Arbuscular mycorrhizal fungal spore-associated bacteria affect mycorrhizal colonization,plant growth and potato pathogens

Arbuscular mycorrhizal (AM) fungi and their bacterial associates are essential living components of the soil microbiota. From a total of 385 bacteria previously isolated from spores of AM fungi (AMB), 10 were selected based on ability to inhibit growth of plant pathogens. Effects of these isolates on AM fungal colonization, plant growth in potato (Solanum tuberosum L.) and inhibition of pathogens was investigated. AM fungal root colonization of potato was 7-fold higher in the presence of the Pseudomonas FWC70 isolate in a greenhouse and was 6–9-fold higher in the presence of the three isolates Pseudomonas FWC70, Stenotrophomonas FWC94 and Arthrobacter FWC110 in an outdoor pot experiment. Several growth traits of potato were stimulated by the Pseudomonas isolates FWC16, FWC30 and FWC70 and by the Stenotrophomonas isolate FWC14. All three Pseudomonas isolates showed inhibition against Erwinia carotovora, Phytophthora infestans and Verticillium dahliae but Stenotrophomonas isolates were variable. Protease(s), siderophores and indole acetic acid were produced by all isolates. Chitinase(s) were produced by all Stenotrophomonas and phosphate-solubilizing activity by all Pseudomonas isolates, the Stenotrophomonas FWC14 isolate and the Arthrobacter FWC110 isolate. We conclude that some AMB are multifunctional and production of extracellular enzymes and bioactive compounds are likely mechanisms for their multifunctional activities. Our results show that some AMB are likely to contribute to the often described ability of AM fungi to inhibit pathogens, acquire mineral nutrients and modify plant root growth.     

Cause and duration of mustard incorporation effects on soil-borne plant pathogenic fungi

Two fungal plant pathogens, Rhizoctonia solani AG 2-2 and Fusarium oxysporum f.sp. lini, were studied in relation to general responses of soil fungi and bacteria following incorporation of Brassica juncea. Our aim was to understand to what extent the changes in the biological and physicochemical characteristics of the soil could explain the effects on the studied pathogens and diseases, and to determine the temporal nature of the responses. Short-term effects of mustard incorporation (up to 4 months) were investigated in a microcosm experiment, and compared with a treatment where composted plant material was incorporated. In a field experiment, the responses were followed up to 11 months after removal or incorporation of a mustard crop. In general, responses in the variables measured changed more after incorporation of fresh mustard material than after addition of similar amounts of composted plant material (microcosms) or after removal of the mustard crop (field). The soil inoculum potential of R. solani AG 2-2 decreased directly after incorporation of mustard, but increased later to disease levels above those in the untreated soil. Neither of these effects could be explained by changes in the population density of R. solani AG 2-2. Fusarium spp. were less influenced, although an increase in the suppressiveness to Fusarium wilt was observed after mustard incorporation as compared with the treatment where mustard was removed. The microbial responses to mustard incorporation were more pronounced for bacteria than for fungi. After an initial substantial increase, the bacterial density decreased but remained above the levels in the control treatment throughout the experimental periods. The bacterial community structure was modified up to 8 months after mustard incorporation. We conclude that incorporation of fresh mustard influences soil microbial communities, especially the bacteria, and has a potential to control the pathogenic activity of R. solani 2-2 on a short-term perspective. The time dependency in microbial responses is important and should be taken into consideration for the evaluation of the potential of Brassicas to control plant disease on a field scale.     

连作土壤微生物区系分析、调控及高通量研究方法

土壤连作后导致土壤微生物生态失衡、病原微生物富集、有益微生物减少,土壤微生物从细菌主导型向真菌主导型转化,使病原菌更容易侵染植物而引发植物的各种土传病害。施用微生物有机肥可以将失衡的微生物区系恢复到健康的状态,从而可以起到防治土传病害的作用。本文围绕连作引起的土壤中各大类微生物数量和种类的变化以及连作土壤施用微生物有机肥修复后其微生物数量和种类的变化进行了综述,并通过与传统技术比较,介绍了454高通量测序研究方法的优越性,指出了其在土壤微生物区系研究中的重要性。     

Effects of soil application of olive mill wastewaters on the structure and function of the community of arbuscular mycorrhizal fungi

Recycling of olive mill wastewaters (OMW) into agricultural soils is a controversial issue since benefits to soil fertility should counterbalance potential short-term toxicity effects. We investigated the short-term effects of OMW on the soil-plant system, regarding the diversity, structure and root colonization capacity of arbuscular mycorrhizal (AM) fungi and the respective growth response of Vicia faba L, commonly used as green manure in olive-tree plantations. A compartmentalized pot system was used that allowed the establishment of an AM fungal community in one compartment (feeder) and the application of three OMW dose levels in an adjacent second compartment (receiver). At 0, 10, and 30 days after OMW treatment (DAT), V. faba pre-germinated seeds were seeded in the receiver compartment. At harvest, shoot and root dry weights, AM fungal root colonization, soil hyphal length and P availability were recorded in the receiver compartment. In addition, OMW effects on AM fungal diversity in plant roots were studied by DGGE. A transient effect of OMW application was observed; plant growth and AM fungal colonization were initially inhibited, whereas soil hyphal length was stimulated, but in most cases differences were absent when seeding was performed 30 DAT. Similarly, changes induced in the structure of the root AM fungal community were of transient nature. Cloning and sequencing of all the major DGGE bands showed that roots were colonized by Glomus spp. The transient effects of OMW on the structure and function of AM fungi could be attributed to OMW-derived phytoxicity to V. faba plants or to an indirect effect via alteration of soil nutritional status. The high OMW dose significantly increased soil P availability in the presence of AM fungi, suggesting efficient involvement of AM fungi in organic-P minerilization. Overall our results indicate that soil application of OMW would cause transient changes in the AM fungal colonization of V. faba plants, which, would not impair their long-term plant growth promoting ability.     

De-coupling of root–microbiome associations followed by antagonist inoculation improves rhizosphere soil suppressiveness

It was hypothesized that disruption of the root–microbiome association creates empty rhizosphere niches that could be filled by both soilborne pathogens and beneficial microbes. The effect of de-coupling root–microbiome associations related to improve soil suppressiveness was investigated in cucumber using the pathogen Fusarium oxysporum f. sp. Cucumerinum (FOC) and its antagonist Bacillus amyloliquefaciens SQR9 (SQR9) system. The root–soil microbiome association of cucumber was disrupted by applying the fungicide carbendazim to the soil, and then FOC or/and its antagonist SQR9 were inoculated in the rhizosphere. In the fungicide treatment, the FOC wilt disease incidence was significantly increased by 13.3 % on average compared to the FOC treatment without fungicide. However, when the fungicide treatment was applied to the soil with SQR9 and FOC, the SQR9 effectively reduced the disease incidence, and improved cucumber plant growth compared to a no fungicide control. These results indicate that de-coupling of root–microbiome associations followed by antagonist inoculation can improve rhizosphere soil suppressiveness, which may help to develop strategies for efficient application of rhizosphere beneficial microbes in agriculture.     

Plant microcosm studies demonstrating bioremediation of cyanide toxicity by Trichoderma and Fusarium spp.

The biodegradation of cyanide by Trichoderma and Fusarium spp. growing in association with plant roots in microcosms was investigated with CN^– at 50 or 100 mg/kg. Pea and wheat seeds germinated and plants grew only when seeds were inoculated with the fungi, probably because the plant/fungal association was capable of promoting cyanide catabolism. Inoculation by fungi also increased plant shoot lengths and the biomass of shoots and root compared with control plants without CN^– and fungi. Such plant/fungal association shows potential as a land remediation system.     

Non-streptomycete actinomycetes as biocontrol agents of soil-borne fungal plant pathogens and as plant growth promoters

Among soil microorganisms, bacteria and fungi and to a lesser extent actinomycetes, have received considerable attention as biocontrol agents of soil-borne fungal plant pathogens and as plant growth promoters. Within actinomycetes, Streptomyces spp. have been investigated predominantly, mainly because of their dominance on, and the ease of isolation from, dilution plates and because of the commercial interest shown on the antibiotics produced by certain Streptomyces spp. Many of non-streptomycete actinomycetes (NSA) taxa are therefore rarely reported in literature dealing with routine isolations of biocontrol agents and/or plant growth promoters from plant and soil. It is clear that special isolation methods need to be employed in routine isolations to selectively isolate NSA. Some interesting information exists, albeit in relatively few reports compared to that on other microorganisms, on the biological activities of NSA, especially in relation to their mechanisms of action in the biological control of soil-borne fungal plant pathogens and plant growth promotion. This review presents an overview of this information and seeks to encourage further investigations into what may be considered a relatively unexplored area of research. Certain soil environmental factors, especially in horticultural systems, could be manipulated to render the soil conducive for the biological activities of NSA. A variety of NSA isolated by selective methods have not only shown to be rhizosphere competent but also adapted for an endophytic life in root cortices. Some of the NSA, including endophytic strains that have shown potential to suppress soil-borne fungal plant pathogens, are able to employ one or more mechanisms of antagonism including antibiosis, hyperparasitism and the production of cell-wall degrading enzymes. Strains of NSA promote plant growth by producing plant growth regulators. Enhancement of plant growth by the antagonists are considered to help the host by producing compensatory roots that mask the impact of root diseases.     

The invasive plant Solidago canadensis L. suppresses local soil pathogens through allelopathy

Recent studies suggest that invasive plants pose a significant effect on local soil pathogens, which in turn affects on the plant invasion. However, the mechanisms by which invasive plants affect soil pathogens were less well known. We conducted four experiments to test the hypothesis that the invasive plant species Solidago canadensis L. may affect soilborne pathogens through exudation of allelochemicals. Two common soilborne pathogens Pythium ultimum and Rhizoctonia solani were used in the study. Tomato (Lycopersicon esculentum Mill) variety Qianhong No.1 which is sensitive to soil pathogens P. ultimum and R. solani was used to indicate pathogenic activity (in terms of seedling mortality and damping-off). Extracts from root and rhizome of S. canadensis significantly suppressed the growth and pathogenic activity of both pathogens under Petri dish culture and sand culture (experiments 1 and 2), providing direct evidence that S. canadensis exerts allelopathic effects on these pathogens. Subsequently, a pathogen inoculation experiment under sand culture showed that pathogenic activity of both P. ultimum and R. solani was lower under the soil with S. canadensis compared to that under the soil with a common native plant Kummerowia striata (Thunb.) Schindl (experiment 3), implying that invasive S. canadensis had but native K. striata did not have allelopathic effects on soil pathogens through root and rhizome exudation. Finally, results from field soil tests showed that mortality and damping-off rate of tomato seedlings were significantly lower under the soils collected from the fields dominated by S. canadensis than that dominated by native plants at both sampling sites, suggesting that suppression of pathogens also occurs in the field. From the present experimental results we suggest that invasive S. canadensis may acquire spreading advantage in non-native habitat by using “novel weapons” to inhibit not only local plants but also soilborne pathogens.     

Adaptation of plants and arbuscular mycorrhizal fungi to coal tailings in Indiana

We tested the potential for arbuscular mycorrhizal fungi to mediate plant adaptation to mine soil conditions utilizing a full factorial experiment involving two fungal communities, two ecotypes of plants and two soil types. We found that plants grew larger with fungal communities derived from mine soil regardless of the soil type in which they were grown. There was no evidence that the plants suffered from aluminum toxicity; however, plants grown in coal tailings produced far less biomass than those grown in low-nutrient clay soil. Andropogon virginicus L. grown from seeds collected from a coal mine had increased allocation to roots in sterile soil. Plantago lanceolata L. grown from seeds collected from a coal mine also showed an increased allocation to roots. We concluded that harsh edaphic conditions may help reinforce the symbiotic relationship between plants and AM fungi, resulting in more beneficial symbionts.     

Trichoderma–plant–pathogen interactions

Biological control involves the use of beneficial organisms, their genes, and/or products, such as metabolites, that reduce the negative effects of plant pathogens and promote positive responses by the plant. Disease suppression, as mediated by biocontrol agents, is the consequence of the interactions between the plant, pathogens, and the microbial community. Antagonists belonging to the genus Trichoderma are among the most commonly isolated soil fungi. Due to their ability to protect plants and contain pathogen populations under different soil conditions, these fungi have been widely studied and commercially marketed as biopesticides, biofertilizers and soil amendments. Trichoderma spp. also produce numerous biologically active compounds, including cell wall degrading enzymes, and secondary metabolites. Studies of the three-way relationship established with Trichoderma, the plant and the pathogen are aimed at unravelling the mechanisms involved in partner recognition and the cross-talk used to maintain the beneficial association between the fungal antagonist and the plant. Several strategies have been used to identify the molecular factors involved in this complex tripartite interaction including genomics, proteomics and, more recently, metabolomics, in order to enhance our understanding. This review presents recent advances and findings regarding the biocontrol-resulting events that take place during the Trichoderma–plant–pathogen interaction. We focus our attention on the biological aspects of this topic, highlighting the novel findings concerning the role of Trichoderma in disease suppression. A better understanding of these factors is expected to enhance not only the rapid identification of effective strains and their applications but also indicate the potentials for improvement of natural strains of Trichoderma.     

Plant pathogen protection by arbuscular mycorrhizas: A role for fungal diversity?

Arbuscular mycorrhizal (AM) fungi can confer protection to host plants against some root pathogens, and several mechanisms for these phenomena have been proposed. If AM fungal taxa vary in the ways that they limit the negative effects of pathogens on host plants, additive and/or synergistic interactions among members of diverse AM fungal assemblages and communities may result in a greater pathogen protection than is currently predicted. However, in a review of the literature on interactions between AM and pathogenic fungi, we found few examples that compared the effectiveness of single- and multi-species AM fungal assemblages. Here, we briefly recount the generally recognized mechanisms of pathogen protection by AM fungi and present evidence, where appropriate, for functional diversity among AM fungal taxa with regard to these mechanisms. We propose that functional complementarity of AM fungal taxa in interactions with pathogens could mimic, or even be the cause of, previously observed relationships between AM fungal diversity and plant productivity.     

Fungal diversity in set-aide agricultural soil investigated using terminal-restriction fragment length polymorphism

As part of the restoration of biodiversity on former agricultural land there has been focused on methods to enhance the rate of transition from agricultural land towards natural grasslands or forest ecosystems. Management practices such as sowing seed mixtures and inoculating soil of later successional stages have been used. The aim of this study was to determine the effects of a managed plant community on the diversity of soil fungi in a newly abandoned agricultural land. A field site was set up consisting of 20 plots where the plant diversity was managed by either sowing 15 plant species, or natural colonization was allowed to occur. The plant mixture contained five species each of grasses, legumes and forbs that all were expected to occur at the site. A subset of the plots (five from each treatment) was inoculated with soil cores from a late successional stage. The plant community composition was subject to a principal component analysis based on the coverage of each species. Five years after abandonment, soil samples were taken from the plots, DNA was extracted and the ITS region of the rDNA gene was amplified using fluorescently labelled fungal specific primers (ITS 1F/ITS 4). The PCR products were digested using HinfI and TaqI and sequenced. Results from both restriction enzymes were combined and a principal component analysis performed on the presence/absence of fragments. Also the fungal diversity expressed as number of restriction fragments were analysed. There was significantly higher fungal species richness in the experimental plots compared to the forest and field soils, but no differences between sown and naturally colonized plots. The different plant treatments did not influence the below ground fungal community composition. Soil water content on the other hand had an impact on the fungal community composition.     

Ectomycorrhizal Fungi and Associated Bacteria Provide Protection Against Heavy Metals in Inoculated Pine (Pinus Sylvestris L.) Seedlings

The roles of ectomycorrhizal fungi and bacteria associated with corresponding fungal species in distribution of heavy metals within roots and shoots of inoculated pine (Pinus sylvestris L.) seedlings were determined in this study. The mycorrhizal fungi forming different morphotypes were identified by PCR-RFLP using respective primers for an internal spacer transcribed region (ITS) of fungal rDNA. Amongst five fungal species detected, three were identified as Scleroderma citrinum, Amanita muscaria and Lactarius rufus. These fungi used for inoculation of pine seedlings significantly reduced translocation of Zn(II), Cd(II) or Pb(II) from roots to shoots, and the pattern of metal-accumulation was dependent on the fungal species. Ectomycorrhizae-associated bacteria identified as Pseudomonas were used as an additional component of the pine inoculation. These dual root inoculations resulted in higher accumulation of the metals, especially Zn(II), in the roots compared to the inoculation with fungal species alone. Consequently, dual inoculation of pine seedlings could be a suitable approach for plant protection against heavy metals and successful planting of metal-polluted soils.     

How distinct are arbuscular mycorrhizal fungal communities associating with grapevines?

Grapevines form associations with arbuscular mycorrhizal (AM) fungi. These root-dwelling fungi have the potential to contribute to crop vigor, productivity, pathogen protection, and nutrient content in grapes. In this study the arbuscular mycorrhizal fungal communities of grapevines and the surrounding interrow and native vegetation are compared. We found over 40 different taxa associating with both vines and interrow vegetation, but these communities differed based on host plant identity. These differences were apparent even after accounting for differences in soil chemical properties and differences in host plant diversity between vinerows and interrows, indicating that Vitis preferentially interacts with a subset of the viticultural fungal community. Since AM fungal communities play a major role in grapevine health, our results suggest that host identity and the diversity of AM fungal hosts in a vineyard can have strong effects on arbuscular mycorrhizal fungi community structure. In this paper, we used high throughput sequencing of the large subunit rDNA to analyze the diversity of AM fungi growing in a vineyard.     

Mycorrhizal fungi and earthworms reduce antioxidant enzyme activities in maize and sunflower plants grown in Cd-polluted soils

Changes in plant antioxidant enzymes (AOEs) in response to cadmium (Cd) pollution are an important mechanism for plant growth and tolerance to Cd-induced stress. The main objective of this greenhouse study was to determine the combined influence of earthworm and arbuscular mycorrhiza (AM) fungal inoculation and their interactions with Cd on AOEs and proline accumulation in leaves of two major crops under Cd stress. Maize (Zea mays L.) and sunflower (Helianthus annuus L.) plants were exposed to Cd stress (10 and 20 mg kg⁻¹ soil), inoculated with either earthworm (Lumbricus rubellus L.) or AM fungi (Glomus intraradices and Glomus mosseae species) in a pot experiment for three months. Exposure to Cd decreased shoot dry weights, increased shoot Cd and P concentrations, leaf proline accumulation and the activity of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD) and polyphenol oxidase (PPO) in both mycorrhizal and non-mycorrhizal plants and both in the presence and absence of earthworms. Inoculation of both model plants with earthworms and AM fungi decreased shoot Cd concentrations and the activity of all AOEs, except PPO. Although earthworm activity enhanced the proline content of sunflower in Cd-polluted soils, the proline level of both plants remained unaffected by AM fungi. AM fungi and earthworms may decrease the activity of AOEs through a decline in shoot Cd toxicity and concentration, confirming that plant inoculation with these soil organisms improves maize and sunflower tolerance and protection against Cd toxicity. Generally, the effect of AM fungal inoculation on plant responses to Cd addition was greater than that of earthworm activity. Nonetheless, the interactive effect of AM fungus and earthworm is of minor importance for most of the plant AOEs in Cd-polluted soils.     

Reforestation of burned stands: The effect of ectomycorrhizal fungi on Pinus pinaster establishment

The area occupied by Pinus pinaster in Portugal is rapidly diminishing because of forest fires. Ectomycorrhizal fungi form obligate, mutually beneficial associations with P. pinaster which improve plant growth and resistance to adverse conditions. The aim of this work was to assess whether native ectomycorrhizal fungi could be a useful tool in the reforestation of burned areas. The work was conducted in a forest nursery greenhouse, where P. pinaster seedlings were inoculated with compatible ectomycorrhizal fungal isolates: Suillus bovinus, Pisolithus tinctorius, Rhizopogon roseolus, and a mixture of the three fungi, using burned and unburned forest soil as substrate. Inoculation significantly enhanced the growth of P. pinaster, with R. roseolus proving to be the most effective in burned soil, with an 8-fold increase in plant fresh weight. Overall, inoculation stimulated growth most in burned than in unburned soil.This study suggests that inoculation with selected ectomycorrhizal fungi in containerised nurseries can be an advantageous approach for the successful establishment of P. pinaster in burned soil. The obtained results point out to the interest of extending these studies into fire-impacted areas, using ectomycorrhizal fungi as a biological tool.     

Control of tomato bacterial wilt and root-knot diseases by Bacillus thuringiensis CR-371 and Streptomyces avermectinius NBRC14893

Ralstonia solanacearum and Meloidogyne incognita are two soilborne pathogens that cause serious damage and great losses in the production of tomato. For this purpose, a bacterial isolate, Bacillus thuringiensis CR-371, and an actinomyces isolate, Streptomyces avermectinius NBRC14893, were examined for their ability to protect tomato from root-knot nematode and bacterial wilt diseases under glasshouse conditions. Treatment of tomato roots with B. thuringiensis CR-371 and S. avermectinius NBRC14893 followed by challenge inoculation with R. solanacearum and M. incognita significantly decreased disease severity of bacterial wilt alone, root-knot nematode alone, or mixed infection by both pathogens compared to the control. Furthermore, pretreatment of tomato roots with B. thuringiensis CR-371 and S. avermectinius NBRC14893 significantly reduced bacterial proliferation of R. solanacearum both in pathogen alone inoculated plants and in plants co-inoculated with R. solanacearum and M. incognita. In conclusion, our results suggest that the treatment of tomato roots with B. thuringiensis CR-371 and S. avermectinius NBRC14893 simultaneously suppresses bacterial wilt and root-knot nematode diseases. Therefore, B. thuringiensis CR-371 and S. avermectinius NBRC14893 could provide new options for integrated pest management strategies against plant diseases, especially against bacterial-nematode disease complexes that cause synergistic yield losses.     

Root colonisation by arbuscular mycorrhizal, fine endophytic and dark septate fungi across a pH gradient in acid beech forests

Colonisation by root endophytes can be beneficial to plants growing on acid, nutrient-poor soils. Arbuscular mycorrhizal (AM) fungi can supply herbs with nutrients and may give protection against aluminium toxicity. Two other root colonising fungi, fine endophytes (FE) and dark septate fungi (DSE), are less well known but are potentially of benefit to their host plant. AM fungi are the most prevalent symbionts in herbs at neutral to acidic soil pH. At extremely low pH, fungal growth can be limited and AM colonisation is usually rare. Fine and dark septate endophytes, on the other hand, have been observed more often under these conditions. In order to relate endophyte colonisation to a gradient in soil pH, we investigated root colonisation by AM, FE and DSE in Maianthemum bifolium, Galium odoratum, Mercurialis perennis and Stellaria nemorum, from a range of acidic beech forests. With decreasing pH, colonisation by AM decreased, whereas the other two endophytes increased. AM and FE colonisation were inversely correlated in Maianthemum bifolium. We compared changes in root colonisation with those in chemical composition of soil and leaf samples and found a positive correlation between leaf magnesium concentrations and the presence of DSE in Galium odoratum. Aluminium concentration in Maianthemum bifolium tended to be lower when FE colonisation was high, suggesting a possible role for the fungi in plant protection against Al. We suggest that FE and DSE may replace AM fungi in herbaceous vegetation at extremely low pH, counteracting some of the negative effects of high soil acidity on plants.     

Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing

Soil fungi and oomycetes (syn. peronosporomycetes) are the most common causes of pea diseases, and these pathogens often occur in complexes involving several species. Information on the dynamics within this complex of pathogens, and also between the complex of pathogens and other fungi in the development of root disease is limited. In this study, next-generation sequencing of nuclear ribosomal internal transcribed spacer-1 was used to characterize fungal communities in agricultural soils from nine pea fields, in which pea roots showed different degrees of disease. Fungal species richness, diversity, and community composition were analyzed and compared among the different pea soils. After filtering for quality and excluding non-fungal sequences, 55,460 sequences clustering into 434 operational taxonomic units (OTUs), were obtained from the nine soil samples. These sequences were found to correspond to 145–200 OTUs in each soil. The fungal communities in the nine soils were strongly dominated by Ascomycota and Basidiomycota. Phoma, Podospora, Pseudaleuria, and Veronaea, at genus level, correlated to the disease severity index of pea roots; Phoma was most abundant in soils with diseased plants, whereas Podospora, Pseudaleuria, and Veronaea were most abundant in healthy soils. No correlation was found between the disease severity index and the abundance of some of the other fungi and oomycetes normally considered as root pathogens in pea.     

Survey of Soil Fungal Communities in Strawberry Fields by Illumina Amplicon Sequencing

Soil fungal pathogens are the most common cause of diseases in commercial strawberry crops worldwide. Since simultaneous infections by different pathogens can severely damage the crop, understanding the associated fungal communities can be helpful to mitigate crop loss. Herein, we used Illumina metabarcoding to assess the structure of fungal communities in five strawberry production areas in Estonia. Our analysis revealed 990 to 1430 operational taxonomic units (OTUs) per soil sample (pools of eight soil samples per production area). Based on our analyses, Ascomycota (55.5%) and Basidiomycota (25.0%) were the most OTUs-rich. Amongst the 24 most abundant OTUs, Geomyces, Rhodotorula, Verticillium and Microdochium were the most abundant genera, which were found across nearly all the soil samples. The OTUs were also clustered into three distinct groups, corresponding to different functional guilds of fungi. In addition, Fusarium solani, V. dahliae, Rhizoctonia solani and Colletotrichum truncatum were enormously abundant in the fields with disease symptoms, whereas arbuscular mycorrhizal fungi especially Rhizophagus irregularis were considerably more abundant in the fields with healthy plants. These findings provide support that mycorrhizal fungi may play an important role in suppressing pathogens. Our study for the first time shows the usefulness of Illumina technology in surveying the communities of soil fungi in strawberry fields effectively, which may improve available disease management strategies against strawberry diseases.