Soil as a battlefield and a reservoir: linking soil components to the epidemiology of soilborne plant diseases

Soil as a battlefield and a reservoir: linking soil components to the epidemiology of soilborne plant diseases | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Systematic Review Soil as a battlefield and a reservoir: linking soil components to the epidemiology of soilborne plant diseases David Pires, Florabelle Castañeda, Leny Galvez, Mark Angelo Balendres This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8731607/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 12 You are reading this latest preprint version Abstract This paper focuses on how microbial diversity, soil organic matter, and soil structure influence the activities of soilborne pathogens and plant disease epidemiology. Microbial diversity, organic matter, and structure are soil components that can reshape plant-pathogen-soil interactions (the plant disease triangle) by altering nutrient dynamics and the composition of the soil microbiome. When beneficial microorganisms are favored, soil suppressiveness is enhanced by reducing plant pathogen survival, limiting infection success, and restricting inoculum buildup, thereby decreasing disease incidence and severity. However, microbial diversity, soil organic matter, and soil structure may also promote pathogen growth or facilitate cooperative microbial interactions that improve pathogen persistence, thereby elevating disease risk. Future progress requires a shift from descriptive surveys toward functional and predictive approaches, as these soil components are epidemiological factors that can either suppress or intensify the development of plant diseases caused by soilborne plant pathogens. This paper highlights the importance of soil management in regulating microbial community dynamics and supporting plant disease control. biological control microbial ecology plant disease triangle soil organic matter soil suppressiveness Figures Figure 1 1. Introduction Soil is a densely populated and highly competitive ecosystem in which pathogen establishment depends on successful invasion of an existing microbial community. Classical plant disease epidemiology emphasized the disease triangle (host, pathogen, environment), often reducing soil to a passive physical matrix for root growth [ 1 ]. Advances in microbial ecology now demonstrate that microbial diversity is a critical biological factor that modulates all three components of the triangle, influencing pathogen survival, host susceptibility, and environmental filtering, thereby functioning as a biotic modifier of disease emergence rather than an independent triangle component [ 2 ]. Studies have shown that soil’s suppressiveness against plant diseases is linked with the diversity of soil microorganisms, which act against pathogens in several ways, including antibiosis, parasitism, competition, and induced resistance [ 3 – 6 ]. Beyond microbial diversity, soil organic matter (SOM) plays a central role in structuring belowground biological activity. As a primary energy source for the soil microbiome, SOM fuels microbial growth and interaction [ 7 ]. Through microbial decomposition, SOM supports plant growth and defense by releasing nutrients, particularly nitrogen and phosphorus, in forms that plants can readily absorb [ 8 ]. As a result, aside from the naturally occurring organic matter in the soil, supplemental organic fertilizers are used to enhance soil health and increase the soil’s suppressiveness to plant diseases. Another important factor that affects microbial communities and their interactions with SOM is the arrangement of mineral particles, organic matter, and pore spaces into aggregates of various sizes, which dictates soil structure. While both soil texture and soil structure influence water movement, gas diffusion, and microbial diversity, the dynamic, management-responsive heterogeneity of soil structure, shaped by cultural practices and biological activity, makes it a particularly relevant factor in plant disease epidemiology. Porosity and variations in pore sizes profoundly influence soil microbial ecology by creating variations of microhabitats with differing nutrient requirements. Fine pores or micropores tend to remain water-filled and anaerobic, while large pores or macropores drain and aerate quickly; intermediate pores provide a good balance of oxygen, moisture, and carbon for microbial communities [ 9 , 10 ]. By shaping microbial community structure, soil pore characteristics ultimately influence plant–microbe interactions. This paper reviews knowledge on how microbial diversity, SOM, and soil structure influence the activities of soilborne pathogens and plant disease epidemiology. This paper also discusses strategies to improve soil management for controlling soilborne plant diseases and outlines future research directions. Future progress requires a shift from descriptive surveys toward functional and predictive approaches. 2. Influence of soil microbial diversity High microbial diversity constrains pathogen invasion through mechanisms described by the insurance hypothesis and niche saturation [ 11 – 13 ]. In diverse soils, ecological niches are largely occupied, and limiting resources, such as labile carbon and iron, are rapidly sequestered by resident microorganisms, reducing opportunities for invading pathogens to establish and proliferate [ 14 ]. This protective function is reinforced by findings that probiotic diversity itself enhances suppression; for instance, diverse Pseudomonas consortia in the tomato rhizosphere were found to survive better and reduce Ralstonia solanacearum densities more effectively than less diverse communities, via intensified resource competition and interference [ 15 ]. However, this colonization resistance is non-selective and can paradoxically con-strain disease management efforts. For example, Nishisaka et al. [ 16 ] demonstrated that while a Pseudomonas biocontrol strain strongly suppressed Bipolaris sorokiniana in low-diversity soils, the same inoculant failed to confer significant suppression in high-diversity soils, indicating that high background diversity can hinder the establishment of introduced inoculants. From an epidemiological perspective, these processes contribute to both general suppression, driven by overall microbial biomass and competitive exclusion, and specific suppression, mediated by defined antagonistic taxa or functions [ 17 ]. Within this framework, the soil food web emerges as an additional regulatory layer of the battlefield. Free-living nematodes, as integral components of the soil food web, contribute to disease suppression not only through direct predation on pathogens but also indirectly by grazing on microbial populations, restructuring microbial interaction networks, and accelerating nutrient turnover, thereby reinforcing competitive and antagonistic pressures within the microbiome [ 18 – 21 ]. Similarly, soil protists act as key microbial grazers within the soil food web, selectively feeding on bacteria and fungi to modulate community composition, stimulate microbial turnover, and indirectly enhance plant health by reinforcing microbiome-mediated disease suppression [ 22 – 23 ]. Together, these mechanisms reduce the basic reproduction number ( R 0 ) of soilborne pathogens, increasing the threshold required for disease onset and slowing epidemic development at the population level (Fig. 1 ). At the field scale, such reductions in R 0 are expected to manifest as delayed disease establishment, lower secondary infection rates, and increased spatial aggregation of symptomatic plants, ultimately dampening epidemic velocity; however, this is not straightforward in complex environments [ 24 ]. Despite strong conceptual support, translating microbial diversity into predictive epidemiological frameworks remains challenging. A central difficulty lies in disentangling causation from correlation: soils with high microbial diversity often exhibit lower disease incidence, but it is unclear whether diversity drives suppression or whether healthy plants, through carbon-rich root exudation, promote a complexified rhizosphere community through microbial recruitment [ 16 , 25 ]. Moreover, disease suppression does not scale linearly with diversity. Evidence increasingly supports a “diversity–function saturation” effect, in which additional diversity beyond a threshold yields diminishing returns for pathogen suppression, complicating the definition of actionable diversity targets for management [ 3 , 8 ]. Methodological constraints further limit inference. Taxonomic sequencing provides information on community composition but offers limited insight into functional capacity. For example, two soils with similar diversity metrics may differ substantially in their ability to suppress pathogens such as Rhizoctonia or Fusarium , depending on functional traits rather than species richness per se [ 26 ]. Finally, soil heterogeneity obscures key interactions: bulk soil measurements frequently fail to capture the fine scale dynamics occurring in the rhizosphere, where pathogen infection, microbial antagonism, and host defense intersect. Microbial diversity, therefore, represents more than a reservoir of taxa; it constitutes an epidemiological filter that protects plants from soilborne pathogens. While high diversity generally correlates with reduced disease incidence and severity, outcomes are shaped by functional redundancy, community structure, and context-dependent host–microbe–pathogen interactions. In this sense, diverse soils function as biological buffers that dampen pathogen invasion and transmission, transforming soil from a passive inoculum reservoir into an active battlefield where pathogens face sustained biotic resistance [ 3 , 6 , 26 ]. 3. Influence of soil organic matter Soil organic matter (SOM) can enhance soil suppressiveness by limiting the growth and activity of phytopathogens through increases in the diversity, abundance, and functional activity of beneficial microbial communities. For this reason, organic amendments are commonly applied to build SOM and strengthen disease-suppressive soil conditions. However, Bonanomi et al. [ 27 ] reported variable outcomes across studies: 45% observed improved soil suppressiveness, 35% found no significant effects, and 20% documented increased disease incidence. The suppressive potential of an organic amendment depends on both its quality and its interaction with the existing soil microbiome. In general, more readily decomposable materials are more effective in stimulating microbial activity [ 7 ]. Microbial genera frequently linked to plant growth promotion include Microvirga , Acinetobacter , Streptomyces , Bradyrhizobium , and Bacillus , whereas Ureibacillus , Thermogutta , and Sphingopyxis have been associated with suppressive composts [ 28 ]. A meta-analysis by Silva and Canellas [ 29 ] further indicated that increasing organic matter through sustainable biological approaches can reduce pest and disease pressure. Vermicompost, for example, supplies essential macro- and micronutrients (e.g., Ca, Mg, Zn, B, P, K, and N), along with beneficial microorganisms such as nitrogen-fixing and phosphate-solubilizing bacteria [ 30 ]. It also contains plant growth-regulating compounds, including indole-3-acetic acid, gibberellic acid, and kinetin [ 31 ]. Similarly, compost tea can suppress pathogens via antagonistic microbial activity, including competition for nutrients and space, parasitism, antimicrobial metabolite production, and the induction of systemic resistance in plants. In addition, humic substances (HS) may indirectly strengthen plant defenses by limiting pathogens through inhibitory and antagonistic effects. The HS are also considered biostimulants, as they can promote root elongation, enhance germination, alleviate stress impacts, and increase biomass accumulation. They may also influence secondary metabolite production, thereby eliciting plant defense responses and improving resistance [ 32 ]. HS were reported to be highly effective (75.9%) in pest and disease control, although performance depends strongly on their composition and the applied concentration. For instance, HS effects were observed at 40, 150, and 1 mg L⁻¹ in banana, peach, and cucumber, respectively, against Meloidogyne spp., Xanthomonas arboricola , and Fusarium spp. Nevertheless, excessive HS concentrations may induce phytotoxicity [ 27 ]. Plant bacterial diseases also remain difficult to manage because bacteria can enter through natural openings or wounds. Ralstonia solanacearum, the causal agent of bacterial wilt in Solanaceae crops, can persist in soil for extended periods even in the absence of a host, further complicating disease control. Overall, organic matter sources vary in their effectiveness against pests and diseases due to multiple contributing factors, including material origin, molecular composition, the target organism, and the crop system involved. In contrast to reports that SOM enrichment promotes beneficial microbial communities, Du et al. [ 33 ] demonstrated that increasing agricultural SOM can also elevate the proportion of fungal phytopathogens, as determined through fungal internal transcribed spacer (ITS) amplicon sequencing. Their six-year fertilization experiment assessed the impacts of repeated organic amendments (crop straw and fresh manure) on soilborne fungal pathogens. The authors reported that high soil organic carbon (SOC) exerted a stronger influence on phytopathogenic fungi than on saprotrophic or symbiotic fungal groups in agricultural soils. Specifically, crop straw and cattle manure increased the relative abundance of phytopathogens such as Monographella (a pathogen of spring barley) [ 34 ] and Magnaporthe , whereas pig manure promoted Penicillium , Devriesia , and Pestalotiopsis . Organic material applications may introduce a greater diversity and abundance of potential pathogens [ 35 , 36 ], which can compete with beneficial microorganisms. Because organic amendments can also create favorable conditions for pathogen growth, proliferation, and colonization, they may ultimately contribute to the development of soilborne diseases [ 37 ]. Furthermore, evidence suggests that high SOC conditions may promote more positive microbial interactions, such as cooperation and facilitation, rather than competitive relationships among phytopathogens [ 38 ]. Wei et al. [ 39 ] further showed that differences in the initial soil microbiome can influence disease outcomes. Microbiomes associated with healthy plants tended to become less diverse, whereas diseased plant microbiomes showed no consistent diversity shift, exhibiting fewer associated species, fewer connections, and shorter average path lengths, signifying stronger connectivity, faster communication, and efficient transport. These patterns indicate that diseased soils may exhibit stronger positive associations within microbial networks than healthy soils. Collectively, these findings highlight the importance of managing fertilization and organic amendment strategies to regulate microbial community dynamics and support plant disease control. 4. Influence of soil structure Fungal pathogens uniquely explore the soil matrix via hyphal extension, allowing movement through both water-filled and air-filled pores, unlike many bacteria, which rely on continuous water films [ 40 ]. However, hyphal growth is constrained by soil physical architecture, with pore size, connectivity, and tortuosity governing the rate and geometry of spread [ 41 ]. Rhizoctonia solani , a widely studied soilborne pathogen causing root rot and damping-off in numerous crops, has served as a model for linking soil structure to fungal epidemiology. Studies show that fungal spread is primarily driven by microscale pore architecture rather than bulk soil properties: well-connected air-filled pores, cracks, and biopores facilitate hyphal expansion, whereas small, tortuous pores restrict growth even at comparable biomass levels [ 42 ]. These findings underscore soil microstructure as a key determinant of pathogen spread, highlighting how disease risk is sensitive to management practices that alter pore connectivity. Oomycete pathogens, such as Phytophthora and Pythium species, disperse via motile biflagellate zoospores that swim through water-filled soil pores toward host roots, making soil moisture and pore connectivity key determinants of infection [ 43 ]. Zoo-spore movement is constrained when pore throats are smaller than their ~ 6–10 µm diameter, causing physical straining, premature encystment, and restricting dispersal to saturated soil layers or continuous macropore networks [ 44 , 45 ]. Consequently, oomycete epidemiology is largely governed by soil pore architecture and moisture dynamics rather than pathogen abundance alone, highlighting soil moisture regulation and structural management as effective strategies for disease suppression. Bacterial soil pathogens such as R. solanacearum disperse primarily via water films coating soil particles, with movement governed by film continuity and pore connectivity. Motility enables active navigation of heterogeneous pore networks, facilitating access to isolated microhabitats, whereas fragmented water films in drier soils restrict dispersal and shape microbial diversity and community composition [ 46 , 47 ]. In addition, bacterial biofilms modify soil microstructure by coating surfaces and clogging pore throats, altering hydraulic properties, generating localized anaerobic conditions, and enhancing root attachment [ 48 ]. Together, these processes underscore the central role of soil microstructure and hydrology in regulating bacterial pathogen spread and disease risk, beyond pathogen abundance or soil chemistry alone [ 49 , 50 ]. Moreover, soil aggregate size strongly shapes nematode communities. In tea plantations in China, larger soil aggregates (> 2 mm) support higher nematode abundance, diversity, and functional activity compared to smaller aggregates. These findings indicate that soil physical structure, through aggregate-mediated pore space and resource availability, governs nematode distribution and mobility, thereby directly influencing plant-parasitic nematode pressure and subsequent disease risk. Long-term tea cultivation reduced soil food web complexity and altered nematode functional composition, suggesting that soil structural degradation may increase vulnerability to plant diseases by constraining beneficial nematodes and enabling opportunistic pathogens [ 51 ]. The study underscores that managing soil aggregation and maintaining a heterogeneous pore network is critical for sustaining nematode-mediated ecosystem services and mitigating soilborne plant disease. Soil compaction from machinery, foot traffic, or grazing alters soil structure by reducing macropores and increasing bulk density, creating stress on plants while often favoring pathogens. Compacted soils limit aeration, restrict root penetration, and trap ethylene, inducing adaptive responses such as radial swelling, reduced root hair development, and decreased cytoplasmic streaming. These changes weaken plant defenses, modify root architecture, and increase susceptibility to soilborne pathogens. Epidemiologically, compaction correlates with greater root disease severity; increased bulk density has been shown to elevate Fusarium and other root rot incidence, likely through hypoxia and altered water potentials that enhance pathogen activity and stress host roots [ 52 ]. Similarly, Rhizoctonia root rot severity increases under compaction due to restricted root growth and reduced biomass [ 53 ]. Compaction also shifts soil microbial communities, favoring anaerobic prokaryotes and saprotrophic fungi while reducing aerobic prokaryotes and plant-associated fungi [ 54 ]. These findings underscore that soil physical integrity is a key determinant of plant health and disease risk, highlighting the importance of managing compaction in integrated disease management. Similarly, soil physical structure critically influences plant health and disease risk by shaping both root growth and pathogen dynamics. Compaction from machinery, foot traffic, or grazing reduces macropores and increases bulk density, limiting aeration, impeding root penetration, and trapping ethylene, which induces radial swelling, reduces root hair development, and decreases cytoplasmic streaming. These physiological changes weaken plant defenses and increase root susceptibility, while also favoring soilborne pathogens such as Fusarium and Rhizoctonia , whose activity is enhanced under hypoxic and altered water conditions [ 52 – 54 ]. Root system architecture (RSA) further mediates disease risk by determining root distribution relative to pathogen inoculum. In compacted soils, roots exploit macropores or cracks to reach deeper, less pathogen-dense layers, whereas shallow, highly branched roots remain in the topsoil, increasing exposure [ 55 , 56 ]. RSA also shapes microbial communities, influencing pathogen suppression or facilitation through microbial recruitment along soil gradients [ 57 , 58 ]. Soil compaction and aggregate-mediated pore structure regulate the distribution and movement of plant-parasitic nematodes, which, along with fungi and oomycetes, shape the intensity and spatial patterns of root diseases. These interactions highlight that soil physical integrity, root architecture, and microbial communities collectively determine pathogen encounters, disease severity, and crop resilience, emphasizing the integration of soil physics, RSA, and microbial ecology in effective plant disease management. 5. Soil management for soilborne plant disease control If soil is a battlefield, soil management represents the strategic deployment of resources to favor beneficial allies over pathogenic adversaries. Historically, soilborne disease control relied heavily on chemical fumigation, which temporarily suppresses pathogens but also eliminates much of the resident microbiome, creating a biological vacuum often recolonized by opportunistic pathogens. Contemporary approaches instead aim to manipulate soil ecological processes at the level of the soil food-web, promoting suppressive microbial communities and their trophic regulators rather than eliminating pathogens outright. By contrast, reductive soil disinfestation (RSD) increased bacterial diversity, optimized the core microbiome, and stimulated potential disease-suppressive agents, conferring more durable resistance to invasion and improved plant health [ 59 ]. These outcomes illustrate that effective management reshapes not only microbial composition but also trophic interactions within the soil food web, stabilizing suppressive functions through coupled microbial and faunal regulation. Mechanistic work on RSD shows that both the altered abiotic environment (elevated pH, labile carbon) and specific bacterial and fungal groups jointly underpin suppression of damping‑off, highlighting that soil physicochemical conditions and microbiota codetermine outcomes [ 60 ]. Principles of conservation agriculture, including minimal soil disturbance, permanent soil cover, and diversified crop rotations, form the foundation of this shift. Complementary strategies such as organic amendments (e.g., composts and biochar), anaerobic soil disinfestation (ASD), and biofumigant cover crops are used to restructure microbial communities and alter soil physicochemical conditions. Rather than pursuing pathogen eradication, these approaches aim to restore soil food-web complexity, in which microbial competition, antagonism, functional redundancy, and trophic regulation collectively limit pathogen survival, infectivity, transmission efficiency, and ultimately pathogen R 0 [ 61 , 62 ]. Biologically based soil management, however, remains less predictable than chemical control. The most persistent challenge is context dependency: practices that suppress pathogens such as Verticillium in one field may fail in another due to subtle differences in soil chemistry, texture, climate, or baseline microbial composition. Time lag is an additional constraint. Unlike fumigation, which rapidly reduces pathogen inoculum, the development of suppressive soils is gradual and may require multiple seasons, posing economic risks during transitional periods. Trade-offs further complicate implementation. Amendments that stimulate beneficial microorganisms may also favor opportunistic pathogens or saprophytes under certain environmental conditions. Reviews on compost‑based and compost‑derived disease suppression show that disease‑suppressive composts can enhance natural suppressiveness by introducing beneficial microbiota and stimulating general suppression mechanisms such as increased microbial activity, fungistasis, competition for space and nutrients, antibiotic production, and systemic resistance (4,5). Moreover, because soil food-webs are inherently dynamic and context-dependent, increases in trophic complexity do not guarantee uniform outcomes across systems. While direct empirical evidence remains limited, there is a theoretical risk that soilborne pathogens could adapt to persistent biological suppression or exploit transient imbalances within food-web interactions, either by tolerating antagonistic compounds or exploiting alternative ecological niches. Effective soilborne disease management, therefore, requires a paradigm shift from eradication to ecological balance. Despite challenges related to predictability and transition timeframes, integrated strategies combining organic amendments, reduced till-age, and crop diversification offer the most sustainable path forward. By managing soil as a living habitat rather than a substrate, growers can recruit indigenous microbial communities as persistent, self-regenerating defenses against soilborne diseases, reducing long-term dependence on chemical inputs. Long‑term work shows that suppressiveness is largely microbial in origin, involving antibiosis, parasitism, competition, and induced resistance [ 3 – 6 ]. 6. Research outlook and future progress Future advances in soilborne disease research will require a shift from descriptive associations toward mechanistic and predictive frameworks that explicitly link microbial traits, community structure, and epidemiological outcomes. Functional metagenomics and trait-based analyses, combined with network approaches, will be central to identifying the genes, functions, and keystone taxa that constrain pathogen establishment within complex pathobiomes [3-8,63-64]. Longitudinal, high-resolution temporal studies will further be essential to capture microbial transitions that precede disease outbreaks, enabling microbiome-informed early-warning indicators for soilborne epidemics [65]. Emerging technologies now provide the means to integrate microscale root–microbe interactions with applied disease management. Advanced imaging tools and synthetic microbiomes offer complementary platforms to experimentally test causal mechanisms and design pathogen-suppressive communities. Translating these insights into practice will require prescriptive soil management strategies, including engineered microbial consortia, crop breeding for rhizosphere competence, predictive modeling, and improved standardization of organic amendments. Together, these approaches position the soil microbiome as a manipulable interface for precision phytopathology rather than a passive background to disease emergence [3,5,6,66-69]. Declarations CRediT authorship contribution statement David Pires : Conceptualization, Writing - Original Draft, Writing - Reviewing and Editing. Florabelle Castañeda : Writing - Original Draft, Writing - Reviewing and Editing. Leny Galvez : Writing - Original Draft, Writing - Reviewing and Editing. Mark Angelo Balendres : Conceptualization, Writing - Original Draft, Writing - Reviewing and Editing. Funding David Pires is supported by the Portuguese Foundation for Science and Technology ( Fundação para a Ciência e a Tecnologia , FCT) and the European Social Fund under the PhD fellowship 2021.08030.BD. This work was published open access with the support of a transformative agreement provided by Biblioteca do Conhecimento Online (b-on), covering the open access publishing costs. Competing Interests The authors have no financial or non-financial interests to disclose. Author Contribution David Pires : Conceptualization, Writing - Original Draft, Writing - Reviewing and Editing. Florabelle Castañeda : Writing - Original Draft, Writing - Reviewing and Editing. Leny Galvez : Writing - Original Draft, Writing - Reviewing and Editing. Mark Angelo Balendres : Conceptualization, Writing - Original Draft, Writing - Reviewing and Editing. References Scholthof K-BG (2007) The disease triangle: pathogens, the environment and society. Nat Rev Microbiol 5(2):152–156. https://doi.org/10.1038/nrmicro1596 Leveau JHJ (2024) Re-envisioning the plant disease triangle: full integration of the host microbiota and a focal pivot to health outcomes. Annu Rev Phytopathol 62(1):31–47. https://doi.org/10.1146/annurev-phyto-121423-042021 Schlatter D, Kinkel L, Thomashow L, Weller D, Paulitz T (2017) Disease suppressive soils: new insights from the soil microbiome. Phytopathology® 107(11):1284–1297. https://doi.org/10.1094/PHYTO-03-17-0111-RVW De Corato U (2020a) Disease-suppressive compost enhances natural soil suppressiveness against soilborne plant patho-gens: A critical review. Rhizosphere 13:100192. https://doi.org/10.1016/j.rhisph.2020.100192 De Corato U (2020b) Soil microbiota manipulation and its role in suppressing soilborne plant pathogens in organic farming systems under the light of microbiome-assisted strategies. Chem Biol Technol Agric 7(1):17. https://doi.org/10.1186/s40538-020-00183-7 Jayaraman S, Naorem AK, Lal R, Dalal RC, Sinha NK, Patra AK, Chaudhari SK (2021) Disease-suppressive soils—beyond food production: a critical review. J Soil Sci Plant Nutr 21(2):1437–1465. https://doi.org/10.1007/s42729-021-00451-x van der Sloot M, Maerowitz-Mcmahan S, Postma J, Limpens J, De Deyn GB (2024) Soilborne disease suppres-siveness after short and long term application of fermented, composted or fresh organic amendment treatments in arable soils. Appl Soil Ecol 195:105268. https://doi.org/10.1016/j.apsoil.2023.105268 Priyadarshini C, Lal R, Yuan P, Liu W, Adhikari A, Bhandari S, Xia Y (2025) Plant disease suppressiveness en-hancement via soil health management. Biology 14(8):924. https://doi.org/10.3390/biology14080924 Negassa WC, Guber AK, Kravchenko AN, Marsh TL, Hildebrandt B, Rivers ML (2015) Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria. PLoS ONE 10(4):e0123999. https://doi.org/10.1371/journal.pone.0123999 Wang N, Zhang T (2024) Soil pore structure and its research methods: A review. Soil Water Res 19(1):1–24. https://doi.org/10.17221/64/2023-swr van Elsas JD, Chiurazzi M, Mallon CA, Elhottovā D, Krištůfek V, Salles JF (2012) Microbial diversity determines the invasion of soil by a bacterial pathogen. Proceedings of the National Academy of Sciences, 109(4), 1159–1164. https://doi.org/10.1073/pnas.1109326109 Mallon CA, Le Roux X, van Doorn GS, Dini-Andreote F, Poly F, Salles JF (2018) The impact of failure: unsuc-cessful bacterial invasions steer the soil microbial community away from the invader’s niche. ISME J 12(3):728–741. https://doi.org/10.1038/s41396-017-0003-y Li H, Deng Y, Zhang S, Greenberg J, Chen D, Song X, Geng X, Zhuge Y, Li C, Ni G, Hou Y (2025) Nutrient availability and invader density regulate the diversity–invasibility relationship mediated by soil microbes. Funct Ecol 39(10):2717–2729. https://doi.org/10.1111/1365-2435.70137 Loreau M, Barbier M, Filotas E, Gravel D, Isbell F, Miller SJ, Montoya JM, Wang S, Aussenac R, Germain R, Thompson PL, Gonzalez A, Dee LE (2021) Biodiversity as insurance: from concept to measurement and application. Biol Rev 96(5):2333–2354. https://doi.org/10.1111/brv.12756 Hu J, Wei Z, Friman V-P, Gu S, Wang X, Eisenhauer N, Yang T, Ma J, Shen Q, Xu Y, Jousset A (2016) Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression. MBio 7(6). https://doi.org/10.1128/mBio.01790-16 Nishisaka CS, Quevedo HD, Ventura JP, Andreote FD, Mauchline TH, Mendes R (2025) Soil microbial diversity: A key factor in pathogen suppression and inoculant performance. Geoderma 460:117444. https://doi.org/10.1016/j.geoderma.2025.117444 Verdú M, Alcántara JM, Navarro-Cano JA, Goberna M (2023) Transitivity and intransitivity in soil bacterial networks. ISME J 17(12):2135–2139. https://doi.org/10.1038/s41396-023-01540-8 Bongers T, Ferris H (1999) Nematode community structure as a bioindicator in environmental monitoring. Trends Ecol Evol 14(6):224–228. https://doi.org/https://doi.org/10.1016/S0169-5347(98)01583-3 Ferris H, Bongers T, de Goede RGM (2001) A framework for soil food web diagnostics: extension of the nematode faunal analysis concept. Appl Soil Ecol 18(1):13–29. https://doi.org/https://doi.org/10.1016/S0929-1393(01)00152-4 Yeates GW (2003) Nematodes as soil indicators: functional and biodiversity aspects. Biol Fertil Soils 37(4):199–210. https://doi.org/https://doi.org/10.1007/s00374-003-0586-5 Topalović O, Geisen S (2023) Nematodes as suppressors and facilitators of plant performance. New Phytol 238(6):2305–2312. https://doi.org/https://doi.org/10.1111/nph.18925 Xiong W, Song Y, Yang K, Gu Y, Wei Z, Kowalchuk GA, Xu Y, Jousset A, Shen Q, Geisen S (2020) Rhizosphere protists are key determinants of plant health. Microbiome 8(1):27. https://doi.org/10.1186/s40168-020-00799-9 Santoyo G, del Orozco-Mosqueda M C., Babalola OO (2025) How protists contribute to plant growth and health: Exploring new interactions with the plant microbiome. Microbe 7:100361. https://doi.org/10.1016/j.microb.2025.100361 van den Bosch F, McRoberts N, van den Berg F, Madden LV (2008) The basic reproduction number of plant path-ogens: matrix approaches to complex dynamics. Phytopathology® 98(2):239–249. https://doi.org/10.1094/PHYTO-98-2-0239 Vukicevich E, Lowery T, Bowen P, Úrbez-Torres JR, Hart M (2016) Cover crops to increase soil microbial diversity and mitigate decline in perennial agriculture. A review. Agron Sustain Dev 36(3):48. https://doi.org/10.1007/s13593-016-0385-7 Todorović I, Moënne-Loccoz Y, Raičević V, Jovičić-Petrović J, Muller D (2023) Microbial diversity in soils suppressive to Fusarium diseases. Front Plant Sci 14. https://doi.org/10.3389/fpls.2023.1228749 Bonanomi G, Antignani V, Pane C, Scala F (2007) Suppression of soilborne fungal diseases with organic amendments. J Plant Pathol, 311–324. https://www.jstor.org/stable/41998409 Mayerhofer J, Thuerig B, Oberhaensli T, Enderle E, Lutz S, Ahrens CH, Widmer F (2021) Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane. FEMS Microbiol Ecol 97(10):fiab134. https://doi.org/10.1093/femsec/fiab134 Silva RM, Canella LP (2022) Organic matter in the pest and plant disease control: A meta-analysis. Chem Biol Technol Agric 9(1):70. https://doi.org/10.1186/s40538-022-00332-0 Yatoo AM, Rasool S, Ali S, Majid S, Rehman MU, Ali MN, Farooq S (2020) Vermicomposting: An eco-friendly approach for recycling/management of organic wastes. Bioremediation and biotechnology: sustainable approaches to pollution degradation. Springer International Publishing, Cham, pp 167–187. https://doi.org/10.1007/978-3-030-35691-0_8 Ravindran B, Wong JW, Selvam A, Sekaran G (2016) Influence of microbial diversity and plant growth hormones in compost and vermicompost from fermented tannery waste. Bioresour Technol 217:200–204. https://doi.org/10.1016/j.biortech.2016.03.032 Pereira RV, Filgueiras CC, Dória J, Peñaflor MFG, Willett DS (2021) The effects of biostimulants on induced plant defense. Front Agron 3:630596. https://doi.org/10.3389/fagro.2021.630596 Du S, Trivedi P, Wei Z, Feng J, Hu HW, Bi L, Huang Q, Liu YR (2022) The proportion of soilborne fungal pathogens increases with elevated organic carbon in agricultural soils. Msystems 7(2):e01337–e01321. https://doi.org/10.1128/msystems.01337-21 Perry DA (1986) Pathogenicity of Monographella nivalis to spring barley. Trans Br Mycological Soc 86(2):287–293. https://doi.org/10.1016/S0007-1536(86)80158-9 Nicholson FA, Groves SJ, Chambers BJ (2005) Pathogen survival during livestock manure storage and following land application. Bioresour Technol 96(2):135–143. https://doi.org/10.1016/j.biortech.2004.02.030 Vandecasteele B, Muylle H, De Windt I, Van Acker J, Ameloot N, Moreaux K, Coucke P, Debode J (2018) Plant fibers for renewable growing media: Potential of defibration, acidification or inoculation with biocontrol fungi to reduce the N drawdown and plant pathogens. J Clean Prod 203:1143–1154. https://doi.org/10.1016/j.jclepro.2018.08.167 Yang H, Ma J, Rong Z, Zeng D, Wang Y, Hu S, Ye W, Zheng X (2019) Wheat straw return influences nitro-gen-cycling and pathogen associated soil microbiota in a wheat–soybean rotation system. Front Microbiol 10:1811. https://doi.org/10.3389/fmicb.2019.01811 Li M, Wei Z, Wang J, Jousset A, Friman VP, Xu Y, Shen Q, Pommier T (2019) Facilitation promotes invasions in plant-associated microbial communities. Ecol Lett 22(1):149–158. https://doi.org/10.1111/ele.13177 Wei Z, Gu Y, Friman VP, Kowalchuk GA, Xu Y, Shen Q, Jousset A (2019) Initial soil microbiome composition and functioning predetermine future plant health. Sci Adv 5(9):eaaw0759. https://doi.org/10.1126/sciadv.aaw0759 Wösten HaB (2001) Hydrophobins: multipurpose proteins. Annu Rev Microbiol 55(1):625–646. https://doi.org/10.1146/annurev.micro.55.1.625 Aleklett K, Ohlsson P, Bengtsson M, Hammer E (2021) Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips. ISME J 15:1782–1793. https://doi.org/10.1038/s41396-020-00886-7 Falconer RE, Battaia G, Schmidt S, Baveye P, Chenu C, Otten W (2015) Microscale Heterogeneity Explains Ex-perimental Variability and Non-Linearity in Soil Organic Matter Mineralisation. PLoS ONE 10(5):e0123774. https://doi.org/10.1371/journal.pone.0123774 Yu Y, Elliott M, Chowdhury I, Flury M (2020) Transport Mechanisms of Motile and Nonmotile Phytophthora cac-torum Zoospores in Unsaturated Porous Media. Water Resour Res 57(2). https://doi.org/10.1029/2020wr028249 Erwin DC, Ribeiro OK (1996) Phytophthora diseases worldwide. The American Phytopathological Society, St Paul, Minnesota, p 562 Judelson HS, Blanco FA (2005) The spores of Phytophthora: weapons of the plant destroyer. Nat Rev Microbiol 3:47–58 Carson JK, Gonzalez-QuiñOnes V, Murphy DV, Hinz C, Shaw JA, Gleeson DB (2010) Low pore connectivity increases bacterial diversity in soil. Appl Environ Microbiol 76(12):3936–3942. https://doi.org/10.1128/aem.03085-09 Ebrahimi AN, Or D (2014) Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks. Water Resour Res 50:7406–7429. https://doi:10.1002/2014WR015897 Aufrecht JA, Fowlkes JD, Bible AN, Morrell-Falvey J, Doktycz MJ, Retterer ST (2019) Pore-scale hydrody-namics influence the spatial evolution of bacterial biofilms in a microfluidic porous network. PLoS ONE 14(6):e0218316. https://doi.org/10.1371/journal.pone.0218316 Yang K, Wang X, Hou R, Lu C, Fan Z, Li J, Wang S, Xu Y, Shen Q, Friman V, Wei Z (2023) Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease. Microbiome 11(1):16. https://doi.org/10.1186/s40168-023-01463-8 Chachar Z, Xue X, Fang J, Chen M, Jiarui C, Chen W, Ahmed N, Chachar S, Narejo M, Ahmed N, Fan L, Lai R, Qi Y (2025) Key mechanisms of plant-Ralstonia solanacearum interaction in bacterial wilt pathogenesis. Front Microbiol 16:1521422. https://doi.org/10.3389/fmicb.2025.1521422 He S, Jia H, Zheng Z, Li T, Luo Z, Zhang Y, Wang Y (2022) Responses of soil nematode community within soil aggregates to tea plantation age. Environ Sci Pollut Res 29(56):85114–85127 Tu J (1994) Effects of soil compaction, temperature, and moisture on the development of the Fusarium root rot complex of pea in southwestern Ontario. Phytoprotection 75(3):125–131. https://doi.org/10.7202/706059ar Gill JS, Hunt S, Sivasithamparam K, Smettem KRJ (2004) Root growth altered by compaction of a sandy loam soil affects severity of rhizoctonia root rot of wheat seedlings. Aust J Exp Agric 44(6):595–599. https://doi.org/10.1071/ea02093 Longepierre M, Widmer F, Keller T, Weisskopf P, Colombi T, Six J, Hartmann M (2021) Limited resilience of the soil microbiome to mechanical compaction within four growing seasons of agricultural management. ISME Commun 1(1):44. https://doi.org/10.1038/s43705-021-00046-8 Correa J, Postma JA, Watt M, Wojciechowski T (2019) Soil compaction and the architectural plasticity of root systems. J Exp Bot 70(21):6019–6034. https://doi.org/10.1093/jxb/erz383 Gifford ML, Xu G, Dupuy LX, Vissenberg K, Rebetzke G (2024) Root architecture and rhizosphere–microbe interactions. J Exp Bot 75(2):503–507. https://doi.org/10.1093/jxb/erad488 Galindo-Castañeda T, Hartmann M, Lynch JP (2024) Location: root architecture structures rhizosphere micro-bial associations. J Exp Bot 75(2):594–604. https://doi.org/10.1093/jxb/erad421 Zhang H, Liu Z, Zheng C, Ma H, Zeng M, Yang X (2024) Root system architecture plasticity with beneficial rhi-zosphere microbes: Current findings and future perspectives. Microbiol Res 292:128028. https://doi.org/10.1016/j.micres.2024.128028 Zhou X, Zhang Q, Yan Y, Qu J, Zhou J, Zhao J, Zhang J, Cai Z, Dai C, Huang X (2025) Effects of soil man-agement strategies based on different principles on soil microbial communities and the outcomes for plant health. Biol Control 201:105708. https://doi.org/10.1016/j.biocontrol.2025.105708 Liu L, Huang X, Zhao J, Zhang J, Cai Z (2019) Characterizing the key agents in a disease-suppressed soil managed by reductive soil disinfestation. Appl Environ Microbiol 85(7). https://doi.org/10.1128/AEM.02992-18 van Bruggen AH, Gamliel A, Finckh MR (2016) Plant disease management in organic farming systems. Pest Man-agement Sci 72(1):30–44. https://doi.org/10.1002/ps.4145 Panth M, Hassler SC, Baysal-Gurel F (2020) Methods for management of soilborne diseases in crop production. Agriculture 10(1):16. https://doi.org/10.3390/agriculture10010016 Vayssier-Taussat M, Albina E, Citti C, Cosson J-F, Jacques M-A, Lebrun M-H, Le Loir Y, Ogliastro M, Petit M-A, Roumagnac P, Candresse T (2014) Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics. Frontiers in Cellular and Infection Microbiology, 4. https://doi.org/10.3389/fcimb.2014.00029 Bass D, Stentiford GD, Wang H-C, Koskella B, Tyler CR (2019) The pathobiome in animal and plant diseases. Trends Ecol Evol 34(11):996–1008. https://doi.org/10.1016/j.tree.2019.07.012 Fournier P, Pellan L, Jaswa A, Cambon MC, Chataigner A, Bonnard O, Raynal M, Debord C, Poeydebat C, Labarthe S, Delmotte F, This P, Vacher C (2025) Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology. Environ Microbiome 20(1):37. https://doi.org/10.1186/s40793-025-00691-9 Mazzola M, Freilich S (2017) Prospects for biological soilborne disease control: application of indigenous versus synthetic microbiomes. Phytopathology® 107(3):256–263. https://doi.org/10.1094/PHYTO-09-16-0330-RVW Niu B, Wang W, Yuan Z, Sederoff RR, Sederoff H, Chiang VL, Borriss R (2020) Microbial interactions within multiple-strain biological control agents impact soilborne plant disease. Front Microbiol 11. https://doi.org/10.3389/fmicb.2020.585404 Qiao Y, Wang Z, Sun H, Guo H, Song Y, Zhang H, Ruan Y, Xu Q, Huang Q, Shen Q, Ling N (2024) Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects. Microbiome 12(1):101. https://doi.org/10.1186/s40168-024-01814-z Bashizi T, Kim M-J, Lim K, Lee G, Tagele S, Shin J-H (2025) Application of a synthetic microbial community to enhance pepper resistance against Phytophthora capsici. Plants 14(11):1625. https://doi.org/10.3390/plants14111625 Additional Declarations No competing interests reported. Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 10 Mar, 2026 Reviews received at journal 02 Mar, 2026 Reviews received at journal 24 Feb, 2026 Reviews received at journal 23 Feb, 2026 Reviewers agreed at journal 17 Feb, 2026 Reviewers agreed at journal 09 Feb, 2026 Reviewers agreed at journal 29 Jan, 2026 Reviewers agreed at journal 29 Jan, 2026 Reviewers invited by journal 29 Jan, 2026 Editor assigned by journal 29 Jan, 2026 Submission checks completed at journal 29 Jan, 2026 First submitted to journal 29 Jan, 2026 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8731607","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Systematic Review","associatedPublications":[],"authors":[{"id":583365545,"identity":"cdbbc0c4-46b2-40e7-84e8-2833f24332e0","order_by":0,"name":"David Pires","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAxElEQVRIiWNgGAWjYDCCA2DEIEe6FmO4AA8xWkAgsYFoLXw3cg8erqioS99wvMfwcUUNQ549IS2SN/ISDp45czh3w5kzxoZnjjEUE7TF4MwZg4ONbQdyN9xIS5NsYGNI7CFOy7+6dIP7z4Ba/hGj5XgPUEsDc4LBDeZjko1tRGiRPN6XcLDh2GHDmWeSDxs29kkU8xwgoIXvMO/hjw01dfJ8xw82Pmz4ZpPH3kDIGrR4kEggqAEj6ojRMgpGwSgYBSMMAACQu0eYlIqKhgAAAABJRU5ErkJggg==","orcid":"","institution":"University of Évora","correspondingAuthor":true,"prefix":"","firstName":"David","middleName":"","lastName":"Pires","suffix":""},{"id":583365546,"identity":"840415c0-ef93-4dfd-a51a-d3297eb635fa","order_by":1,"name":"Florabelle Castañeda","email":"","orcid":"","institution":"De La Salle University","correspondingAuthor":false,"prefix":"","firstName":"Florabelle","middleName":"","lastName":"Castañeda","suffix":""},{"id":583365547,"identity":"4e10cc35-d213-45fd-aec8-e3ad0145047f","order_by":2,"name":"Leny Galvez","email":"","orcid":"","institution":"Department of Agriculture","correspondingAuthor":false,"prefix":"","firstName":"Leny","middleName":"","lastName":"Galvez","suffix":""},{"id":583365548,"identity":"934bc5c9-8fe1-45c1-b5c8-d4c9ea4c4c8d","order_by":3,"name":"Mark Angelo Balendres","email":"","orcid":"","institution":"De La Salle University","correspondingAuthor":false,"prefix":"","firstName":"Mark","middleName":"Angelo","lastName":"Balendres","suffix":""}],"badges":[],"createdAt":"2026-01-29 12:39:10","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8731607/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8731607/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":101936091,"identity":"901e4628-b746-405e-b5f4-bedd42083b0a","added_by":"auto","created_at":"2026-02-05 08:37:24","extension":"jpeg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":985297,"visible":true,"origin":"","legend":"\u003cp\u003eConceptual framework illustrating how soil biological diversity and management shape the epidemiology of soilborne plant pathogens. Left panel: low-diversity soils function as permissive pathogen reservoirs, where weak microbial competition and limited soil food web regulation allow efficient pathogen reproduction (\u003cem\u003eR\u003c/em\u003e\u003csub\u003e0\u003c/sub\u003e \u0026gt; 1), and disease spread. Middle panel: high-diversity soils exhibit strong biotic resistance, mediated by dense microbial communities and trophic interactions, that reduce pathogen reproduction (\u003cem\u003eR\u003c/em\u003e\u003csub\u003e0\u003c/sub\u003e \u0026lt; 1) and prevent epidemic thresholds from being reached. Right panel: sustainable agronomic practices promote this transition by restructuring soil biological interactions and enabling the selective enrichment of beneficial soil biota, shifting soils from passive reservoirs toward suppressive, food-web-regulated disease states.\u003c/p\u003e","description":"","filename":"floatimage1.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-8731607/v1/77fa25238acb328799c11606.jpeg"},{"id":101943632,"identity":"f22db268-ebfb-4550-8e8a-fd4e854622ba","added_by":"auto","created_at":"2026-02-05 09:42:36","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1511704,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8731607/v1/8526e321-1d71-4ccb-849f-d71a560e8828.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Soil as a battlefield and a reservoir: linking soil components to the epidemiology of soilborne plant diseases","fulltext":[{"header":"1. Introduction","content":"\u003cp\u003eSoil is a densely populated and highly competitive ecosystem in which pathogen establishment depends on successful invasion of an existing microbial community. Classical plant disease epidemiology emphasized the disease triangle (host, pathogen, environment), often reducing soil to a passive physical matrix for root growth [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. Advances in microbial ecology now demonstrate that microbial diversity is a critical biological factor that modulates all three components of the triangle, influencing pathogen survival, host susceptibility, and environmental filtering, thereby functioning as a biotic modifier of disease emergence rather than an independent triangle component [\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. Studies have shown that soil\u0026rsquo;s suppressiveness against plant diseases is linked with the diversity of soil microorganisms, which act against pathogens in several ways, including antibiosis, parasitism, competition, and induced resistance [\u003cspan additionalcitationids=\"CR4 CR5\" citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eBeyond microbial diversity, soil organic matter (SOM) plays a central role in structuring belowground biological activity. As a primary energy source for the soil microbiome, SOM fuels microbial growth and interaction [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. Through microbial decomposition, SOM supports plant growth and defense by releasing nutrients, particularly nitrogen and phosphorus, in forms that plants can readily absorb [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. As a result, aside from the naturally occurring organic matter in the soil, supplemental organic fertilizers are used to enhance soil health and increase the soil\u0026rsquo;s suppressiveness to plant diseases.\u003c/p\u003e \u003cp\u003eAnother important factor that affects microbial communities and their interactions with SOM is the arrangement of mineral particles, organic matter, and pore spaces into aggregates of various sizes, which dictates soil structure. While both soil texture and soil structure influence water movement, gas diffusion, and microbial diversity, the dynamic, management-responsive heterogeneity of soil structure, shaped by cultural practices and biological activity, makes it a particularly relevant factor in plant disease epidemiology. Porosity and variations in pore sizes profoundly influence soil microbial ecology by creating variations of microhabitats with differing nutrient requirements. Fine pores or micropores tend to remain water-filled and anaerobic, while large pores or macropores drain and aerate quickly; intermediate pores provide a good balance of oxygen, moisture, and carbon for microbial communities [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. By shaping microbial community structure, soil pore characteristics ultimately influence plant\u0026ndash;microbe interactions.\u003c/p\u003e \u003cp\u003eThis paper reviews knowledge on how microbial diversity, SOM, and soil structure influence the activities of soilborne pathogens and plant disease epidemiology. This paper also discusses strategies to improve soil management for controlling soilborne plant diseases and outlines future research directions. Future progress requires a shift from descriptive surveys toward functional and predictive approaches.\u003c/p\u003e"},{"header":"2. Influence of soil microbial diversity","content":"\u003cp\u003eHigh microbial diversity constrains pathogen invasion through mechanisms described by the insurance hypothesis and niche saturation [\u003cspan additionalcitationids=\"CR12\" citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. In diverse soils, ecological niches are largely occupied, and limiting resources, such as labile carbon and iron, are rapidly sequestered by resident microorganisms, reducing opportunities for invading pathogens to establish and proliferate [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. This protective function is reinforced by findings that probiotic diversity itself enhances suppression; for instance, diverse \u003cem\u003ePseudomonas\u003c/em\u003e consortia in the tomato rhizosphere were found to survive better and reduce \u003cem\u003eRalstonia solanacearum\u003c/em\u003e densities more effectively than less diverse communities, via intensified resource competition and interference [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eHowever, this colonization resistance is non-selective and can paradoxically con-strain disease management efforts. For example, Nishisaka \u003cem\u003eet al.\u003c/em\u003e [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e] demonstrated that while a Pseudomonas biocontrol strain strongly suppressed \u003cem\u003eBipolaris sorokiniana\u003c/em\u003e in low-diversity soils, the same inoculant failed to confer significant suppression in high-diversity soils, indicating that high background diversity can hinder the establishment of introduced inoculants. From an epidemiological perspective, these processes contribute to both general suppression, driven by overall microbial biomass and competitive exclusion, and specific suppression, mediated by defined antagonistic taxa or functions [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. Within this framework, the soil food web emerges as an additional regulatory layer of the battlefield. Free-living nematodes, as integral components of the soil food web, contribute to disease suppression not only through direct predation on pathogens but also indirectly by grazing on microbial populations, restructuring microbial interaction networks, and accelerating nutrient turnover, thereby reinforcing competitive and antagonistic pressures within the microbiome [\u003cspan additionalcitationids=\"CR19 CR20\" citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eSimilarly, soil protists act as key microbial grazers within the soil food web, selectively feeding on bacteria and fungi to modulate community composition, stimulate microbial turnover, and indirectly enhance plant health by reinforcing microbiome-mediated disease suppression [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. Together, these mechanisms reduce the basic reproduction number (\u003cem\u003eR\u003c/em\u003e\u003csub\u003e0\u003c/sub\u003e) of soilborne pathogens, increasing the threshold required for disease onset and slowing epidemic development at the population level (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). At the field scale, such reductions in \u003cem\u003eR\u003c/em\u003e\u003csub\u003e0\u003c/sub\u003e are expected to manifest as delayed disease establishment, lower secondary infection rates, and increased spatial aggregation of symptomatic plants, ultimately dampening epidemic velocity; however, this is not straightforward in complex environments [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eDespite strong conceptual support, translating microbial diversity into predictive epidemiological frameworks remains challenging. A central difficulty lies in disentangling causation from correlation: soils with high microbial diversity often exhibit lower disease incidence, but it is unclear whether diversity drives suppression or whether healthy plants, through carbon-rich root exudation, promote a complexified rhizosphere community through microbial recruitment [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e, \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e]. Moreover, disease suppression does not scale linearly with diversity. Evidence increasingly supports a \u0026ldquo;diversity\u0026ndash;function saturation\u0026rdquo; effect, in which additional diversity beyond a threshold yields diminishing returns for pathogen suppression, complicating the definition of actionable diversity targets for management [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eMethodological constraints further limit inference. Taxonomic sequencing provides information on community composition but offers limited insight into functional capacity. For example, two soils with similar diversity metrics may differ substantially in their ability to suppress pathogens such as \u003cem\u003eRhizoctonia\u003c/em\u003e or \u003cem\u003eFusarium\u003c/em\u003e, depending on functional traits rather than species richness per se [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. Finally, soil heterogeneity obscures key interactions: bulk soil measurements frequently fail to capture the fine scale dynamics occurring in the rhizosphere, where pathogen infection, microbial antagonism, and host defense intersect.\u003c/p\u003e \u003cp\u003eMicrobial diversity, therefore, represents more than a reservoir of taxa; it constitutes an epidemiological filter that protects plants from soilborne pathogens. While high diversity generally correlates with reduced disease incidence and severity, outcomes are shaped by functional redundancy, community structure, and context-dependent host\u0026ndash;microbe\u0026ndash;pathogen interactions. In this sense, diverse soils function as biological buffers that dampen pathogen invasion and transmission, transforming soil from a passive inoculum reservoir into an active battlefield where pathogens face sustained biotic resistance [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"3. Influence of soil organic matter","content":"\u003cp\u003eSoil organic matter (SOM) can enhance soil suppressiveness by limiting the growth and activity of phytopathogens through increases in the diversity, abundance, and functional activity of beneficial microbial communities. For this reason, organic amendments are commonly applied to build SOM and strengthen disease-suppressive soil conditions. However, Bonanomi \u003cem\u003eet al.\u003c/em\u003e [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e] reported variable outcomes across studies: 45% observed improved soil suppressiveness, 35% found no significant effects, and 20% documented increased disease incidence. The suppressive potential of an organic amendment depends on both its quality and its interaction with the existing soil microbiome. In general, more readily decomposable materials are more effective in stimulating microbial activity [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. Microbial genera frequently linked to plant growth promotion include \u003cem\u003eMicrovirga\u003c/em\u003e, \u003cem\u003eAcinetobacter\u003c/em\u003e, \u003cem\u003eStreptomyces\u003c/em\u003e, \u003cem\u003eBradyrhizobium\u003c/em\u003e, and \u003cem\u003eBacillus\u003c/em\u003e, whereas \u003cem\u003eUreibacillus\u003c/em\u003e, \u003cem\u003eThermogutta\u003c/em\u003e, and \u003cem\u003eSphingopyxis\u003c/em\u003e have been associated with suppressive composts [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eA meta-analysis by Silva and Canellas [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e] further indicated that increasing organic matter through sustainable biological approaches can reduce pest and disease pressure. Vermicompost, for example, supplies essential macro- and micronutrients (e.g., Ca, Mg, Zn, B, P, K, and N), along with beneficial microorganisms such as nitrogen-fixing and phosphate-solubilizing bacteria [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. It also contains plant growth-regulating compounds, including indole-3-acetic acid, gibberellic acid, and kinetin [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]. Similarly, compost tea can suppress pathogens via antagonistic microbial activity, including competition for nutrients and space, parasitism, antimicrobial metabolite production, and the induction of systemic resistance in plants.\u003c/p\u003e \u003cp\u003eIn addition, humic substances (HS) may indirectly strengthen plant defenses by limiting pathogens through inhibitory and antagonistic effects. The HS are also considered biostimulants, as they can promote root elongation, enhance germination, alleviate stress impacts, and increase biomass accumulation. They may also influence secondary metabolite production, thereby eliciting plant defense responses and improving resistance [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. HS were reported to be highly effective (75.9%) in pest and disease control, although performance depends strongly on their composition and the applied concentration. For instance, HS effects were observed at 40, 150, and 1 mg L⁻\u0026sup1; in banana, peach, and cucumber, respectively, against \u003cem\u003eMeloidogyne\u003c/em\u003e spp., \u003cem\u003eXanthomonas arboricola\u003c/em\u003e, and \u003cem\u003eFusarium\u003c/em\u003e spp. Nevertheless, excessive HS concentrations may induce phytotoxicity [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. Plant bacterial diseases also remain difficult to manage because bacteria can enter through natural openings or wounds. Ralstonia solanacearum, the causal agent of bacterial wilt in Solanaceae crops, can persist in soil for extended periods even in the absence of a host, further complicating disease control. Overall, organic matter sources vary in their effectiveness against pests and diseases due to multiple contributing factors, including material origin, molecular composition, the target organism, and the crop system involved.\u003c/p\u003e \u003cp\u003eIn contrast to reports that SOM enrichment promotes beneficial microbial communities, Du \u003cem\u003eet al.\u003c/em\u003e [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e] demonstrated that increasing agricultural SOM can also elevate the proportion of fungal phytopathogens, as determined through fungal internal transcribed spacer (ITS) amplicon sequencing. Their six-year fertilization experiment assessed the impacts of repeated organic amendments (crop straw and fresh manure) on soilborne fungal pathogens. The authors reported that high soil organic carbon (SOC) exerted a stronger influence on phytopathogenic fungi than on saprotrophic or symbiotic fungal groups in agricultural soils. Specifically, crop straw and cattle manure increased the relative abundance of phytopathogens such as \u003cem\u003eMonographella\u003c/em\u003e (a pathogen of spring barley) [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e] and \u003cem\u003eMagnaporthe\u003c/em\u003e, whereas pig manure promoted \u003cem\u003ePenicillium\u003c/em\u003e, \u003cem\u003eDevriesia\u003c/em\u003e, and \u003cem\u003ePestalotiopsis\u003c/em\u003e. Organic material applications may introduce a greater diversity and abundance of potential pathogens [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e, \u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e], which can compete with beneficial microorganisms. Because organic amendments can also create favorable conditions for pathogen growth, proliferation, and colonization, they may ultimately contribute to the development of soilborne diseases [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eFurthermore, evidence suggests that high SOC conditions may promote more positive microbial interactions, such as cooperation and facilitation, rather than competitive relationships among phytopathogens [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. Wei \u003cem\u003eet al.\u003c/em\u003e [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e] further showed that differences in the initial soil microbiome can influence disease outcomes. Microbiomes associated with healthy plants tended to become less diverse, whereas diseased plant microbiomes showed no consistent diversity shift, exhibiting fewer associated species, fewer connections, and shorter average path lengths, signifying stronger connectivity, faster communication, and efficient transport. These patterns indicate that diseased soils may exhibit stronger positive associations within microbial networks than healthy soils. Collectively, these findings highlight the importance of managing fertilization and organic amendment strategies to regulate microbial community dynamics and support plant disease control.\u003c/p\u003e"},{"header":"4. Influence of soil structure","content":"\u003cp\u003eFungal pathogens uniquely explore the soil matrix via hyphal extension, allowing movement through both water-filled and air-filled pores, unlike many bacteria, which rely on continuous water films [\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]. However, hyphal growth is constrained by soil physical architecture, with pore size, connectivity, and tortuosity governing the rate and geometry of spread [\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]. \u003cem\u003eRhizoctonia solani\u003c/em\u003e, a widely studied soilborne pathogen causing root rot and damping-off in numerous crops, has served as a model for linking soil structure to fungal epidemiology. Studies show that fungal spread is primarily driven by microscale pore architecture rather than bulk soil properties: well-connected air-filled pores, cracks, and biopores facilitate hyphal expansion, whereas small, tortuous pores restrict growth even at comparable biomass levels [\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]. These findings underscore soil microstructure as a key determinant of pathogen spread, highlighting how disease risk is sensitive to management practices that alter pore connectivity.\u003c/p\u003e \u003cp\u003eOomycete pathogens, such as \u003cem\u003ePhytophthora\u003c/em\u003e and \u003cem\u003ePythium\u003c/em\u003e species, disperse via motile biflagellate zoospores that swim through water-filled soil pores toward host roots, making soil moisture and pore connectivity key determinants of infection [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e]. Zoo-spore movement is constrained when pore throats are smaller than their ~\u0026thinsp;6\u0026ndash;10 \u0026micro;m diameter, causing physical straining, premature encystment, and restricting dispersal to saturated soil layers or continuous macropore networks [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e, \u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e]. Consequently, oomycete epidemiology is largely governed by soil pore architecture and moisture dynamics rather than pathogen abundance alone, highlighting soil moisture regulation and structural management as effective strategies for disease suppression.\u003c/p\u003e \u003cp\u003eBacterial soil pathogens such as \u003cem\u003eR. solanacearum\u003c/em\u003e disperse primarily via water films coating soil particles, with movement governed by film continuity and pore connectivity. Motility enables active navigation of heterogeneous pore networks, facilitating access to isolated microhabitats, whereas fragmented water films in drier soils restrict dispersal and shape microbial diversity and community composition [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e, \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e]. In addition, bacterial biofilms modify soil microstructure by coating surfaces and clogging pore throats, altering hydraulic properties, generating localized anaerobic conditions, and enhancing root attachment [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e]. Together, these processes underscore the central role of soil microstructure and hydrology in regulating bacterial pathogen spread and disease risk, beyond pathogen abundance or soil chemistry alone [\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e, \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eMoreover, soil aggregate size strongly shapes nematode communities. In tea plantations in China, larger soil aggregates (\u0026gt;\u0026thinsp;2 mm) support higher nematode abundance, diversity, and functional activity compared to smaller aggregates. These findings indicate that soil physical structure, through aggregate-mediated pore space and resource availability, governs nematode distribution and mobility, thereby directly influencing plant-parasitic nematode pressure and subsequent disease risk. Long-term tea cultivation reduced soil food web complexity and altered nematode functional composition, suggesting that soil structural degradation may increase vulnerability to plant diseases by constraining beneficial nematodes and enabling opportunistic pathogens [\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e]. The study underscores that managing soil aggregation and maintaining a heterogeneous pore network is critical for sustaining nematode-mediated ecosystem services and mitigating soilborne plant disease.\u003c/p\u003e \u003cp\u003eSoil compaction from machinery, foot traffic, or grazing alters soil structure by reducing macropores and increasing bulk density, creating stress on plants while often favoring pathogens. Compacted soils limit aeration, restrict root penetration, and trap ethylene, inducing adaptive responses such as radial swelling, reduced root hair development, and decreased cytoplasmic streaming. These changes weaken plant defenses, modify root architecture, and increase susceptibility to soilborne pathogens. Epidemiologically, compaction correlates with greater root disease severity; increased bulk density has been shown to elevate Fusarium and other root rot incidence, likely through hypoxia and altered water potentials that enhance pathogen activity and stress host roots [\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e]. Similarly, Rhizoctonia root rot severity increases under compaction due to restricted root growth and reduced biomass [\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e]. Compaction also shifts soil microbial communities, favoring anaerobic prokaryotes and saprotrophic fungi while reducing aerobic prokaryotes and plant-associated fungi [\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e]. These findings underscore that soil physical integrity is a key determinant of plant health and disease risk, highlighting the importance of managing compaction in integrated disease management.\u003c/p\u003e \u003cp\u003eSimilarly, soil physical structure critically influences plant health and disease risk by shaping both root growth and pathogen dynamics. Compaction from machinery, foot traffic, or grazing reduces macropores and increases bulk density, limiting aeration, impeding root penetration, and trapping ethylene, which induces radial swelling, reduces root hair development, and decreases cytoplasmic streaming. These physiological changes weaken plant defenses and increase root susceptibility, while also favoring soilborne pathogens such as \u003cem\u003eFusarium\u003c/em\u003e and \u003cem\u003eRhizoctonia\u003c/em\u003e, whose activity is enhanced under hypoxic and altered water conditions [\u003cspan additionalcitationids=\"CR53\" citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e]. Root system architecture (RSA) further mediates disease risk by determining root distribution relative to pathogen inoculum. In compacted soils, roots exploit macropores or cracks to reach deeper, less pathogen-dense layers, whereas shallow, highly branched roots remain in the topsoil, increasing exposure [\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e, \u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e]. RSA also shapes microbial communities, influencing pathogen suppression or facilitation through microbial recruitment along soil gradients [\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e, \u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e]. Soil compaction and aggregate-mediated pore structure regulate the distribution and movement of plant-parasitic nematodes, which, along with fungi and oomycetes, shape the intensity and spatial patterns of root diseases. These interactions highlight that soil physical integrity, root architecture, and microbial communities collectively determine pathogen encounters, disease severity, and crop resilience, emphasizing the integration of soil physics, RSA, and microbial ecology in effective plant disease management.\u003c/p\u003e"},{"header":"5. Soil management for soilborne plant disease control","content":"\u003cp\u003eIf soil is a battlefield, soil management represents the strategic deployment of resources to favor beneficial allies over pathogenic adversaries. Historically, soilborne disease control relied heavily on chemical fumigation, which temporarily suppresses pathogens but also eliminates much of the resident microbiome, creating a biological vacuum often recolonized by opportunistic pathogens. Contemporary approaches instead aim to manipulate soil ecological processes at the level of the soil food-web, promoting suppressive microbial communities and their trophic regulators rather than eliminating pathogens outright. By contrast, reductive soil disinfestation (RSD) increased bacterial diversity, optimized the core microbiome, and stimulated potential disease-suppressive agents, conferring more durable resistance to invasion and improved plant health [\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e]. These outcomes illustrate that effective management reshapes not only microbial composition but also trophic interactions within the soil food web, stabilizing suppressive functions through coupled microbial and faunal regulation. Mechanistic work on RSD shows that both the altered abiotic environment (elevated pH, labile carbon) and specific bacterial and fungal groups jointly underpin suppression of damping‑off, highlighting that soil physicochemical conditions and microbiota codetermine outcomes [\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e].\u003c/p\u003e \u003cp\u003ePrinciples of conservation agriculture, including minimal soil disturbance, permanent soil cover, and diversified crop rotations, form the foundation of this shift. Complementary strategies such as organic amendments (e.g., composts and biochar), anaerobic soil disinfestation (ASD), and biofumigant cover crops are used to restructure microbial communities and alter soil physicochemical conditions. Rather than pursuing pathogen eradication, these approaches aim to restore soil food-web complexity, in which microbial competition, antagonism, functional redundancy, and trophic regulation collectively limit pathogen survival, infectivity, transmission efficiency, and ultimately pathogen \u003cem\u003eR\u003c/em\u003e\u003csub\u003e0\u003c/sub\u003e [\u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e61\u003c/span\u003e, \u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e62\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eBiologically based soil management, however, remains less predictable than chemical control. The most persistent challenge is context dependency: practices that suppress pathogens such as \u003cem\u003eVerticillium\u003c/em\u003e in one field may fail in another due to subtle differences in soil chemistry, texture, climate, or baseline microbial composition. Time lag is an additional constraint. Unlike fumigation, which rapidly reduces pathogen inoculum, the development of suppressive soils is gradual and may require multiple seasons, posing economic risks during transitional periods.\u003c/p\u003e \u003cp\u003eTrade-offs further complicate implementation. Amendments that stimulate beneficial microorganisms may also favor opportunistic pathogens or saprophytes under certain environmental conditions. Reviews on compost‑based and compost‑derived disease suppression show that disease‑suppressive composts can enhance natural suppressiveness by introducing beneficial microbiota and stimulating general suppression mechanisms such as increased microbial activity, fungistasis, competition for space and nutrients, antibiotic production, and systemic resistance (4,5). Moreover, because soil food-webs are inherently dynamic and context-dependent, increases in trophic complexity do not guarantee uniform outcomes across systems. While direct empirical evidence remains limited, there is a theoretical risk that soilborne pathogens could adapt to persistent biological suppression or exploit transient imbalances within food-web interactions, either by tolerating antagonistic compounds or exploiting alternative ecological niches.\u003c/p\u003e \u003cp\u003eEffective soilborne disease management, therefore, requires a paradigm shift from eradication to ecological balance. Despite challenges related to predictability and transition timeframes, integrated strategies combining organic amendments, reduced till-age, and crop diversification offer the most sustainable path forward. By managing soil as a living habitat rather than a substrate, growers can recruit indigenous microbial communities as persistent, self-regenerating defenses against soilborne diseases, reducing long-term dependence on chemical inputs. Long‑term work shows that suppressiveness is largely microbial in origin, involving antibiosis, parasitism, competition, and induced resistance [\u003cspan additionalcitationids=\"CR4 CR5\" citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e].\u003c/p\u003e"},{"header":"6. Research outlook and future progress","content":"\u003cp\u003eFuture advances in soilborne disease research will require a shift from descriptive associations toward mechanistic and predictive frameworks that explicitly link microbial traits, community structure, and epidemiological outcomes. Functional metagenomics and trait-based analyses, combined with network approaches, will be central to identifying the genes, functions, and keystone taxa that constrain pathogen establishment within complex pathobiomes [3-8,63-64]. Longitudinal, high-resolution temporal studies will further be essential to capture microbial transitions that precede disease outbreaks, enabling microbiome-informed early-warning indicators for soilborne epidemics [65].\u003c/p\u003e\n\u003cp\u003eEmerging technologies now provide the means to integrate microscale root–microbe interactions with applied disease management. Advanced imaging tools and synthetic microbiomes offer complementary platforms to experimentally test causal mechanisms and design pathogen-suppressive communities. Translating these insights into practice will require prescriptive soil management strategies, including engineered microbial consortia, crop breeding for rhizosphere competence, predictive modeling, and improved standardization of organic amendments. Together, these approaches position the soil microbiome as a manipulable interface for precision phytopathology rather than a passive background to disease emergence [3,5,6,66-69].\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eCRediT authorship contribution statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDavid Pires\u003c/strong\u003e: Conceptualization, Writing - Original Draft, Writing - Reviewing and Editing. \u003cstrong\u003eFlorabelle Casta\u0026ntilde;eda\u003c/strong\u003e: Writing - Original Draft, Writing - Reviewing and Editing. \u003cstrong\u003eLeny Galvez\u003c/strong\u003e: Writing - Original Draft, Writing - Reviewing and Editing. \u003cstrong\u003eMark Angelo Balendres\u003c/strong\u003e: Conceptualization, Writing - Original Draft, Writing - Reviewing and Editing.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDavid Pires is supported by the Portuguese Foundation for Science and Technology (\u003cem\u003eFunda\u0026ccedil;\u0026atilde;o para a Ci\u0026ecirc;ncia e a Tecnologia\u003c/em\u003e, FCT) and the European Social Fund under the PhD fellowship 2021.08030.BD. This work was published open access with the support of a transformative agreement provided by \u003cem\u003eBiblioteca do Conhecimento Online\u003c/em\u003e (b-on), covering the open access publishing costs.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting Interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors have no financial or non-financial interests to disclose.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contribution\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDavid Pires : Conceptualization, Writing - Original Draft, Writing - Reviewing and Editing. Florabelle Casta\u0026ntilde;eda : Writing - Original Draft, Writing - Reviewing and Editing. Leny Galvez : Writing - Original Draft, Writing - Reviewing and Editing. Mark Angelo Balendres : Conceptualization, Writing - Original Draft, Writing - Reviewing and Editing.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eScholthof K-BG (2007) The disease triangle: pathogens, the environment and society. Nat Rev Microbiol 5(2):152\u0026ndash;156. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/nrmicro1596\u003c/span\u003e\u003cspan address=\"10.1038/nrmicro1596\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLeveau JHJ (2024) Re-envisioning the plant disease triangle: full integration of the host microbiota and a focal pivot to health outcomes. Annu Rev Phytopathol 62(1):31\u0026ndash;47. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1146/annurev-phyto-121423-042021\u003c/span\u003e\u003cspan address=\"10.1146/annurev-phyto-121423-042021\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSchlatter D, Kinkel L, Thomashow L, Weller D, Paulitz T (2017) Disease suppressive soils: new insights from the soil microbiome. Phytopathology\u0026reg; 107(11):1284\u0026ndash;1297. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1094/PHYTO-03-17-0111-RVW\u003c/span\u003e\u003cspan address=\"10.1094/PHYTO-03-17-0111-RVW\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDe Corato U (2020a) Disease-suppressive compost enhances natural soil suppressiveness against soilborne plant patho-gens: A critical review. Rhizosphere 13:100192. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.rhisph.2020.100192\u003c/span\u003e\u003cspan address=\"10.1016/j.rhisph.2020.100192\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDe Corato U (2020b) Soil microbiota manipulation and its role in suppressing soilborne plant pathogens in organic farming systems under the light of microbiome-assisted strategies. Chem Biol Technol Agric 7(1):17. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/s40538-020-00183-7\u003c/span\u003e\u003cspan address=\"10.1186/s40538-020-00183-7\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eJayaraman S, Naorem AK, Lal R, Dalal RC, Sinha NK, Patra AK, Chaudhari SK (2021) Disease-suppressive soils\u0026mdash;beyond food production: a critical review. J Soil Sci Plant Nutr 21(2):1437\u0026ndash;1465. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1007/s42729-021-00451-x\u003c/span\u003e\u003cspan address=\"10.1007/s42729-021-00451-x\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003evan der Sloot M, Maerowitz-Mcmahan S, Postma J, Limpens J, De Deyn GB (2024) Soilborne disease suppres-siveness after short and long term application of fermented, composted or fresh organic amendment treatments in arable soils. Appl Soil Ecol 195:105268. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.apsoil.2023.105268\u003c/span\u003e\u003cspan address=\"10.1016/j.apsoil.2023.105268\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePriyadarshini C, Lal R, Yuan P, Liu W, Adhikari A, Bhandari S, Xia Y (2025) Plant disease suppressiveness en-hancement via soil health management. Biology 14(8):924. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3390/biology14080924\u003c/span\u003e\u003cspan address=\"10.3390/biology14080924\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eNegassa WC, Guber AK, Kravchenko AN, Marsh TL, Hildebrandt B, Rivers ML (2015) Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria. PLoS ONE 10(4):e0123999. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1371/journal.pone.0123999\u003c/span\u003e\u003cspan address=\"10.1371/journal.pone.0123999\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWang N, Zhang T (2024) Soil pore structure and its research methods: A review. Soil Water Res 19(1):1\u0026ndash;24. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.17221/64/2023-swr\u003c/span\u003e\u003cspan address=\"10.17221/64/2023-swr\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003evan Elsas JD, Chiurazzi M, Mallon CA, Elhottovā D, Krištůfek V, Salles JF (2012) Microbial diversity determines the invasion of soil by a bacterial pathogen. Proceedings of the National Academy of Sciences, 109(4), 1159\u0026ndash;1164. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1073/pnas.1109326109\u003c/span\u003e\u003cspan address=\"10.1073/pnas.1109326109\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMallon CA, Le Roux X, van Doorn GS, Dini-Andreote F, Poly F, Salles JF (2018) The impact of failure: unsuc-cessful bacterial invasions steer the soil microbial community away from the invader\u0026rsquo;s niche. ISME J 12(3):728\u0026ndash;741. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s41396-017-0003-y\u003c/span\u003e\u003cspan address=\"10.1038/s41396-017-0003-y\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi H, Deng Y, Zhang S, Greenberg J, Chen D, Song X, Geng X, Zhuge Y, Li C, Ni G, Hou Y (2025) Nutrient availability and invader density regulate the diversity\u0026ndash;invasibility relationship mediated by soil microbes. Funct Ecol 39(10):2717\u0026ndash;2729. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1111/1365-2435.70137\u003c/span\u003e\u003cspan address=\"10.1111/1365-2435.70137\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLoreau M, Barbier M, Filotas E, Gravel D, Isbell F, Miller SJ, Montoya JM, Wang S, Aussenac R, Germain R, Thompson PL, Gonzalez A, Dee LE (2021) Biodiversity as insurance: from concept to measurement and application. Biol Rev 96(5):2333\u0026ndash;2354. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1111/brv.12756\u003c/span\u003e\u003cspan address=\"10.1111/brv.12756\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHu J, Wei Z, Friman V-P, Gu S, Wang X, Eisenhauer N, Yang T, Ma J, Shen Q, Xu Y, Jousset A (2016) Probiotic diversity enhances rhizosphere microbiome function and plant disease suppression. MBio 7(6). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1128/mBio.01790-16\u003c/span\u003e\u003cspan address=\"10.1128/mBio.01790-16\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eNishisaka CS, Quevedo HD, Ventura JP, Andreote FD, Mauchline TH, Mendes R (2025) Soil microbial diversity: A key factor in pathogen suppression and inoculant performance. Geoderma 460:117444. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.geoderma.2025.117444\u003c/span\u003e\u003cspan address=\"10.1016/j.geoderma.2025.117444\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eVerd\u0026uacute; M, Alc\u0026aacute;ntara JM, Navarro-Cano JA, Goberna M (2023) Transitivity and intransitivity in soil bacterial networks. ISME J 17(12):2135\u0026ndash;2139. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s41396-023-01540-8\u003c/span\u003e\u003cspan address=\"10.1038/s41396-023-01540-8\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBongers T, Ferris H (1999) Nematode community structure as a bioindicator in environmental monitoring. Trends Ecol Evol 14(6):224\u0026ndash;228. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/https://doi.org/10.1016/S0169-5347(98)01583-3\u003c/span\u003e\u003cspan address=\"10.1016/S0169-5347(98)01583-3\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFerris H, Bongers T, de Goede RGM (2001) A framework for soil food web diagnostics: extension of the nematode faunal analysis concept. Appl Soil Ecol 18(1):13\u0026ndash;29. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/https://doi.org/10.1016/S0929-1393(01)00152-4\u003c/span\u003e\u003cspan address=\"10.1016/S0929-1393(01)00152-4\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYeates GW (2003) Nematodes as soil indicators: functional and biodiversity aspects. Biol Fertil Soils 37(4):199\u0026ndash;210. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/https://doi.org/10.1007/s00374-003-0586-5\u003c/span\u003e\u003cspan address=\"10.1007/s00374-003-0586-5\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTopalović O, Geisen S (2023) Nematodes as suppressors and facilitators of plant performance. New Phytol 238(6):2305\u0026ndash;2312. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/https://doi.org/10.1111/nph.18925\u003c/span\u003e\u003cspan address=\"10.1111/nph.18925\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eXiong W, Song Y, Yang K, Gu Y, Wei Z, Kowalchuk GA, Xu Y, Jousset A, Shen Q, Geisen S (2020) Rhizosphere protists are key determinants of plant health. Microbiome 8(1):27. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/s40168-020-00799-9\u003c/span\u003e\u003cspan address=\"10.1186/s40168-020-00799-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSantoyo G, del Orozco-Mosqueda M C., Babalola OO (2025) How protists contribute to plant growth and health: Exploring new interactions with the plant microbiome. Microbe 7:100361. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.microb.2025.100361\u003c/span\u003e\u003cspan address=\"10.1016/j.microb.2025.100361\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003evan den Bosch F, McRoberts N, van den Berg F, Madden LV (2008) The basic reproduction number of plant path-ogens: matrix approaches to complex dynamics. Phytopathology\u0026reg; 98(2):239\u0026ndash;249. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1094/PHYTO-98-2-0239\u003c/span\u003e\u003cspan address=\"10.1094/PHYTO-98-2-0239\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eVukicevich E, Lowery T, Bowen P, \u0026Uacute;rbez-Torres JR, Hart M (2016) Cover crops to increase soil microbial diversity and mitigate decline in perennial agriculture. A review. Agron Sustain Dev 36(3):48. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1007/s13593-016-0385-7\u003c/span\u003e\u003cspan address=\"10.1007/s13593-016-0385-7\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTodorović I, Mo\u0026euml;nne-Loccoz Y, Raičević V, Jovičić-Petrović J, Muller D (2023) Microbial diversity in soils suppressive to Fusarium diseases. Front Plant Sci 14. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3389/fpls.2023.1228749\u003c/span\u003e\u003cspan address=\"10.3389/fpls.2023.1228749\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBonanomi G, Antignani V, Pane C, Scala F (2007) Suppression of soilborne fungal diseases with organic amendments. J Plant Pathol, 311\u0026ndash;324. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.jstor.org/stable/41998409\u003c/span\u003e\u003cspan address=\"https://www.jstor.org/stable/41998409\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMayerhofer J, Thuerig B, Oberhaensli T, Enderle E, Lutz S, Ahrens CH, Widmer F (2021) Indicative bacterial communities and taxa of disease-suppressing and growth-promoting composts and their associations to the rhizoplane. FEMS Microbiol Ecol 97(10):fiab134. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/femsec/fiab134\u003c/span\u003e\u003cspan address=\"10.1093/femsec/fiab134\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSilva RM, Canella LP (2022) Organic matter in the pest and plant disease control: A meta-analysis. Chem Biol Technol Agric 9(1):70. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/s40538-022-00332-0\u003c/span\u003e\u003cspan address=\"10.1186/s40538-022-00332-0\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYatoo AM, Rasool S, Ali S, Majid S, Rehman MU, Ali MN, Farooq S (2020) Vermicomposting: An eco-friendly approach for recycling/management of organic wastes. Bioremediation and biotechnology: sustainable approaches to pollution degradation. Springer International Publishing, Cham, pp 167\u0026ndash;187. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1007/978-3-030-35691-0_8\u003c/span\u003e\u003cspan address=\"10.1007/978-3-030-35691-0_8\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eRavindran B, Wong JW, Selvam A, Sekaran G (2016) Influence of microbial diversity and plant growth hormones in compost and vermicompost from fermented tannery waste. Bioresour Technol 217:200\u0026ndash;204. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.biortech.2016.03.032\u003c/span\u003e\u003cspan address=\"10.1016/j.biortech.2016.03.032\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePereira RV, Filgueiras CC, D\u0026oacute;ria J, Pe\u0026ntilde;aflor MFG, Willett DS (2021) The effects of biostimulants on induced plant defense. Front Agron 3:630596. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3389/fagro.2021.630596\u003c/span\u003e\u003cspan address=\"10.3389/fagro.2021.630596\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDu S, Trivedi P, Wei Z, Feng J, Hu HW, Bi L, Huang Q, Liu YR (2022) The proportion of soilborne fungal pathogens increases with elevated organic carbon in agricultural soils. Msystems 7(2):e01337\u0026ndash;e01321. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1128/msystems.01337-21\u003c/span\u003e\u003cspan address=\"10.1128/msystems.01337-21\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePerry DA (1986) Pathogenicity of Monographella nivalis to spring barley. Trans Br Mycological Soc 86(2):287\u0026ndash;293. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/S0007-1536(86)80158-9\u003c/span\u003e\u003cspan address=\"10.1016/S0007-1536(86)80158-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eNicholson FA, Groves SJ, Chambers BJ (2005) Pathogen survival during livestock manure storage and following land application. Bioresour Technol 96(2):135\u0026ndash;143. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.biortech.2004.02.030\u003c/span\u003e\u003cspan address=\"10.1016/j.biortech.2004.02.030\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eVandecasteele B, Muylle H, De Windt I, Van Acker J, Ameloot N, Moreaux K, Coucke P, Debode J (2018) Plant fibers for renewable growing media: Potential of defibration, acidification or inoculation with biocontrol fungi to reduce the N drawdown and plant pathogens. J Clean Prod 203:1143\u0026ndash;1154. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.jclepro.2018.08.167\u003c/span\u003e\u003cspan address=\"10.1016/j.jclepro.2018.08.167\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYang H, Ma J, Rong Z, Zeng D, Wang Y, Hu S, Ye W, Zheng X (2019) Wheat straw return influences nitro-gen-cycling and pathogen associated soil microbiota in a wheat\u0026ndash;soybean rotation system. Front Microbiol 10:1811. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3389/fmicb.2019.01811\u003c/span\u003e\u003cspan address=\"10.3389/fmicb.2019.01811\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi M, Wei Z, Wang J, Jousset A, Friman VP, Xu Y, Shen Q, Pommier T (2019) Facilitation promotes invasions in plant-associated microbial communities. Ecol Lett 22(1):149\u0026ndash;158. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1111/ele.13177\u003c/span\u003e\u003cspan address=\"10.1111/ele.13177\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWei Z, Gu Y, Friman VP, Kowalchuk GA, Xu Y, Shen Q, Jousset A (2019) Initial soil microbiome composition and functioning predetermine future plant health. Sci Adv 5(9):eaaw0759. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1126/sciadv.aaw0759\u003c/span\u003e\u003cspan address=\"10.1126/sciadv.aaw0759\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eW\u0026ouml;sten HaB (2001) Hydrophobins: multipurpose proteins. Annu Rev Microbiol 55(1):625\u0026ndash;646. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1146/annurev.micro.55.1.625\u003c/span\u003e\u003cspan address=\"10.1146/annurev.micro.55.1.625\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAleklett K, Ohlsson P, Bengtsson M, Hammer E (2021) Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips. ISME J 15:1782\u0026ndash;1793. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s41396-020-00886-7\u003c/span\u003e\u003cspan address=\"10.1038/s41396-020-00886-7\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFalconer RE, Battaia G, Schmidt S, Baveye P, Chenu C, Otten W (2015) Microscale Heterogeneity Explains Ex-perimental Variability and Non-Linearity in Soil Organic Matter Mineralisation. PLoS ONE 10(5):e0123774. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1371/journal.pone.0123774\u003c/span\u003e\u003cspan address=\"10.1371/journal.pone.0123774\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYu Y, Elliott M, Chowdhury I, Flury M (2020) Transport Mechanisms of Motile and Nonmotile Phytophthora cac-torum Zoospores in Unsaturated Porous Media. Water Resour Res 57(2). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1029/2020wr028249\u003c/span\u003e\u003cspan address=\"10.1029/2020wr028249\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eErwin DC, Ribeiro OK (1996) Phytophthora diseases worldwide. The American Phytopathological Society, St Paul, Minnesota, p 562\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eJudelson HS, Blanco FA (2005) The spores of Phytophthora: weapons of the plant destroyer. Nat Rev Microbiol 3:47\u0026ndash;58\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eCarson JK, Gonzalez-Qui\u0026ntilde;Ones V, Murphy DV, Hinz C, Shaw JA, Gleeson DB (2010) Low pore connectivity increases bacterial diversity in soil. Appl Environ Microbiol 76(12):3936\u0026ndash;3942. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1128/aem.03085-09\u003c/span\u003e\u003cspan address=\"10.1128/aem.03085-09\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEbrahimi AN, Or D (2014) Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks. Water Resour Res 50:7406\u0026ndash;7429. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi:10.1002/2014WR015897\u003c/span\u003e\u003cspan address=\"https://doi:10.1002/2014WR015897\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAufrecht JA, Fowlkes JD, Bible AN, Morrell-Falvey J, Doktycz MJ, Retterer ST (2019) Pore-scale hydrody-namics influence the spatial evolution of bacterial biofilms in a microfluidic porous network. PLoS ONE 14(6):e0218316. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1371/journal.pone.0218316\u003c/span\u003e\u003cspan address=\"10.1371/journal.pone.0218316\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYang K, Wang X, Hou R, Lu C, Fan Z, Li J, Wang S, Xu Y, Shen Q, Friman V, Wei Z (2023) Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease. Microbiome 11(1):16. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/s40168-023-01463-8\u003c/span\u003e\u003cspan address=\"10.1186/s40168-023-01463-8\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChachar Z, Xue X, Fang J, Chen M, Jiarui C, Chen W, Ahmed N, Chachar S, Narejo M, Ahmed N, Fan L, Lai R, Qi Y (2025) Key mechanisms of plant-Ralstonia solanacearum interaction in bacterial wilt pathogenesis. Front Microbiol 16:1521422. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3389/fmicb.2025.1521422\u003c/span\u003e\u003cspan address=\"10.3389/fmicb.2025.1521422\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHe S, Jia H, Zheng Z, Li T, Luo Z, Zhang Y, Wang Y (2022) Responses of soil nematode community within soil aggregates to tea plantation age. Environ Sci Pollut Res 29(56):85114\u0026ndash;85127\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTu J (1994) Effects of soil compaction, temperature, and moisture on the development of the Fusarium root rot complex of pea in southwestern Ontario. Phytoprotection 75(3):125\u0026ndash;131. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.7202/706059ar\u003c/span\u003e\u003cspan address=\"10.7202/706059ar\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGill JS, Hunt S, Sivasithamparam K, Smettem KRJ (2004) Root growth altered by compaction of a sandy loam soil affects severity of rhizoctonia root rot of wheat seedlings. Aust J Exp Agric 44(6):595\u0026ndash;599. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1071/ea02093\u003c/span\u003e\u003cspan address=\"10.1071/ea02093\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLongepierre M, Widmer F, Keller T, Weisskopf P, Colombi T, Six J, Hartmann M (2021) Limited resilience of the soil microbiome to mechanical compaction within four growing seasons of agricultural management. ISME Commun 1(1):44. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s43705-021-00046-8\u003c/span\u003e\u003cspan address=\"10.1038/s43705-021-00046-8\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eCorrea J, Postma JA, Watt M, Wojciechowski T (2019) Soil compaction and the architectural plasticity of root systems. J Exp Bot 70(21):6019\u0026ndash;6034. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/jxb/erz383\u003c/span\u003e\u003cspan address=\"10.1093/jxb/erz383\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGifford ML, Xu G, Dupuy LX, Vissenberg K, Rebetzke G (2024) Root architecture and rhizosphere\u0026ndash;microbe interactions. J Exp Bot 75(2):503\u0026ndash;507. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/jxb/erad488\u003c/span\u003e\u003cspan address=\"10.1093/jxb/erad488\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGalindo-Casta\u0026ntilde;eda T, Hartmann M, Lynch JP (2024) Location: root architecture structures rhizosphere micro-bial associations. J Exp Bot 75(2):594\u0026ndash;604. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/jxb/erad421\u003c/span\u003e\u003cspan address=\"10.1093/jxb/erad421\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang H, Liu Z, Zheng C, Ma H, Zeng M, Yang X (2024) Root system architecture plasticity with beneficial rhi-zosphere microbes: Current findings and future perspectives. Microbiol Res 292:128028. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.micres.2024.128028\u003c/span\u003e\u003cspan address=\"10.1016/j.micres.2024.128028\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhou X, Zhang Q, Yan Y, Qu J, Zhou J, Zhao J, Zhang J, Cai Z, Dai C, Huang X (2025) Effects of soil man-agement strategies based on different principles on soil microbial communities and the outcomes for plant health. Biol Control 201:105708. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.biocontrol.2025.105708\u003c/span\u003e\u003cspan address=\"10.1016/j.biocontrol.2025.105708\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLiu L, Huang X, Zhao J, Zhang J, Cai Z (2019) Characterizing the key agents in a disease-suppressed soil managed by reductive soil disinfestation. Appl Environ Microbiol 85(7). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1128/AEM.02992-18\u003c/span\u003e\u003cspan address=\"10.1128/AEM.02992-18\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003evan Bruggen AH, Gamliel A, Finckh MR (2016) Plant disease management in organic farming systems. Pest Man-agement Sci 72(1):30\u0026ndash;44. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1002/ps.4145\u003c/span\u003e\u003cspan address=\"10.1002/ps.4145\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePanth M, Hassler SC, Baysal-Gurel F (2020) Methods for management of soilborne diseases in crop production. Agriculture 10(1):16. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3390/agriculture10010016\u003c/span\u003e\u003cspan address=\"10.3390/agriculture10010016\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eVayssier-Taussat M, Albina E, Citti C, Cosson J-F, Jacques M-A, Lebrun M-H, Le Loir Y, Ogliastro M, Petit M-A, Roumagnac P, Candresse T (2014) Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics. Frontiers in Cellular and Infection Microbiology, 4. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3389/fcimb.2014.00029\u003c/span\u003e\u003cspan address=\"10.3389/fcimb.2014.00029\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBass D, Stentiford GD, Wang H-C, Koskella B, Tyler CR (2019) The pathobiome in animal and plant diseases. Trends Ecol Evol 34(11):996\u0026ndash;1008. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.tree.2019.07.012\u003c/span\u003e\u003cspan address=\"10.1016/j.tree.2019.07.012\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFournier P, Pellan L, Jaswa A, Cambon MC, Chataigner A, Bonnard O, Raynal M, Debord C, Poeydebat C, Labarthe S, Delmotte F, This P, Vacher C (2025) Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology. Environ Microbiome 20(1):37. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/s40793-025-00691-9\u003c/span\u003e\u003cspan address=\"10.1186/s40793-025-00691-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMazzola M, Freilich S (2017) Prospects for biological soilborne disease control: application of indigenous versus synthetic microbiomes. Phytopathology\u0026reg; 107(3):256\u0026ndash;263. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1094/PHYTO-09-16-0330-RVW\u003c/span\u003e\u003cspan address=\"10.1094/PHYTO-09-16-0330-RVW\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eNiu B, Wang W, Yuan Z, Sederoff RR, Sederoff H, Chiang VL, Borriss R (2020) Microbial interactions within multiple-strain biological control agents impact soilborne plant disease. Front Microbiol 11. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3389/fmicb.2020.585404\u003c/span\u003e\u003cspan address=\"10.3389/fmicb.2020.585404\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eQiao Y, Wang Z, Sun H, Guo H, Song Y, Zhang H, Ruan Y, Xu Q, Huang Q, Shen Q, Ling N (2024) Synthetic community derived from grafted watermelon rhizosphere provides protection for ungrafted watermelon against Fusarium oxysporum via microbial synergistic effects. Microbiome 12(1):101. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/s40168-024-01814-z\u003c/span\u003e\u003cspan address=\"10.1186/s40168-024-01814-z\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBashizi T, Kim M-J, Lim K, Lee G, Tagele S, Shin J-H (2025) Application of a synthetic microbial community to enhance pepper resistance against Phytophthora capsici. Plants 14(11):1625. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3390/plants14111625\u003c/span\u003e\u003cspan address=\"10.3390/plants14111625\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"microbial-ecology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"meco","sideBox":"Learn more about [Microbial Ecology](https://www.springer.com/journal/248)","snPcode":"248","submissionUrl":"https://submission.nature.com/new-submission/248/3","title":"Microbial Ecology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"biological control, microbial ecology, plant disease triangle, soil organic matter, soil suppressiveness","lastPublishedDoi":"10.21203/rs.3.rs-8731607/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8731607/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThis paper focuses on how microbial diversity, soil organic matter, and soil structure influence the activities of soilborne pathogens and plant disease epidemiology. Microbial diversity, organic matter, and structure are soil components that can reshape plant-pathogen-soil interactions (the plant disease triangle) by altering nutrient dynamics and the composition of the soil microbiome. When beneficial microorganisms are favored, soil suppressiveness is enhanced by reducing plant pathogen survival, limiting infection success, and restricting inoculum buildup, thereby decreasing disease incidence and severity. However, microbial diversity, soil organic matter, and soil structure may also promote pathogen growth or facilitate cooperative microbial interactions that improve pathogen persistence, thereby elevating disease risk. Future progress requires a shift from descriptive surveys toward functional and predictive approaches, as these soil components are epidemiological factors that can either suppress or intensify the development of plant diseases caused by soilborne plant pathogens. This paper highlights the importance of soil management in regulating microbial community dynamics and supporting plant disease control.\u003c/p\u003e","manuscriptTitle":"Soil as a battlefield and a reservoir: linking soil components to the epidemiology of soilborne plant diseases","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-02-05 08:37:20","doi":"10.21203/rs.3.rs-8731607/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-03-10T14:39:10+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-03-02T22:38:56+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-02-24T16:49:27+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-02-23T07:59:24+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"150770873622155176624700493371373280127","date":"2026-02-17T17:09:29+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"99162177757271487944919978358956635456","date":"2026-02-09T08:43:20+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"5926657375391969060048014574912970111","date":"2026-01-30T02:23:24+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"322783159723295168275821416295034489417","date":"2026-01-30T01:24:30+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2026-01-29T15:53:53+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-01-29T13:57:21+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-01-29T13:55:57+00:00","index":"","fulltext":""},{"type":"submitted","content":"Microbial Ecology","date":"2026-01-29T11:59:37+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"microbial-ecology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"meco","sideBox":"Learn more about [Microbial Ecology](https://www.springer.com/journal/248)","snPcode":"248","submissionUrl":"https://submission.nature.com/new-submission/248/3","title":"Microbial Ecology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"e93d714f-7ef6-473d-98e3-5f2f737d383f","owner":[],"postedDate":"February 5th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-05-05T15:38:21+00:00","versionOfRecord":[],"versionCreatedAt":"2026-02-05 08:37:20","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8731607","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8731607","identity":"rs-8731607","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}