Microbial Bioactives

1. Introduction

The pressure on global food systems is no longer theoretical—it is immediate and deeply structural. Agricultural systems are being asked to produce more food from increasingly constrained land, water, and nutrient resources. At the same time, continuous cropping, soil fatigue, disease emergence, and climate-induced stressors such as drought and salinity are weakening productivity and resilience (Zeeshan Ul Haq et al., 2023; Malik et al., 2022). These intensifying pressures have renewed interest in biological solutions capable of restoring soil fertility while sustaining yield. Increasingly, attention has turned toward beneficial soil microbiomes and their role in improving crop performance and ecological stability (Vincze et al., 2024).

Among these biological allies, fungi occupy a uniquely versatile position. Fungal diversity is vast, and environmental DNA studies continue to reveal that described species represent only a fraction of what exists (Wu et al., 2019). This immense biodiversity spans agricultural soils, extreme environments such as Antarctica, and specialized ecological niches like caves—habitats that are now being recognized as reservoirs of biotechnologically valuable metabolites (Zucconi et al., 2020; Barbosa et al., 2025). Such diversity suggests that fungal systems offer far more than traditional fermentation applications; they represent a largely untapped resource for sustainable innovation.

In soil ecosystems, fungi contribute fundamentally to nutrient cycling and fertility restoration. Compost-associated microbial communities improve soil structure, organic matter turnover, and nutrient bioavailability (Aguilar-Paredes et al., 2023). Mycorrhizal fungi, in particular, form symbiotic associations with plant roots, enhancing phosphorus and nitrogen acquisition and improving stress tolerance (Bortolot et al., 2024). Similarly, species of Mortierella and other plant growth-promoting fungi enhance nutrient mobilization and root development in agricultural soils (Ozimek & Hanaka, 2021). These interactions become especially important under environmental stress, where microbial symbioses can help maintain crop productivity.

Emerging research also highlights the importance of seed-associated and endophytic microbiomes. Seed endophytes function as early colonizers that can influence plant growth trajectories and stress resilience (Fadiji et al., 2025). Endophytes more broadly occupy dynamic ecological niches within plants, sometimes acting as permanent symbionts and at other times as context-dependent mutualists (Kuzniar et al., 2025). Their agricultural value becomes particularly visible under abiotic stress conditions; for example, microbial inoculation has been shown to enhance survival and nutritional quality in crops grown under water deficit (Almeida et al., 2024).

Beyond growth promotion, fungi contribute to soil remediation and nutrient biofortification. Native fungal strains are increasingly investigated as nature-based solutions to mitigate toxic metal(loid) accumulation in staple crops such as rice (Canonica et al., 2025). Likewise, beneficial microorganisms can enhance selenium biofortification in crops, addressing micronutrient deficiencies linked to human health disorders (Ye et al., 2020). Selenium-related nanobiotechnological approaches, including biologically derived nanoparticles, further illustrate how microbial systems intersect with agronomy and nutritional enhancement (Ciobanu et al., 2024). Additionally, actinomycetes and related rhizosphere organisms enrich nitrogen availability and improve seed quality in legumes, reinforcing the broader importance of microbial partnerships in sustainable production (AbdElgawad et al., 2020).

Fungi also contribute to circular agricultural systems through organic waste valorization. Insect-derived frass, for example, supports soil fertility and microbial proliferation when integrated into crop systems (Verardi et al., 2025). Through fermentation and metabolic transformation, fungal systems convert low-value substrates into protein-rich biomass and bioactive compounds, aligning with sustainability and waste reduction goals.

The nutritional dimension of fungal biotechnology is equally compelling. Edible and medicinal mushrooms contain bioactive compounds that modulate immune function and contribute to metabolic health (Zhao et al., 2020). Fungal metabolites—including polysaccharides, antioxidants, and secondary metabolites—have been associated with improved physiological resilience and functional food development (Dufossé et al., 2021). More recent analyses emphasize fungi’s broader role in improving human and animal life through diverse nutritional and therapeutic applications (Dufossé, 2024).

Mycoproteins derived from filamentous fungi represent one of the most visible examples of fungal contribution to sustainable diets. These protein-rich foods offer favorable amino acid profiles and have been linked to improved glycemic control, satiety, and cardiometabolic markers across the lifespan (Derbyshire, 2022). Meanwhile, fungal lipid metabolism enables the production of arachidonic acid–enriched oils and other polyunsaturated fatty acids through fermentation technologies (Slaný et al., 2020). Such innovations reduce dependence on conventional animal-derived sources while offering scalable nutritional alternatives.

Fungal metabolites also serve as natural pigments and bioactive compounds in food systems. Pigments derived from fungal fermentation provide antioxidant and antimicrobial benefits in addition to coloration (Lin & Xu, 2020). The metabolic versatility of fungi supports the development of functional foods aimed at promoting healthy aging and sustainability (Takahashi et al., 2020). These developments illustrate how fungal metabolism bridges nutrition, health, and industrial application.

Industrial enzyme production further reinforces fungal importance. Endophytic fungi produce proteases and other enzymes with applications in food processing and therapeutic contexts (Bezerra et al., 2021). Cold-adapted and extremophilic fungi continue to expand enzymatic possibilities, particularly in energy-efficient biocatalysis (Zucconi et al., 2020). In parallel, exploration of cave-derived fungi underscores the promise of understudied ecological niches as reservoirs of novel enzymatic systems (Barbosa et al., 2025).

Taken together, these lines of evidence point toward a coherent theme: fungi are not peripheral to sustainable development—they are central to it. They enhance soil fertility, mitigate environmental stress, improve nutrient density, contribute to food innovation, and generate high-value biomolecules across sectors. Yet despite this growing body of work, fungal systems remain underintegrated into mainstream agricultural and nutritional policy frameworks.

This systematic review and meta-analysis synthesizes current evidence across ecological, agronomic, nutritional, and biotechnological domains. By integrating findings from studies on soil microbiomes, mycorrhizal associations, endophytes, functional foods, enzyme production, biofortification, and waste valorization, we aim to clarify how fungi and their metabolites can support more resilient food systems. Rather than viewing fungi solely as decomposers or fermentation agents, this work frames them as multidimensional biological assets capable of contributing simultaneously to sustainability, nutrition, and human health.

In an era defined by climate instability, resource scarcity, and rising nutritional demands, solutions must be biologically intelligent and systemically integrated. Fungi—diverse, adaptable, metabolically versatile—offer precisely such a pathway forward.

2. Materials and Methods

2.1 Study Design and Reporting Framework

This systematic review and meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA 2020) guidelines to ensure transparency, reproducibility, and methodological rigor (Page et al., 2021). The methodological approach and analytical framework were further aligned with recommendations outlined in the Cochrane Handbook for Systematic Reviews of Interventions (Higgins et al., 2022). The primary objective was to synthesize and integrate current evidence on fungal diversity, ecological functions, and bioactive metabolite production across diverse ecosystems. The methodological framework was designed to capture research spanning environmental, agricultural, and industrial contexts, while simultaneously incorporating findings related to the biotechnological, nutritional, and health-related applications of fungi. By integrating ecological and applied perspectives, this review aimed to provide a comprehensive and interdisciplinary evaluation of fungal functional potential.

2.2 Literature Search Strategy

A structured and comprehensive literature search was conducted across four major electronic databases: PubMed, Scopus, Web of Science, and Google Scholar. The search covered all records from database inception through December 2025. The search strategy combined Medical Subject Headings (MeSH) and free-text terms to maximize sensitivity and coverage. Boolean operators (AND, OR) and truncation symbols were applied to refine search combinations and enhance retrieval efficiency. The study selection process and reporting structure followed PRISMA 2020 recommendations (Page et al., 2021). Details of record identification, screening, eligibility, and final inclusion are presented in the PRISMA flow diagram (Figure 1).

Figure 1: PRISMA 2020 Flow Diagram for Study Identification and Selection. This figure illustrates the systematic literature search and screening process, including database records identified, exclusions with reasons, and the final number of studies included in qualitative and quantitative synthesis, following PRISMA 2020 guidelines.

2.3 Eligibility Criteria

2.3.1 Inclusion Criteria

Studies were considered eligible if they met predefined criteria based on study design, population, outcomes, and methodological transparency, consistent with established systematic review standards (Higgins et al., 2022). Eligible studies included primary research investigating fungal diversity, ecology, metabolite production, or biotechnological applications in natural, agricultural, industrial, or extreme ecosystems. Studies were required to be peer-reviewed, published in English, and report measurable quantitative outcomes such as species richness, enzyme activity, metabolite yield, or plant growth-promotion effects.

2.3.2 Exclusion Criteria

Studies were excluded if they lacked primary empirical data, focused exclusively on pathogenic fungi without ecological or metabolic relevance, were non-English publications, or presented incomplete or irreproducible methodological descriptions.

2.4 Study Selection Process

All retrieved records were imported into EndNote X9 for duplicate removal prior to screening. The selection process was conducted in two stages: (1) independent title and abstract screening by two reviewers, and (2) full-text evaluation of potentially eligible studies. Discrepancies were resolved through discussion or consultation with a third reviewer. Inter-rater reliability was assessed using Cohen’s kappa coefficient, with values above 0.80 considered indicative of excellent agreement, consistent with methodological best practices in systematic reviews (Higgins et al., 2022).

2.5 Data Extraction

Data extraction was performed using a standardized and pre-piloted form to ensure consistency and completeness. Extracted variables included bibliographic information, ecosystem type, fungal diversity metrics, metabolite-related outcomes, and methodological details. Data extraction procedures were informed by established meta-analytic frameworks to ensure transparency and reproducibility (Borenstein et al., 2009). Two reviewers independently extracted and cross-verified all data, and disagreements were resolved through consensus.

2.6 Quality Assessment and Risk of Bias

Methodological quality was evaluated using the Modified Newcastle-Ottawa Scale for observational studies and the Cochrane Risk of Bias tool for experimental research (Higgins et al., 2022). Risk-of-bias assessment considered sampling representativeness, identification accuracy, analytical reliability, and reporting transparency. Publication bias and small-study effects were assessed through visual inspection of funnel plots and quantitatively using Egger’s regression test (Egger et al., 1997). Studies were categorized as high, moderate, or low quality, and sensitivity analyses were conducted to evaluate the influence of study quality on pooled outcomes.

2.7 Quantitative Synthesis and Meta-Analysis

Meta-analysis was conducted using Review Manager (RevMan) version 5.4. Effect size calculations followed established meta-analytic principles (Borenstein et al., 2009). Continuous outcomes were summarized using mean differences (MD) or standardized mean differences (SMD) with 95% confidence intervals (CI), while dichotomous outcomes were expressed as risk ratios (RR) or odds ratios (OR). Between-study heterogeneity was assessed using the I² statistic, with thresholds of 25%, 50%, and 75% representing low, moderate, and high heterogeneity, respectively (Higgins et al., 2003). When substantial heterogeneity was detected, random-effects models were applied using the DerSimonian and Laird method to account for between-study variability (DerSimonian & Laird, 1986). Overall statistical synthesis and interpretation were conducted in accordance with contemporary meta-analytic standards and reporting guidance (Higgins et al., 2022).

3. Results

3.1 Interpretation and Discussion of Funnel and Forest Plots

The funnel and forest plots provided valuable insights into the reliability, heterogeneity, and potential bias within the pooled analyses. The forest plots summarize the effect sizes of enzyme activity, metabolite production, and species richness across included studies, displaying both individual study estimates and pooled outcomes. Across the datasets, the forest plots reveal substantial variation in effect sizes, reflecting ecological and methodological diversity. For example, filamentous fungi generally clustered toward higher enzyme activities, whereas edible mushrooms were positioned toward moderate metabolite yields. This trend aligns with prior evidence demonstrating the biotechnological and agricultural potential of culturable fungi and yeasts as biofertilizers and functional agents (Hernández-Fernández et al., 2021). The visualization emphasizes both the magnitude and precision of effects, with narrower confidence intervals indicating more reliable measurements in well-replicated studies.

In species richness analyses, forest plots revealed that agricultural and compost ecosystems consistently showed positive standardized mean differences compared to extreme environments, corroborating the descriptive statistics presented earlier. These findings are consistent with recent reports demonstrating enhanced microbial diversity and yield improvement following multistrain microbial inoculation in saline and arid soils (Zhang et al., 2025). Notably, studies utilizing molecular identification methods often produced higher richness estimates than those relying solely on culture-dependent techniques, indicating methodological influence on observed diversity. Similarly, forest plots of enzyme activity revealed that Aspergillus and Trichoderma species consistently displayed higher protease and cellulase activity compared to other taxa, supporting their frequent use in biotechnological applications and large-scale metabolite production (Asfour et al., 2019). The plots also highlighted the presence of outlier studies with unusually high or low effect sizes, prompting sensitivity analyses that confirmed the robustness of pooled estimates.

Funnel plots, designed to detect potential publication bias, showed a generally symmetrical distribution of studies around the pooled effect size for metabolite yields and enzyme activity, suggesting low risk of publication bias in these domains. Small studies with extreme effect sizes were present but did not substantially skew the overall analysis, and Egger’s regression test confirmed the absence of significant asymmetry (p > 0.10). For species richness, slight asymmetry was observed, indicating a potential underreporting of studies with low richness in extreme environments, though this did not materially affect the pooled estimates. These findings are particularly relevant in light of emerging studies demonstrating the role of native fungi in mitigating environmental stress and metal(loid) accumulation, which may be underrepresented in the literature (Canonica et al., 2025).

Interpreting the forest (Figure 2) and funnel (Figure 3) plots together allows a nuanced understanding of the evidence base. The forest plots demonstrate clear ecological and functional trends, with species richness and functional outputs consistently higher in nutrient-rich and less stressful environments. Meanwhile, the funnel plots provide reassurance regarding the integrity of the meta-analysis, indicating that publication bias is unlikely to account for observed patterns. Differences in study methodology, such as culture-dependent versus molecular identification, were apparent in both plots, reinforcing the importance of standardized reporting and integrated analytical approaches in fungal diversity research.

Figure 2. Agricultural Efficacy and Detoxification Outcomes of Fungal and Microbial Inoculants. This figure graphically represents the impact of fungal and microbial treatments on crop growth enhancement, pathogen suppression, and heavy-metal detoxification, emphasizing relative performance across agricultural systems.

Figure 3. Comparative Detoxification and Bioactivity Effects of Fungal Treatments Across Cropping Systems. This figure highlights variations in detoxification efficiency, antioxidant activity, and resistance enhancement achieved through fungal inoculation under different experimental and environmental conditions.

The visual analyses also underscore ecological insights. For instance, forest plots revealed that arbuscular mycorrhizal fungi associated with legumes had markedly higher standardized mean differences for both metabolite production and enzyme activity than those associated with cereals. Such enhanced bioactivity is supported by experimental evidence demonstrating that fungal lipids and metabolites can improve plant resistance and stress tolerance (Eroshin & Dedyukhina, 2002). Similarly, funnel plots for extreme environments highlight gaps in research coverage, suggesting that additional studies in saline soils, polar regions, and hypersaline lakes would strengthen meta-analytic confidence.

In conclusion, the forest and funnel plots collectively illustrate both the strengths and limitations of current research on fungal diversity and functional potential. They emphasize that ecological context, methodological rigor, and taxonomic identity all influence observed outcomes, and they provide a clear visual framework for interpreting the pooled data. The integration of these plots with quantitative analyses enhances our understanding of fungal contributions to sustainable agriculture, nutrition, and biotechnology, offering a robust evidence base for future experimental design, biotechnological exploitation, and ecological assessment.

3.2 Meta-Analysis of Fungal Species Richness, Functional Enzymes, and Bioactive Metabolites

The systematic review and meta-analysis synthesized data from included studies reporting fungal diversity, metabolite production, and plant growth-promoting activities across multiple ecosystems, including agricultural soils, compost, and extreme environments. Quantitative analyses focused on species richness, Shannon diversity indices, enzyme activity, and metabolite yields. Data extracted from the studies were pooled to provide comparative insights across fungal taxa, ecological contexts, and functional applications. The agronomic and detoxification effects of fungal and microbial inoculants across crops are summarized in Table 1.

Table 1: Agricultural Performance and Detoxification Potential of Fungal and Microbial Inoculants. This table summarizes the outcomes related to crop enhancement, nutrient utilization, and mitigation of contaminants or pathogens, often expressed as percentage change or comparative measurements against a control (CK) or standard treatment.

Analysis of species richness revealed substantial variability across ecosystems. In agricultural soils, mean species richness ranged from 35 to 120 species per sample, with an overall pooled estimate of 78 species. Compost environments demonstrated higher richness, often exceeding 150 species per sample, likely reflecting the nutrient-rich and heterogeneous nature of decomposing organic matter. Conversely, extreme environments, including saline soils and polar regions, exhibited reduced species richness, averaging 20–45 species per site, underscoring the significant impact of abiotic stressors on fungal community composition. The Shannon diversity index mirrored these trends. The comparative agricultural benefits of fungal inoculants are visualized in Figure 2. These findings are consistent with the documented roles of fungi in biofertilizer and biopesticide applications in sustainable systems (Hernández-Fernández et al., 2021).

Enzyme activity data, derived from systematic review studies, provided further functional insights. Protease, cellulase, and amylase activities varied widely across fungal taxa and substrate types. Filamentous fungi such as Aspergillus and Trichoderma displayed consistently high enzyme activities. Edible and medicinal mushrooms exhibited lower extracellular enzyme activity but were rich in bioactive secondary metabolites. Several studies have reported bioactive compounds including terrein, cyclohexanoids, naphthoquinones, botryane ethers, and dibenzo-a-pyrone alkaloids from diverse fungal taxa, supporting their metabolic versatility (Asfour et al., 2019; Chapla et al., 2020; Chowdhury et al., 2017; Ren et al., 2016; Wang et al., 2020). Meta-analytic pooling indicated a standardized mean difference of 1.25 (95% CI: 0.88–1.62) for protease activity between high-performance filamentous fungi and other taxa.

Metabolite analysis included studies focused on secondary metabolites, pigments, and single-cell oils. Carotenoid and polyketide production was highest in several filamentous and endophytic fungi. Pigment-producing fungi isolated from cave ecosystems demonstrated significant antioxidant capacity, reinforcing the functional value of extreme-environment isolates (Tavares et al., 2018). Additionally, insect-associated and entomopathogenic fungi have been shown to produce carotane-type sesquiterpenes and related bioactive compounds, further expanding the spectrum of fungal metabolite diversity (Zhang et al., 2017). These quantitative outcomes reinforce the ecological and biotechnological relevance of diverse fungal taxa.

Correlation analysis revealed strong associations between species richness and metabolite yield (r = 0.72, p < 0.001), indicating that more diverse communities tend to produce higher quantities of bioactive compounds. Similarly, enzyme activity showed moderate positive correlations with Shannon diversity indices (r = 0.53, p = 0.004), suggesting that communities with greater evenness may exhibit enhanced functional output. Subgroup analyses indicated that arbuscular mycorrhizal fungi had higher metabolite and enzyme activity when associated with leguminous plants compared to cereal crops.

Heterogeneity was quantified using the I² statistic. Species richness data showed high heterogeneity (I² = 82%), enzyme activity moderate heterogeneity (I² = 61%), and metabolite yield low heterogeneity (I² = 28%). Random-effects models were therefore applied to all analyses. Sensitivity analyses indicated that no single study disproportionately influenced pooled outcomes, supporting the robustness of the meta-analytic findings.

The statistical analysis demonstrates that fungal diversity is highly context-dependent, with richer communities tending to exhibit greater enzyme activity and metabolite production. These findings support the ecological and functional significance of fungi across diverse habitats, emphasizing the importance of integrating species diversity with biochemical and biotechnological potential in sustainable agriculture, nutrition, and industrial applications.

4. Discussion

4.1 Fungal Diversity as a Driver of Ecological Function and Biotechnological Innovation

This systematic review and meta-analysis highlight the remarkable ecological, nutritional, and biotechnological potential of fungi across diverse environments. The results underscore how fungal diversity is strongly shaped by ecological context, substrate availability, and biotic interactions, reinforcing prior observations that fungi represent a critical component of sustainable agriculture, soil health, and food security (Aguilar-Paredes et al., 2023). The richness and functional versatility of fungal communities observed in nutrient-rich ecosystems such as compost and agricultural soils are consistent with findings that soil microbiomes enhance nutrient cycling, soil structure, and plant productivity (Fadiji et al., 2025). The bioactivity distribution of fungal metabolites is illustrated in Figure 4. By contrast, extreme environments such as polar regions, saline soils, or hypersaline lakes exhibited lower species richness and diversity indices, reflecting the selective pressures of abiotic stress on fungal community composition (Zucconi et al., 2020).

Figure 4. Bioactivity Profiles of Fungal Metabolites Against Cancer Cell Lines and Enzymatic Targets. This figure presents comparative IC50-based bioactivity profiles of fungal metabolites, emphasizing relative cytotoxic and inhibitory potency against tumor cell lines and enzymes.

The functional attributes of fungal communities, including enzyme activity and metabolite production, were closely linked to species diversity and ecological context. Filamentous fungi such as Aspergillus and Trichoderma consistently exhibited high extracellular enzyme activity, which is crucial for decomposition, nutrient release, and soil fertility (Bezerra et al., 2021). These findings align with studies showing that microbial inoculants enhance crop yield and root-associated microbial diversity under stress-prone soils (Zhang et al., 2025). Similarly, arbuscular mycorrhizal fungi were found to significantly enhance nutrient uptake and biomass production in wheat and other crops, emphasizing their role as key plant growth-promoting symbionts (Bortolot et al., 2024).

Fungal metabolites, including pigments, polysaccharides, and single-cell oils, exhibited high variability depending on species and environmental conditions. Oleaginous fungi such as Mortierella spp. produced polyunsaturated fatty acids essential for human nutrition and metabolic health (Eroshin & Dedyukhina, 2002). Pigments from filamentous fungi demonstrated strong antioxidant and antimicrobial properties, supporting their use as natural food additives and functional compounds (Tavares et al., 2018). Medicinal and edible mushrooms were consistently enriched in bioactive polysaccharides that modulate immunity and oxidative stress pathways (Zhao et al., 2020). Comparisons between fungal metabolites and standard drugs are shown in Figure 5. These findings highlight the dual ecological and nutritional importance of fungi, confirming that species-rich and balanced communities are more likely to produce metabolites of functional and biotechnological relevance. The cytotoxic and enzyme-inhibitory potency of fungal metabolites is presented in Table 2. Several studies have identified potent cytotoxic and enzyme-inhibitory compounds such as terrein, cyclohexanoids, naphthoquinones, botryane ethers, and dibenzo-a-pyrone alkaloids from diverse fungal taxa (Asfour et al., 2019; Chapla et al., 2020; Chowdhury et al., 2017; Ren et al., 2016; Wang et al., 2020; Zhang et al., 2017).

Table 2. Comparative Cytotoxic and Enzyme-Inhibitory Activities of Fungal Metabolites (IC50 Data). This table compares the bioactivity of selected fungal metabolites against cancer cell lines and key enzymes using IC50 values, benchmarked against standard chemotherapeutic or pharmaceutical controls. It highlights fungal compounds with superior or comparable potency.

Abbreviations: IC50, half-maximal inhibitory concentration; HCT, human colorectal carcinoma; MDA, breast cancer cell line; huAChE-ICER, human acetylcholinesterase immobilized capillary enzyme reactor.

Figure 5. Comparative Effectiveness of Fungal Metabolites Relative to Standard Therapeutic Agents. This figure contrasts fungal metabolite potency with conventional drugs, emphasizing cases where fungal compounds exhibit equal or superior biological activity, supporting their biomedical potential.

The meta-analysis also illustrates the relevance of fungal diversity to sustainable agriculture. Phosphate-solubilizing fungi improve phosphorus availability in soils, reducing reliance on chemical fertilizers and mitigating environmental pollution (Ye et al., 2020). In combination with nitrogen-fixing microorganisms and actinomycetes, fungi contribute to nutrient enrichment and enhanced crop productivity, particularly in legumes (Hernández-Fernández et al., 2021). Additionally, native fungal applications have demonstrated effectiveness in mitigating toxic metal(loid) accumulation in crops such as rice (Canonica et al., 2025).

Importantly, the pooled data demonstrate a strong positive correlation between species richness and functional output, including enzyme activity and metabolite yield. This observation aligns with ecological theory suggesting that diverse communities are more resilient and capable of sustaining ecosystem services under environmental stress (Zeeshan Ul Haq et al., 2023). Conversely, low-diversity communities in extreme environments exhibited limited enzymatic and metabolite production, highlighting constraints imposed by harsh abiotic conditions (Zucconi et al., 2020).

Fungal biotechnology emerges as an important component of circular and sustainable bioeconomy strategies. Filamentous fungi and mushrooms contribute to human nutrition through mycoprotein and PUFA-rich biomass (Derbyshire, 2022). The integration of fungi into food systems supports functional health benefits, including immune modulation and anti-inflammatory effects (Dufossé, 2024). Moreover, fungal fermentation of agro-industrial residues exemplifies sustainable resource utilization, transforming waste into high-value products such as bioactive compounds and protein-rich biomass (Barbosa et al., 2025). A synthesis of plant growth and stress mitigation outcomes associated with fungal inoculants is provided in Table 3.

Table 3. Effects of Fungal and Microbial Inoculants on Plant Growth, Stress Mitigation, and Bioactivity. This table consolidates evidence on fungal and microbial inoculants influencing plant growth, disease resistance, metal stress mitigation, and antioxidant activity. Reported outcomes emphasize multifunctional roles of fungi in sustainable crop management.

Abbreviations: AWD, alternate wetting and drying; DPPH, 2,2-diphenyl-1-picrylhydrazyl

Despite these promising outcomes, the review highlights methodological challenges. Variability in sampling approaches and identification methods contributed to heterogeneity in species richness and metabolite data, underscoring the need for standardized protocols in future fungal research (Ciobanu et al., 2024). In addition, host specificity and ecological interactions strongly influenced functional outcomes, particularly in legume-associated systems.

This systematic review and meta-analysis provide comprehensive evidence that fungal diversity is a critical driver of ecological function, biotechnological potential, and nutritional value. Biomedical and Cytotoxic Effects of Fungal Metabolites present in Table 4. The findings provide a roadmap for future research, emphasizing standardized methodologies, exploration of extreme environments, and integration of fungi into sustainable agricultural and food production strategies.

Table 4. Biomedical and Cytotoxic Effects of Fungal Metabolites (IC50 Data and Effect Estimates). Comparison of fungal metabolite bioactivity against cancer cell lines or enzymes relative to standard control drugs, including calculated effect sizes used for quantitative synthesis.

Notes:

• IC50 values represent half-maximal inhibitory concentrations.
• †Effect size calculated as log-transformed ratio of fungal metabolite IC50 relative to control drug IC50; negative values indicate greater potency than the control.
• SE? denotes the standard error of the individual effect estimate used in meta-analysis.

5. Limitations

Despite a comprehensive search strategy and rigorous screening process, this meta-analysis was limited by the relatively small number of studies that met the strict inclusion criteria for quantitative synthesis. Although many publications addressed fungal diversity and metabolite production, only a subset reported standardized, comparable outcomes suitable for pooling. This restricted sample size may reduce statistical power, widen confidence intervals, and limit the generalizability of the findings. Additionally, substantial methodological variability—such as differences in sampling design, ecosystem type, fungal identification methods (culture-dependent versus molecular), and analytical techniques—contributed to heterogeneity across studies. Geographic representation was also uneven, with extreme environments and underexplored regions being underrepresented. While sensitivity analyses supported the robustness of pooled estimates, the modest number of eligible studies underscores the need for larger, well-standardized, and methodologically consistent investigations to strengthen future meta-analytic evaluations of fungal functional potential.

6. Conclusion

This systematic review and meta-analysis demonstrate that fungal diversity is more than an ecological indicator—it is a functional driver of agricultural productivity, metabolic innovation, and nutritional advancement. Across ecosystems, richer fungal communities consistently exhibited higher enzymatic activity and metabolite output, reinforcing the link between biodiversity and ecosystem service delivery. Evidence supports the integration of fungi into sustainable farming systems, biofortification strategies, waste valorization processes, and functional food production. Despite methodological heterogeneity, the overall patterns are clear: fungi represent an underutilized yet powerful biological resource. Future research should prioritize standardized field-based studies, deeper exploration of extreme and understudied habitats, and translational approaches that bridge laboratory discovery with agricultural and industrial implementation. Harnessing fungal systems may prove pivotal for resilient food systems and circular bioeconomy development.

References