scholarly journals Grapevine wood microbiome analysis identifies key fungal pathogens and potential interactions with the bacterial community implicated in grapevine trunk disease appearance

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Bekris Fotios ◽  
Vasileiadis Sotirios ◽  
Papadopoulou Elena ◽  
Samaras Anastasios ◽  
Testempasis Stefanos ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Amplicon Sequencing ◽  
Strong Interactions ◽  
Dependent Manner ◽  
Grapevine Trunk Diseases ◽  
Bacterial Microbiome ◽  
Trunk Diseases ◽  
Fungal Microbiome ◽  
Potential Interactions

Abstract Background Grapevine trunk diseases (GTDs) is a disease complex caused by wood pathogenic fungi belonging to genera like Phaeomoniella, Phaeoacremonium, Fomitiporia, Eutypa and members of the family Botryosphaeriaceae. However, the co-occurrence of these fungi in symptomatic and asymptomatic vines at equivalent abundances has questioned their role in GTDs. Hence, we still lack a good understanding of the fungi involved in GTDs, their interactions and the factors controlling their assemblage in vines. We determined the fungal and bacterial microbiome in wood tissues of asymptomatic and symptomatic vines of three main Greek cultivars (Agiorgitiko, Xinomavro, Vidiano), each cultivated in geographically distinct viticultural zones, using amplicon sequencing. Results We noted that cultivar/biogeography (lumped factor) was the strongest determinant of the wood fungal microbiome (p < 0.001, 22.7%), while GTD symptoms condition had a weaker but still significant effect (p < 0.001, 3.5%), being prominent only in the cultivar Xinomavro. Several fungal Amplicon Sequence Variants (ASVs), reported as GTD-associated pathogens like Kalmusia variispora, Fomitiporia spp., and Phaemoniella chlamydosporα (most dominant in our study), were positively correlated with symptomatic vines in a cultivar/viticultural zone dependent manner. Random Forest analysis pointed to P. chlamydosporα, K. variispora, A. alternata and Cladosporium sp., as highly accurate predictors of symptomatic vines (0% error rate). The wood bacterial microbiome showed similar patterns, with biogeography/cultivar being the main determinant (p < 0.001, 25.5%) of its composition, followed by the GTD status of vines (p < 0.001, 5.2%). Differential abundance analysis revealed a universal positive correlation (p < 0.001) of Bacillus and Streptomyces ASVs with asymptomatic vines. Network analysis identified a significant negative co-occurrence network between these bacterial genera and Phaemoniella, Phaeoacrominum and Seimatosporium. These results point to a plant beneficial interaction between Bacillus/Streptomyces and GTD pathogens. Conclusions Our study (a) provides evidence that GTD symptomatic plants support a wood fungal microbiome, showing cultivar and biogeography-dependent patterns, that could be used as a proxy to distinguish between healthy and diseased vines, (b) points to strong interactions between the bacterial and fungal wood microbiome in asymptomatic vines that should be further pursued in the quest for discovery of novel biocontrol agents.

scholarly journals Production of Phytotoxic Metabolites by Botryosphaeriaceae in Naturally Infected and Artificially Inoculated Grapevines

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 802
Author(s):  
Pierluigi Reveglia ◽  
Regina Billones-Baaijens ◽  
Jennifer Millera Millera Niem ◽  
Marco Masi ◽  
Alessio Cimmino ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Protocatechuic Acid ◽  
Physiological Factors ◽  
Diplodia Seriata ◽  
Grapevine Trunk Diseases ◽  
Botryosphaeria Dieback ◽  
Trunk Diseases ◽  
One Year ◽  
Pathogen Dna

Grapevine trunk diseases (GTDs) are considered a serious problem to viticulture worldwide. Several GTD fungal pathogens produce phytotoxic metabolites (PMs) that were hypothesized to migrate to the foliage where they cause distinct symptoms. The role of PMs in the expression of Botryosphaeria dieback (BD) symptoms in naturally infected and artificially inoculated wood using molecular and analytical chemistry techniques was investigated. Wood samples from field vines naturally infected with BD and one-year-old vines inoculated with Diplodia seriata, Spencermartinsia viticola and Dothiorella vidmadera were analysed by cultural isolations, quantitative PCR (qPCR) and targeted LC-MS/MS to detect three PMs: (R)-mellein, protocatechuic acid and spencertoxin. (R)-mellein was detected in symptomatic naturally infected wood and vines artificially inoculated with D. seriata but was absent in all non-symptomatic wood. The amount of (R)-mellein detected was correlated with the amount of pathogen DNA detected by qPCR. Protocatechuic acid and spencertoxin were absent in all inoculated wood samples. (R)-mellein may be produced by the pathogen during infection to break down the wood, however it was not translocated into other parts of the vine. The foliar symptoms previously reported in vineyards may be due to a combination of PMs produced and climatic and physiological factors that require further investigation.

The compositional turnover of grapevine-associated plant pathogenic fungal communities are greater among intraindividual microhabitats and terroirs than among healthy and Esca-diseased plants

2021 ◽  
Author(s):  
Adrienn Geiger ◽  
Zoltán Karácsony ◽  
Richárd Golen ◽  
Kálmán Zoltán Váczy ◽  
József Geml
Keyword(s):  
Pathogenic Fungi ◽  
Wine Industry ◽  
Fungal Communities ◽  
Opportunistic Pathogens ◽  
Grapevine Trunk Diseases ◽  
Esca Disease ◽  
Dna Metabarcoding ◽  
Trunk Diseases ◽  
Fungal Dna ◽  
Key Questions

Grapevine trunk diseases (GTD) are a major threat to the wine industry, causing yield loss and dieback of grapevines. While the increasing damage caused by GTDs in recent decades have spurred several studies on grapevine-associated pathogenic fungi, key questions about the emergence and severity of GTDs remain unanswered, including possible differences in plant pathogenic fungal communities in asymptomatic and symptomatic grapevines. We generated fungal DNA metabarcoding data from soil, bark, and perennial wood samples from asymptomatic and symptomatic grapevines sampled in three terroirs. We observed larger compositional differences in plant pathogenic fungi among different plants parts within grapevine plants than among individual grapevines. This is driven by the dominance of GTD-associated fungi in perennial wood and non-GTD pathogens in soil, as well as by the lack of significant differences among asymptomatic and Esca symptomatic grapevines. These results suggest that fungi generally associated with Esca disease belong to the core grapevine microbiome and likely are commensal endophytes and/or latent saprotrophs, some of which can act as opportunistic pathogens on stressed plants. In addition, we found significant compositional differences among sampling sites, particularly in soil, which suggest a certain influence of local edaphic and mesclimatic factors on plant pathogenic fungal communities. Furthermore, the observed differences among terroirs in plant pathogenic fungal communities in grapevine woody parts indicate that environmental factors likely are important for the development of Esca disease and further studies are needed to investigate the abiotic conditions on fungal compositional dynamics in Esca-affected plants.

scholarly journals Host genetic control of succession in the switchgrass leaf fungal microbiome

2021 ◽  
Author(s):  
Acer VanWallendael ◽  
Gian Maria Niccolo Benucci ◽  
Pedro Beschoren da Costa ◽  
Linnea Fraser ◽  
Gregory Bonito ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Panicum Virgatum ◽  
Genetic Locus ◽  
Growing Season ◽  
Amplicon Sequencing ◽  
Immune Genes ◽  
Time Space ◽  
Genome Wide ◽  
Host Genetic ◽  
Fungal Microbiome

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across three additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association mapping and RNA-sequencing to show that three cysteine-rich receptor-like kinases were linked to a genetic locus associated with microbiome structure. These genes were more highly expressed in genotypes susceptible to fungal pathogens, which were central to microbial covariance networks, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

scholarly journals Fungal community associated with grapevine wood lesions in Lebanon

OENO One ◽  
2014 ◽  
Vol 48 (4) ◽  
pp. 293
Author(s):  
Elia Choueiri ◽  
Fouad Jreijiri ◽  
Paulette Chlela ◽  
Valérie Mayet ◽  
Gwénaelle Comont ◽  
...  
Keyword(s):  
Cross Sections ◽  
Fungal Community ◽  
Fungal Pathogens ◽  
Numerical Evaluation ◽  
Grapevine Trunk Diseases ◽  
Mediterranean Countries ◽  
Esca Disease ◽  
Trunk Diseases ◽  
Micro Organisms

<p style="text-align: justify;"><strong>Aims</strong>: To detect and identify the cultivable microorganisms putatively associated with esca disease in representative Lebanese vineyards.</p><p style="text-align: justify;"><strong>Methods and results</strong>: Two field surveys were conducted in Lebanon in 2005 and 2007 to study the fungal community associated with grapevine wood lesions. A total of 68 vines showing typical esca symptoms were randomly sampled in 17 vineyards and cross sections were obtained of cordons and trunks. The shape and type of inner necrosis and discoloration were examined and isolations were made from the symptomatic wood. Isolation results showed that inner necrosis and isolated fungi were similar to those previously found elsewhere, namely in Central Europe or Mediterranean countries. Additionally, three methods for numerical evaluation of micro-organisms found were compared.</p><p style="text-align: justify;"><strong>Conclusion</strong>: Most fungal pathogens generally associated with grapevine trunk diseases were detected, of which the basidiomycete <em>Fomitiporia mediterranea</em> and species of the ascomycete family <em>Botryosphaeriaceae</em> were the most frequently encountered. Additionally, a large diversity of other wood colonizing micro-organisms was detected. The putative role of some of the obtained micro-organisms in the process of wood degradation related to esca disease is discussed.</p><p style="text-align: justify;"><strong>Significance and impact of the study</strong>: This isolation study is presently the most completed that was carried out with grapevine wood samples collected in Lebanon. Besides, it is the first to provide isolation results based on a classification of inner necrosis in five categories and to compare three criteria for numerical evaluation. This study also tends to further highlight that <em>Botryosphaeriaceae</em> species are common wood inhabiting fungi that should be associated with esca.</p>

scholarly journals Relationship Between the Xylem Anatomy of Grapevine Rootstocks and Their Susceptibility to Phaeoacremonium minimum and Phaeomoniella chlamydospora

2021 ◽  
Vol 12 ◽  
Author(s):  
Charis K. Ramsing ◽  
David Gramaje ◽  
Sara Mocholí ◽  
Javier Agustí ◽  
Félix Cabello Sáenz de Santa María ◽  
...  
Keyword(s):  
Surface Area ◽  
Fungal Pathogens ◽  
Xylem Anatomy ◽  
Dna Concentration ◽  
Phaeomoniella Chlamydospora ◽  
Grapevine Trunk Diseases ◽  
Potential Association ◽  
Trunk Diseases ◽  
Stem Surface Area ◽  
Detrimental Impact

Fungal grapevine trunk diseases (GTDs) are some of the most pressing threats to grape production worldwide. While these diseases are associated with several fungal pathogens, Phaeomoniella chlamydospora and Phaeoacremonium minimum are important contributors to esca and Petri diseases. Recent research has linked grapevine xylem diameter with tolerance to Pa. chlamydospora in commercial rootstocks. In this study, we screen over 25 rootstocks for xylem characteristics and tolerance to both Pa. chlamydospora and Pm. minimum. Tolerance was measured by fungal incidence and DNA concentration (quantified via qPCR), while histological analyses were used to measure xylem characteristics, including xylem vessels diameter, density, and the proportion of the stem surface area covered by xylem vessels. Rootstocks were grouped into different classes based on xylem characteristics to assess the potential association between vasculature traits and pathogen tolerance. Our results revealed significant differences in all the analyzed xylem traits, and also in DNA concentration for both pathogens among the tested rootstocks. They corroborate the link between xylem vessels diameter and tolerance to Pa. chlamydospora. In Pm. minimum, the rootstocks with the widest xylem diameter proved the most susceptible. This relationship between vasculature development and pathogen tolerance has the potential to inform both cultivar choice and future rootstock breeding to reduce the detrimental impact of GTDs worldwide.

scholarly journals Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics

mSystems ◽  
2021 ◽  
Author(s):  
Vittorio Tracanna ◽  
Adam Ossowicki ◽  
Marloes L. C. Petrus ◽  
Sam Overduin ◽  
Barbara R. Terlouw ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Amplicon Sequencing ◽  
Plant Pathogenic Fungi ◽  
Content Type ◽  
Major Threat ◽  
Wide Range

Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops.

Evaluation of Biological and Chemical Pruning Wound Protectants to Control Grapevine Trunk Diseases Pathogens Eutypa lata and Neofusicoccum parvum

2021 ◽  
Author(s):  
Robert Blundell ◽  
Akif Eskalen
Keyword(s):  
Recovery Rate ◽  
Fungal Pathogens ◽  
Field Trials ◽  
Positive Control ◽  
Neofusicoccum Parvum ◽  
Eutypa Lata ◽  
Grapevine Trunk Diseases ◽  
Pruning Wound ◽  
Wound Protection ◽  
Trunk Diseases

Grapevine trunk diseases, caused by many different fungal pathogens, are one of the most economically important diseases affecting the grapevine industry worldwide. Pruning wounds are the main point of entry for these fungal pathogens and thus, disease control is focused on preventative pruning wound protection by chemical products and/or biological control agents (BCAs). In this study we evaluated a broad variety of already registered or at the experimental stage of chemical and BCAs in greenhouse and in field trials for the protection of table- and wine-grape vines against infection of Eutypa lata and Neofusicoccum parvum, major pathogens responsible for Eutypa and Botryosphaeria dieback, respectively. Our study showed that Trichoderma asperellum and Trichoderma gamsii consistently provided pruning wound protection in greenhouse and field trials, with a mean percent disease control (MPDC) of 88% and 100% for E. lata and N. parvum, respectively, when compared to the water treated-inoculated positive control (P<0.05). The chemical protectants, thiophanate-methyl + myclobutanil and fluopyram and trifloxystrobin were also able to effectively protect wounds with a MPDC of up to 86% when compared to the water treated-inoculated positive control (P<0.05). When biological treatments were evaluated for recovery from treated canes at the end of the growing season, Trichoderma-based treatments had a rate of recovery between 0 and 100%, Aureobasidium-based treatments had a recovery rate between 25 and 100%, and Bacillus-based treatments had a recovery rate between 0 and 25%.

scholarly journals Effectiveness of Natural Antifungal Compounds in Controlling Infection by Grapevine Trunk Disease Pathogens through Pruning Wounds

2015 ◽  
Vol 81 (18) ◽  
pp. 6474-6483 ◽  
Author(s):  
Rebeca Cobos ◽  
Rosa María Mateos ◽  
José Manuel Álvarez-Pérez ◽  
Miguel Angel Olego ◽  
Silvia Sevillano ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Field Trials ◽  
Economic Benefits ◽  
Chitosan Oligosaccharide ◽  
Promising Alternative ◽  
Content Type ◽  
Phaeomoniella Chlamydospora ◽  
Grapevine Trunk Diseases ◽  
Trunk Diseases

ABSTRACTGrapevine trunk fungal pathogens, such asDiplodia seriataandPhaeomoniella chlamydospora, can infect plants through pruning wounds. They cause grapevine trunk diseases and are involved in grapevine decline. Accordingly, the protection of pruning wounds is crucial for the management of grapevine trunk diseases. The efficacy of different natural antifungals in inhibiting the growth of several fungi causing grapevine trunk diseases was evaluatedin vitro. The fungi showing greaterin vitroefficacy were tested on autoclaved grape wood assays againstD. seriataandP. chlamydospora. Based on results from these assays, chitosan oligosaccharide, vanillin, and garlic extract were selected for further evaluation on pruning wounds inoculated withD. seriataandP. chlamydosporain field trials. A significant decrease in plant mortality was observed after 2 years of growth in the plants treated with the different natural antifungals compared to the mortality rate observed in infected plants that were not treated with antifungals. Also, the infection rate for the inoculated pathogens was significantly reduced in plants treated with the selected natural antifungals. Therefore, natural antifungals represent a promising alternative for disease control and could provide significant economic benefits for the grape-growing industry.

scholarly journals The Influence of Temperature on the Growth, Sporulation, Colonization, and Survival of Trichoderma spp. in Grapevine Pruning Wounds

Agronomy ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1771
Author(s):  
Guzmán Carro-Huerga ◽  
Sara Mayo-Prieto ◽  
Álvaro Rodríguez-González ◽  
Samuel Álvarez-García ◽  
Santiago Gutiérrez ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Climatic Conditions ◽  
Plant Diseases ◽  
Trichoderma Spp ◽  
Grapevine Trunk Diseases ◽  
Winter Conditions ◽  
Different Temperatures ◽  
Influence Of Temperature On ◽  
Trunk Diseases ◽  
Native Strains

Trichoderma is a genus of fungi used for the biological control of plant diseases and a large number of its bio-formulates are available in the market. However, its efficacy under field conditions remains unclear, especially for the protection of grapevine plants against Grapevine Trunk Diseases (GTDs). These diseases are caused by a complex of fungal pathogens whose main point of entrance into the affected plants is through pruning wounds. In this research, different Trichoderma native strains have been evaluated according to their ability to grow at different temperatures and their capacity to colonize pruning wounds in adverse climatic conditions. Strains from section Trichoderma have adapted to cooler conditions. On the other hand, strains from clade Harzianum/Virens grow at higher temperatures. However, differences can also be found between strains inside the same clade/section. Native strains were able to colonize more than 70% of vine pruning wounds in winter conditions. The Trichoderma strain T154 showed a significantly higher re-isolation degree from vine plants and its concentration was optimized for spraying onto vine plants. In conclusion, Trichoderma native strains are better adapted to survive in a changing environment, and they could give better protection to grapevine plants in co-evolution with each specific vineyard.

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