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19 pages, 3204 KiB

Open AccessArticle

Hot Water Treatment Causes Lasting Alteration to the Grapevine (Vitis vinifera L.) Mycobiome and Reduces Pathogenic Species Causing Grapevine Trunk Diseases

by Sarah B. Lade, Dora Štraus, Arnau Buñol and Jonàs Oliva

J. Fungi 2022, 8(5), 485; https://doi.org/10.3390/jof8050485 - 6 May 2022

Cited by 2 | Viewed by 2463

Abstract

The effective management of grapevine trunk diseases (GTDs) is an ongoing challenge. Hot water treatment (HWT) is an environmentally friendly and economically viable option; however, the short-term effects of HWT on grapevine (Vitis vinifera L.) health and production are not fully understood. [...] Read more.

The effective management of grapevine trunk diseases (GTDs) is an ongoing challenge. Hot water treatment (HWT) is an environmentally friendly and economically viable option; however, the short-term effects of HWT on grapevine (Vitis vinifera L.) health and production are not fully understood. The aim of this study was to compare the effects of HWT on plant growth and fungal community structure in nursery stock until plants were completely established in the field. We assessed eleven graft and three rootstock varieties from four local nurseries in a region of Catalonia (NE Spain) where GTDs are a serious threat. After treatment, the plants were left to grow under field conditions for two growing seasons. Metabarcoding of the ITS region was used to study the mycobiomes of plant graft unions and root collars. We also assessed the influence of plant physiological indicators in community composition. Hot water treatment caused lasting changes in GTD communities in both the root collar and graft union that were not always characterized as a reduction of GTD-related fungi. However, HWT reduced the relative abundance of some serious GTD-associated pathogens such as Cadophora luteo-olivacea in graft tissues, and Phaeomoniella chlamydospora and Neofusicoccum parvum in the root collar. Treatment had the greatest influence on the total and GTD-related fungal communities of Chardonnay and Xarel·lo, respectively. Total community variation was driven by treatment and nursery in rootstocks, whereas HWT most significantly affected the GTD community composition in R-110 rootstock. In conclusion, changes in fungal abundance were species-specific and mostly dependent on the plant tissue type; however, HWT did reduce plant biomass accumulation in the short-term. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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17 pages, 2191 KiB

Open AccessArticle

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

by David Gramaje, Aleš Eichmeier, Milan Spetik, María Julia Carbone, Rebeca Bujanda, Jessica Vallance and Patrice Rey

J. Fungi 2022, 8(5), 421; https://doi.org/10.3390/jof8050421 - 20 Apr 2022

Cited by 15 | Viewed by 3080

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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19 pages, 2448 KiB

Open AccessArticle

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

by Milan Špetík, Josef Balík, Pavel Híc, Eliška Hakalová, Kateřina Štůsková, Lucie Frejlichová, Jan Tříska and Aleš Eichmeier

J. Fungi 2022, 8(4), 357; https://doi.org/10.3390/jof8040357 - 30 Mar 2022

Cited by 4 | Viewed by 2826

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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19 pages, 3757 KiB

Open AccessArticle

Diversity of Neofusicoccum parvum for the Production of the Phytotoxic Metabolites (-)-Terremutin and (R)-Mellein

by Patricia Trotel-Aziz, Guillaume Robert-Siegwald, Olivier Fernandez, Catarina Leal, Sandra Villaume, Jean-François Guise, Eliane Abou-Mansour, Marc-Henri Lebrun and Florence Fontaine

J. Fungi 2022, 8(3), 319; https://doi.org/10.3390/jof8030319 - 19 Mar 2022

Cited by 12 | Viewed by 3858

Abstract

Two Neofusicoccumparvum isolates and a UV mutant were characterized for their phytotoxin production in vitro, their pathogenicity on grapevine, and their genome sequenced. The isolate Np-Bt67 produced high level of (-)-terremutin, but almost no (R)-mellein, and it was the most [...] Read more.

Two Neofusicoccumparvum isolates and a UV mutant were characterized for their phytotoxin production in vitro, their pathogenicity on grapevine, and their genome sequenced. The isolate Np-Bt67 produced high level of (-)-terremutin, but almost no (R)-mellein, and it was the most aggressive on grapevine, triggering apoplexy. Similar symptoms were not induced by purified (-)-terremutin. The isolate Bourgogne S-116 (Np-B) produced 3-fold less (-)-terremutin and high amounts of (R)-mellein, but it was less aggressive on grapevine than Np-Bt67. The UV9 mutant obtained from Np-B (NpB-UV9) no longer produced (-)-terremutin but overproduced (R)-mellein by 2.5-fold, and it was as pathogenic as its parent. NpB-UV9 differed from its parent by simple mutations in two genes (transcription factor UCR-NP2_6692, regulatory protein UCR-NP2_9007), not located neither near (R)-mellein, nor (-)-terremutin biosynthetic genes, but likely involved in the control of (-)-terremutin biosynthesis. Grapevine immunity was disturbed upon challenge with these pathogens or purified phytotoxins, leading to an upregulation of SA-dependent defenses, while (-)-terremutin interfered with host JA/ET-dependent defenses. Our results suggest that neither (-)-terremutin nor (R)-mellein alone is essential for the pathogenicity of N. parvum on grapevine, since isolate/mutant non-producing these toxins in vitro is pathogenic. However, these phytotoxins could play a quantitative role in the infection process. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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19 pages, 3701 KiB

Open AccessArticle

Minimal versus Intensive: How the Pruning Intensity Affects Occurrence of Grapevine Leaf Stripe Disease, Wood Integrity, and the Mycobiome in Grapevine Trunks

by Christian Kraus, Carolin Rauch, Elisa Maria Kalvelage, Falk Hubertus Behrens, Dagmar d’Aguiar, Cornelia Dubois and Michael Fischer

J. Fungi 2022, 8(3), 247; https://doi.org/10.3390/jof8030247 - 28 Feb 2022

Cited by 8 | Viewed by 3307

Abstract

Previous works on grapevine-trunk diseases indicate that minimal or non-pruning of the grapevine under certain circumstances can significantly reduce the risk of symptom expression. Nevertheless, knowledge of the mechanisms behind these observations are limited. Therefore, it was the aim of this study to [...] Read more.

Previous works on grapevine-trunk diseases indicate that minimal or non-pruning of the grapevine under certain circumstances can significantly reduce the risk of symptom expression. Nevertheless, knowledge of the mechanisms behind these observations are limited. Therefore, it was the aim of this study to investigate in more detail the effect of pruning intensity on the grapevine trunk by means of trunk integrity and the fungal community in the wood tissue. Two German vineyards partially trained in vertical-shoot position and semi-minimally pruned hedges were chosen for this survey due to the accessibility of multi-annual esca-monitoring data. The results revealed that only in one of the two vineyards was the incidence of external esca symptoms significantly reduced over a period of five years (2017–2021) by minimal pruning, which was up to 73.7% compared to intensive pruning. In both vineyards, the trunks of intensively pruned vines not only had more pruning wounds on the trunk (by 86.0% and 72.9%, respectively) than minimally pruned vines, but also exhibited a larger (by 19.3% and 14.7%, respectively) circumference of the trunk head. In addition, the percentage of white rot and necrosis in the trunks of esca-positive and esca-negative vines was analyzed and compared between the two pruning intensities; hereby, significant differences were only found for esca-negative ‘Dornfelder’ vines, in which the proportion of necrosis was higher for intensively pruned vines (23.0%) than for minimally pruned vines (11.5%). The fungal communities of the differently pruned vine trunks were mainly dominated by four genera, which are also associated with GTDs: Diplodia, Eutypa, Fomitiporia and Phaeomoniella. All in all, the fungal diversity and community composition did not differ between minimally and intensively pruned, esca-positive vines. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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23 pages, 6144 KiB

Open AccessArticle

Assessment of a New Copper-Based Formulation to Control Esca Disease in Field and Study of Its Impact on the Vine Microbiome, Vine Physiology and Enological Parameters of the Juice

by Vincenzo Mondello, Christelle Lemaître-Guillier, Patricia Trotel-Aziz, Régis Gougeon, Alberto Acedo, Philippe Schmitt-Kopplin, Marielle Adrian, Cátia Pinto, Olivier Fernandez and Florence Fontaine

J. Fungi 2022, 8(2), 151; https://doi.org/10.3390/jof8020151 - 31 Jan 2022

Cited by 8 | Viewed by 3625

Abstract

Copper-based preparations have been used for more than 100 years in viticulture to control downy mildew caused by Plasmopara viticola. LC2017, and a new low-copper-based formulation, has been developed to control grapevine trunk diseases (GTDs). Previous greenhouse studies showed the potential of [...] Read more.

Copper-based preparations have been used for more than 100 years in viticulture to control downy mildew caused by Plasmopara viticola. LC2017, and a new low-copper-based formulation, has been developed to control grapevine trunk diseases (GTDs). Previous greenhouse studies showed the potential of LC2017 to control GTDs by both fungistatic and plant defense elicitor effects. Here, we further characterize the effects of LC2017 in the field determining its impact on: (i) incidence of Esca, (ii) the vine microbiome, (iii) the vine physiology and (iv) enological parameters of juices. We observed a progressive decrease of cumulate Esca incidence in treated vines over the years with annual fluctuation related to the known erratic emergence of GTD symptoms. Neither harmful effects of LC2017 on the vine microbiota, nor on vine physiology were observed (at both transcriptomic and metabolomic levels). Similarly, no impact of LC2017 was observed on the enological properties of berries except for sugar content in juice from esca-diseased vines. The most important result concerns the transcriptomic profiles: that of diseased and LC2017 treated vines differs from that of disease untreated ones, showing a treatment effect. Moreover, the transcriptomic profile of diseased and LC2017-treated vines is similar to that of untreated asymptomatic vines, suggesting control of the disease. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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18 pages, 2800 KiB

Open AccessArticle

Untargeted and Targeted LC-MS/MS Based Metabolomics Study on In Vitro Culture of Phaeoacremonium Species

by Pierluigi Reveglia, Maria Luisa Raimondo, Marco Masi, Alessio Cimmino, Genoveffa Nuzzo, Gaetano Corso, Angelo Fontana, Antonia Carlucci and Antonio Evidente

J. Fungi 2022, 8(1), 55; https://doi.org/10.3390/jof8010055 - 6 Jan 2022

Cited by 10 | Viewed by 2989

Abstract

Grapevine (Vitis vinifera L.) can be affected by many different biotic agents, including tracheomycotic fungi such as Phaeomoniella chlamydospora and Phaeoacremonium minimum, which are the main causal agent of Esca and Petri diseases. Both fungi produce phytotoxic naphthalenone polyketides, namely scytalone [...] Read more.

Grapevine (Vitis vinifera L.) can be affected by many different biotic agents, including tracheomycotic fungi such as Phaeomoniella chlamydospora and Phaeoacremonium minimum, which are the main causal agent of Esca and Petri diseases. Both fungi produce phytotoxic naphthalenone polyketides, namely scytalone and isosclerone, that are related to symptom development. The main objective of this study was to investigate the secondary metabolites produced by three Phaeoacremonium species and to assess their phytotoxicity by in vitro bioassay. To this aim, untargeted and targeted LC-MS/MS-based metabolomics were performed. High resolution mass spectrometer UHPLC-Orbitrap was used for the untargeted profiling and dereplication of secondary metabolites. A sensitive multi reaction monitoring (MRM) method for the absolute quantification of scytalone and isosclerone was developed on a UPLC-QTrap. Different isolates of P. italicum, P. alvesii and P. rubrigenum were grown in vitro and the culture filtrates and organic extracts were assayed for phytotoxicity. The toxic effects varied within and among fungal isolates. Isosclerone and scytalone were dereplicated by matching retention times and HRMS and MS/MS data with pure standards. The amount of scytalone and isosclerone differed within and among fungal species. To our best knowledge, this is the first study that applies an approach of LC-MS/MS-based metabolomics to investigate differences in the metabolic composition of organic extracts of Phaeoacremonium species culture filtrates. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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21 pages, 2793 KiB

Open AccessArticle

Variation in Fungal Community in Grapevine (Vitis vinifera) Nursery Stock Depends on Nursery, Variety and Rootstock

by Sarah B. Lade, Dora Štraus and Jonàs Oliva

J. Fungi 2022, 8(1), 47; https://doi.org/10.3390/jof8010047 - 3 Jan 2022

Cited by 19 | Viewed by 3354

Abstract

Grapevine trunk diseases (GTDs) are caused by cryptic complexes of fungal pathogens and have become a growing problem for new grapevine (Vitis vinifera) plantations. We studied the role of the nursery, variety, and rootstock in the composition of the fungal communities [...] Read more.

Grapevine trunk diseases (GTDs) are caused by cryptic complexes of fungal pathogens and have become a growing problem for new grapevine (Vitis vinifera) plantations. We studied the role of the nursery, variety, and rootstock in the composition of the fungal communities in root collars and graft unions of planting material in Catalonia (NE Spain). We compared necrosis and fungal communities in graft unions and root collars at harvest, and then after three months of cold storage. We evaluated combinations of eleven red and five white varieties with four common rootstocks coming from six nurseries. Fungal communities were characterized by isolation and metabarcoding of the ITS2 region. Our data suggests that nursery followed by rootstock and variety had significant effects on necrosis and fungal community structure in graft and root tissues. Within the plant, we found large differences in terms fungal community distribution between graft and root tissues. Graft unions housed a significantly higher relative abundance of GTD-related Operational Taxonomic Units (OTUs) than root collars. More severe necrosis was correlated with a lower relative abundance of GTD-related OTUs based on isolation and metabarcoding analyses. Our results suggest that nurseries and therefore their plant production practices play a major role in determining the fungal and GTD-related fungal community in grapevine plants sold for planting. GTD variation across rootstocks and varieties could be explored as a venue for minimizing pathogen load in young plantations. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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18 pages, 3105 KiB

Open AccessArticle

The Mycorrizal Status in Vineyards Affected by Esca

by Lucia Landi, Renzo Foglia, Sergio Murolo and Gianfranco Romanazzi

J. Fungi 2021, 7(10), 869; https://doi.org/10.3390/jof7100869 - 16 Oct 2021

Cited by 8 | Viewed by 2711

Abstract

In this work we analyzed the relationship among native arbuscular mycorrhizal fungi (AMF) and vine roots affected by esca, a serious grapevine trunk disease. The AMF symbiosis was analyzed on the roots of neighboring plants (symptomatic and asymptomatic to esca) in 14 sites [...] Read more.

In this work we analyzed the relationship among native arbuscular mycorrhizal fungi (AMF) and vine roots affected by esca, a serious grapevine trunk disease. The AMF symbiosis was analyzed on the roots of neighboring plants (symptomatic and asymptomatic to esca) in 14 sites of three vineyards in Marche region (central–eastern Italy). The AMF colonization intensity, identified by non-vital staining, showed higher value in all esca symptomatic plants (ranging from 24.6% to 61.3%) than neighboring asymptomatic plants (from 17.4% to 57.6%). The same trend of Glomeromycota phylum abundance was detected by analyzing fungal operational taxonomic units (OTUs) linked to the AMF community, obtained by amplicon high throughput analysis of ITS 1 region. Overall, the highest amount of OTUs was detected on roots from symptomatic plants (0.42%), compared to asymptomatic roots (0.29%). Specific primer pairs for native Rhizophagus irregularis and Funneliformis mosseae AMF species, were designed in 28S rRNA and large subunit (LSU) ribosomal RNA, respectively, and droplet digital PCR protocol for absolute quantification was set up. A higher number of DNA copies of both fungal species were detected more frequently in symptomatic than asymptomatic vines. Our study suggests a relationship between esca and native AMF in grapevine. These results underline the importance of native rhizosphere microbial communities for a better knowledge of grapevine esca disease. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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22 pages, 10857 KiB

Open AccessEditor’s ChoiceArticle

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

by María Julia Carbone, Sandra Alaniz, Pedro Mondino, Matías Gelabert, Ales Eichmeier, Dorota Tekielska, Rebeca Bujanda and David Gramaje

J. Fungi 2021, 7(9), 686; https://doi.org/10.3390/jof7090686 - 25 Aug 2021

Cited by 38 | Viewed by 5660

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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24 pages, 5917 KiB

Open AccessArticle

Comparative Study of Secreted Proteins, Enzymatic Activities of Wood Degradation and Stilbene Metabolization in Grapevine Botryosphaeria Dieback Fungi

by Clément Labois, Elodie Stempien, Justine Schneider, Christine Schaeffer-Reiss, Christophe Bertsch, Mary-Lorène Goddard and Julie Chong

J. Fungi 2021, 7(7), 568; https://doi.org/10.3390/jof7070568 - 16 Jul 2021

Cited by 13 | Viewed by 2848

Abstract

Botryosphaeriaceae fungi are plant pathogens associated with Botryosphaeria dieback. To better understand the virulence factors of these fungi, we investigated the diversity of secreted proteins and extracellular enzyme activities involved in wood degradation and stilbene metabolization in Neofusicoccum parvum and Diplodia seriata, [...] Read more.

Botryosphaeriaceae fungi are plant pathogens associated with Botryosphaeria dieback. To better understand the virulence factors of these fungi, we investigated the diversity of secreted proteins and extracellular enzyme activities involved in wood degradation and stilbene metabolization in Neofusicoccum parvum and Diplodia seriata, which are two major fungi associated with grapevine B. dieback. Regarding the analysis of proteins secreted by the two fungi, our study revealed that N. parvum, known to be more aggressive than D. seriata, was characterized by a higher quantity and diversity of secreted proteins, especially hydrolases and oxidoreductases that are likely involved in cell wall and lignin degradation. In addition, when fungi were grown with wood powder, the extracellular laccase and Mn peroxidase enzyme activities were significantly higher in D. seriata compared to N.parvum. Importantly, our work also showed that secreted Botryosphaeriaceae proteins produced after grapevine wood addition are able to rapidly metabolize the grapevine stilbenes. Overall, a higher diversity of resveratrol and piceatannol metabolization products was found with enzymes of N. parvum compared to D. seriata. This study emphasizes the diversity of secreted virulence factors found in B. dieback fungi and suggests that some resveratrol oligomers produced in grapevine wood after pathogen attack could be formed via pathogenic fungal oxidases. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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25 pages, 15786 KiB

Open AccessArticle

Trunk Surgery as a Tool to Reduce Foliar Symptoms in Diseases of the Esca Complex and Its Influence on Vine Wood Microbiota

by Andrea Pacetti, Samuele Moretti, Catia Pinto, Stéphane Compant, Sibylle Farine, Christophe Bertsch and Laura Mugnai

J. Fungi 2021, 7(7), 521; https://doi.org/10.3390/jof7070521 - 29 Jun 2021

Cited by 23 | Viewed by 4421

Abstract

In the last few years, trunk surgery has gained increasing attention as a method to reduce foliar symptoms typical of some of the Esca complex diseases. The technique relies on the mechanical removal of decayed wood by a chainsaw. A study on a [...] Read more.

In the last few years, trunk surgery has gained increasing attention as a method to reduce foliar symptoms typical of some of the Esca complex diseases. The technique relies on the mechanical removal of decayed wood by a chainsaw. A study on a 14-year-old Cabernet Sauvignon vineyard was carried out to validate the efficacy of trunk surgery and explore possible explanations behind it. Three levels of treatment were applied to three of the most characteristic symptoms associated with some diseases of the Esca complex, such as leaf stripe symptoms (LS), wilted shoots (WS) and apoplexy (APP). The most promising results were obtained by complete trunk surgery, where the larger decay removal allowed lower symptom re-expression. According to the wood types analyzed (decay, medium and sound wood), different changes in microbiota were observed. Alpha-diversity generally decreased for bacteria and increased for fungi. More specifically, main changes were observed for Fomitiporia mediterranea abundance that decreased considerably after trunk surgery. A possible explanation for LS symptom reduction after trunk surgery could be the microbiota shifting caused by the technique itself affecting a microbic-shared biochemical pathway involved in symptom expression. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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18 pages, 1840 KiB

Open AccessArticle

Impacts of Sodium Arsenite on Wood Microbiota of Esca-Diseased Grapevines

by Emilie Bruez, Philippe Larignon, Christophe Bertsch, Guillaume Robert-Siegwald, Marc-Henri Lebrun, Patrice Rey and Florence Fontaine

J. Fungi 2021, 7(7), 498; https://doi.org/10.3390/jof7070498 - 22 Jun 2021

Cited by 20 | Viewed by 2583

Abstract

Although sodium arsenite was widely used in Europe until its ban in 2003, its effects on microorganisms is not clearly understood. To improve our understanding of sodium arsenite curative effect on GTDs, grapevines displaying esca-foliar symptoms from different French regions (Alsace, Champagne, Languedoc) [...] Read more.

Although sodium arsenite was widely used in Europe until its ban in 2003, its effects on microorganisms is not clearly understood. To improve our understanding of sodium arsenite curative effect on GTDs, grapevines displaying esca-foliar symptoms from different French regions (Alsace, Champagne, Languedoc) were treated or not with sodium arsenite, and analyzed for their wood microbiota. Using metabarcoding, we identified the fungal and bacterial taxa composition of microbiota colonizing woody trunk tissues. Large differences in fungal microbiota composition between treated and untreated grapevines were observed while no major impacts were observed on bacteria microbiota. The main fungal species detected in untreated necrotic woody tissues was Fomitiporia mediterranea (63–94%), a fungal pathogen associated with esca. The relative abundance of this fungal species significantly decreased after sodium arsenite treatment in the three vineyards, in particular in white-rot necrotic tissues and their borders (−90%). F. mediterranea was the most sensitive to sodium arsenite among fungi from grapevine woody tissues. These results strongly suggest that the effect of sodium arsenite on GTDs is due to its ability to efficiently and almost specifically eliminate F. mediterranea from white-rot necrotic tissues, allowing saprobic fungi to colonize the tissues previously occupied by this pathogenic fungus. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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23 pages, 3564 KiB

Open AccessArticle

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

by David Gramaje, Carmen Berlanas, María del Pilar Martínez-Diz, Emilia Diaz-Losada, Livio Antonielli, Sabrina Beier, Markus Gorfer, Monika Schmoll and Stéphane Compant

J. Fungi 2020, 6(4), 255; https://doi.org/10.3390/jof6040255 - 29 Oct 2020

Cited by 12 | Viewed by 3868

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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White Rot Fungi (Hymenochaetales) and Esca of Grapevine: Insights from Recent Microbiome Studies

by Giovanni Del Frari, Helena Oliveira and Ricardo Boavida Ferreira

J. Fungi 2021, 7(9), 770; https://doi.org/10.3390/jof7090770 - 17 Sep 2021

Cited by 23 | Viewed by 3749

Abstract

Esca is a major grapevine trunk disease that heavily affects vineyards in the Northern hemisphere. The etiology and epidemiology of this disease have been subject of dispute ever since the earliest disease reports. The reason behind such debate is the presence of multiple [...] Read more.

Esca is a major grapevine trunk disease that heavily affects vineyards in the Northern hemisphere. The etiology and epidemiology of this disease have been subject of dispute ever since the earliest disease reports. The reason behind such debate is the presence of multiple internal and external symptoms, as well as several putative and confirmed wood pathogens. While the role of pathogenic fungi, as causal agents of wood symptoms, has been thoroughly assessed, their role in the expression of leaf symptoms remains to be fully elucidated. In this review, we analyzed etiological and epidemiological data, with a special focus on the microbiological aspect of esca and the involvement of Hymenochaetales (Basidiomycota). Vineyard studies have associated leaf symptoms with the presence of white rot, most frequently caused by Fomitiporia mediterranea (Hymenochaetales), while tracheomycotic fungi are commonly found, with similar abundance, in symptomatic and asymptomatic vines. Pathogenicity trials have excluded a direct effect of Hymenochaetales species in triggering leaf symptoms, while the data concerning the role of tracheomycotic fungi remains controversial. Recent microbiome studies confirmed that F. mediterranea is more abundant in leaf-symptomatic vines, and treatments that effectively control leaf symptoms, such as sodium arsenite spray and trunk surgery, act directly on the abundance of F. mediterranea or on the presence of white rot. This suggest that the simultaneous presence of Hymenochaetales and tracheomycotic fungi is a pre-requisite for leaf symptoms; however, the relation among fungal pathogens, grapevine and other biotic and abiotic factors needs further investigation. Full article

(This article belongs to the Special Issue Application of Omics Technologies for a Deeper Insight into the Study of Fungal Trunk Pathogens of Grapevine)

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