Occurrence and Diversity of Black-Foot Disease Fungi in Symptomless Grapevine Nursery Stock in Spain

Health Status of Ready-to-Plant Grapevine Nursery Material in Canada Regarding Young Vine Decline Fungi

Young vine decline (YVD), caused by several taxonomically different fungi, results in the decline and death of grapevines within a few years after planting. Infection can occur in nursery mother blocks and/or at several stages in the nursery propagation process, but the final plant material may remain asymptomatic. Four nurseries that sell ready-to-plant grapevines in Canada were sampled to evaluate the health status with regard to YVD fungi, including Botryosphaeriaceae spp., Cadophora luteo-olivacea, Dactylonectria macrodidyma, Dactylonectria torresensis, Phaeoacremonium minimum, and Phaeomoniella chlamydospora. Plants representing three cultivars, 'Chardonnay', 'Merlot', and 'Pinot noir', either grafted onto '3309C' rootstock or self-rooted, were provided by the nurseries. Samples from the roots, base of the rootstock or self-rooted cultivar, graft-union, and scion were collected from each plant. DNA was extracted, and the total abundance of each fungus was quantified using Droplet Digital PCR. Results revealed that 99% of plants harbored at least one of the fungi studied, with a mean of three different fungal species that were present per grapevine. Droplet Digital PCR results showed that the abundance of the different fungi significantly varied between different sections of each plant, individual plants for each cultivar, and cultivars from the same nursery. Necrosis measurements were recorded from the base of the rootstock or self-rooted cultivars and did not correlate with fungal abundance recorded in that section for each grapevine, but necrosis was consistent across cultivars within nurseries. Five different rootstocks were compared from one nursery, and results showed no differences between rootstocks and their health status. Among all nurseries, C. luteo-olivacea was the most prevalent fungus (97% of the plants), while D. macrodidyma was the least commonly found (13% of the plants). This study shows that ready-to-plant nursery material sold in Canada is likely to be infected with several YVD fungi and that presence and abundance of fungi vary significantly among individual grapevines and nurseries.

Identification and Characterization of Neocosmospora silvicola Causing Canker Disease on Pinus armandii in China

Chinese white pine, Pinus armandii, is a source of high-quality timber and an afforestation tree in China, which plays an important ecological and social role in water and soil conservation. Recently, a new canker disease has been reported in Longnan City, Gansu Province, where P. armandii is mainly distributed. In this study, the causal agent was isolated from diseased samples and identified as a fungal pathogen, Neocosmospora silvicola, based on morphological characteristics and molecular analyses (internal transcribed spacer, large subunit, RNA polymerase II, and translation elongation factor-1α). Pathogenicity tests on P. armandii revealed that N. silvicola isolates caused a 60% average mortality rate in artificially inoculated 2-year-old seedlings. The pathogenicity of these isolates was also observed on the branches of 10-year-old P. armandii trees with a 100% mortality rate. These results agree with the isolation of N. silvicola from diseased plants, suggesting the possible role of this fungus in the decline of P. armandii plants. Mycelial growth of N. silvicola was fastest on potato dextrose agar medium, and growth occurred at pH values ranging from 4.0 to 11.0 with temperatures between 5 and 40°C. The fungus also grew rapidly in complete darkness compared with other light conditions. Of the eight carbon and seven nitrogen sources tested, starch and sodium nitrate, respectively, were highly efficient in supporting the mycelial growth of N. silvicola. The ability of N. silvicola to grow at low temperatures (5°C) may explain its occurrence in the Longnan area of Gansu Province. This article is the first report of N. silvicola as an important fungal pathogen causing branch and stem cankers on Pinus tree species, which remains a threat to the forests.

Duplex Real-Time PCR Assays for the Simultaneous Detection and Quantification of Botryosphaeriaceae Species Causing Canker Diseases in Woody Crops

Woody canker diseases caused by fungi of the Botryosphaeriaceae family are producing increasing losses in many economically important woody crops, including almond. To develop a molecular tool for the detection and quantification of the most aggressive and threatening species is of main importance. This will help to prevent the introduction of these pathogens in new orchards and to conveniently apply the appropriate control measures. Three reliable, sensitive and specific duplex qPCR assays using TaqMan probes have been designed for the detection and quantification of (a) Neofusicoccum parvum and the Neofusicoccum genus, (b) N. parvum and the Botryosphaeriaceae family and (c) Botryosphaeria dothidea and the Botryosphaeriaceae family. The multiplex qPCR protocols have been validated on artificially and naturally infected plants. Direct systems to process plant materials, without DNA purification, allowed high-throughput detection of Botryosphaeriaceae targets even in asymptomatic tissues. These results validate the qPCR using the direct sample preparation method as a valuable tool for Botryosphaeria dieback diagnosis allowing a large-scale analysis and the preventive detection of latent infection.

Detection of Ilyonectria pseudodestructans from Potato by RNase H-Dependent PCR (rhPCR) and rh-Quantitative PCR (rhqPCR)

Ilyonectria pseudodestructans, a plant pathogen that is known to cause root rot on fruit trees such as grapevine and apple, has recently been reported to also cause tuber decay in potato. The increasing risk of this pathogen on various horticultural crops makes it essential to develop a rapid and accurate detection method. In this study, an RNase H-dependent PCR (rhPCR) protocol and a modified probe-based rh-quantitative PCR (rhqPCR) protocol for I. pseudodestructans detection were developed. Both the forward and reverse primers for rhPCR and rhqPCR carry an RNA nucleotide at the site where a single-nucleotide polymorphism between I. pseudodestructans and strains of other Ilyonectria spp. is located, and the rhqPCR also contains a fluorescent-labeled target-specific probe. The primers were designed based on the sequence of the histone H3 gene and could amplify a DNA fragment of 73 bp. In the specificity test, by alignment via the BLASTn tool, the RNA nucleotide bases on both the forward and the reverse primers were identical to the corresponding genomic site of 16 of 17 (94.1%) database-available I. pseudodestructans strains, and different from 43 of 44 (97.7%) database-available strains of other Ilyonectria spp. When the rhPCR and rhqPCR protocols were applied on 11 I. pseudodestructans strains and 46 other strains of different species of plant pathogens, all of the I. pseudodestructans strains generated positive reactions whereas all of the other strains were negative, which indicated an excellent specificity of the primers. In the sensitivity test, the lowest DNA template amount for a positive reaction using the rhPCR and rhqPCR methods was 2 pg for I. pseudodestructans genomic DNA. When testing the rhqPCR method on gBlock, the lowest number of molecules for a positive reaction was six. These results indicated a high sensitivity of the protocol for I. pseudodestructans detection. To our knowledge, this is the first report of a probe-based rhqPCR to be applied to plant disease diagnosis; in addition, this is also the first rapid molecular protocol to detect I. pseudodestructans. The new rhPCR and rhqPCR methods have a potential to be applied by plant disease diagnostic labs for their routine work.

Vineyard Management and Physicochemical Parameters of Soil Affect Native Trichoderma Populations, Sources of Biocontrol Agents against Phaeoacremonium minimum

Native strains of Trichoderma in vineyard soil represent an opportunity for reducing the incidence of grapevine trunk diseases (GTDs) in vineyards. Moreover, its relationship with the environment (physicochemical soil characteristics and farming management practices) remains unclear. In the current study, a survey was carried out on farming management used by viticulturists, and soil samples were studied to analyze their physicochemical properties and to isolate Trichoderma strains. Later, statistical analyses were performed to identify possible correlations between Trichoderma populations, soil management and soil characteristics. In addition, in vitro tests, including antibiosis and mycoparasitism, were performed to select those Trichoderma strains able to antagonize Phaeoacremonium minimum. In this study a positive correlation was found between the iron content and pH in the soil, and a lower pH increases Trichoderma populations in soils. Vineyard management also affects Trichoderma populations in the soil, negatively in the case of fertilization and tillage and positively in the case of herbicide spraying. Two Trichoderma native strains were selected as potential biocontrol agents (Trichoderma gamsii T065 and Trichoderma harzianum T087) using antibiosis and mycoparasitism as mechanisms of action. These results led to the conclusion that native Trichoderma strains hold great potential as biological control agents and as producers of secondary metabolites.

In Silico functional and phylogenetic analyses of fungal immunomodulatory proteins of some edible mushrooms

Mushrooms are a well known source of many bioactive and nutritional compounds with immense applicability in both the pharmaceutical and food industries. They are widely used to cure various kinds of ailments in traditional medicines. They have a low amount of fats and cholesterol and possess a high number of proteins. Immunomodulators have the ability which can improve immunity and act as defensive agents against pathogens. One such class of immunomodulators is fungal immunomodulatory proteins (FIPs). FIPs have potential roles in the treatment of cancer, and immunostimulatory effects and show anti-tumor activities. In the current study, 19 FIPs from edible mushrooms have been used for comparison and analysis of the conserved motifs. Phylogenetic analysis was also carried out using the FIPs. The conserved motif analysis revealed that some of the motifs strongly supported their identity as FIPs while some are novel. The fungal immunomodulatory proteins are important and have many properties which can be used for treating ailments and diseases and this preliminary study can be used for the identification and functional characterization of the proposed novel motifs and in unraveling the potential roles of FIPs for developing newer drugs.

Fungal Grapevine Trunk Diseases in Romanian Vineyards in the Context of the International Situation

Vitis vinifera, known as the common grape vine, represents one of the most important fruit crops in the world. Romania is a wine-producing country with a rich and long tradition in viticulture. In the last decade, increasing reports of damage caused by grapevine trunk diseases (GTDs) have raised concerns in all wine producing countries. Up to now, no study was performed regarding the GTDs situation in Romania, an important grapevine grower in Europe. In this study, we aim, after a comprehensive presentation of the fungal GTDs worldwide, to review the scientific information related to these diseases in Romania in order to open a national platform in an international framework. In order to achieve this, we consulted over 500 references from different scientific databases and cited 309 of them. Our review concludes that, in Romania, there is little amount of available literature on this matter. Three out of six fungal GTDs are reported and well documented in all of the Romanian viticultural zones (except for viticultural zone 4). These are Eutypa dieback, Phomopsis dieback, and Esca disease. Of the fungal pathogens considered responsible Eutypa lata, Phomopsis viticola and Stereum hirsutum are the most studied and well documented in Romania. Management measures are quite limited, and they mostly include preventive measures to stop the GTDs spread and the removal of affected grapevines.

The road to molecular identification and detection of fungal grapevine trunk diseases

Grapevine is regarded as a highly profitable culture, being well spread worldwide and mostly directed to the wine-producing industry. Practices to maintain the vineyard in healthy conditions are tenuous and are exacerbated due to abiotic and biotic stresses, where fungal grapevine trunk diseases (GTDs) play a major role. The abolishment of chemical treatments and the intensification of several management practices led to an uprise in GTD outbreaks. Symptomatology of GTDs is very similar among diseases, leading to underdevelopment of the vines and death in extreme scenarios. Disease progression is widely affected by biotic and abiotic factors, and the prevalence of the pathogens varies with country and region. In this review, the state-of-the-art regarding identification and detection of GTDs is vastly analyzed. Methods and protocols used for the identification of GTDs, which are currently rather limited, are highlighted. The main conclusion is the utter need for the development of new technologies to easily and precisely detect the presence of the pathogens related to GTDs, allowing to readily take phytosanitary measures and/or proceed to plant removal in order to establish better vineyard management practices. Moreover, new practices and methods of detection, identification, and quantification of infectious material would allow imposing greater control on nurseries and plant exportation, limiting the movement of infected vines and thus avoiding the propagation of fungal inoculum throughout wine regions.

Genetic Diversity and Population Structure of Cylindrocarpon-like Fungi Infecting Ginseng Roots in Northeast China

Northeast China is well known for cultivating ginseng (Panax ginseng and P. quinquefolius). Ginseng roots are threatened by the infection of the most notorious Cylindrocarpon-like fungi (CLF), which are a complex containing important soilborne pathogens. Although the disease is economically important, little is known about the genetic diversity and population structure of the pathogenic CLF complex. This knowledge will help in developing effective disease management strategies. To conduct this study, diseased ginseng roots were collected from 12 regions representing the main ginseng-growing areas in Northeast China, and CLF were isolated. A total of 169 isolates with CLF anamorph were identified in two Dactylonectria species and six Ilyonectria species using morphological and molecular methods. Cross pathogenicity tests showed that all species were pathogenic to both P. ginseng and P. quinquefolius, and most of them had slightly stronger aggressiveness in P. ginseng. The analysis of partial sequences of the Histone H3 gene generated a high level of genetic diversity and geographic differentiation. A total of 132 variable sites were detected in 169 sequences, which formed 20 haplotypes with a haplotype diversity of 0.824. Genetic differentiation was positively correlated with geographic distance. The geographic populations in the range of Changbai Mountain were distinctly discriminated from those in other non-Changbai Mountain populations. No significant genetic differentiation was found between ginseng hosts. Cylindrocarpon-like fungi causing ginseng root diseases are geographically correlated in the genetic distance in Northeast China and should be managed correspondingly.

Grapevine nursery propagation material as source of fungal trunk disease pathogens in Uruguay

Grapevine fungal trunk diseases (GTDs) have become a serious problem for grapevines worldwide. Nursery vines infected during the propagation process are considered one of the main ways of dissemination of GTD pathogens. In this study, we examined the status of GTDs in grapevine planting material, from rootstocks and scion mother cuttings to grafted rooted vines ready to plant, according to the local nursery propagation process. During 2018-2019, internal symptoms of GTDs were examined in 2400 propagation materials and fungal isolations were carried out from a subsample of 1026 selected materials. Our results revealed that nursery grapevine plants produced in Uruguay have a high incidence of GTDs, regardless of the scion/rootstock combination. Typical brown to black streaks and sectorial wood necrosis were observed in materials on all propagation stages, with a markedly increasing incidence throughout the nursery process, reaching almost 100% in grafted rooted vines ready to plant. Botryosphaeria dieback, Petri disease and black-foot disease were the main GTDs found. The results showed that Botryosphaeria dieback and Petri disease pathogens infect materials from the early stages of the process, with a marked increase towards the end of the plant production process, whereas black-foot disease pathogens were found exclusively in vines ready to plant. Diaporthe dieback pathogens were also detected in materials in all stages but in a low proportion (less than 10% of infected material). Based on single locus analysis, the 180 isolates selected were placed into eight genera and 89% identified within 22 fungal species associated with GTDs, with Phaeoacremonium oleae and Diaporthe terebinthifolii as new records on grapevine worldwide. Our results have concluded that locally produced vines are one of the main ways of dissemination of GTD pathogens and showed that a nursery sanitation programme is required to reduce the incidence of these diseases.

Grapevine trunk diseases of cold-hardy varieties grown in Northern Midwest vineyards coincide with canker fungi and winter injury

Grapevine trunk diseases make up a disease complex associated with several vascular fungal pathogenic species. Surveys to characterize the composition of grapevine trunk diseases have been conducted for most major grape growing regions of the world. This study presents a similar survey characterizing the fungi associated with grapevine trunk diseases of cold-hardy interspecific hybrid grape varieties grown nearly exclusively in the atypical harsh winter climate of Northern Midwestern United states vineyards. From the 172 samples collected in 2019, 640 isolates obtained by culturing were identified by ITS sequencing and represent 420 sample-unique taxa. From the 420 representative taxa, opportunistic fungi of the order Diaporthales including species of Cytospora and Diaporthe were most frequently identified. Species of Phaeoacremonium, Paraconiothyrium, and Cadophora were also prevalent. In other milder Mediterranean growing climates, species of Xylariales and Botryosphaeriales are often frequently isolated but in this study they were isolated in small numbers. No Phaeomoniellales taxa were isolated. We discuss the possible compounding effects of winter injury, the pathogens isolated, and management strategies. Additionally, difficulties in researching and understanding the grapevine trunk disease complex are discussed.

Exploring the Temporal Dynamics of the Fungal Microbiome in Rootstocks, the Lesser-Known Half of the Grapevine Crop

Rootstocks are the link between the soil and scion in grapevines, can provide tolerance to abiotic and biotic stresses, and regulate yield and grape quality. The vascular system of grapevine rootstocks in nurseries is still an underexplored niche for research, despite its potential for hosting beneficial and pathogenic microorganisms. The purpose of this study was to investigate the changes in the composition of fungal communities in 110 Richter and 41 Berlandieri rootstocks at four stages of the grapevine propagation process. Taxonomic analysis revealed that the fungal community predominantly consisted of phylum Ascomycota in all stages of the propagation process. The alpha-diversity of fungal communities differed among sampling times for both rootstocks, with richness and fungal diversity in the vascular system decreasing through the propagation process. The core microbiome was composed of the genera Cadophora, Cladosporium, Penicillium and Alternaria in both rootstocks, while the pathogenic genus Neofusicoccum was identified as a persistent taxon throughout the propagation process. FUNguild analysis showed that the relative abundance of plant pathogens associated with trunk diseases increased towards the last stage in nurseries. Fungal communities in the vascular system of grapevine rootstocks differed between the different stages of the propagation process in nurseries. Numerous genera associated with potential biocontrol activity and grapevine trunk diseases were identified. Understanding the large diversity of fungi in the rootstock vascular tissue and the interactions between fungal microbiota and grapevine will help to develop sustainable strategies for grapevine protection.

Molecular and Pathogenic Characterization of Cylindrocarpon-like Anamorphs Causing Root and Basal Rot of Almonds

Three almond nurseries were prospected in the South of Spain (Sevilla) to evaluate the sanitary status of the nursery plant material. Samples consisted of main roots, secondary roots and six-month-old basal stems ‘GxN-15’, ‘Nemaguard’, ‘Cadaman’, ‘Rootpac-40’ and ‘Rootpac-20’ rootstocks planted in the soil, and twigs of mother plants from ‘Lauranne’, ‘Guara’, ‘Marcona’, ‘Marta’ and ‘Ferragnes’ almond cultivars. Endophytic and potential pathogenic fungi were identified in mother plants and 70 Cylindrocarpon-like anamorph isolates were detected in the root system and basal stems of analyzed rootstocks. Based on partial sequencing of the his3 gene and multilocus phylogenetic analysis of the concatenated ITS, tub2, his3 and tef1-α partial sequences, seven Cylindrocarpon-like anamorph species were identified as Dactylonectria torresensis, D. novozelandica, D. macrodidyma, Ilyonectria liriodendri, Neonectria sp. 1, N. quercicola and Cylindrocladiella variabilis. Pathogenicity was assessed on young healthy detached twigs of ‘Guara’ almond cultivar and one-year-old ‘Lauranne’ potted almonds grafted onto ‘GxN-15’ rootstocks. Among the seven Cylindrocarpon-like anamorph species, I. liriodendri, Neonectria sp. 1 and N. quercicola were the most aggressive. Inoculated detached shoots developed necrotic lesions 15 days after inoculation. Inoculated trees showed sectorized necrosis in the main and secondary roots and the basal stem of the rootstock 5 months after inoculation. The most aggressive species were able to cause necrosis also in the grafted cultivar, and I. liriodendri, and N. quercicola also reduced the root biomass. This is the first report of Cylindrocarpon-like anamorph species causing root and basal rot of almonds.

Lignans Extract from Knotwood of Norway Spruce—A Possible New Weapon against GTDs

Grapevine trunk diseases (GTDs) pose a major threat to the wine industry worldwide. Currently, efficient biological methods or chemical compounds are not available for the treatment of infected grapevines. In the present study, we used an extract from the knotwood of spruce trees as a biological control against GTDs. Our in vitro trial was focused on the antifungal effects of the extract against the most common GTD pathogens—Cadophora luteo-olivacea, Dactylonectria torresensis, Diaporthe ampelina, Diaporthe bohemiae, Diplodia seriata, Eutypa lata, and Phaeoacremonium minimum. Our in vitro trial revealed a high antifungal effect of the extract against all tested fungi. The inhibition rates varied among the different species from 30% to 100% using 1 mg·mL⁻¹ extract. Subsequently, the efficiency of the extract was supported by an in planta experiment. Commercial grafts of Vitis vinifera were treated with the extract and planted. The total genomic DNA of grapevines was extracted 10 days and 180 days after the treatment. The fungal microbial diversities of the treated/untreated plants were compared using high-throughput amplicon sequencing (HTAS). Treated plants showed 76.9% lower relative abundance of the genus Diaporthe and 70% lower relative abundance of the genus Phaeoacremonium 10 days after treatment. A similar scenario was observed for the genus Cadophora 180 days after treatment, where treated plants showed 76% lower relative abundance of this genus compared with untreated grapevines.

Detection and identification of “black foot” pathogens of grapes in Crimea

At the present stage of development, stable economic efficiency of viticulture is possible if a decrease in the viability of grape plants, accompanied by a decrease in their productivity and lifecycle reduction, is prevented. Progressive grapevine weakening can be caused by both climate change and affection of perennial wood by the complexes of phytopathogenic fungi. In the last two decades, in all major grape-cultivating states, the root rot or “black foot” of grapes has been attributed to the most harmful diseases of perennial wood, especially in nurseries and young plantations. Presently, 30 fungal species are known to be associated with this disease, with the most common genera being Campylocarpon, Cylindrocladiella, Dactylonectria, Ilyonectria, Neonectria, Pleiocarpon, and Thelonectria. The article presents the results of laboratory researches and field experiments aimed at studying the etiology of inhibition of grape plant development in the conditions of Crimea. For the period from 2017 to 2021, in the vineyards of Mountain-Valley, South-Western and Central-Steppe Crimea, the affection of bushes of grape varieties ‘Moldova’, ‘Aligote’, ‘Arcadia’, ‘Lora’, ‘Rkatsiteli’ with the disease "black foot" or root rot of grapes was diagnosed for the first time. Using of molecular biological approach based on the polymerase chain reaction (PCR) made it possible to establish that “black foot” pathogens in Crimean vineyards include Dactylonectria macrodidyma (Halleen, Schroers & Crous) L. Lombard & Crous, 2014 and Ilyonectria destructans (Zinssm.) Rossman, L. Lombard & Crous, 2015.

The microbiota of the grapevine holobiont: A key component of plant health

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Grapevine interacts different microbiota living around and within its tissues

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Addition of microbial genes to plant genome gives supplementary functions to the holobiont

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The composition of grapevine microbiota varies according to endogenous and exogenous factors

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Microbiota variations can lead to perturbations of grapevine metabolism

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The link between symptom emergence of dieback and microbial imbalance is currently studied

Background

Grapevine is a woody, perennial plant of high economic importance worldwide. Like other plants, it lives in close association with large numbers of microorganisms. Bacteria, fungi and viruses are structured in communities, and each individual can be beneficial, neutral or harmful to the plant. In this sense, microorganisms can interact with each other and regulate plant functions (including immunity) and even provide new ones. Thus, the grapevine associated with its microbial communities constitutes a supra-organism, also called a holobiont, whose functioning is linked to established plant-microorganism interactions.

Aim of review

The overall health of the plant may be conditioned by the diversity and structure of microbial communities. Consequently, an optimal microbial composition will consist of a microbial balance allowing the plant to be healthy. Conversely, an imbalance of microbial populations could lead to (or be generated by) a decline of the plant. The microbiome is an active component of the host also responsive to biotic and abiotic changes; in that respect, a better understanding of the most important drivers of the composition of plant microbiomes is needed.

Key scientific concepts of review

This article presents the current state of the art about the grapevine microbiota and its composition according to the plant compartments and the influencing factors. We also focus on situations of imbalance, in particular during plant disease or decline. Finally, we discuss the possible interest of microbial engineering in an agrosystem such as viticulture.

Drought Influences Fungal Community Dynamics in the Grapevine Rhizosphere and Root Microbiome

Plant roots support complex microbial communities that can influence nutrition, plant growth, and health. In grapevine, little is known about the impact of abiotic stresses on the belowground microbiome. In this study, we examined the drought-induced shifts in fungal composition in the root endosphere, the rhizosphere and bulk soil by internal transcribed spacer (ITS) high-throughput amplicon sequencing (HTAS). We imposed three irrigation regimes (100%, 50%, and 25% of the field capacity) to one-year old grapevine rootstock plants cv. SO₄ when plants had developed 2–3 roots. Root endosphere, rhizosphere, and bulk soil samples were collected 6- and 12-months post-plantation. Drought significantly modified the overall fungal composition of all three compartments, with the root endosphere compartment showing the greatest divergence from well-watered control (100%). The overall response of the fungal microbiota associated with black-foot disease (Dactylonectria and “Cylindrocarpon” genera) and the potential biocontrol agent Trichoderma to drought stress was consistent across compartments, namely that their relative abundances were significantly higher at 50–100% than at 25% irrigation regime. We identified a significant enrichment in several fungal genera such as the arbuscular mycorrhizal fungus Funneliformis during drought at 25% watering regime within the roots. Our results reveal that drought stress, in addition to its well-characterized effects on plant physiology, also results in the restructuring of grapevine root microbial communities, and suggest the possibility that members of the altered grapevine microbiota might contribute to plant survival under extreme environmental conditions.

Evaluation of Sown Cover Crops and Spontaneous Weed Flora as a Potential Reservoir of Black-Foot Pathogens in Organic Viticulture

Simple Summary

Black-foot is an important grapevine disease caused by a soil-borne fungal pathogens complex, which are collectively known as Cylindrocarpon-like asexual morphs. In organic viticulture, both sown and native cover crop species can act as potential reservoirs of black-foot associated fungi. In our study a wide survey of cover crops grown in organic vineyards was conducted over a diverse range of climatic zones in six different European countries to acquire information about the presence of Cylindrocarpon-like asexual morphs on their roots. Several fungal species associated with black-foot disease were found on some of the cover crops evaluated in all the countries. These results provide valuable information for a reasoned choice of cover crop species, or a species mix, that can be used in organic viticulture. This is particularly important for maximizing their benefits and reducing potential problems in vineyards.

Abstract

(1) Background. An extensive survey of grapevine-sown cover crops and spontaneous weed flora was conducted from 2019 to 2020 in organic vineyards in six European countries (France, Italy, Romania, Slovenia, Spain, Switzerland). Our main objective was to detect and identify the presence of Cylindrocarpon-like asexual morphs species associated with black-foot disease on their roots. (2) Methods. Fungal isolations from root fragments were performed on culture media. Cylindrocarpon-like asexual morph species were identified by analyzing the DNA sequence data of the histone H3 (his3) gene region. In all, 685 plants belonging to different botanical families and genera were analyzed. Cylindrocarpon-like asexual morphs were recovered from 68 plants (9.9% of the total) and approximately 0.97% of the plated root fragments. (3) Results. Three fungal species (Dactylonectria alcacerensis, Dactylonectria torresensis, Ilyonectria robusta) were identified. Dactylonectria torresensis was the most frequent, and was isolated from many cover crop species in all six countries. A principal component analysis with the vineyard variables showed that seasonal temperatures and organic matter soil content correlated positively with Cylindrocarpon-like asexual morphs incidence. (4) Conclusions. The presence of Cylindrocarpon-like asexual morphs on roots of cover crops suggests that they can potentially act as alternative hosts for long-term survival or to increase inoculum levels in vineyard soils.

Survey of Trunk Pathogens in South African Olive Nurseries

Several fungal trunk pathogens are associated with olive trunk diseases in South Africa. Little is known regarding the inoculum sources of these pathogens in the olive industry, and no specific management strategies are in place. The aim of this study was to investigate the status of olive nurseries in South Africa, with regard to the presence of trunk pathogens in olive plant material, to determine whether nursery material can be considered inoculum sources contributing to long-distance dispersal of these pathogens. Isolations were made from asymptomatic cuttings from mother blocks (stage 1), asymptomatic and symptomatic rooted cuttings (stage 2), and 1- to 2-year-old trees (stage 3) of eight cultivars in two nurseries. Known olive trunk pathogens of Nectriaceae, Diaporthaceae, Botrysphaeriaceae, Togniniaceae, Phaeomoniellaceae, and Pleurostomataceae were recovered. Neofusicoccum australe was detected in a single stage 1 cutting. Stage 3 material showed the highest incidence of fungi from these families, with Pleurostoma richardsiae having the highest incidence in both nurseries (82.2 and 36.7% of the 1- to 2-year-old trees). Phaeoacremonium parasiticum was present in 28.9% of the trees from one nursery (stage 3). The remaining pathogens occurred in ≤13.3% of the material. These results indicate that nursery propagation material from mother blocks harbors low levels of trunk pathogens and that additional infections occur during the nursery process. Management strategies should focus on the prevention and elimination of infections in mother blocks as well as during the propagation process to ensure that pathogen-free material is delivered to producers.

Field evaluation of biocontrol agents against black-foot and Petri diseases of grapevine

BACKGROUND

Black-foot and Petri diseases are the main fungal diseases associated with young grapevine decline. Two field experiments were established to evaluate the preventive effect of two potential biocontrol agents (BCAs), that is Streptomyces sp. E1 + R4 and Pythium oligandrum Po37, and three BCA-commercial products containing Trichoderma atroviride SC1, Trichoderma koningii TK7 and Pseudomonas fluorescens + Bacillus atrophaeus on fungal infection in grafted plants and plant growth parameters.

RESULTS

The effectiveness of some BCA in reducing the incidence and severity of both diseases was dependent on the plant part analyzed and the plant age. No single BCA application was able to control both diseases. Streptomyces sp. E1 + R4 were able to reduce significantly the infection of the most prevalent black-foot disease fungi while P. oligandrum Po37 and Trichoderma spp. were able to reduce significantly Phaeomoniella chlamydospora and Phaeoacremonium minimum (Petri disease) infection. BCA treatments had no effect on the shoot weight, and root weight was significantly lower in all BCA treatments with respect to the control.

CONCLUSIONS

The combination of the disease-suppressive activity of two or more beneficial microbes in a biocontrol preparation is required to prevent infection by black-foot and Petri disease fungi in vineyards.

Comparative Genomic Analysis of Dactylonectria torresensis Strains from Grapevine, Soil and Weed Highlights Potential Mechanisms in Pathogenicity and Endophytic Lifestyle

The soil-borne fungus Dactylonectria torresensis is the most common causal agent of black-foot disease in Europe. However, there is a lack of understanding on how this fungus can provoke plant symptoms. In this study, we sequenced, annotated and analyzed the genomes of three isolates of D. torresensis collected from asymptomatic vine, weed and soil. Sequenced genomes were further compared to those of 27 fungal species including root and aerial pathogens, white rot degraders, indoor biodeterioration agents, saprotrophs, dark septate endophytes and mycorrhiza. Strains of D. torresensis present genomes with between 64 and 65 Mbp and with up to 18,548 predicted genes for each strain. Average Nucleotide Identity (ANI) shows that strains are different according to genome contents. Clusters of orthologous groups were compared, and clusters of genes related to necroses were particularly detected in all strains of D. torresensis (necrosis inducing peptides and proteins, and ethylene inducing peptides) as well as several genes involved in resistance against fungicides frequently used in viticulture such as copper. Interestingly, an expanded high number of genes related to carbohydrate-active enzymes were detected in each Dactylonectria strain, especially those related to glycoside hydrolases that could be involved in penetration of plant tissues or pathogenicity. An increased number of candidate genes for CAZyme classes AA9 and AA3-1 supports the ability of strains to efficiently degrade plant material. High numbers of genes of D. torresensis related to secretome and small secreted proteins were further characterized. Moreover, the presence of several gene clusters such as fujikurin-like genes was detected and were normally found in Fusariumfujikuroi, that have been linked to fungal pathogenicity. The phenotypes of the three strains investigated showed further difference in light response. We found that Dactylonectria strains have an increased number of photoreceptor encoding genes and we showed sequence alterations. Altogether, the results highlight several gene clusters present in D. torresensis strains that could be linked to endophytic lifestyle, pathogenicity, plant maceration and degradation of plant tissues as well as adaptation to soil contaminated with metals and metalloids and light response.

Droplet Digital PCR Technology for Detection of Ilyonectria liriodendri from Grapevine Environmental Samples

Black-foot disease is one of the most important soilborne diseases affecting planting material in grapevine nurseries and young vineyards. Accurate, early, and specific detection and quantification of black-foot disease causing fungi are essential to alert growers and nurseries to the presence of the pathogens in soil, and to prevent the spread of these pathogens through grapevines using certified pathogen-free planting material and development of resistance. We comparatively assessed the accuracy, efficiency, and specificity of droplet digital PCR (ddPCR) and real-time PCR (qPCR) techniques for the detection and quantification of Ilyonectria liriodendri in bulk and rhizosphere soils, as well as grapevine endorhizosphere. Fungal abundance was not affected by soil-plant fractions. Both techniques showed a high degree of correlation across the samples assessed (R² = 0.95) with ddPCR being more sensitive to lower target concentrations. Roots of asymptomatic vines were found to be a microbial niche that is inhabited by black-foot disease fungi.