to prioritize original research contributions and minimize citation bias, with a time span from 1 January 2003 to 31 December 2024. Data cleaning involved removing duplicates using EndNote X20 (95% title–author similarity threshold) and manually excluding irrelevant studies (e.g., marine or medical applications). A total of 3964 papers related to microbial improvement of soil were included in the analysis (Figure 1). The Chinese literature data source was determined through keyword searches in the China National Knowledge Infrastructure (CNKI) database, restricted to journals indexed in the Chinese Science Citation Database (CSCD), Peking University Core, or Engineering Index (EI) to ensure quality. In the advanced search box, the query “microbial agents + soil improvement” was used with a time limit from 2003 to 2024, and non-English publications were cross-checked by bilingual researchers to align with the study scope. After rigorous screening, 118 relevant papers from Chinese sources were retained. All raw datasets are publicly accessible via the WoS and CNKI platforms, ensuring transparency and reproducibility. Data validation included duplicate removal and manual verification by independent researchers to confirm consistency with inclusion criteria.

2.2. Analysis Method

VOSviewer (version 1.6.20) software analyzed publication volume, annual keyword trends, and institutional collaborations in the Web of Science [19] (Figure 2). The literature from the CNKI database was not considered because the actual number after screening to highlight duplicates and the irrelevant literature was below 60, making it difficult to form a statistical pattern. Keyword co-occurrence/clustering networks were constructed to visualize research hotspots, with a minimum keyword occurrence threshold set to 12 to filter low-frequency noise and enhance thematic clarity. Temporal keyword evolution maps highlighted shifting priorities, while country–institution collaboration networks were also generated to assess global partnerships. VOSviewer settings utilized the Louvain clustering algorithm and association strength normalization to optimize network interpretability. Annual publication counts and top journal rankings since 2003 were plotted using Origin Pro (2021). These bibliometric approaches revealed the field’s current landscape, research foci, and future directions [20].

3. Bibliometric Analysis

3.1. Global Publication Trend Analysis

From 2003 to 2024, SCI-indexed publications on soil-improving microbial agents increased annually, with distinct growth phases (Figure 2). The period 2003–2014 showed high growth rates, while 2015–2024 exhibited slower relative growth but larger absolute increases due to an expanded publication base. Post-2015 trends followed an exponential trajectory (Figure 2), indicating accelerated research output alongside methodological diversification. While the overall publication trend shows an increase, the temporary decline in citations after 2022 may reflect research constraints due to the impact of the epidemic and delays in indexing articles in the Web of Science database.
Clarivate’s 2024 Journal Citation Reports identified contributions from 104 countries, with significant output disparities (Figure 2 and Figure 3). China led with 1928 publications (continuous 20-year growth), followed by the United States (789 publications, 19.8% of global output), both maintaining upward trends.
At the institutional level, the Chinese Academy of Sciences (CAS) is the most prolific institution in the world, with 477 papers. The U.S. Department of Agriculture’s Agricultural Research Service (USDA ARS) and University of Florida published 45 and 43 papers, respectively (Figure S1 and Table S2).

3.2. Visualization Analysis of High-Frequency Keyword Co-Occurrence

Between 2003 and 2024, 9821 keywords were identified in microbial agent research for soil improvement, with 169 high-frequency keywords (occurrence > 12, defined as hotspots) highlighting research hotspots after manual deletion of duplicate keywords (Figure 4, Table 1 and Table S4). During 2013–2023, terms including “soil”, “diversity”, “nitrogen”, “carbon”, “rhizosphere”, “plant-growth”, and “bacteria” emerged as central nodes in the keyword network.
The co-occurrence network clustered into three modules, representing core research themes. The red module (“biochar”, “microbial community”, “phytoremediation”, “heavy metals”, “bioremediation”) focused on biochar-induced microbial community dynamics and their roles in nutrient cycling, particularly phytoremediation mechanisms for heavy metal contamination. The green module (“microbiome”, “rhizosphere”, “sustainable agriculture”, “biocontrol”, “metagenomics”, “plant-microbe interactions”, “arbuscular mycorrhizal fungi”) emphasized rhizosphere microbiome functions, exploring stress resistance enhancement through microbial symbiosis and arbuscular mycorrhizal fungi to advance sustainable agriculture. The blue module (“soil microbes”, “soil organic carbon”, “bacteria”, “fungi”, “microbial biomass”, “phosphorus”, “nitrogen”) underscored the microbial regulation of soil organic carbon cycling and nutrient (N/P) transformation mechanisms.

3.3. Analysis of Research Hotspots and Emerging Trends

Since keywords effectively summarize the main research themes, we further employed keyword clustering networks to provide an overview of changes in research hotspots within the field of microbial agents for soil improvement over the past 20 years. Figure 5a illustrates the annual variations in the keyword co-occurrence network, showing the keywords that were predominant between 2010 and 2023, which indicates a significant increase in research hotspots during this period (Table S3). This trend aligns with the rapid growth in publication volume observed from 2015 to 2023, as shown in Figure 2, Figure 5b shows the annual changes in keyword hotspots from 2018 to 2024 (Table S3), which transition from purple to green to yellow. The purple keywords include “microbial biomass”, “nitrogen”, “nutrient cycling”, “rhizobacteria”, “heavy metals”, and “remediation”; the green keywords are “microbial diversity”, “soil microbes”, “rhizosphere”, “biochar”, and “sustainable agriculture”; and the yellow keywords include “bacterial community”, “soil health”, “ecological restoration”, “microbial agent” and “metagenomics”. The results demonstrate a shift in research trends within this field: around 2018, the focus was primarily on the role of microorganisms in soil remediation and nutrient cycling. After 2021, the attention shifted toward the application of molecular biological techniques, as well as the diversity and community composition of microorganisms. More recently, emphasis has been placed on the role of microorganisms in plant disease resistance and growth promotion.

4. Classification of Microbial Agents

Microbial agents and fertilizers are widely utilized for soil improvement globally, demonstrating benefits in agricultural productivity and environmental sustainability [21]. To elucidate their mechanisms, challenges, and applications, microbial agents are classified through multiple criteria based on global research, industry standards, and bibliometric findings (Table 2). These distinctions are classified by form as liquid or solid formulations, composition as single-strain or composite agents, functional roles encompassing organic composting, soil remediation, disease resistance, and growth promotion, and microbial types including bacterial, fungal, or actinomycete agents [22]. Proper application of these agents enhances crop yields, soil quality, and ecological protection, offering a theoretical foundation for optimizing agricultural practices [23].

4.1. Microbial Agent Formulation Types

Microbial agents can be categorized by their formulation type into liquid and solid microbial agents. Liquid microbial agents are typically prepared by suspending or concentrating microbial strains obtained from fermentation, which are then mixed with other components, such as nutrients and trace elements. This type of microbial agent has advantages such as ease of preparation process and short activation and initiation times, allowing for rapid activation of the reactor and improved processing efficiency. Therefore, it holds significant potential for development and application in practice [26]. For example, Previous studies isolated the FE-1 fungal strain from farmland and formulated it into a liquid microbial agent [36]. This agent effectively degrades fomesafen in the soil and promotes root growth in plants, thereby reducing the impact of pesticide residues on crops. Compared with liquid microbial agents, solid microbial agents have a longer shelf life and lower strain loss rate, making them easier to store and transport. This is significant for reducing the transportation and usage costs of the agents. Solid formulations have a shelf life of up to 12 months, but activation takes 24–48 h, which may delay farm time; liquid formulations have an activation time of <6 h but require cold-chain transportation. Recent research has shown that, even after different periods of storage, the composting effects of solid microbial agents remain similar [37]. These agents can effectively improve compost maturity and shorten the composting cycle, further demonstrating the advantages of solid microbial agents in terms of shelf-life and strain stability. Furthermore, research has demonstrated that the application of both liquid and solid microbial agents can significantly increase soil urease activity, thereby increasing the total nitrogen content in plants, expanding the leaf area, and substantially increasing the chlorophyll content (as measured by a soil–plant analysis development (SPAD) meter). This leads to an increase in the net photosynthetic rate of leaves, with yield improvements of 26.9% and 34.4%, respectively, compared with those of treatments without microbial agents [38].

4.2. Classification of Microbial Species and Functional Characteristics of Microbial Agents

Microbial agents are categorized by microbial type into bacterial, fungal, and actinomycete agents. Bacterial agents, including Bacillus spp., lactic acid bacteria, rhizobia, and Pseudomonas spp., enhance soil fertility and structure through metabolic diversity and rapid reproduction [39]. For example, Bacillus siamensis promotes garlic growth and alters soil enzyme activity via protease activity, siderophore production, and phosphorus solubilization [40]. Fungal agents such as arbuscular mycorrhizal (AM) fungi improve crop nitrogen uptake while reducing soil N2O emissions through regulation of nitrification/denitrification genes [41]. Actinomycete agents, notably Streptomyces spp., suppress plant pathogens via antagonism and parasitism, with Streptomyces albus demonstrating superior biocontrol efficacy against cucumber root-knot nematodes [35].
Functionally, microbial agents are classified as growth-promoting, composting, disease-resistance, or bioremediation agents. Growth-promoting agents enhance nutrient uptake and stress tolerance through hormone secretion and nutrient solubilization. Their combined application with bioorganic fertilizers elevates soil organic matter, phosphorus, potassium, and microbial biomass in tea chrysanthemum systems [42]. Composting agents, including Bacillus subtilis–Aspergillus niger consortia, accelerate organic matter degradation and compost maturation [43]. Disease-resistance agents utilize actinomycetes—responsible for 67% of antibiotic production—to combat pathogens through antibiotic synthesis and nutrient competition [44]. Bioremediation agents such as Bacillus licheniformis mitigate heavy metal toxicity and pollutant residues, restoring soil microecosystem functionality [45].

4.3. Microbial Agents Can Be Classified on the Basis of Their Composition

Microbial agents can be classified into single microbial agents and composite microbial agents on the basis of their composition. Single microbial agents (e.g., preparations containing only Bacillus subtilis) have limited functionality and environmental adaptability but are highly targeted and suitable for specific disease control; compound microbial agents (e.g., EM microbial agents) can improve adaptability through multibacterial synergy, but at an increased cost. Many studies have demonstrated that the degradation or transformation of many organic substances requires the synergistic action of multiple microorganisms [39]. Composite microbial agents, which are prepared by mixing two or more strains with different functions at a specific ratio, offer stronger adaptability and stability than single microbial agents do, fully leveraging the synergistic advantages of the microbial community for optimal application results [46]. Since the 1970s, in countries such as the United States, Japan, and those in Europe, various composite microbial agents have been successfully developed, with the most successful being the effective microorganism (EM) agent developed by Professor Teruo Higa of the University of Ryukyu in the early 1980s, which has been widely used in more than 90 countries for agriculture, animal husbandry, and environmental remediation, yielding significant economic, ecological, and social benefits [46]. The research on microbial agents in China started later but has developed rapidly, and several microbial agents have now been introduced, such as the successfully developed “Shenwei” microbial ecological formulation, which, after extensive experimental application, has begun to be widely used in agriculture, animal husbandry, and environmental applications, achieving good societal, economic, and ecological benefits [47]. The use of this microbial agent not only reduces the amount of chemical fertilizers needed but also degrades harmful substances in the soil, enhances soil fertility, and improves soil resistance and resilience, thereby improving the soil environment.

5. Soil Improvement Effects of Microbial Agents and Influencing Factors

5.1. Role of Microorganisms in the Regulation of Soil Physicochemical Properties

Microorganisms play a crucial role in regulating nutrient cycling and transformation in soil and plants, serving as indispensable and highly active biological agents in soil. To varying degrees, the abundance and diversity of microorganisms in the soil control the direction of soil nutrient transformation, the types of compounds produced, and the exchange flux in the soil. Soil microorganisms play a key role in nutrient cycling, particularly for elements such as C, N, and P, by participating in processes such as autotrophic carbon fixation, by driving the soil carbon cycle, and by regulating soil phosphorus availability, making them important contributors to soil health regulation [48] (Figure 6 and Table 3).

5.1.1. Microorganisms Are Involved in the Assimilation and Mineralization of Organic Carbon

Microorganisms regulate the soil carbon balance by participating in the assimilation and mineralization of organic carbon. The extracellular and intracellular enzymes secreted by microorganisms are key factors contributing to soil enzymatic activity, with the extracellular enzymes that catalyze the transformation of organic and inorganic substances in soil being the primary agents driving soil organic carbon mineralization [57] (Figure 6 and Table 3). Recent studies on the soil carbon pump theory suggest that, after the exterior modification of recalcitrant organic substrates into small, easily absorbable molecules through extracellular enzymes, microorganisms carry out internal turnover, leading to the iterative accumulation of microbial residues and promoting the formation of organic matter. This process ultimately results in the stabilization of such compounds in the soil via the microbial “entombing effect”, which significantly contributes to the accumulation of soil organic carbon (SOC) [58]. The physiological characteristics of individual microorganisms and the ecological traits of microbial communities regulate the diversity of soil ecological functions, thereby influencing soil mineralization. The production of microbial residues is controlled by three physiological characteristics: the microbial growth rate (MGR), the carbon use efficiency (CUE), and the microbial biomass turnover rate (MTR) [59]. Studies have shown a significant correlation between soil CUE and soil SOC, and since the composition and diversity of soil microbial communities are key factors influencing soil CUE, the contribution of soil microorganisms to CUE and SOC is highly important. However, the mechanisms by which individual microorganisms and microbial communities drive soil carbon accumulation through assimilation still require further investigation [60,61].

5.1.2. Regulatory Role of Microorganisms in Soil Biological Nitrogen Fixation

Biological nitrogen fixation (BNF) in soil mainly occurs through the following pathways: (1) symbiosis with leguminous plants to form root nodules; (2) associative nitrogen fixation without root nodule formation; and (3) nitrogen fixation by bacteria such as cyanobacteria, Azotobacter, and Clostridia [62,63] (Figure 6 and Table 3). In addition, the efficiency of biological nitrogen fixation can be enhanced through the exogenous application of organic materials, microbial agents, and other measures. Inoculation with nitrogen-fixing bacteria can also promote biological nitrogen fixation; however, challenges include competition for nutrients with indigenous microbial communities, unstable host‒symbiont compatibility, and difficulty in ensuring nitrogen fixation capacity throughout the entire lifecycle [64]. Biological nitrogen fixation involves the conversion of atmospheric nitrogen ( N 2 ) into ammonium ( NH 4 + ), which is then oxidized in the soil by ammonia-oxidizing archaea and bacteria to form nitrate ( NO 3 - ) or further converted into nitrate ( NO 3 - ) through nitrite oxidation by nitrifying bacteria. However, biological nitrogen fixation produces the byproduct N 2 O , a potent greenhouse gas that exacerbates the atmospheric greenhouse effect. Soil microorganisms carrying genes for N 2 O reductase (encoded by nosZ) can reduce N 2 O to N 2 [63,65] (Figure 6 and Table 3). Thus, it is evident that microorganisms play crucial roles in driving the soil nitrogen cycle and regulating soil nitrogen availability.

5.1.3. Microbial Regulation of Soil Phosphorus Availability

Plants acquire phosphorus primarily from soil, where it exists as organic (bound in recalcitrant compounds) and inorganic forms. While organic phosphorus requires microbial mineralization to release plant-available inorganic phosphate (Pi), inorganic phosphorus dominates (60–80% of total soil phosphorus) yet is largely immobilized through adsorption or mineral fixation [66]. Only 1% of inorganic phosphorus exists as soluble forms (e.g., water-soluble Pi bound to low-molecular-weight organics), directly accessible to plants. Plant roots enhance Pi mobilization via phosphatase secretion, aided by microbial activity. Soil microorganisms sustain phosphorus availability through three key functions: (1) solubilizing mineral phosphorus, (2) mineralizing organic phosphorus, and (3) facilitating plant uptake and translocation [67] (Figure 7 and Table 3). By balancing organic-inorganic phosphorus conversion and enriching soil organic phosphorus pools, microbes ensure sustained nutrient supply for soil–plant ecosystem health.

5.1.4. Microbial Improvement of Soil Physical Structure

Soil aggregates, critical for nutrient storage and ecosystem function, maintain water stability, root development, and erosion resistance (Figure 7 and Table 3). Their formation requires cementing agents (e.g., humus, polysaccharides, microbial secretions) and aggregation forces (e.g., wet–dry cycles, biological activity). Humus, the primary stabilizing agent, originates from microbial transformation of organic matter. Biological forces—particularly microbial activity, root growth, and burrowing fauna—drive aggregate development [68].
Microorganisms enhance aggregation through three mechanisms: (1) secreting extracellular polymeric substances (EPS) to bind particles, (2) utilizing cell surface charges for electrostatic adhesion, and (3) entangling particles via fungal/actinobacterial hyphae [69] (Figure 7 and Table 3). Microbial spatial heterogeneity further facilitates aggregate formation, with diverse communities synergistically improving soil structure. Thus, microorganisms are pivotal in establishing stable aggregate networks [70].

5.2. Microbial Improvement of the Soil Biological Environment

The ecological effects of microorganisms on improving the soil environment are reflected primarily in an increase in the population of beneficial microorganisms, an inhibition of pathogen growth, an increase in soil resistance, the degradation of harmful substances in the soil, and restoration of the soil biological environment.

5.2.1. Microbial Resistance to Stress and Control of Soil Pests and Diseases

Soil microorganisms play vital roles in countering biotic and abiotic stresses, directly influencing soil health and plant resilience [69]. Beneficial microbes enhance soil disease resistance through competition, predation, parasitism, and secretion of antagonistic compounds (Figure 7 and Table 3). Their adaptive strategies to environmental stress include: (1) metabolic adaptation via altered pathways to produce stress-specific metabolites; (2) dynamic regulation of gene expression timing and intensity; and (3) cooperative resource-sharing networks that suppress pathogen colonization [70]. For instance, bacterial-fungal synergies enable resource exchange while maintaining ecological equilibrium [71]. Such interconnected microbial networks enhance soil–plant health, underscoring microbial biotherapy as a promising strategy to enrich beneficial taxa, reduce pathogens, and improve soil resilience.

5.2.2. Microbial Control of Pollution and Degradation of Harmful Substances

Soil microorganisms critically transform and detoxify pollutants such as petroleum hydrocarbons, microplastics, and heavy metals, which disrupt microbial communities and soil ecosystem functions [72,73]. Petroleum remediation relies on bioaugmentation with microbial agents, as biostimulation alone often fails to degrade complex hydrocarbons. Enzymatic processes—including oxidation, reduction, and decarboxylation—break hydrocarbons into CO2, H2O, and benign byproducts [74]. For microplastics, extracellular enzymes and radicals depolymerize plastics into oligomers, which are mineralized into CO2, H2O, and N2 [75] (Figure 7 and Table 3). Fungal-dominated communities exhibit superior degradation efficiency compared to bacteria, highlighting the importance of enhancing fungal diversity [76,77].
Heavy metal remediation leverages microbial bioadsorption, immobilization, and redox reactions. Microorganisms chelate metal ions via extracellular polymeric substances (EPS) or intracellular sequestration, offering an eco-friendly alternative to physicochemical methods that risk secondary pollution [78]. These mechanisms—combined with metal ion-EPS complexation—enable efficient, low-cost immobilization of contaminants [79,80].

5.3. Microorganisms as Predictors of Soil Health

Soil microorganisms naturally respond strongly to various physicochemical changes in soil, showing direct or indirect reactions to changes in the soil environment, making them sensitive indicators of soil health [81]. Following the inoculation of microbial agents into the soil, these agents interact with the soil ecosystem through various mechanisms, including antagonism, competition, metabolic inhibition, and symbiosis, and their proper application can positively influence microbial activity, diversity, and community structure within soil [82]. The diversity, biomass, abundance, health and community structure of microorganisms in soil, as determined by metagenomics techniques, are closely related to soil environmental conditions, such as soil-borne diseases, soil pollution, nutrient content, soil texture and soil structure. For example, studies have shown that soil pathogens and viruses can serve as indicators for diagnosing soil health and quality, while the activity of soil enzymes can reflect the physical and chemical properties, microbial activity, and biodiversity of soil, all of which are closely linked to the functional diversity of soil [83]. Additionally, research has shown that the ratio of microbial biomass carbon to soil organic carbon (Cmic:Corg) serves as an indicator of soil organic carbon status, with values exceeding the reference ratio found in mature forests, indicating an accumulation of organic carbon, whereas values below this threshold suggest a depletion [84] (Figure 7). Microorganisms are sensitive indicators of soil health, and specific microbial groups are strongly correlated with soil variables, playing a crucial role in guiding the application of targeted microbial inoculants or the use of microbiome engineering techniques to modulate soil microbial communities and improve soil health.
Determination of soil microbiota through microbial red macrogenomic engineering techniques and prediction of soil health based on soil microbiota has become a prominent research focus. In studies on the comprehensive assessment and prediction of soil health, microbial communities have demonstrated predictive accuracy rates ranging from 50% to 95% for soil quality indices and 80% for overall soil health indices [85]. Recent studies have combined macrogenomics (e.g., functional gene phoD abundance to predict phosphorus effectiveness) and stable isotope probes (SIPs, which track 13C-labeled microbial metabolic activity) to develop predictive models of soil health. For example, generalized linear modeling (GLM) allows quantitative assessment of soil denitrification potential through the negative correlation between nosZ gene abundance and N2O emissions [64]. In addition, 15N isotope tracing revealed the contribution of AM fungi to plant N uptake [65], providing new indicators of microbial regulation of soil health. These findings indicate the feasibility of using the microbiome to predict soil health status.

5.4. Limitations of Microbial Agent Application

Current research identifies six key limitations in microbial agent use for soil improvement: (1) competition with indigenous microbiota, poor environmental adaptability, and limited proliferation post-inoculation [86]; (2) variable efficacy under field conditions; (3) methodological constraints in microbial research requiring advanced technological integration; (4) high cultivation costs and complexity; (5) insufficient understanding of multi-strain synergies and long-term safety; (6) limited functionality under extreme environments, with rare efficient strain availability [87].
Globally, microbial agent technologies are well-established, whereas China’s later-starting research has focused on strain selection but lags in field application and commercialization. Unregulated usage, including misuse and overapplication, further complicates implementation. Despite these challenges, expanding microbial agent applications in pollution control remains a critical priority amid escalating environmental crises.

6. Conclusions

Over the past three decades, global research on microbial inoculants for soil improvement has expanded rapidly, driven by technological advancements and societal demands. China, facing urgent ecological and economic challenges, emerges as the largest contributor to Web of Science publications in this field, followed by the United States, with both nations leading disciplinary frontiers (Figure S1). Bibliometric analysis (2003–2024) highlights the Chinese Academy of Sciences as the top institution in publication output, citations, and international collaboration (Figure S1). Key journals, including Frontiers in Microbiology, Science of the Total Environment, Soil Biology & Biochemistry, and Applied Soil Ecology, underpin scholarly advancements (Figure S2 and Table S1). While China demonstrates strengths in theoretical research, harmonizing ecological restoration with sustainable development remains a critical priority, it needs to establish a ‘microbe-plant–soil’ interdisciplinary research platform, prioritize funding for long-term field trials (e.g., the Saline Fungus Combined Restoration Project), and incorporate the ecological benefits of microbial agents into its agricultural subsidy policy in order to promote the deeper integration of ecological restoration and sustainable agricultural development(Figure S3).
International research has shown quantifiable progress with microbial inoculants, with an approximate 38-fold increase in relevant SCI publications from 14 in 2003 to 552 in 2024. Studies have demonstrated significant progress in microbial inoculants for soil improvement, focusing on biodiversity, soil carbon/nitrogen cycling, microbial community assembly, and pollution bioremediation [88,89]. Macrogenomics has revealed the central role of functional genes in petroleum hydrocarbon degradation, while heterologous expression of laccase genes (laccases) has led to an increase in the efficiency of polyethylene degradation by fungi. In addition, synthetic biology tools are being used to construct highly efficient composite fungicides, providing a new direction for bioremediation technology [88,89]. China, despite its extensive theoretical research on soil microbial zonation characteristics, rhizosphere microbial interactions, and functional diversity [90], started relatively late in applied studies of microbial inoculants. The CNKI database reveals only over a hundred related publications, indicating insufficient empirical research and an urgent need to refine practical application frameworks.
Bibliometric analysis highlights three core research priorities: (1) enhancing functional strain screening via high-throughput sequencing to isolate key species adaptable to soil environments, capable of improving fertility and ecosystem health [88]; (2) deciphering microbial interspecies interactions and soil-microbe signaling pathways [89]; (3) identifying environmental drivers of inconsistent field efficacy through inoculation trials [91]. Future research should focus on three major directions: (1) cross-domain bacterial agent development: constructing bacteria–fungus–archaea consortium (e.g., Bacillus-Aspergillus–Methanotrophs synergistic system), which has been shown to have a higher yield-increasing effect than a single bacterial agent in field trials; (2) intelligent optimization technology: combined with machine learning models (e.g., Random Forest algorithm to predict fungicide adaptability), it realizes dynamic regulation of inoculation strategy; (3) eco-certification system: establish soil health grading standards based on microbial biomarkers (e.g., Cmic:Corg ratio, nosZ gene abundance) to promote both policy- and market-driven incentives. Current limitations stem from incomplete mechanistic understanding, delayed effects of inoculants, and field performance variability. Integrating laboratory and field experiments to develop synergistic “microbial–physicochemical remediation” systems will advance cost-effective, eco-friendly solutions. This approach not only addresses the shortcomings of conventional techniques but also drives innovation in soil restoration engineering, supporting China’s ecological agriculture and sustainable development goals.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agronomy15051223/s1, Figure S1: Collaboration network of the top 39 most productive institutes; Figure S2: Collaborative networks of the top 20 journals with the highest number of publications; Figure S3: Collaborative network of the top 75 authors with the highest number of publications;Table S1: Top 10 most productive journals; TableS2: Top 15 most productive journals; Table S3: Average year of the 20 most frequent keywords; Table S4: Keyword Frequency Table.

Author Contributions

Conceptualization, M.T. and T.F.; methodology, M.T.; software, M.T.; validation, M.T., T.F., H.Y., and X.H.; formal analysis, M.T., X.H., and H.Y.; investigation, M.T., X.H., and H.Y.; resources, T.F.; data curation, M.T.; writing—original draft preparation, M.T.; writing—review and editing, M.T., T.F., C.W., X.H., and H.Y.; visualization, M.T.; supervision, T.F.; project administration, T.F.; funding acquisition, T.F. All authors have read and agreed to the published version of the manuscript.

Funding

This study was supported by the National Key Research and Development Program of China (No. 2022YFB4202103), the National Natural Science Foundation of China (No. 42371114), the Open Fund Project of the Engineering Technology Innovation Center for Ecological Protection and Restoration in the Middle Yellow River, Ministry of Natural Resources (No. 2025034). The funding agencies had no role in the study design, data interpretation, or decision to submit the manuscript for publication.

Data Availability Statement

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

Conflicts of Interest

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

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Figure 1. Research methodology steps.
Figure 1. Research methodology steps.
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Figure 2. Statistics on publication counts and annual publication counts in 20 countries, 2003 to 2024. Shows the change in the number of articles published in the field of microbial agents for soil improvement in the last 20 years and the number of articles published in each country. This sentence is translated into English to ensure scientific accuracy. Data from the Web of Science TM Core Collection.
Figure 2. Statistics on publication counts and annual publication counts in 20 countries, 2003 to 2024. Shows the change in the number of articles published in the field of microbial agents for soil improvement in the last 20 years and the number of articles published in each country. This sentence is translated into English to ensure scientific accuracy. Data from the Web of Science TM Core Collection.
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Figure 3. Analysis of cooperation networks in the top 20 countries (2003–2024). Collaboration network of the top 20 most productive countries. The node size increases with the number of publications of each country. The distance between two nodes decreases with the increase in their association strength. The thickness of the linking lines increases with the number of co-authored documents published by two countries. The different colors of the nodes represent the different clusters of countries.
Figure 3. Analysis of cooperation networks in the top 20 countries (2003–2024). Collaboration network of the top 20 most productive countries. The node size increases with the number of publications of each country. The distance between two nodes decreases with the increase in their association strength. The thickness of the linking lines increases with the number of co-authored documents published by two countries. The different colors of the nodes represent the different clusters of countries.
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Figure 4. Co-occurrence network analysis of keywords in soil microbial research. Keywords are represented by tags and circles. The sizes of the tags and circles indicate the importance of the keywords. The greater the weight of keywords is, the larger the tags and circles of the project are. The color of the item is determined by the cluster to which the item belongs. The lines between items represent links. The closer the distance between keywords and the denser the lines are, the stronger the correlation.
Figure 4. Co-occurrence network analysis of keywords in soil microbial research. Keywords are represented by tags and circles. The sizes of the tags and circles indicate the importance of the keywords. The greater the weight of keywords is, the larger the tags and circles of the project are. The color of the item is determined by the cluster to which the item belongs. The lines between items represent links. The closer the distance between keywords and the denser the lines are, the stronger the correlation.
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Figure 5. Interannual evolution of hotspots in the soil microbial research keyword co-occurrence network from (a) 2003–2024 and (b) 2018–2024. The image shows the year-to-year change in keywords (research hotspots); the color shift from dark blue to yellow indicates the transition of research hotspots appearing from 2003 to 2024 (for example, (a) dark blue a = 2003, yellow = 2024; (b) dark blue a = 2018, yellow = 2024), and the size of the circle indicates the weight of the keyword—the bigger the circle, the higher the weight.
Figure 5. Interannual evolution of hotspots in the soil microbial research keyword co-occurrence network from (a) 2003–2024 and (b) 2018–2024. The image shows the year-to-year change in keywords (research hotspots); the color shift from dark blue to yellow indicates the transition of research hotspots appearing from 2003 to 2024 (for example, (a) dark blue a = 2003, yellow = 2024; (b) dark blue a = 2018, yellow = 2024), and the size of the circle indicates the weight of the keyword—the bigger the circle, the higher the weight.
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Figure 6. The main process of microbially mediated regulation of soil physical and chemical properties. The figure depicts the essential roles of soil microorganisms in mediating biogeochemical cycles (carbon, nitrogen, and phosphorus cycles), highlighting their indispensable contributions to soil formation, development, and amelioration processes.
Figure 6. The main process of microbially mediated regulation of soil physical and chemical properties. The figure depicts the essential roles of soil microorganisms in mediating biogeochemical cycles (carbon, nitrogen, and phosphorus cycles), highlighting their indispensable contributions to soil formation, development, and amelioration processes.
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Figure 7. The main functional framework showing the mechanisms by which microorganisms affect soil health. Soil microorganisms are sensitive to changes in soil conditions, the relationship between soil microorganisms and soil health, and the mechanisms by which microorganisms purify, repair, and improve soil physicochemical properties by participating in a variety of biochemical processes and thereby maintaining soil health (for example, microbial communities dominated by fungi degraded microplastics significantly more efficiently than bacteria, a finding that provides direct evidence for targeted regulation of functional microbes for remediation of contaminated soils.).
Figure 7. The main functional framework showing the mechanisms by which microorganisms affect soil health. Soil microorganisms are sensitive to changes in soil conditions, the relationship between soil microorganisms and soil health, and the mechanisms by which microorganisms purify, repair, and improve soil physicochemical properties by participating in a variety of biochemical processes and thereby maintaining soil health (for example, microbial communities dominated by fungi degraded microplastics significantly more efficiently than bacteria, a finding that provides direct evidence for targeted regulation of functional microbes for remediation of contaminated soils.).
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Table 1. The top 10 keywords for research on soil improvement by microbial agents.
Table 1. The top 10 keywords for research on soil improvement by microbial agents.
RankKeywordFrequencyTotal Link Strength
1rhizosphere156254
2biochar159202
3microbial community159184
4soil microbes120118
5phytoremediation103133
6bacteria105197
7sustainable agriculture68101
8nitrogen55102
9heavy metals5782
10soil microbial community5064
Note: the top 10 most frequently occurring keywords extracted by the bibliometric analysis software and their total link strength.
Table 2. Classification of functional characteristics of microbial agents.
Table 2. Classification of functional characteristics of microbial agents.
ClassificationCategorizationFunctional CharacteristicApplicationReferences
Dosage formLiquid agents(1) Advantages such as ease of preparation, ease of application, short activation time, and rapid effectiveness.
(2) The ability to prevent soil-borne diseases, maintain the balance of rhizosphere microbial communities, and degrade toxic substances. 		Applicable for seed/root treatment, drip irrigation/fertigation, and water purification/pollutant degradation.[24]
Solid agents(1) Promoting plant growth and increasing yield.
(2) Enhancing the activity of urease and transaminase in soil, increasing the content of available nitrogen, and promoting nitrogen absorption. 		Enhances long-term soil enhancement with latent-phase efficacy while functioning as basal fertilizer.[24,25]
Composite methodSingle agents(1) Single function, with limited adaptability.
(2) Targeted antagonism against pathogens, pests, and soil-borne diseases. 		Resolving single soil environment issues.[25]
Composite agents(1) Compared to single microbial agents, composite agents are more efficient and stable in soil, promoting crop growth.
(2) They can significantly increase the nitrogen, phosphorus, and soluble leaf protein content in plants, thereby promoting plant growth. 		Improve soil health and crop growth; inoculate leguminous crops to suppress wilt.[26]
Functional characteristicOrganic material composting agents(1) Induces rapid thermophilic phase, enhancing organic matter conversion.
(2) Eradicate pathogens, nematode eggs, and compost contaminants.
(3) Effectively degrade odor-producing organic macromolecules and suppress putrefactive microorganisms. 		Decompose diverse organic materials (e.g., straw, manure, distillers’ grains, plant litter, sewage sludge).[27]
Soil remediation agents(1) Promote the formation of soil aggregates, increase soil porosity, improve soil structure, and alleviate compaction.
(2) Regulate soil pH, degrade pesticide residues, and immobilize heavy metals, mitigating salinization and alkalization.
(3) Enhance soil water and nutrient retention capacity, promoting stable and high crop yields. 		Remediate compacted/acidic soils and agrochemical/heavy metal co-contaminated sites.[28]
Disease-resistance agents(1) Inhibit the proliferation of soil pathogens, effectively preventing root rot, damping-off, root-knot nematodes, and other replant diseases.
(2) Enhance crop stress resistance, improving tolerance to early frost, cold, and lodging. 		Applicable to field crops such as wheat, corn, and soybeans, as well as economic crops like vegetables, fruit trees, and medicinal plants.[29,30]
Growth-promoting agents(1) Provide or activate nutrients, stimulate root growth, and increase yield.
(2) Improve the quality of agricultural products by participating in the synthesis of plant cell materials, enhancing the content of beneficial components such as proteins, sugars, vitamins, and amino acids. 		Applicable to field crops such as wheat, corn, and soybeans, as well as economic crops like vegetables, fruit trees, and medicinal plants.[31,32]
Microbial speciesBacterial agents(1) Diverse in species, with strong reproductive ability and complex metabolism.
(2) Enhance soil fertility, improve soil structure, increase soil bacterial population, and combat soil pests and diseases. 		Enhances phosphorus/potassium solubilization and soil transformation while suppressing pathogenic microbes.[33]
Fungal agents(1) Form a network-like mycelial structure, increasing contact opportunities with contaminants on particulate surfaces.
(2) Degrade diverse organic pollutants, including polycyclic aromatic hydrocarbons, petroleum hydrocarbons, and halogenated hydrocarbons.
(3) Enrich indigenous microbiota, synergizing with native microbes-plant roots to boost remediation. 		It is suitable for the remediation of sites with organic and composite contamination, as well as for land with poor soil structure.[34]
Actinomycete agents(1) Assist plants in nutrient absorption.
(2) Control the spread of plant pathogens, exhibiting strong antagonistic and parasitic effects on pathogenic organisms.
(3) Actinomycetes secondary metabolites exhibit antimicrobial activity, enhance crop growth/yield, ameliorate soil ecology, and demonstrate eco-friendliness. 		It can produce antibiotics and is used for wastewater treatment, as well as for the chemical control of root-knot nematodes.[35]
Note: The table summarizes four microbial agent classification methods, their features, and applications. Microbial agents may belong to multiple categories (e.g., a liquid formulation of Bacillus spp. can function as both a growth-promoting and disease-resistance agent).
Table 3. Microbial species involved in the regulation of soil physicochemical properties and their functions.
Table 3. Microbial species involved in the regulation of soil physicochemical properties and their functions.
Microbial FunctionMechanismGenus/SpeciesReferencesFirst AuthorYear
Carbon CycleMicrobial decomposition of organic matter, CO2 fixation via photosynthesis.Cyanobacteria, Streptomyces[49]Falkowski, P.G.2008
Nitrogen CycleNitrogen fixation, nitrification, denitrification, and ammonification.Rhizobium, Nitrosomonas[50]Kuypers, M.M.M.2018
Phosphorus CycleSolubilization, mineralization, and uptake via phosphatases.Pseudomonas,Bacillus[51]Richardson, A.E.2009
Soil Microbes Resist Pests/DiseasesAntibiotic production, induced systemic resistance (ISR).Pseudomonas Fluorescens,Bacillus Subtilis[52]Pieterse, C.M.J.2014
Microbial Degradation of PetroleumHydrocarbon degradation via oxygenases and biosurfactants.Pseudomonas Putida,Alcanivorax Borkumensis[53]Denaro, R.2021
Microbial Degradation of PesticidesEnzymatic breakdown (e.g., hydrolases, oxidoreductases).Arthrobacter,Pseudomonas[54]Singh, B.K.2009
Microbial Heavy Metal ToleranceBiosorption, bioaccumulation, and detoxification via metallothioneins.Geobacter,Cupriavidus Metallidurans[55]Nies, D.1999
Plastic DegradationEnzymatic hydrolysisIdeonella Sakaiensis,Aspergillus Niger[56]Yoshida, S.2016
Note: The content of the table explains the various functions and processes in which microorganisms are involved in regulating the physical and chemical properties of soil shown in Figure 6 and Figure 7. These include the carbon cycle, nitrogen cycle, phosphorus cycle, the resistance of microorganisms to soil pests and diseases, the degradation of pesticide pollution, petroleum degradation, enhanced tolerance to heavy metals, plastic degradation, as well as regulatory mechanisms and references.
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Tan, M.; Feng, T.; Wang, C.; Hao, X.; Yu, H. Effects of Microbial Agents on Soil Improvement—A Review and Bibliometric Analysis. Agronomy 2025, 15, 1223. https://doi.org/10.3390/agronomy15051223

AMA Style

Tan M, Feng T, Wang C, Hao X, Yu H. Effects of Microbial Agents on Soil Improvement—A Review and Bibliometric Analysis. Agronomy. 2025; 15(5):1223. https://doi.org/10.3390/agronomy15051223

Chicago/Turabian Style

Tan, Mengdi, Tianjiao Feng, Cong Wang, Xiaozhen Hao, and Hang Yu. 2025. "Effects of Microbial Agents on Soil Improvement—A Review and Bibliometric Analysis" Agronomy 15, no. 5: 1223. https://doi.org/10.3390/agronomy15051223

APA Style

Tan, M., Feng, T., Wang, C., Hao, X., & Yu, H. (2025). Effects of Microbial Agents on Soil Improvement—A Review and Bibliometric Analysis. Agronomy, 15(5), 1223. https://doi.org/10.3390/agronomy15051223

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