Diversity of Rhizospheric Fungal Genera in Vegetable Crops of Burkina Faso

Diversity of Rhizospheric Fungal Genera in Vegetable Crops of Burkina Faso | 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 Article Diversity of Rhizospheric Fungal Genera in Vegetable Crops of Burkina Faso Dianda Zoéyandé Oumarou, Kiemdé Rasmané, Tiendrebeogo Nebnoma Romaric, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6821486/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Vegetable cultivation is a cornerstone of socio-economic development in Burkina Faso, ensuring food security and providing income for local communities. However, soil-borne pathogenic fungi, commonly referred to as soil-borne fungi, threaten crop productivity by causing significant yield losses. These fungi play diverse ecological roles, acting as either pathogens or beneficial organisms, making their characterization essential for sustainable agricultural management. This study aimed to inventory and characterize fungal communities in the rhizosphere of vegetable crops across multiple regions of Burkina Faso. Using the suspension-dilution method combined with macroscopic and microscopic analyses, 11 fungal genera were identified: Penicillium , Aspergillus , Absidia, Trichoderma , Rhizopus , Fusarium, Alternaria , Curvularia , Metarhizium , Pythium , and Colletotrichum . Among these, Trichoderma and Fusarium were the dominant species. Fungal diversity varied among rhizospheres, with tomato and eggplant exhibiting the highest richness (9 genera each). Pathogenicity tests revealed that Fusarium isolates, particularly the F5 isolate, induced severe symptoms in tomato plants, highlighting their pathogenic potential. Conversely, Trichoderma isolates demonstrated high antagonistic activity, inhibiting pathogenic Fusarium and Alternaria strains by more than 60%. These findings highlight the dual role of rhizospheric fungi as both threats and biocontrol agents, providing critical insights for developing integrated pest management strategies to enhance vegetable production in Burkina Faso. Biological sciences/Ecology Biological sciences/Microbiology Biological sciences/Plant sciences Rhizospheres Fungal diversity Pathogenicity Antagonism Burkina Faso Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 INTRODUCTION Vegetable production is critical for household food security and income generation in Burkina Faso, particularly in urban and peri-urban areas 1 , 23 . In the Sudano-Sahelian zone, vegetable farming is primarily dominated by onion, tomato, and cabbage crops. However, the productivity of these systems is constrained by suboptimal cultivation practices, soil health, pests and diseases, and local climate conditions 3 . The rhizosphere is at the heart of these systems, a biologically active zone surrounding plant roots that hosts complex microbial communities. Fungi are key components of these communities, playing diverse roles in the functionality of agroecosystems and can be broadly categorized into three functional groups: (i) symbiotic fungi, such as arbuscular mycorrhizal fungi (AMF), which enhance nutrient acquisition and improve plant resilience to abiotic stresses 4 – 6 ; (ii) saprophytic fungi, which contribute to organic matter decomposition and nutrient cycling 7 ; and (iii) pathogenic fungi, which cause economically significant diseases, including vascular wilts, root rots, and leaf spots, with genera such as Fusarium and Alternaria commonly implicated 8 – 11 . The composition and activity of rhizospheric fungal communities are influenced by several agronomic and environmental factors, including crop type 12 , agricultural practices 13 , crop rotation schemes 14 , and production methods (organic vs. conventional) 15 . Additionally, practices such as soil sterilization, grafting, and prolonged exposure to agrochemical residues can significantly alter rhizosphere microbial dynamics, with implications for plant health and the sustainability of cropping systems 16 , 17 . Despite the recognized importance of fungal communities in maintaining soil health and plant productivity, little is known about rhizospheric fungi's diversity and functional roles of rhizospheric fungi in Burkina Faso's vegetable production systems. This knowledge gap is particularly concerning given the potential for seeds, composts, and soils to act as reservoirs of phytopathogenic fungi, posing risks to crop health. Therefore, a comprehensive understanding of rhizosphere fungal diversity is crucial for informing sustainable crop management strategies, mitigating disease risks, and enhancing the resilience of horticultural systems in the region. MATERIAL AND METHODS Sampling sites Rhizosphere soil samples were collected in eight provinces in four regions of Burkina Faso. All sampling locations are shown in Fig. 1. Sampling methods Soil samples were collected from the rhizosphere of plants in crop fields located in the Hauts-Bassins, Centre, and Centre-West regions of Burkina Faso. Samples were collected using a soil auger, with stringent precautions taken to prevent cross-contamination, including the systematic disinfection of tools with 90% ethyl alcohol. A composite sample was formed for each plot by combining five subsamples collected diagonally to ensure representativeness. Each composite sample consisted of approximately 250 grams of soil taken from a depth of 15–20 cm. Samples were placed in sterile polyethylene bags, transported to the phytopathology laboratory, and stored at 4°C until further analysis. Isolation of fungi from soil Fungal isolation followed the suspension dilution using the method described by Davet and Roxel (1997) 18 . For each sample, 1 g of soil was transferred into a 15 ml tube containing 10 ml of sterile distilled water. The suspension was agitated for one hour to dislodge spores and mycelial fragments, creating a stock solution. Decimal dilutions were subsequently prepared by transferring 1 ml of the stock solution to 9 ml of sterile distilled water. From each dilution, 0.2ml was plated onto Potato Dextrose Agar (PDA) in petri dishes. To obtain a 10-¹ dilution. The plates were incubated at 25°C for 7 days to facilitate the development of fungal colonies. Fungal Colony Count and Species Load Fungal colonies were enumerated, preliminarily characterized, and purified. Colony-forming units (CFU) per gram of soil were calculated using direct colony counts. To ensure reliability, only Petri dishes containing 15–150 colonies in two consecutive dilutions were considered for enumeration 19 . Two replicates of each selected dilution were used for colony counting. The CFU per gram of soil was determined using the formula: \(\:N=\frac{\text{S}\text{u}\text{m}\:\text{o}\text{f}\:\text{c}\text{o}\text{l}\text{o}\text{n}\text{i}\text{e}}{\text{V}\text{m}\text{l}\left(\text{n}1+0.1\text{n}2\right)\text{X}\text{d}1}\) where N: number of CFU per gram of soil; V: volume of solution deposited; n1: number of dishes considered at the first dilution retained; n2 : Number of dishes considered at the second dilution retained; d1: Factor of the first dilution kept. Inventory of fungal genera After incubation, the fungal colonies were examined under a binocular microscope to characterize morphological structures, including hyphae, conidiophores, and conidia. Genera were identified using the identification key by 20 Analysis of fungal genus diversity Fungal diversity was assessed using several indices, including species richness, Shannon's diversity index (H'), Piélou's equitability index (E), and Simpson's index (D). Species richness corresponds to the number of fungal species identified in a given sample. The Shannon-Weaver diversity index (H') is calculated according to the formula H' = - Σ ((ni / N) × log₂ (ni / N)), where ni is the number of individuals of species i and N is the total number of individuals. This index considers both species richness and relative abundance. It is minimal (H' = 0) when all individuals belong to a single species and tends to species richness (S) when species are equally represented in the community 21 . Piélou's Equitability Index (E) measures the regularity of the distribution of individuals among species. It is expressed as the ratio E = H' / log₂(S), with a value between 0 and 1. An index close to 0 indicates a marked dominance of a single species, while an index close to 1 reflects a balanced distribution of individuals between species. Simpson's index (D) assesses the probability that two individuals randomly selected from a sample belong to the same species: D = Σ [ni(ni − 1)] / [N(N − 1)]. Where ni is the number of individuals of species i and N is the total number of individuals. For a more intuitive interpretation, the index 1 - D is often used: a value close to 1 indicates high diversity, while a value close to 0 indicates low diversity 22 . Pathogenicity evaluation The pathogenicity of isolated fungi was tested on tomato ( Solanum lycopersicum ) plants of the UC 82 B variety, known for its earliness, fruit firmness, and good productivity. Conidial suspensions were standardized to (10 8 ) conidia/ml using 0.05% Tween 80 for dispersion. Each isolate was inoculated onto three-week-old plants by applying 1 ml of suspension to the crown base and wounded leaves using a sterile syringe. A completely randomized block design was implemented, with 10 plants per isolate and control plants treated only with 0.05% Tween 80. Pathogenicity was assessed 40 days after planting (DAP) using disease incidence and severity indices. Disease Incidence (I) is the percentage of plants showing symptoms such as necrosis, chlorosis, or mortality. The calculation was based on the formula proposed by 23 . I = Σ \(\:\left(\frac{n}{N}\right)*\) 100, where I: average incidence per sample; n: number of diseased plants; N: total number of plants observed (N = 12). Disease severity was scored at the 40th percentile using a five-class scale 24 . Disease severity was assessed using a visual scale inspired by 25 , based on the intensity of the observed symptoms. The scale has five levels: a score of 1 indicates the absence of symptoms; 3 corresponds to wilting and slight chlorosis affecting one to three leaves, representing about 10% of the foliage; 5 reflects moderate damage, with about 25% of the leaves and branches showing symptoms; 7 indicates more severe damage, affecting about 50% of the foliage; finally, a score of 9 is given when almost 75% of the leaves and branches are affected by wilting, chlorosis, defoliation and, finally, plant death. The severity index was calculated using the formula of 25 . Is = Σ((Xi*ni)/(N*Z))*100; where 𝐼𝑠 = Disease severity index of the isolate, 𝑋𝑖 = Disease severity i on the plant, 𝑛𝑖 = number of replicates of severity i, 𝑁 = Total number of plants observed. (N = 6) and 𝑍 = highest severity scale (Z= 9). Evaluation of antagonistic potential The antagonistic activity of Trichoderma isolates against pathogenic fungi was evaluated using a dual-culture method 26 . Petri dishes with a 90 mm diameter were filled with 20 mL of PDA medium. Mycelial explants 6 mm in diameter of each pathogenic species and the antagonist were placed on the same axis, equidistant from the center of the dish, at a distance of 5 cm 27 . The plates were sealed and incubated under a 12-hour light-dark cycle at 22–25°C for 7 days. Pathogen-only cultures served as controls. Each pathogen-antagonist combination was replicated four times. The antagonism coefficients (ᶏ) were calculated as follows: ᶏ = (1 - Rtrait/Rtem)*100 where ᶏ: antagonism coefficient; Rtem: mean growth radius of the pathogens alone without Trichoderma ; Rtrait: mean growth radius of the pathogens in the presence of Trichoderma 26 . Data Analysis Data averages were calculated using Microsoft Excel and analyzed using analysis of variance (ANOVA), followed by the Student-Newman-Keuls multiple comparison test at a 5% significance level, using XLSTAT 2016 software. Diversity indices were computed using PAST software. RESULTS Fungal load in the rhizosphere The total fungal load varied significantly among the crops studied (Table 1 ). Tomato rhizosphere soils exhibited the highest fungal load, followed by bell pepper. Conversely, the lowest fungal loads were observed in soils cultivated with chili, eggplant, and onion, which showed no significant differences among themselves (Table 1 ). Table 1 Fungal load in different rhizospheres Speculations Total fungal load (10 4 CFU/g soil) Tomato 7,4 a Eggplant + bell pepper 2,4 c Bell Pepper 4,7 b Pepper 1,8 d Onion 2,1 c Eggplant 1,9 c Valeur de F 42,062 Probabilité 0,000 Significatif HRS Legend : CFU : colony-format unit ; Stat : Statistical values ; HSR : highly significant. The numbers in the same column with the same alphabetical letter do not differ significantly at the 5% threshold (Student Newman Keuls test). Diversity Indices The number of fungal individuals and genera varied significantly across the different rhizospheres. The tomato rhizosphere exhibited the highest abundance, with 108 individuals, followed by eggplant (64) and bell pepper (20). In contrast, lower counts were observed in the rhizospheres of eggplant + bell pepper (5), onion (4), and chili (7). Specific richness, expressed as the number of fungal genera, was similar in several rhizospheres, including eggplant + bell pepper, onion, chili, and bell pepper (four genera each). However, tomato and eggplant rhizospheres demonstrated greater richness with nine genera each, suggesting higher taxonomic diversity. Simpson's index (1-D) revealed that the rhizospheres of chili and bell pepper had the lowest diversity (Table 2 ). Onion, eggplant, and tomato rhizospheres exhibited moderate diversity levels, with the tomato rhizosphere displaying slightly higher diversity. The Shannon index (H') further confirmed tomato and eggplant rhizospheres as the most diverse, while bell pepper rhizosphere had the lowest diversity among the samples analyzed. Piélou's equitability index (E) highlighted a perfectly equitable distribution of fungal genera in the onion rhizosphere (Table 2 ). High equitability was also observed in eggplant and chili rhizospheres, while other rhizospheres displayed slightly less balanced distributions Table 2 Diversity Indices Diversity indices Rhizospheres Eggplant Eggplant + Bell Pepper Onion Pipper Bell Pepper Tomato Specific Richness (S)) 9 4 4 4 4 9 Individuals 64 5 4 7 20 108 Simpson_1-D 0,78 0,72 0,75 0,69 0,67 0,79 Shannon_H 1,71 1,33 1,38 1,27 1,20 1,71 Piélou equitability (E) 0,77 0,96 1 0,9 0,86 0,78 Rhizosphere Mycoflora The isolation of fungal communities from various rhizosphere soils revealed significant diversity, with 27 species distributed across 11 fungal genera identified through macroscopic and microscopic examination of colonies obtained via the suspension dilution method. The identified genera included Aspergillus , Absidia , Fusarium , Rhizopus , Penicillium , Trichoderma , Colletotrichum , Metarhizium , Alternaria , Curvularia , and Pythium (Fig. 3). The mycological analysis indicated considerable variation in fungal diversity across the rhizospheres studied. The rhizospheres of tomato and eggplant exhibited the highest fungal richness, with nine genera identified. In contrast, the rhizospheres associated with pepper, chili, onion, and the mixed rhizosphere of eggplant + pepper demonstrated lower diversity, with only four fungal genera detected in each case (Fig. 2). The distribution and abundance of fungal genera varied distinctly among the crops studied. For example, Absidia and Curvularia were exclusively associated with the tomato rhizosphere, where they were detected with 100% prevalence. Similarly, Metarhizium and Pythium were isolated solely from the eggplant rhizosphere. Conversely, specific genera, such as Trichoderma and Aspergillus , were ubiquitous, being present across all rhizospheres examined. Other genera displayed a more selective distribution. For instance, Fusarium and Rhizopus were detected in five of the six agricultural plots, while Colletotrichum isolates were predominantly obtained from the rhizospheres of tomato and eggplant, accounting for 50% of the total isolates from each crop. Additionally, Alternaria and Penicillium were identified in three rhizosphere environments, indicating a moderate distribution level across crops (Fig. 3). Characteristics of the identified genera The morphological characteristics, both macroscopic and microscopic, of the isolated fungi were described for each fungal genus. These observations are detailed in Fig. 3. Growth Rate of Isolated Fungi The analysis of the average growth rate of the isolated fungi, presented in Table 3 , reveals a significant (p \(\:<\:0.001;\:F-value\:=\:263.91)\:\) variation between the different fungal genera. Rhizopus sp. had the highest growth rate (1.87 mm/hour), followed by species of the genus Trichoderma (1.35 mm/hour). Intermediate values for mycelial growth rate come from the genera Penicillium (0.57 mm/ hour), Metarhizium (0.55 mm/ hour), Fusarium (0.481 mm/ Hour), Phytium (0.46 mm/ hour), Colletotrichum (0.45 mm/ hour) and Alternaria (0.36 mm/ Hour). Curvularia was the slowest growing of all genera studied (0.20 mm/hour). Table 3 Growth rate of isolated fungi Fungal genera Radial growth (mm)/ Hour Rhizopus 1,87 a Trichoderma 1,35 b Pénicilium 0,57 c Metharizium 0,55 c Fusarium 0,48 cd Pytium 0,46 cd Alternaria 0,36 d Curvularia Colletotrichum 0,20 e 0.45 cd Stat F-value 263,91 Probability 0,0001 Significant HS Legend : Highly significant (HS) Pathogenicity of isolates from inventoried fungal genera All fungal isolates from the inventoried genera demonstrated pathogenicity on inoculated tomato plants, inducing distinct symptoms. Necrotic spots were observed on the leaves of plants inoculated with Alternaria and Colletotrichum isolates (Fig. 4A). In contrast, plants inoculated with Fusarium isolates exhibited yellowing of leaves, followed by desiccation and wilting (Fig. 4B). The re-isolation of these fungal genera from symptomatic plant tissues confirmed Koch's postulates, verifying their pathogenic role. In vitro antagonistic effect of Trichoderma on Alternaria and Fusarium isolates The antagonistic interactions between three Trichoderma isolates (T1A, T1H, and T1L) and two pathogen isolates ( Alternaria A1 and Fusarium F2) were evaluated in co-culture experiments on Petri dishes (Fig. 5). Visual observations after seven days revealed that the Trichoderma isolates T1A sporulated extensively on the pathogens, colonizing up to two-thirds of the Petri dish surface. By day 9, Alternaria (A1) had become entirely overgrown by Trichoderma (T1A), demonstrating a strong antagonistic capacity (Fig. 5A). Quantitative analysis of inhibition rates, as determined by the Newman-Keuls test at a 5% significance threshold, indicated minor variations between isolates. Although no statistically significant differences were detected, the co-culture of Trichoderma isolates T1A with Alternaria isolate A1 exhibited the highest inhibition rate (88%). In contrast, the lowest inhibition rate (68%) was observed in the co-culture of Trichoderma isolate T1H with Alternaria A1 (Fig. 6). DISCUSSION Statistical analysis revealed significant differences in fungal load among the rhizospheres of the vegetable crops studied. Tomato exhibited the highest fungal load, while chili showed the lowest. The elevated fungal abundance in tomato rhizospheres may be attributed to greater root exudation, which provides substrates for fungal growth, as suggested by 28 and 29 . In contrast, the reduced fungal load observed in chili and pepper rhizospheres may be linked to the production of antimicrobial compounds, such as capsaicinoids, which inhibit microbial colonization 30 . Higher specific richness observed in the rhizospheres of tomato and eggplant underscores the remarkable taxonomic diversity in these crops. This diversity likely reflects differences in root exudate composition and the availability of diverse ecological niches, as noted by 10 , 11 . Quantitative metrics, such as Simpson's index, confirm the greater fungal diversity in the rhizospheres of tomato and eggplant compared to chili and pepper, highlighting the critical role of plant-microbe interactions in shaping rhizosphere communities. The equitability observed in onion rhizospheres, followed by eggplant and chili, suggests a more homogeneous distribution of fungal genera. This balanced coexistence may result from reduced competitive dominance of any single genus, allowing for a more equitable coexistence 18 . The isolation of 27 fungal species across 11 genera emphasizes the microbiological richness of vegetable rhizospheres. Ubiquitous genera, such as Trichoderma and Aspergillus , were detected in all rhizospheres, consistent with their opportunistic nature and high environmental adaptability 30 . On the other hand, specific associations, such as Absidia and Curvularia in tomato or Metarhizium and Pythium i n eggplant, reflect distinct ecological preferences and plant-microbe interactions, as observed by 31 . Differences in growth rates among fungal genera provide insight into their ecological strategies. Rhizopus sp., which exhibited the fastest growth rate, aligns with its opportunistic colonizer behavior. Similarly, Trichoderma spp. demonstrated rapid growth and competitive abilities, consistent with its antagonistic mechanisms and potential as a biocontrol agent, as reported by 32 , 33 . Moderate growth rates observed in genera such as Penicillium and Fusarium may reflect their adaptation to stable environmental niches, while the slower growth of Curvularia suggests a niche specialization strategy. Pathogenicity tests revealed that isolates of Fusarium (F2, F5) and Alternaria (A1) induced severe symptoms in inoculated tomato plants, including leaf necrosis, wilting, and desiccation. The variability in pathogenicity among isolates may stem from genetic differences within fungal species, as well as environmental factors influencing virulence, such as nutrient availability and soil conditions 26 . Specific virulence factors, such as mycotoxins produced by Fusarium or cutinase enzymes secreted by Alternaria , likely contribute to their aggressive pathogenic behavior. The antagonistic activity of Trichoderma isolates against Fusarium and Alternaria highlights its competitive capacity and biocontrol potential. Visual observations in co-culture experiments demonstrated that Trichoderma isolates T1A exhibited rapid sporulation and colonization, effectively suppressing pathogen growth. Although statistical analysis revealed no significant differences between isolates, T1A exhibited the highest inhibition rate (88%) against Alternaria A1, consistent with its high mycoparasitic activity 32 , 33 . These findings align with previous studies 34 , 35 that emphasize the potential of Trichoderma as a biocontrol agent in sustainable vegetable production. However, environmental variability and formulation challenges must be addressed to optimize its field efficacy. The results highlight the significance of fungal diversity and natural antagonists in preserving soil health and controlling plant diseases. Greater species richness in the rhizospheres of tomato and eggplant, coupled with the effectiveness of Trichoderma , opens avenues for developing integrated biocontrol strategies. Sustainable agricultural practices, such as crop rotation, the use of pathogen-free seeds, and organic amendments, can help maintain microbial balance and suppress pathogenic fungi. The widespread use of untreated seeds and compost by farmers, as reported by 9 , introduces both saprophytic and pathogenic fungi into soils, further influencing rhizosphere composition. While compost amendments enhance microbial richness, as previously demonstrated 36 , 37 , they may also contribute to pathogen transmission. Addressing these challenges is crucial for optimizing soil health and ensuring the sustainability of vegetable production systems. Conclusion This study highlights the high fungal diversity in vegetable rhizospheres, comprising 27 species across 11 genera, including the dominant genera Trichoderma and Fusarium . The rhizospheres of tomato and eggplant exhibited the highest fungal load and diversity, while chili and pepper showed lower richness and abundance. Pathogenicity tests identified Fusarium and Alternaria as key contributors to disease development, emphasizing their importance in disease management strategies. The antagonistic activity of Trichoderma isolates demonstrated their potential as biocontrol agents, with isolate T1A exhibiting the most potent inhibitory effects against pathogens. These findings suggest that sustainable agricultural practices, such as crop rotation, the use of healthy seeds, and organic soil amendments, are essential for maintaining microbial balance and optimizing soil health. The integration of biocontrol strategies leveraging Trichoderma and other beneficial fungi represents a promising avenue for sustainable vegetable production. Declarations Conflict of Interest There is no conflict of interest Author Contribution DZO : Conceptualization; Funding acquisition; Methodology; Resources; Roles/Writing - original draft; prepared figures and tables 1-6KR, KR, ZTC : Methodology; Formal analysis; Roles/Writing - original draft;ORS : Conceptualization; Funding acquisition; Methodology; Formal analysis; Roles/Writing - original draft; Writing - review & editing ; prepared figures 1-6 Acknowledgments This work benefited from the facilities of the Feed the Future Innovation Lab for Current and Emerging Threats to Crops provided by the United States Agency for International Development (USAID) [cooperative agreement No: 7200AA21LE00005] Fruits and vegetables and Soil-bornes pathogens, Burkina National Research Fund for Development [FONRID/AAP8/NCP/PC/2021] (FONRID, Burkina Faso). 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Oumarou","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA8UlEQVRIiWNgGAWjYFCDw0DMw2DDA+YwNsgRrSUNpsWYCC0HwFoOMxDUwi+Rnfi5ouIwA99x5mcP3tSclzFn7334gXGHAU4tkjNyN0ueOXOYQfIwm7nhnGO3eSx7jhtLMJ7BrcXgRu4Gyca2wwwGhxnMpHnYbvMY3EhjkGBs+4NPy+afEC3s36R5/p3jMbj/jPkHYxteW7ZBbeExk+ZtOwC0hY1NAp8WyZ632ywbzqTzSB7mKZOc25fMY3Amjc0iEY9f+NlzN99sqLCW4zt/fJvEm2929gbHjzHf+IgnxGCAB5WbQFDDKBgFo2AUjAJ8AAAXl1J116zQxwAAAABJRU5ErkJggg==","orcid":"","institution":"Centre National de Recherches Scientifiques et Technologiquees","correspondingAuthor":true,"prefix":"","firstName":"Dianda","middleName":"Zoéyandé","lastName":"Oumarou","suffix":""},{"id":475779594,"identity":"18e37d8a-7013-4e6b-af72-26f74f423528","order_by":1,"name":"Kiemdé Rasmané","email":"","orcid":"","institution":"Centre National de Recherches Scientifiques et Technologiquees","correspondingAuthor":false,"prefix":"","firstName":"Kiemdé","middleName":"","lastName":"Rasmané","suffix":""},{"id":475779595,"identity":"b9f9a0dc-3879-4e67-96f7-8bfe56164665","order_by":2,"name":"Tiendrebeogo Nebnoma Romaric","email":"","orcid":"","institution":"Université Thomas SANKARA, Centre Universitaire de Tenkodogo","correspondingAuthor":false,"prefix":"","firstName":"Tiendrebeogo","middleName":"Nebnoma","lastName":"Romaric","suffix":""},{"id":475779596,"identity":"97701b30-ad0a-4133-b30d-0c3dceea987e","order_by":3,"name":"Zombré Tinlé Cyrille","email":"","orcid":"","institution":"Centre National de Recherches Scientifiques et Technologiquees","correspondingAuthor":false,"prefix":"","firstName":"Zombré","middleName":"Tinlé","lastName":"Cyrille","suffix":""},{"id":475779597,"identity":"f37c166f-225a-47a3-a5fc-d685324baff5","order_by":4,"name":"Ouedraogo Rimnoma Serge","email":"","orcid":"","institution":"the Pennsylvania State University","correspondingAuthor":false,"prefix":"","firstName":"Ouedraogo","middleName":"Rimnoma","lastName":"Serge","suffix":""}],"badges":[],"createdAt":"2025-06-04 14:23:31","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6821486/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6821486/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":85423468,"identity":"34d8a330-47b0-42d1-bd0b-2b1bb0ff83d8","added_by":"auto","created_at":"2025-06-25 16:09:33","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":617319,"visible":true,"origin":"","legend":"\u003cp\u003eLegend not included with this version.\u003c/p\u003e","description":"","filename":"Figure1.png","url":"https://assets-eu.researchsquare.com/files/rs-6821486/v1/c137e827e5d8ad8a5e083d26.png"},{"id":85423467,"identity":"d0437a43-038c-42f9-8062-76d3a2ca4ea2","added_by":"auto","created_at":"2025-06-25 16:09:33","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":103989,"visible":true,"origin":"","legend":"\u003cp\u003eLegend not included with this version.\u003c/p\u003e","description":"","filename":"Figure2.png","url":"https://assets-eu.researchsquare.com/files/rs-6821486/v1/77ab9085adcea809cd5acdb2.png"},{"id":85422640,"identity":"53d09038-3777-450c-acf8-3aab2d08cf79","added_by":"auto","created_at":"2025-06-25 16:01:33","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1484210,"visible":true,"origin":"","legend":"\u003cp\u003eLegend not included with this version.\u003c/p\u003e","description":"","filename":"Figure3.png","url":"https://assets-eu.researchsquare.com/files/rs-6821486/v1/bfb4146d3865c5953b360e9b.png"},{"id":85422641,"identity":"41869b46-daef-4564-bf8a-854347651a55","added_by":"auto","created_at":"2025-06-25 16:01:33","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":1031723,"visible":true,"origin":"","legend":"\u003cp\u003eLegend not included with this version.\u003c/p\u003e","description":"","filename":"Figure4.png","url":"https://assets-eu.researchsquare.com/files/rs-6821486/v1/2b298d0e8d348b48b4a2a669.png"},{"id":85422643,"identity":"fe801f67-9a76-4b52-a76c-e8f9d8e897e6","added_by":"auto","created_at":"2025-06-25 16:01:33","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":1237610,"visible":true,"origin":"","legend":"\u003cp\u003eLegend not included with this version.\u003c/p\u003e","description":"","filename":"Figure5.png","url":"https://assets-eu.researchsquare.com/files/rs-6821486/v1/28281c337564f01430a07f3b.png"},{"id":85422646,"identity":"4fdc0f1b-78b2-40ac-8016-309b56eb052a","added_by":"auto","created_at":"2025-06-25 16:01:33","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":144171,"visible":true,"origin":"","legend":"\u003cp\u003eLegend not included with this version.\u003c/p\u003e","description":"","filename":"Figure6.png","url":"https://assets-eu.researchsquare.com/files/rs-6821486/v1/a9907251aa2fbb1928301355.png"},{"id":96363210,"identity":"5d485f1c-d20e-459a-8366-29a5aff39fa8","added_by":"auto","created_at":"2025-11-20 10:05:30","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":7055885,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6821486/v1/c8aad8f3-6c3c-4230-ae37-5cbb5ffa117f.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Diversity of Rhizospheric Fungal Genera in Vegetable Crops of Burkina Faso","fulltext":[{"header":"INTRODUCTION","content":"\u003cp\u003eVegetable production is critical for household food security and income generation in Burkina Faso, particularly in urban and peri-urban areas\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e,\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u003c/sup\u003e. In the Sudano-Sahelian zone, vegetable farming is primarily dominated by onion, tomato, and cabbage crops. However, the productivity of these systems is constrained by suboptimal cultivation practices, soil health, pests and diseases, and local climate conditions\u003csup\u003e\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe rhizosphere is at the heart of these systems, a biologically active zone surrounding plant roots that hosts complex microbial communities. Fungi are key components of these communities, playing diverse roles in the functionality of agroecosystems and can be broadly categorized into three functional groups: (i) symbiotic fungi, such as arbuscular mycorrhizal fungi (AMF), which enhance nutrient acquisition and improve plant resilience to abiotic stresses \u003csup\u003e\u003cspan additionalcitationids=\"CR5\" citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u003c/sup\u003e ; (ii) saprophytic fungi, which contribute to organic matter decomposition and nutrient cycling\u003csup\u003e\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u003c/sup\u003e; and (iii) pathogenic fungi, which cause economically significant diseases, including vascular wilts, root rots, and leaf spots, with genera such as \u003cem\u003eFusarium\u003c/em\u003e and \u003cem\u003eAlternaria\u003c/em\u003e commonly implicated \u003csup\u003e\u003cspan additionalcitationids=\"CR9 CR10\" citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe composition and activity of rhizospheric fungal communities are influenced by several agronomic and environmental factors, including crop type\u003csup\u003e\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u003c/sup\u003e, agricultural practices \u003csup\u003e\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u003c/sup\u003e, crop rotation schemes \u003csup\u003e\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u003c/sup\u003e, and production methods (organic vs. conventional) \u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e. Additionally, practices such as soil sterilization, grafting, and prolonged exposure to agrochemical residues can significantly alter rhizosphere microbial dynamics, with implications for plant health and the sustainability of cropping systems\u003csup\u003e\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e,\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eDespite the recognized importance of fungal communities in maintaining soil health and plant productivity, little is known about rhizospheric fungi's diversity and functional roles of rhizospheric fungi in Burkina Faso's vegetable production systems. This knowledge gap is particularly concerning given the potential for seeds, composts, and soils to act as reservoirs of phytopathogenic fungi, posing risks to crop health. Therefore, a comprehensive understanding of rhizosphere fungal diversity is crucial for informing sustainable crop management strategies, mitigating disease risks, and enhancing the resilience of horticultural systems in the region.\u003c/p\u003e"},{"header":"MATERIAL AND METHODS","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eSampling sites\u003c/h2\u003e \u003cp\u003eRhizosphere soil samples were collected in eight provinces in four regions of Burkina Faso. All sampling locations are shown in Fig.\u0026nbsp;1.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eSampling methods\u003c/h3\u003e\n\u003cp\u003eSoil samples were collected from the rhizosphere of plants in crop fields located in the Hauts-Bassins, Centre, and Centre-West regions of Burkina Faso. Samples were collected using a soil auger, with stringent precautions taken to prevent cross-contamination, including the systematic disinfection of tools with 90% ethyl alcohol. A composite sample was formed for each plot by combining five subsamples collected diagonally to ensure representativeness. Each composite sample consisted of approximately 250 grams of soil taken from a depth of 15\u0026ndash;20 cm. Samples were placed in sterile polyethylene bags, transported to the phytopathology laboratory, and stored at 4\u0026deg;C until further analysis.\u003c/p\u003e\n\u003ch3\u003eIsolation of fungi from soil\u003c/h3\u003e\n\u003cp\u003eFungal isolation followed the suspension dilution using the method described by Davet and Roxel (1997)\u003csup\u003e\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u003c/sup\u003e. For each sample, 1 g of soil was transferred into a 15 ml tube containing 10 ml of sterile distilled water. The suspension was agitated for one hour to dislodge spores and mycelial fragments, creating a stock solution. Decimal dilutions were subsequently prepared by transferring 1 ml of the stock solution to 9 ml of sterile distilled water. From each dilution, 0.2ml was plated onto Potato Dextrose Agar (PDA) in petri dishes. To obtain a 10-\u0026sup1; dilution. The plates were incubated at 25\u0026deg;C for 7 days to facilitate the development of fungal colonies.\u003c/p\u003e\n\u003ch3\u003eFungal Colony Count and Species Load\u003c/h3\u003e\n\u003cp\u003eFungal colonies were enumerated, preliminarily characterized, and purified. Colony-forming units (CFU) per gram of soil were calculated using direct colony counts. To ensure reliability, only Petri dishes containing 15\u0026ndash;150 colonies in two consecutive dilutions were considered for enumeration\u003csup\u003e\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u003c/sup\u003e. Two replicates of each selected dilution were used for colony counting. The CFU per gram of soil was determined using the formula:\u003c/p\u003e \u003cp\u003e \u003cspan class=\"InlineEquation\"\u003e \u003cspan class=\"mathinline\"\u003e\\(\\:N=\\frac{\\text{S}\\text{u}\\text{m}\\:\\text{o}\\text{f}\\:\\text{c}\\text{o}\\text{l}\\text{o}\\text{n}\\text{i}\\text{e}}{\\text{V}\\text{m}\\text{l}\\left(\\text{n}1+0.1\\text{n}2\\right)\\text{X}\\text{d}1}\\)\u003c/span\u003e \u003c/span\u003e where N: number of CFU per gram of soil; V: volume of solution deposited; n1: number of dishes considered at the first dilution retained; n2 : Number of dishes considered at the second dilution retained; d1: Factor of the first dilution kept.\u003c/p\u003e\n\u003ch3\u003eInventory of fungal genera\u003c/h3\u003e\n\u003cp\u003eAfter incubation, the fungal colonies were examined under a binocular microscope to characterize morphological structures, including hyphae, conidiophores, and conidia. Genera were identified using the identification key by \u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u003c/sup\u003e\u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eAnalysis of fungal genus diversity\u003c/h2\u003e \u003cp\u003eFungal diversity was assessed using several indices, including species richness, Shannon's diversity index (H'), Pi\u0026eacute;lou's equitability index (E), and Simpson's index (D).\u003c/p\u003e \u003cp\u003eSpecies richness corresponds to the number of fungal species identified in a given sample.\u003c/p\u003e \u003cp\u003eThe Shannon-Weaver diversity index (H') is calculated according to the formula H' = - Σ ((ni / N) \u0026times; log₂ (ni / N)), where ni is the number of individuals of species i and N is the total number of individuals. This index considers both species richness and relative abundance. It is minimal (H' = 0) when all individuals belong to a single species and tends to species richness (S) when species are equally represented in the community \u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003ePi\u0026eacute;lou's Equitability Index (E) measures the regularity of the distribution of individuals among species. It is expressed as the ratio E\u0026thinsp;=\u0026thinsp;H' / log₂(S), with a value between 0 and 1. An index close to 0 indicates a marked dominance of a single species, while an index close to 1 reflects a balanced distribution of individuals between species.\u003c/p\u003e \u003cp\u003eSimpson's index (D) assesses the probability that two individuals randomly selected from a sample belong to the same species: D\u0026thinsp;=\u0026thinsp;Σ [ni(ni \u0026minus;\u0026thinsp;1)] / [N(N \u0026minus;\u0026thinsp;1)].\u003c/p\u003e \u003cp\u003eWhere ni is the number of individuals of species i and N is the total number of individuals. For a more intuitive interpretation, the index 1 - D is often used: a value close to 1 indicates high diversity, while a value close to 0 indicates low diversity \u003csup\u003e\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003ePathogenicity evaluation\u003c/h3\u003e\n\u003cp\u003eThe pathogenicity of isolated fungi was tested on tomato (\u003cem\u003eSolanum lycopersicum\u003c/em\u003e) plants of the UC 82 B variety, known for its earliness, fruit firmness, and good productivity. Conidial suspensions were standardized to (10\u003csup\u003e8\u003c/sup\u003e) conidia/ml using 0.05% Tween 80 for dispersion. Each isolate was inoculated onto three-week-old plants by applying 1 ml of suspension to the crown base and wounded leaves using a sterile syringe. A completely randomized block design was implemented, with 10 plants per isolate and control plants treated only with 0.05% Tween 80.\u003c/p\u003e \u003cp\u003ePathogenicity was assessed 40 days after planting (DAP) using disease incidence and severity indices.\u003c/p\u003e \u003cp\u003eDisease Incidence (I) is the percentage of plants showing symptoms such as necrosis, chlorosis, or mortality. The calculation was based on the formula proposed by \u003csup\u003e\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eI\u0026thinsp;=\u0026thinsp;Σ\u003cspan class=\"InlineEquation\"\u003e\u003cspan class=\"mathinline\"\u003e\\(\\:\\left(\\frac{n}{N}\\right)*\\)\u003c/span\u003e\u003c/span\u003e100, where I: average incidence per sample; n: number of diseased plants; N: total number of plants observed (N\u0026thinsp;=\u0026thinsp;12). Disease severity was scored at the 40th percentile using a five-class scale\u003csup\u003e\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eDisease severity was assessed using a visual scale inspired by \u003csup\u003e\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e\u003c/sup\u003e, based on the intensity of the observed symptoms. The scale has five levels: a score of 1 indicates the absence of symptoms; 3 corresponds to wilting and slight chlorosis affecting one to three leaves, representing about 10% of the foliage; 5 reflects moderate damage, with about 25% of the leaves and branches showing symptoms; 7 indicates more severe damage, affecting about 50% of the foliage; finally, a score of 9 is given when almost 75% of the leaves and branches are affected by wilting, chlorosis, defoliation and, finally, plant death.\u003c/p\u003e \u003cp\u003eThe severity index was calculated using the formula of \u003csup\u003e\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e\u003c/sup\u003e. Is\u0026thinsp;=\u0026thinsp;Σ((Xi*ni)/(N*Z))*100; where \u0026#119868;\u0026#119904; = Disease severity index of the isolate, \u0026#119883;\u0026#119894; = Disease severity i on the plant, \u0026#119899;\u0026#119894; = number of replicates of severity i, \u0026#119873; = Total number of plants observed. (N\u0026thinsp;=\u0026thinsp;6) and \u0026#119885; = highest severity scale (Z= 9).\u003c/p\u003e\n\u003ch3\u003eEvaluation of antagonistic potential\u003c/h3\u003e\n\u003cp\u003eThe antagonistic activity of \u003cem\u003eTrichoderma\u003c/em\u003e isolates against pathogenic fungi was evaluated using a dual-culture method\u003csup\u003e\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u003c/sup\u003e. Petri dishes with a 90 mm diameter were filled with 20 mL of PDA medium. Mycelial explants 6 mm in diameter of each pathogenic species and the antagonist were placed on the same axis, equidistant from the center of the dish, at a distance of 5 cm \u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e\u003c/sup\u003e. The plates were sealed and incubated under a 12-hour light-dark cycle at 22\u0026ndash;25\u0026deg;C for 7 days. Pathogen-only cultures served as controls. Each pathogen-antagonist combination was replicated four times. The antagonism coefficients (ᶏ) were calculated as follows:\u003c/p\u003e \u003cp\u003eᶏ = (1 - Rtrait/Rtem)*100 where ᶏ: antagonism coefficient; Rtem: mean growth radius of the pathogens alone without \u003cem\u003eTrichoderma\u003c/em\u003e; Rtrait: mean growth radius of the pathogens in the presence of \u003cem\u003eTrichoderma\u003c/em\u003e \u003csup\u003e\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eData Analysis\u003c/h2\u003e \u003cp\u003eData averages were calculated using Microsoft Excel and analyzed using analysis of variance (ANOVA), followed by the Student-Newman-Keuls multiple comparison test at a 5% significance level, using XLSTAT 2016 software. Diversity indices were computed using PAST software.\u003c/p\u003e \u003c/div\u003e"},{"header":"RESULTS","content":"\u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eFungal load in the rhizosphere\u003c/h2\u003e \u003cp\u003eThe total fungal load varied significantly among the crops studied (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Tomato rhizosphere soils exhibited the highest fungal load, followed by bell pepper. Conversely, the lowest fungal loads were observed in soils cultivated with chili, eggplant, and onion, which showed no significant differences among themselves (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eFungal load in different rhizospheres\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"2\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSpeculations\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTotal fungal load (10\u003csup\u003e4\u003c/sup\u003e CFU/g soil)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTomato\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e7,4 \u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEggplant\u0026thinsp;+\u0026thinsp;bell pepper\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2,4 \u003csup\u003ec\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eBell Pepper\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e4,7 \u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePepper\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1,8 \u003csup\u003ed\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eOnion\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e2,1 \u003csup\u003ec\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eEggplant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e1,9 \u003csup\u003ec\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eValeur de F\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e42,062\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eProbabilit\u0026eacute;\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e0,000\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSignificatif\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHRS\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003cb\u003eLegend : CFU\u003c/b\u003e : colony-format unit ; \u003cb\u003eStat\u003c/b\u003e : Statistical values ; HSR : highly significant. The numbers in the same column with the same alphabetical letter do not differ significantly at the 5% threshold (Student Newman Keuls test).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eDiversity Indices\u003c/h2\u003e \u003cp\u003eThe number of fungal individuals and genera varied significantly across the different rhizospheres. The tomato rhizosphere exhibited the highest abundance, with 108 individuals, followed by eggplant (64) and bell pepper (20). In contrast, lower counts were observed in the rhizospheres of eggplant\u0026thinsp;+\u0026thinsp;bell pepper (5), onion (4), and chili (7).\u003c/p\u003e \u003cp\u003eSpecific richness, expressed as the number of fungal genera, was similar in several rhizospheres, including eggplant\u0026thinsp;+\u0026thinsp;bell pepper, onion, chili, and bell pepper (four genera each). However, tomato and eggplant rhizospheres demonstrated greater richness with nine genera each, suggesting higher taxonomic diversity.\u003c/p\u003e \u003cp\u003eSimpson's index (1-D) revealed that the rhizospheres of chili and bell pepper had the lowest diversity (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Onion, eggplant, and tomato rhizospheres exhibited moderate diversity levels, with the tomato rhizosphere displaying slightly higher diversity. The Shannon index (H') further confirmed tomato and eggplant rhizospheres as the most diverse, while bell pepper rhizosphere had the lowest diversity among the samples analyzed.\u003c/p\u003e \u003cp\u003ePi\u0026eacute;lou's equitability index (E) highlighted a perfectly equitable distribution of fungal genera in the onion rhizosphere (Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). High equitability was also observed in eggplant and chili rhizospheres, while other rhizospheres displayed slightly less balanced distributions\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eDiversity Indices\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\" morerows=\"1\" rowspan=\"2\"\u003e \u003cp\u003eDiversity indices\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"7\" nameend=\"c8\" namest=\"c2\"\u003e \u003cp\u003eRhizospheres\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003eEggplant\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eEggplant\u0026thinsp;+\u0026thinsp;Bell Pepper\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eOnion\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003ePipper\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eBell Pepper\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eTomato\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSpecific Richness (S))\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003e9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e9\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eIndividuals\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003e64\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e20\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e108\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSimpson_1-D\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003e0,78\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0,72\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e0,75\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0,69\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e0,67\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e0,79\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eShannon_H\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c3\" namest=\"c2\"\u003e \u003cp\u003e1,71\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1,33\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1,38\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1,27\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e1,20\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e1,71\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c2\" namest=\"c1\"\u003e \u003cp\u003ePi\u0026eacute;lou equitability (E)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e0,77\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e0,96\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e0,9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e0,86\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e0,78\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec15\" class=\"Section2\"\u003e \u003ch2\u003eRhizosphere Mycoflora\u003c/h2\u003e \u003cp\u003eThe isolation of fungal communities from various rhizosphere soils revealed significant diversity, with 27 species distributed across 11 fungal genera identified through macroscopic and microscopic examination of colonies obtained via the suspension dilution method. The identified genera included \u003cem\u003eAspergillus\u003c/em\u003e, \u003cem\u003eAbsidia\u003c/em\u003e, \u003cem\u003eFusarium\u003c/em\u003e, \u003cem\u003eRhizopus\u003c/em\u003e, \u003cem\u003ePenicillium\u003c/em\u003e, \u003cem\u003eTrichoderma\u003c/em\u003e, \u003cem\u003eColletotrichum\u003c/em\u003e, \u003cem\u003eMetarhizium\u003c/em\u003e, \u003cem\u003eAlternaria\u003c/em\u003e, \u003cem\u003eCurvularia\u003c/em\u003e, and \u003cem\u003ePythium\u003c/em\u003e (Fig.\u0026nbsp;3).\u003c/p\u003e \u003cp\u003eThe mycological analysis indicated considerable variation in fungal diversity across the rhizospheres studied. The rhizospheres of tomato and eggplant exhibited the highest fungal richness, with nine genera identified. In contrast, the rhizospheres associated with pepper, chili, onion, and the mixed rhizosphere of eggplant\u0026thinsp;+\u0026thinsp;pepper demonstrated lower diversity, with only four fungal genera detected in each case (Fig.\u0026nbsp;2).\u003c/p\u003e \u003cp\u003eThe distribution and abundance of fungal genera varied distinctly among the crops studied. For example, \u003cem\u003eAbsidia\u003c/em\u003e and \u003cem\u003eCurvularia\u003c/em\u003e were exclusively associated with the tomato rhizosphere, where they were detected with 100% prevalence. Similarly, \u003cem\u003eMetarhizium\u003c/em\u003e and \u003cem\u003ePythium\u003c/em\u003e were isolated solely from the eggplant rhizosphere. Conversely, specific genera, such as \u003cem\u003eTrichoderma\u003c/em\u003e and \u003cem\u003eAspergillus\u003c/em\u003e, were ubiquitous, being present across all rhizospheres examined.\u003c/p\u003e \u003cp\u003eOther genera displayed a more selective distribution. For instance, \u003cem\u003eFusarium\u003c/em\u003e and \u003cem\u003eRhizopus\u003c/em\u003e were detected in five of the six agricultural plots, while \u003cem\u003eColletotrichum\u003c/em\u003e isolates were predominantly obtained from the rhizospheres of tomato and eggplant, accounting for 50% of the total isolates from each crop. Additionally, \u003cem\u003eAlternaria\u003c/em\u003e and \u003cem\u003ePenicillium\u003c/em\u003e were identified in three rhizosphere environments, indicating a moderate distribution level across crops (Fig.\u0026nbsp;3).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec16\" class=\"Section2\"\u003e \u003ch2\u003eCharacteristics of the identified genera\u003c/h2\u003e \u003cp\u003eThe morphological characteristics, both macroscopic and microscopic, of the isolated fungi were described for each fungal genus. These observations are detailed in Fig.\u0026nbsp;3.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec17\" class=\"Section2\"\u003e \u003ch2\u003eGrowth Rate of Isolated Fungi\u003c/h2\u003e \u003cp\u003eThe analysis of the average growth rate of the isolated fungi, presented in Table\u0026nbsp;\u003cspan refid=\"Tab3\" class=\"InternalRef\"\u003e3\u003c/span\u003e, reveals a significant (p \u003cspan class=\"InlineEquation\"\u003e\u003cspan class=\"mathinline\"\u003e\\(\\:\u0026lt;\\:0.001;\\:F-value\\:=\\:263.91)\\:\\)\u003c/span\u003e\u003c/span\u003evariation between the different fungal genera. \u003cem\u003eRhizopus\u003c/em\u003e sp. had the highest growth rate (1.87 mm/hour), followed by species of the genus \u003cem\u003eTrichoderma\u003c/em\u003e (1.35 mm/hour). Intermediate values for mycelial growth rate come from the genera \u003cem\u003ePenicillium\u003c/em\u003e (0.57 mm/ hour), \u003cem\u003eMetarhizium\u003c/em\u003e (0.55 mm/ hour), \u003cem\u003eFusarium\u003c/em\u003e (0.481 mm/ Hour), \u003cem\u003ePhytium\u003c/em\u003e (0.46 mm/ hour), \u003cem\u003eColletotrichum\u003c/em\u003e (0.45 mm/ hour) and \u003cem\u003eAlternaria\u003c/em\u003e (0.36 mm/ Hour). \u003cem\u003eCurvularia\u003c/em\u003e was the slowest growing of all genera studied (0.20 mm/hour).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab3\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eGrowth rate of isolated fungi\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003eFungal genera\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003eRadial growth (mm)/ Hour\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003e\u003cem\u003eRhizopus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e1,87\u003csup\u003ea\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003e\u003cem\u003eTrichoderma\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e1,35\u003csup\u003eb\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003e\u003cem\u003eP\u0026eacute;nicilium\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e0,57\u003csup\u003ec\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003e\u003cem\u003eMetharizium\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e0,55\u003csup\u003ec\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003e\u003cem\u003eFusarium\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e0,48\u003csup\u003ecd\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003e\u003cem\u003ePytium\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e0,46\u003csup\u003ecd\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003e\u003cem\u003eAlternaria\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e0,36\u003csup\u003ed\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"3\" nameend=\"c3\" namest=\"c1\"\u003e \u003cp\u003e\u003cem\u003eCurvularia\u003c/em\u003e\u003c/p\u003e \u003cp\u003e\u003cem\u003eColletotrichum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e0,20\u003csup\u003ee\u003c/sup\u003e\u003c/p\u003e \u003cp\u003e0.45\u003csup\u003ecd\u003c/sup\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colspan=\"2\" morerows=\"2\" nameend=\"c2\" namest=\"c1\" rowspan=\"3\"\u003e \u003cp\u003e\u003cb\u003eStat\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eF-value\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e263,91\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eProbability\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003e0,0001\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003eSignificant\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"2\" nameend=\"c5\" namest=\"c4\"\u003e \u003cp\u003eHS\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"1\" nameend=\"c6\" namest=\"c6\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003ctfoot\u003e \u003ctr\u003e\u003ctd colspan=\"6\"\u003e\u003cb\u003eLegend\u003c/b\u003e: Highly significant (HS)\u003c/td\u003e\u003c/tr\u003e \u003c/tfoot\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec18\" class=\"Section2\"\u003e \u003ch2\u003ePathogenicity of isolates from inventoried fungal genera\u003c/h2\u003e \u003cp\u003eAll fungal isolates from the inventoried genera demonstrated pathogenicity on inoculated tomato plants, inducing distinct symptoms. Necrotic spots were observed on the leaves of plants inoculated with \u003cem\u003eAlternaria\u003c/em\u003e and \u003cem\u003eColletotrichum\u003c/em\u003e isolates (Fig.\u0026nbsp;4A). In contrast, plants inoculated with \u003cem\u003eFusarium\u003c/em\u003e isolates exhibited yellowing of leaves, followed by desiccation and wilting (Fig.\u0026nbsp;4B). The re-isolation of these fungal genera from symptomatic plant tissues confirmed Koch's postulates, verifying their pathogenic role.\u003c/p\u003e \u003cp\u003e \u003cb\u003eIn vitro antagonistic effect of\u003c/b\u003e \u003cb\u003eTrichoderma\u003c/b\u003e \u003cb\u003eon\u003c/b\u003e \u003cb\u003eAlternaria\u003c/b\u003e \u003cb\u003eand\u003c/b\u003e \u003cb\u003eFusarium\u003c/b\u003e \u003cb\u003eisolates\u003c/b\u003e\u003c/p\u003e \u003cp\u003eThe antagonistic interactions between three \u003cem\u003eTrichoderma\u003c/em\u003e isolates (T1A, T1H, and T1L) and two pathogen isolates (\u003cem\u003eAlternaria\u003c/em\u003e A1 and \u003cem\u003eFusarium\u003c/em\u003e F2) were evaluated in co-culture experiments on Petri dishes (Fig.\u0026nbsp;5). Visual observations after seven days revealed that the \u003cem\u003eTrichoderma\u003c/em\u003e isolates T1A sporulated extensively on the pathogens, colonizing up to two-thirds of the Petri dish surface. By day 9, \u003cem\u003eAlternaria\u003c/em\u003e (A1) had become entirely overgrown by \u003cem\u003eTrichoderma\u003c/em\u003e (T1A), demonstrating a strong antagonistic capacity (Fig.\u0026nbsp;5A).\u003c/p\u003e \u003cp\u003eQuantitative analysis of inhibition rates, as determined by the Newman-Keuls test at a 5% significance threshold, indicated minor variations between isolates. Although no statistically significant differences were detected, the co-culture of \u003cem\u003eTrichoderma\u003c/em\u003e isolates T1A with\u003c/p\u003e \u003cp\u003e \u003cem\u003eAlternaria\u003c/em\u003e isolate A1 exhibited the highest inhibition rate (88%). In contrast, the lowest inhibition rate (68%) was observed in the co-culture of \u003cem\u003eTrichoderma\u003c/em\u003e isolate T1H with \u003cem\u003eAlternaria\u003c/em\u003e A1 (Fig.\u0026nbsp;6).\u003c/p\u003e \u003c/div\u003e"},{"header":"DISCUSSION","content":"\u003cp\u003eStatistical analysis revealed significant differences in fungal load among the rhizospheres of the vegetable crops studied. Tomato exhibited the highest fungal load, while chili showed the lowest. The elevated fungal abundance in tomato rhizospheres may be attributed to greater root exudation, which provides substrates for fungal growth, as suggested by \u003csup\u003e28\u003c/sup\u003e and \u003csup\u003e29\u003c/sup\u003e. In contrast, the reduced fungal load observed in chili and pepper rhizospheres may be linked to the production of antimicrobial compounds, such as capsaicinoids, which inhibit microbial colonization\u003csup\u003e\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eHigher specific richness observed in the rhizospheres of tomato and eggplant underscores the remarkable taxonomic diversity in these crops. This diversity likely reflects differences in root exudate composition and the availability of diverse ecological niches, as noted by\u003csup\u003e\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e,\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u003c/sup\u003e. Quantitative metrics, such as Simpson's index, confirm the greater fungal diversity in the rhizospheres of tomato and eggplant compared to chili and pepper, highlighting the critical role of plant-microbe interactions in shaping rhizosphere communities. The equitability observed in onion rhizospheres, followed by eggplant and chili, suggests a more homogeneous distribution of fungal genera. This balanced coexistence may result from reduced competitive dominance of any single genus, allowing for a more equitable coexistence\u003csup\u003e\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe isolation of 27 fungal species across 11 genera emphasizes the microbiological richness of vegetable rhizospheres. Ubiquitous genera, such as \u003cem\u003eTrichoderma\u003c/em\u003e and \u003cem\u003eAspergillus\u003c/em\u003e, were detected in all rhizospheres, consistent with their opportunistic nature and high environmental adaptability \u003csup\u003e\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e\u003c/sup\u003e. On the other hand, specific associations, such as Absidia and \u003cem\u003eCurvularia\u003c/em\u003e in tomato or \u003cem\u003eMetarhizium\u003c/em\u003e and \u003cem\u003ePythium i\u003c/em\u003en eggplant, reflect distinct ecological preferences and plant-microbe interactions, as observed by \u003csup\u003e\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eDifferences in growth rates among fungal genera provide insight into their ecological strategies. \u003cem\u003eRhizopus\u003c/em\u003e sp., which exhibited the fastest growth rate, aligns with its opportunistic colonizer behavior. Similarly, \u003cem\u003eTrichoderma\u003c/em\u003e spp. demonstrated rapid growth and competitive abilities, consistent with its antagonistic mechanisms and potential as a biocontrol agent, as reported by \u003csup\u003e\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e,\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u003c/sup\u003e. Moderate growth rates observed in genera such as \u003cem\u003ePenicillium\u003c/em\u003e and \u003cem\u003eFusarium\u003c/em\u003e may reflect their adaptation to stable environmental niches, while the slower growth of \u003cem\u003eCurvularia\u003c/em\u003e suggests a niche specialization strategy.\u003c/p\u003e \u003cp\u003ePathogenicity tests revealed that isolates of Fusarium (F2, F5) and \u003cem\u003eAlternaria\u003c/em\u003e (A1) induced severe symptoms in inoculated tomato plants, including leaf necrosis, wilting, and desiccation. The variability in pathogenicity among isolates may stem from genetic differences within fungal species, as well as environmental factors influencing virulence, such as nutrient availability and soil conditions \u003csup\u003e\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u003c/sup\u003e. Specific virulence factors, such as mycotoxins produced by \u003cem\u003eFusarium\u003c/em\u003e or cutinase enzymes secreted by \u003cem\u003eAlternaria\u003c/em\u003e, likely contribute to their aggressive pathogenic behavior.\u003c/p\u003e \u003cp\u003eThe antagonistic activity of Trichoderma isolates against \u003cem\u003eFusarium\u003c/em\u003e and \u003cem\u003eAlternaria\u003c/em\u003e highlights its competitive capacity and biocontrol potential. Visual observations in co-culture experiments demonstrated that \u003cem\u003eTrichoderma\u003c/em\u003e isolates T1A exhibited rapid sporulation and colonization, effectively suppressing pathogen growth. Although statistical analysis revealed no significant differences between isolates, T1A exhibited the highest inhibition rate (88%) against \u003cem\u003eAlternaria\u003c/em\u003e A1, consistent with its high mycoparasitic activity\u003csup\u003e\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e,\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u003c/sup\u003e. These findings align with previous studies \u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e,\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u003c/sup\u003e that emphasize the potential of \u003cem\u003eTrichoderma\u003c/em\u003e as a biocontrol agent in sustainable vegetable production. However, environmental variability and formulation challenges must be addressed to optimize its field efficacy.\u003c/p\u003e \u003cp\u003eThe results highlight the significance of fungal diversity and natural antagonists in preserving soil health and controlling plant diseases. Greater species richness in the rhizospheres of tomato and eggplant, coupled with the effectiveness of \u003cem\u003eTrichoderma\u003c/em\u003e, opens avenues for developing integrated biocontrol strategies. Sustainable agricultural practices, such as crop rotation, the use of pathogen-free seeds, and organic amendments, can help maintain microbial balance and suppress pathogenic fungi.\u003c/p\u003e \u003cp\u003eThe widespread use of untreated seeds and compost by farmers, as reported by \u003csup\u003e\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e\u003c/sup\u003e, introduces both saprophytic and pathogenic fungi into soils, further influencing rhizosphere composition. While compost amendments enhance microbial richness, as previously demonstrated\u003csup\u003e\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e,\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e\u003c/sup\u003e, they may also contribute to pathogen transmission. Addressing these challenges is crucial for optimizing soil health and ensuring the sustainability of vegetable production systems.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eThis study highlights the high fungal diversity in vegetable rhizospheres, comprising 27 species across 11 genera, including the dominant genera \u003cem\u003eTrichoderma\u003c/em\u003e and \u003cem\u003eFusarium\u003c/em\u003e. The rhizospheres of tomato and eggplant exhibited the highest fungal load and diversity, while chili and pepper showed lower richness and abundance. Pathogenicity tests identified \u003cem\u003eFusarium\u003c/em\u003e and \u003cem\u003eAlternaria\u003c/em\u003e as key contributors to disease development, emphasizing their importance in disease management strategies. The antagonistic activity of Trichoderma isolates demonstrated their potential as biocontrol agents, with isolate T1A exhibiting the most potent inhibitory effects against pathogens.\u003c/p\u003e \u003cp\u003eThese findings suggest that sustainable agricultural practices, such as crop rotation, the use of healthy seeds, and organic soil amendments, are essential for maintaining microbial balance and optimizing soil health. The integration of biocontrol strategies leveraging Trichoderma and other beneficial fungi represents a promising avenue for sustainable vegetable production.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch2\u003eConflict of Interest\u003c/h2\u003e \u003cp\u003eThere is no conflict of interest\u003c/p\u003e\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eDZO : Conceptualization; Funding acquisition; Methodology; Resources; Roles/Writing - original draft; prepared figures and tables 1-6KR, KR, ZTC : Methodology; Formal analysis; Roles/Writing - original draft;ORS : Conceptualization; Funding acquisition; Methodology; Formal analysis; Roles/Writing - original draft; Writing - review \u0026amp; editing ; prepared figures 1-6\u003c/p\u003e\u003ch2\u003eAcknowledgments\u003c/h2\u003e\n\u003cp\u003eThis work benefited from the facilities of the Feed the Future Innovation Lab for Current and Emerging Threats to Crops provided by the United States Agency for International Development (USAID) [cooperative agreement No: 7200AA21LE00005] Fruits and vegetables and Soil-bornes pathogens, Burkina National Research Fund for Development [FONRID/AAP8/NCP/PC/2021] (FONRID, Burkina Faso).\u003c/p\u003e\n\u003ch2\u003eData availability statement (mandatory)\u003c/h2\u003e\n\u003cp\u003eData from this study will be made available to the journal as needed via the corresponding author\u0026apos;s e-mail address.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eHama-Ba, F., Parkouda, C., Kamga, R., Tenkouano, A. \u0026amp; Diawara, B. 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Res.\u003c/em\u003e \u003cb\u003e82\u003c/b\u003e, 287\u0026ndash;297 (2012).\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"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":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Rhizospheres, Fungal diversity, Pathogenicity, Antagonism, Burkina Faso","lastPublishedDoi":"10.21203/rs.3.rs-6821486/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6821486/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eVegetable cultivation is a cornerstone of socio-economic development in Burkina Faso, ensuring food security and providing income for local communities. However, soil-borne pathogenic fungi, commonly referred to as soil-borne fungi, threaten crop productivity by causing significant yield losses. These fungi play diverse ecological roles, acting as either pathogens or beneficial organisms, making their characterization essential for sustainable agricultural management.\u003c/p\u003e \u003cp\u003eThis study aimed to inventory and characterize fungal communities in the rhizosphere of vegetable crops across multiple regions of Burkina Faso. Using the suspension-dilution method combined with macroscopic and microscopic analyses, 11 fungal genera were identified: \u003cem\u003ePenicillium\u003c/em\u003e, \u003cem\u003eAspergillus\u003c/em\u003e, \u003cem\u003eAbsidia, Trichoderma\u003c/em\u003e, \u003cem\u003eRhizopus\u003c/em\u003e, \u003cem\u003eFusarium, Alternaria\u003c/em\u003e, \u003cem\u003eCurvularia\u003c/em\u003e, \u003cem\u003eMetarhizium\u003c/em\u003e, \u003cem\u003ePythium\u003c/em\u003e, and \u003cem\u003eColletotrichum\u003c/em\u003e. Among these, \u003cem\u003eTrichoderma\u003c/em\u003e and \u003cem\u003eFusarium\u003c/em\u003e were the dominant species. Fungal diversity varied among rhizospheres, with tomato and eggplant exhibiting the highest richness (9 genera each).\u003c/p\u003e \u003cp\u003ePathogenicity tests revealed that Fusarium isolates, particularly the F5 isolate, induced severe symptoms in tomato plants, highlighting their pathogenic potential. Conversely, \u003cem\u003eTrichoderma\u003c/em\u003e isolates demonstrated high antagonistic activity, inhibiting pathogenic Fusarium and Alternaria strains by more than 60%. These findings highlight the dual role of rhizospheric fungi as both threats and biocontrol agents, providing critical insights for developing integrated pest management strategies to enhance vegetable production in Burkina Faso.\u003c/p\u003e","manuscriptTitle":"Diversity of Rhizospheric Fungal Genera in Vegetable Crops of Burkina Faso","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-06-25 16:01:28","doi":"10.21203/rs.3.rs-6821486/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"ee066dd7-112b-4831-949b-4d3854ae1054","owner":[],"postedDate":"June 25th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":50521167,"name":"Biological sciences/Ecology"},{"id":50521168,"name":"Biological sciences/Microbiology"},{"id":50521169,"name":"Biological sciences/Plant sciences"}],"tags":[],"updatedAt":"2025-11-14T04:53:08+00:00","versionOfRecord":[],"versionCreatedAt":"2025-06-25 16:01:28","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6821486","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6821486","identity":"rs-6821486","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}