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Grapevine trunk diseases (GTDs) are a complex group of diseases, that lead to major economic losses in all wine producing countries. The investigation of biocontrol agents (BCAs) capable to forestall or at least minimize the development of GTDs has, recently, become a priority. Nursery experiments were set up to (i) assess the biocontrol effect of Trichoderma atroviride SC1 and Bacillus subtilis PTA-271, alone and in simultaneous application, against Botryosphaeria dieback (BOT) and black foot (BF) associated pathogens during the grapevine propagation process, and (ii) evaluate the success of the BCA inoculation during the grapevine propagation process, using qRT-PCR techniques.The results demonstrated a significant reduction on the percentage of potentially infected plants and the percentage of fungal isolation from wood fragments of BOT and BF pathogens in nursery material treated with Ta SC1 and Bs PTA-271 respectively. In one of the experiments, the simultaneous treatments with Bs PTA-271 and Ta SC1 presented a reduction on both percentage, potentially infected plants and fungal isolation, from wood fragments of BOT and BF pathogens.These biological treatments may be a relevant component of an integrated approach, using complementary management strategies to limit infection by GTDs pathogens, but further research is still needed to elucidate the effectiveness of Bs PTA-271 and the benefits to be simultaneously applied with Ta SC1 for the control of GTDs pathogens in nurseries. This article is protected by copyright. All rights reserved.

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 alphadiversity 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., This work has been partially supported by Ministerstvo Školství, Mládeže a Tělovýchovy (CZ.02.1.01./0.0/0.0/16_017/0002334) and the “José Castillejo” program (CAS 18/00065). D. Gramaje was supported by the Ramón y Cajal Program, Spanish Government (RYC-2017-23098). We thank M. Maldonado-González and M. Andrés-Sodupe for the technical support.

Xylem anatomy may change in response to environmental or biotic stresses. Vascular occlusion, an anatomical modification of mature xylem, contributes to plant resistance and susceptibility to different stresses. In woody organs, xylem occlusions have been examined as part of the senescence process, but their presence and function in leaves remain obscure. In grapevine, many stresses are associated with premature leaf senescence inducing discolorations and scorched tissue in leaves. However, we still do not know whether the leaf senescence process follows the same sequence of physiological events and whether leaf xylem anatomy is affected in similar ways. In this study, we quantified vascular occlusions in midribs from leaves with symptoms of the grapevine disease esca, magnesium deficiency and autumn senescence. We found higher amounts of vascular occlusions in leaves with esca symptoms (in 27% of xylem vessels on average), whereas the leaves with other symptoms (as well as the asymptomatic controls) had far fewer occlusions (in 3% of vessels). Therefore, we assessed the relationship between xylem occlusions and esca leaf symptoms in four different countries (California in the USA, France, Italy and Spain) and eight different cultivars. We monitored the plants over the course of the growing season, confirming that vascular occlusions do not evolve with symptom age. Finally, we investigated the hydraulic integrity of leaf xylem vessels by optical visualization of embolism propagation during dehydration. We found that the occlusions lead to hydraulic dysfunction mainly in the peripheral veins compared with the midribs in esca symptomatic leaves. These results open new perspectives on the role of vascular occlusions during the leaf senescence process, highlighting the uniqueness of esca leaf symptoms and its consequence on leaf physiology.

A field survey conducted on asymptomatic grapevine propagation material from nurseries and symptomatic young grapevines throughout different regions of Algeria yielded a collection of 70 Phaeoacremonium-like isolates and three Cadophora-like isolates. Based on morphology and DNA sequence data of b-tubulin (tub2) and actin, five Phaeoacremonium species were identified including Phaeoacremonium minimum (22 isolates), Phaeoacremonium venezuelense (19 isolates), Phaeoacremonium parasiticum (17 isolates), Phaeoacremonium australiense (8 isolates), and Phaeoacremonium iranianum (4 isolates). The latter two species (P. australiense and P. iranianum) were reported for the first time in Algeria. Multilocus phylogenetic analyses (internal transcribed spacer, tub2, and translation elongation factor 1-a) and morphological features, allowed the description of the three isolates belonging to the genus Cadophora (WAMC34, WAMC117, and WAMC118) as a novel species, named Cadophora sabaouae sp. nov. Pathogenicity tests were conducted on grapevine cuttings cultivar Cardinal. All the identified species were pathogenic on grapevine cuttings., Ministerstvo Školství, Mládeže a Tělovýchovy Grant/Award Number: CZ-02-1-01/0-0/0-0/16-025/0007314 Technologická Agentura České Republiky Grant/Award Number: TJ02000096 Spanish Government, Ramon y Cajal program Grant/Award Number: RYC-2017-23098

[EN] Grapevine trunk diseases (GTDs) are a big threat for global viticulture. Without effective chemicals, biocontrol strategies are developed as alternatives to better cope with environmental concerns. A combination of biological control agents (BCAs) could even improve sustainable disease management through complementary ways of protection. In this study, we evaluated the combination of Bacillus subtilis (Bs) PTA-271 and Trichoderma atroviride (Ta) SC1 for the protection of Chardonnay and Tempranillo rootlings against Neofusicoccum parvum Bt67, an aggressive pathogen associated to Botryosphaeria dieback (BD). Indirect benefits offered by each BCA and their combination were then characterized in planta, as well as their direct benefits in vitro. Results provide evidence that (1) the cultivar contributes to the beneficial effects of Bs PTA-271 and Ta SC1 against N. parvum, and that (2) the in vitro BCA mutual antagonism switches to the strongest fungistatic effect toward Np-Bt67 in a three-way confrontation test. We also report for the first time the beneficial potential of a combination of BCA against Np-Bt67 especially in Tempranillo. Our findings highlight a common feature for both cultivars: salicylic acid (SA)-dependent defenses were strongly decreased in plants protected by the BCA, in contrast with symptomatic ones. We thus suggest that (1) the high basal expression of SA-dependent defenses in Tempranillo explains its highest susceptibility to N. parvum, and that (2) the cultivar-specific responses to the beneficial Bs PTA-271 and Ta SC1 remain to be further investigated., Funding This work was supported by a French Grant from the Region GRAND-EST France and the City of GRAND-REIMS France through the BIOVIGNE Ph.D. program, whose functioning is supported by BELCHIM Crop Protection France. DG was supported by the Ramon y Cajal program, Spanish Government (RyC-2017-23098).

[EN] 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., Funding This research was founded by FEDER funding through a State Program of I + D + i oriented to the Challenges of Society (RTA2015-00015-C02-00), supported by The National Institute for Agricultural and Food Research and Technology (INIA). DG was supported by the Ramon y Cajal program, Spanish Government (RyC-2017-23098). This research has been developed as a result of a mobility stay funded by the Erasmus+ KA1 Erasmus Mundus Joint Master Degrees Programme of the European Commission under the PLANT HEALTH Project.

Plant compartments provide unique niches that lead to specific microbial associations. The microbiota colonizing the endophytic compartment (endorhizosphere) and the rhizosphere contribute to productivity, plant growth, phytoremediation and carbon sequestration. The main objective of this study was to investigate how fungal communities are enriched in different habitats outside and inside of grapevine roots. For this purpose, the spatial dynamics of the fungal communities associated with three soil-plant compartments (bulk soil, rhizosphere and endorhizosphere) were characterized by ITS high-throughput amplicon sequencing (HTAS). Fungal communities were largely affected in their diversity and composition by soil-plant compartments, whereas the spatial variation (i.e. across five vineyards) was low. The endorhizosphere compartment differed most from the other two, suggesting that the root tissues entail a barrier for fungal colonization. The results of functional prediction via FUNGuild suggested an increase in the relative abundances of potential plant pathogens, endophytes and arbuscular mycorrhiza, and a decrease in wood, dung and undefined saprotrophs from bulk soil towards the endorhizosphere. Roots of asymptomatic vines were a microbial niche that is inhabited by soilborne fungi associated with grapevine trunk diseases, which opens up new perspectives in the study of the endophytic role of these pathogens on grapevines. Results obtained in this study provide helpful information to better know how the host shapes its microbiome and the implications for vineyard productivity and management., David Gramaje was supported by the DOC-INIA program from theINIA, co-funded by the European Social Fund. María del Pilar Martínez-Diz was supported by the FPI-INIA program from the INIA.

Novel species of fungi described in this study include those from various countries as follows: Australia, Chaetomella pseudocircinoseta and Coniella pseudodiospyri on Eucalyptus microcorys leaves, Cladophialophora eucalypti, Teratosphaeria dunnii and Vermiculariopsiella dunnii on Eucalyptus dunnii leaves, Cylindrium grande and Hypsotheca eucalyptorum on Eucalyptus grandis leaves, Elsinoe salignae on Eucalyptus saligna leaves, Marasmius lebeliae on litter of regenerating subtropical rainforest, Phialoseptomonium eucalypti (incl. Phialoseptomonium gen. nov.) on Eucalyptus grandis × camaldulensis leaves, Phlogicylindrium pawpawense on Eucalyptus tereticornis leaves, Phyllosticta longicauda as an endophyte from healthy Eustrephus latifolius leaves, Pseudosydowia eucalyptorum on Eucalyptus sp. leaves, Saitozyma wallum on Banksia aemula leaves, Teratosphaeria henryi on Corymbia henryi leaves. Brazil, Aspergillus bezerrae, Backusella azygospora, Mariannaea terricola and Talaromyces pernambucoensis from soil, Calonectria matogrossensis on Eucalyptus urophylla leaves, Calvatia brasiliensis on soil, Carcinomyces nordestinensis on Bromelia antiacantha leaves, Dendryphiella stromaticola on small branches of an unidentified plant, Nigrospora brasiliensis on Nopalea cochenillifera leaves, Penicillium alagoense as a leaf endophyte on a Miconia sp., Podosordaria nigrobrunnea on dung, Spegazzinia bromeliacearum as a leaf endophyte on Tilandsia catimbauensis, Xylobolus brasiliensis on decaying wood. Bulgaria, Kazachstania molopis from the gut of the beetle Molops piceus. Croatia, Mollisia endocrystallina from a fallen decorticated Picea abies tree trunk. Ecuador, Hygrocybe rodomaculata on soil. Hungary, Alfoldia vorosii (incl.Alfoldia gen. nov.) from Juniperus communis roots, Kiskunsagia ubrizsyi (incl. Kiskunsagia gen. nov.) from Fumana procumbens roots. India, Aureobasidium tremulum as laboratory contaminant, Leucosporidium himalayensis and Naganishia indica from windblown dust on glaciers. Italy, Neodevriesia cycadicola on Cycas sp. leaves, Pseudocercospora pseudomyrticola on Myrtus communis leaves, Ramularia pistaciae on Pistacia lentiscus leaves, Neognomoniopsis quercina (incl. Neognomoniopsis gen. nov.) on Quercus ilex leaves. Japan, Diaporthe fructicola on Passiflora edulis × P. edulis f. flavicarpa fruit, Entoloma nipponicum on leaf litter in a mixed Cryptomeria japonica and Acer spp. forest. Macedonia, Astraeus macedonicus on soil. Malaysia, Fusicladium eucalyptigenum on Eucalyptus sp. twigs, Neoacrodontiella eucalypti (incl. Neoacrodontiella gen. nov.) on Eucalyptus urophylla leaves. Mozambique, Meliola gorongosensis on dead Philenoptera violacea leaflets. Nepal, Coniochaeta dendrobiicola from Dendriobium lognicornu roots. New Zealand, Neodevriesia sexualis and Thozetella neonivea on Archontophoenix cunninghamiana leaves. Norway, Calophoma sandfjordenica from a piece of board on a rocky shoreline, Clavaria parvispora on soil, Didymella finnmarkica from a piece of Pinus sylvestris driftwood. Poland, Sugiyamaella trypani from soil. Portugal, Colletotrichum feijoicola from Acca sellowiana. Russia, Crepidotus tobolensis on Populus tremula debris, Entoloma ekaterinae, Entoloma erhardii and Suillus gastroflavus on soil, Nakazawaea ambrosiae from the galleries of Ips typographus under the bark of Picea abies. Slovenia, Pluteus ludwigii on twigs of broadleaved trees. South Africa, Anungitiomyces stellenboschiensis (incl. Anungitiomyces gen. nov.) and Niesslia stellenboschiana on Eucalyptus sp. leaves, Beltraniella pseudoportoricensis on Podocarpus falcatus leaf litter, Corynespora encephalarti on Encephalartos sp. leaves, Cytospora pavettae on Pavetta revoluta leaves, Helminthosporium erythrinicola on Erythrina humeana leaves, Helminthosporium syzygii on a Syzygium sp. barkcanker, Libertasomyces aloeticus on Aloe sp. leaves, Penicillium lunae from Musa sp. fruit, Phyllosticta lauridiae on Lauridia tetragona leaves, Pseudotruncatella bolusanthi (incl. Pseudotruncatellaceae fam. nov.) and Dactylella bolusanthi on Bolusanthus speciosus leaves. Spain, Apenidiella foetida on submerged plant debris, Inocybe grammatoides on Quercus ilex subsp. ilex forest humus, Ossicaulis salomii on soil, Phialemonium guarroi from soil. Thailand, Pantospora chromolaenae on Chromolaena odorata leaves. Ukraine, Cadophora helianthi from Helianthus annuus stems. USA, Boletus pseudopinophilus on soil under slash pine, Botryotrichum foricae, Penicillium americanum and Penicillium minnesotense from air. Vietnam, Lycoperdon vietnamense on soil. Morphological and culture characteristics are supported by DNA barcodes.

Trabajo desarrollado bajo la financiación del proyecto “Soil Hydrology research platform underpinning innovation to manage water scarcity in European and Chinese cropping Systems” (773903), coordinado por José Alfonso Gómez Calero, investigador del Instituto de Agricultura Sostenible (IAS)., Among the agricultural practices promoted by the Common Agricultural Policy to increase soil functions, the use of cover crops is a recommended tool to improve the sustainability of Mediterranean woody crops such as olive orchards. However, there is a broad range of cover crop typologies in relation to its implementation, control and species composition. In that sense, the influence of different plant species on soil quality indicators in olive orchards remains unknown yet. This study describes the effects of four treatments based on the implementation of different ground covers (CC-GRA: sown cover crop with gramineous, CC-MIX: sown cover crop with a mixture of species and CC-NAT: cover crop with spontaneous vegetation) and conventional tillage (TILL) on soil erosion, soil physicochemical and biological properties after 8 years of cover crop establishment. Our results demonstrated that the presence of a temporary cover crop (CC), compared to a soil under tillage (TILL), can reduce soil losses and maintain good soil physicochemical properties and modify greatly the structure and diversity of soil bacterial communities and its functioning. The presence of a homogeneous CC of gramineous (Lolium rigidum or Lolilum multiflorum) (CC-GR) for 8 years increased the functional properties of the soil as compared to TILL; although the most relevant change was a modification on the bacterial community composition that was clearly different from the rest of treatments. On the other hand, the use of a mixture of plant species (CC-MIX) as a CC for only two years although did not modify greatly the structure and diversity of soil bacterial communities compared to the TILL soil, induced significant changes on the functional properties of the soil and reverted those properties to a level similar to that of an undisturbed soil that had maintained a natural cover of spontaneous vegetation for decades (CC-NAT)., This work was supported by the EU SoilMan project (grant number 01LC1620) funded through the 2015–2016 BiodivERsA COFUND call for research proposals, with national funds through PCIN-2016-048 project by the Spanish Ministry of Economy and Competitiveness (MINECO), SHui project (GA 773903), and by projects PID2019-105793RB-I00, AGL2008-00344 from ‘Ministerio de Ciencia e Innovación’, AGL-2012–37521 from ‘Ministerio de Economia y Competitividad’ of Spain, Project P10-AGR-5908 from ‘Consejería de Economía, Innovación y Ciencia’ Junta de Andalucía, and FEDER financial support from the European Union.

18 Pags.- 2 Tabls.- 1 Fig. © 2020 The Authors. Australian Journal of Grape and Wine Research published by John Wiley & Sons Australia, Ltd on behalf of Australian Society of Viticulture and Oenology Inc. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made., Viticulture is facing emerging challenges not only because of the effect of climate change on yield and composition of grapes, but also of a social demand for environmental‐friendly agricultural management. Adaptation to these challenges is essential to guarantee the sustainability of viticulture. The aim of this review is to present adaptation possibilities from the soil‐hidden, and often disregarded, part of the grapevine, the roots. The complexity of soil–root interactions makes necessary a comprehensive approach taking into account physiology, pathology and genetics, in order to outline strategies to improve viticulture adaptation to current and future threats. Rootstocks are the link between soil and scion in grafted crops, and they have played an essential role in viticulture since the introduction of phylloxera into Europe at the end of the 19th century. This review outlines current and future challenges that are threatening the sustainability of the wine sector and the relevant role that rootstocks can play to face these threats. We describe how rootstocks along with soil management can be exploited as an essential tool to deal with the effects of climate change and of emerging soil‐borne pests and pathogens. Moreover, we discuss the possibilities and limitations of diverse genetic strategies for rootstock breeding., This work is framed in the networking activities of RedVitis (AGL2015‐70931‐REDT) and RedVitis 2.0 (AGL2017‐90759‐REDT), funded by the State Research Agency (AEI) of the Spanish Ministry of Science and Innovation. Ms Diana Marín is beneficiary of postgraduate scholarship funded by Universidad Pública de Navarra (FPI‐UPNA‐2016). Dr Juan Emilio Palomares‐Rius acknowledges the State Research Agency (AEI) of the Spanish Ministry of Science and Innovation for the ‘Ramon y Cajal’ Fellowship RYC‐2017‐22228 and Dr David Gramaje acknowledges Spanish Ministry of Economy and Competitiveness for the ‘Ramon y Cajal’ Fellowship RYC‐2017‐23098.

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 below-ground 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. SO 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., This work was partially supported by project No. TP01010018 and by the infrastructure obtained from project CZ.02.1.01/0.0/0.0/16_017/0002334.

Novel species of fungi described in this study include those from various countries as follows: Algeria, Phaeoacremonium adelophialidum from Vitis vinifera. Antarctica, Comoclathris antarctica from soil. Australia, Coniochaeta salicifolia as endophyte from healthy leaves of Geijera salicifolia, Eremothecium peggii in fruit of Citrus australis, Microdochium ratticaudae from stem of Sporobolus natalensis, Neocelosporium corymbiae on stems of Corymbia variegata, Phytophthora kelmanii from rhizosphere soil of Ptilotus pyramidatus, Pseudosydowia backhousiae on living leaves of Backhousia citriodora, Pseudosydowia indoor oopillyensis, Pseudosydowia louisecottisiae and Pseudosydowia queenslandica on living leaves of Eucalyptus sp. Brazil, Absidia montepascoalis from soil. Chile, Ilyonectria zarorii from soil under Maytenus boaria. Costa Rica, Colletotrichum filicis from an unidentified fern. Croatia, Mollisia endogranulata on deteriorated hardwood. Czech Republic, Arcopilus navicularis from tea bag with fruit tea, Neosetophoma buxi as endophyte from Buxus sempervirens, Xerochrysium bohemicum on surface of biscuits with chocolate glaze and filled with jam. France, Entoloma cyaneobasale on basic to calcareous soil, Fusarium aconidiale from Triticum aestivum, Fusarium juglandicola from buds of Juglans regia. Germany, Tetraploa endophytica as endophyte from Microthlaspi perfoliatum roots. India, Castanediella ambae on leaves of Mangifera indica, Lactifluus kanadii on soil under Castanopsis sp., Penicillium uttarakhandense from soil. Italy, Penicillium ferraniaense from compost. Namibia, Bezerromyces gobabebensis on leaves of unidentified succulent, Cladosporium stipagrostidicola on leaves of Stipagrostis sp., Cymostachys euphorbiae on leaves of Euphorbia sp., Deniquelata hypolithi from hypolith under a rock, Hysterobrevium walvisbayicola on leaves of unidentified tree, Knufia hypolithi and Knufia walvisbayicola from hypolith under a rock, Lapidomyces stipagrostidicola on leaves of Stipagrostis sp., Nothophaeotheca mirabibensis (incl. Nothophaeotheca gen. nov.) on persistent inflorescence remains of Blepharis obmitrata, Paramyrothecium salvadorae on twigs of Salvadora persica, Preussia procaviicola on dung of Procavia sp., Sordaria equicola on zebra dung, Volutella salvadorae on stems of Salvadora persica. Netherlands, Entoloma ammophilum on sandy soil, Entoloma pseudocruentatum on nutrient poor(acid)soil, Entoloma pudens on plant debris, amongst grasses. [...], Leslie W.S. de Freitas and colleagues express their gratitude to Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for scholarships provided to Leslie Freitas and for the research grant provided to André Luiz Santiago; their contribution was financed by the projects ‘Diversity of Mucoromycotina in the different ecosystems of the Atlantic Rainforest of Pernambuco’ (FACEPE–First Projects Program PPP/ FACEPE/CNPq–APQ–0842-2.12/14) and ‘Biology of conservation of fungi s.l. in areas of Atlantic Forest of Northeast Brazil’ (CNPq/ICMBio 421241/ 2017-9) H.B. Lee was supported by the Graduate Program for the Undiscovered Taxa of Korea (NIBR202130202). The study of O.V. Morozova, E.F. Malysheva, V.F. Malysheva, I.V. Zmitrovich, and L.B. Kalinina was carried out within the framework of a research project of the Komarov Botanical Institute RAS (АААА-А19-119020890079-6) using equipment of its Core Facility Centre ‘Cell and Molecular Technologies in Plant Science’. The work of O. V. Morozova, L.B. Kalinina, T. Yu. Svetasheva, and E.A. Zvyagina was financially supported by Russian Foundation for Basic Research project no. 20-04-00349. E.A. Zvyagina and T.Yu. Svetasheva are grateful to A.V. Alexandrova, A.E. Kovalenko, A.S. Baykalova for the loan of specimens, T.Y. James, E.F. Malysheva and V.F. Malysheva for sequencing. J.D. Reyes acknowledges B. Dima for comparing the holotype sequence of Cortinarius bonachei with the sequences in his database. A. Mateos and J.D. Reyes acknowledge L. Quijada for reviewing the phylogeny and S. de la Peña- Lastra and P. Alvarado for their support and help. Vladimir I. Kapitonov and colleagues are grateful to Brigitta Kiss for help with their molecular studies. This study was conducted under research projects of the Tobolsk Complex Scientific Station of the Ural Branch of the Russian Academy of Sciences (N АААА-А19-119011190112-5). E. Larsson acknowledges the Swedish Taxonomy Initiative, SLU Artdatabanken, Uppsala (dha.2019.4.3-13). The study of D.B. Raudabaugh and colleagues was supported by the Schmidt Science Fellows, in partnership with the Rhodes Trust. Gregorio Delgado is grateful to Michael Manning and Kamash Pillai (Eurofins EMLab P&K) for provision of laboratory facilities. Jose G. Maciá-Vicente acknowledges support from the German Research Foundation under grant MA7171/1-1, and from the Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) of the state of Hesse within the framework of the Cluster for Integrative Fungal Research (IPF). Thanks are also due to the authorities of the Cabañeros National Park and Los Alcornocales Natural Park for granting the collection permit and for support during field work. The study of Alina V. Alexandrova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121032300081-7. Michał Gorczak was financially supported by the Ministry of Science and Higher Education through the Faculty of Biology, University of Warsaw intramural grant DSM 0117600- 13. M. Gorczak acknowledges M. Klemens for sharing a photo of the Białowieża Forest logging site and M. Senderowicz for help with preparing the illustration. Ivona Kautmanová and D. Szabóová were funded by the Operational Program of Research and Development and co-financed with the European Fund for Regional Development (EFRD). ITMS 26230120004: ‘Building of research and development infrastructure for investigation of genetic biodiversity of organisms and joining IBOL initiative’. Ishika Bera, Aniket Ghosh, Jorinde Nuytinck and Annemieke Verbeken are grateful to the Director, Botanical Survey of India (Kolkata), Head of the Department of Botany & Microbiology & USIC Dept. HNB Garhwal University, Srinagar, Garhwal for providing research facilities. Ishika Bera and Aniket Ghosh acknowledge the staff of the forest department of Arunachal Pradesh for facilitating the macrofungal surveys to the restricted areas. Sergey Volobuev was supported by the Russian Science Foundation (RSF project N 19-77- 00085). Aleksey V. Kachalkin and colleagues were supported by the Russian Science Foundation (grant No. 19-74-10002). The study of Anna M. Glushakova was carried out as part of the Scientific Project of the State Order of the Government of Russian Federation to Lomonosov Moscow State University No. 121040800174-6. Tracey V. Steinrucken and colleagues were supported by AgriFutures Australia (Rural Industries Research and Development Corporation), through funding from the Australian Government Department of Agriculture, Water and the Environment, as part of its Rural Research and Development for Profit program (PRJ-010527). Neven Matočec and colleagues thank the Croatian Science Foundation for their financial support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). Ana Pošta thanks the Croatian Science Foundation for their support under the grant HRZZ-2018-09-7081. The research of Milan Spetik and co-authors was supported by Internal Grant of Mendel University in Brno No. IGAZF/ 2021-SI1003. K.C. Rajeshkumar thanks SERB, the Department of Science and Technology, Government of India for providing financial support under the project CRG/2020/000668 and the Director, Agharkar Research Institute for providing research facilities. Nikhil Ashtekar thanks CSIR-HRDG, INDIA, for financial support under the SRF fellowship (09/670(0090)/2020-EMRI), and acknowledges the support of the DIC Microscopy Facility, established by Dr Karthick Balasubramanian, B&P (Plants) Group, ARI, Pune. The research of Alla Eddine Mahamedi and co-authors was supported by project No. CZ.02.1.01/0.0/0.0/16_017/0002334, Czech Republic. Tereza Tejklová is thanked for providing useful literature. A. Polhorský and colleagues were supported by the Operational Program of Research and Development and co-financed with the European fund for Regional Development (EFRD), ITMS 26230120004: Building of research and development infrastructure for investigation of genetic biodiversity of organisms and joining IBOL initiative. Yu Pei Tan and colleagues thank R. Chen for her technical support. Ernest Lacey thanks the Cooperative Research Centres Projects scheme (CRCPFIVE000119) for its support. Suchada Mongkolsamrit and colleagues were financially supported by the Platform Technology Management Section, National Center for Genetic Engineering and Biotechnology (BIOTEC), Project Grant No. P19-50231. Dilnora Gouliamova and colleagues were supported by a grant from the Bulgarian Science Fund (KP-06-H31/19). The research of Timofey A. Pankratov was supported by the Russian Foundation for Basic Research (grant No. 19-04-00297a). Gabriel Moreno and colleagues wish to express their gratitude to L. Monje and A. Pueblas of the Department of Drawing and Scientific Photography at the University of Alcalá for their help in the digital preparation of the photographs, and to J. Rejos, curator of the AH herbarium, for his assistance with the specimens examined in the present study. Vit Hubka was supported by the Charles University Research Centre program No. 204069. Alena Kubátová was supported by The National Programme on Conservation and Utilization of Microbial Genetic Resources Important for Agriculture (Ministry of Agriculture of the Czech Republic). The Kits van Waveren Foundation (Rijksherbariumfonds Dr E. Kits van Waveren, Leiden, Netherlands) contributed substantially to the costs of sequencing and travelling expenses for M. Noordeloos. The work of B. Dima was supported by the ÚNKP-20-4 New National Excellence Program of the Ministry for Innovation and Technology from the source of the National Research, Development and Innovation Fund, and by the ELTE Thematic Excellence Programme 2020 supported by the National Research, Development and Innovation Office of Hungary (TKP2020-IKA-05). The Norwegian Entoloma studies received funding from the Norwegian Biodiversity Information Centre (NBIC), and the material was partly sequenced through NorBOL. Gunnhild Marthinsen and Katriina Bendiksen (Natural History Museum, University of Oslo, Norway) are acknowledged for performing the main parts of the Entoloma barcoding work. Asunción Morte is grateful to AEI/FEDER, UE (CGL2016-78946-R) and Fundación Séneca - Agencia de Ciencia y Tecnología de la Región de Murcia (20866/PI/18) for financial support. Vladimír Ostrý was supported by the Ministry of Health, Czech Republic - conceptual development of research organization (National Institute of Public Health – NIPH, IN 75010330). Konstanze Bensch (Westerdijk Fungal Biodiversity Institute, Utrecht) is thanked for correcting the spelling of various Latin epithets.

Cadophora luteo-olivacea is the most prevalent Cadophora species associated with Petri disease and esca of grapevine. Accurate, early, and specific detection and quantification of C. luteo-olivacea are essential to alert growers and nurseries to the presence of the pathogens in soil and to prevent the spread of this pathogen through grapevine planting material. The aim of this study was to develop molecular tools to detect and quantify C. luteo-olivacea inoculum from environmental samples. Species specific primers based on the β-tubulin gene and a TaqMan probe for droplet digital PCR (ddPCR) and quantitative PCR (qPCR) were first developed to detect and quantify purified DNA of the target fungus. Specificity tests showed that the primers were able to amplify the C. luteo-olivacea DNA (20 isolates) while none of the 29 nontarget fungal species (58 isolates) tested were amplified. The ddPCR was shown to be more sensitive compared with qPCR in the detection and quantification of C. luteo-olivacea at very low concentrations and was further selected to accurately detect and quantify the fungus from environmental samples. Twenty-five of the 94 grafting plants (26.6%) analyzed by ddPCR tested positive to C. luteo-olivacea DNA (>3 copies/µl). C. luteo-olivacea was barely detected from vineyard soils. The procedure employed in this study revealed the presence of the pathogen in symptomless vines, which makes implementation of this technique suitable for certification schemes of C. luteo-olivacea-free grapevine planting material.

Grapevine (Vitis vinifera L.) is one of the most economically important cultivated perennial plants worldwide and is susceptible to an array of diseases caused by pathogenic fungi, bacteria, viruses, and oomycetes. In recent decades, extensive efforts have been made to reduce the use of chemical pesticides in viticulture by developing and deploying more sustainable alternative solutions. This Research Topic covers the most recent advances on both basic and applied research on grapevinemicrobe interactions. It provides an overview on (i) the different resistance loci/genes evolved in grapevine species and their application for breeding new resistant cultivars; (ii) the molecular basis of grapevine susceptibility and resistance to pathogens; (iii) the biocontrol and integrated grapevine disease management including induced plant innate immunity by beneficial microbes and natural elicitors; and (iv) the functional properties of endophytic or rhizospheric microbial communities that promote plant health.

The grapevine trunk diseases (GTDs) Botryosphaeria dieback and esca threaten the sustainability of the grapevine industry worldwide. This study aimed to evaluate and compare the efficacy of various liquid (pyraclostrobin + boscalid and thiophanate methyl) and paste (paste + tebuconazole) formulation fungicide treatments, and biological control agents (Trichoderma atroviride SC1 and T. atroviride I-1237), for their potential to prevent infection of grapevine pruning wounds by Diplodia seriata and Phaeomoniella chlamydospora in two field trials over two growing seasons. Treatments were applied to freshly pruned wounds following their label dosages recommendations. After 24 hours, wounds were artificially inoculated with 400 spores of D. seriata or 800 spores of P. chlamydospora. Isolations were made from the treated pruning wounds after 12 months to evaluate the efficacy of the treatments. Fungicide formulations were superior to Trichoderma-based treatments for the control of both pathogens during both growing seasons, with mean percent disease control of 44 to 95% for D. seriata and 46 to 67% for P. chlamydospora. Pyraclostrobin + boscalid was the most effective treatment. Trichoderma atroviride-based treatments did not reduce infection by D. seriata or P. chlamydospora compared to the untreated inoculated control in both vineyards and seasons. This study represents the first vineyard assessment of several chemical and biological treatments to protect pruning wounds against GTDs fungi in Europe and provides growers with tangible preventative control practices to minimize yield losses due to GTDs.

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

The ecology of total fungal communities in grapevine is so far largely derived from studies on culture-dependent methods or cultivation-independent rDNA approaches. Sequencing the ribosomal RNA transcripts (rRNA) would rather reveal the functionally and metabolically active important taxa of the fungal community and provide insights into its activity in the wood. The present study investigated changes in the potentially active fungal communities of internal grapevine wood after Hot-Water Treatment (HWT) in planting material from Czech Republic and Spain at two different times during the propagation process and from two plant zones. We examined fungal communities using both traditional isolation into culture and high-throughput amplicon sequencing (HTAS) of the internal transcribed spacer 2 (ITS2) region in extracted total RNA. HTAS from metatranscriptomic RNA increased the resolution of the fungal community analysis and revealed a highly diverse mycobiota of grapevine wood compared to the traditional method. Fungal diversity differed between grapevine genotypes and showed a temporal variation over the vegetative period. Grapevine planting materials exhibited high fungal diversity after HWT, which demonstrates that the HWT process does not sterilize the internal wood of grapevine. HWT reduced the infection caused by fungal trunk disease pathogens but was not completely effective in eliminating their growth. This study provides important and practically useful insights into the dynamics of active fungal communities in hot-water treated plants, and represents the first study of active fungal communities on grapevine grafted plants by comparing traditional and next-generation sequencing methods., This work was supported by Projects No. LD14051 from the Ministry of Education, Youth and Sports, Czech Republic covered by COST Action FA1303, and No. CZ.02.1.01/0.0/0.0/16_025/0007314 “Multidisciplinary research to increase application potential of nanomaterials in agricultural practice” from EFRR (Grant provider: Ministerstvo školství, mládeže a tělovýchovy České republiky (MŠMT). Access to computing and storage facilities owned by parties and projects contributing to the National Grid Infrastructure MetaCentrum provided under the programme "Projects of Large Research, Development, and Innovations Infrastructures" (CESNET LM2015042), is greatly appreciated. David Gramaje was supported by the DOC-INIA program from the National Institute for Agronomic Research (INIA), co-funded by the European Social Fund. The authors are grateful for the technical assistance of Jesús Alfonso Crespo and Aitor Gavara Vidal.

Background Control of Botrytis bunch rot (BBR) is currently based on the application of fungicides at four timings corresponding to specific growth stages of vines: end of flowering (A), pre-bunch closure (B), veraison (C) and before harvest (D). The current research provides a network meta-analysis of 116 studies conducted between 1963 and 2016 in nine countries, in which 14 strategies (based on combinations of 1, 2, 3, or 4 sprays applied in A, B, C, and/or D) were compared. Results When a one-spray strategy was applied, BBR control was more effective with sprays applied in A, C, or D than B. With a two-spray strategy, strategy AC provided similar control as strategy BC; strategy CD also provided good control. For a 3-spray strategy, the best disease control was consistently obtained with strategy ACD. Four-spray strategy ABCD provided the best control but often involved needless sprays so that the routine application of four sprays is not justified. Conclusions Spraying at timing A seems to be very important for achieving efficient and flexible disease control. Flexibility is reduced by spraying at timing B rather than A. © 2018 Society of Chemical Industry.

BACKGROUND Black-foot disease is one of the main soilborne fungal diseases affecting grapevine production worldwide. Two field experiments were established to evaluate the effect of white mustard cover crop residue amendment and chemical fumigation with propamocarb + fosetyl-Al combined with Trichoderma spp. root treatment on the viability of black-foot inoculum in soil and fungal infection in grafted plants and grapevine seedlings used as bait plants. RESULTS A total of 876 black-foot pathogen isolates were collected from grafted plants and grapevine seedlings used as bait plants in both fields. White mustard biofumigation reduced inoculum of Dactylonectria torresensis and the incidence and severity of black-foot of grapevine, but no added benefit was obtained when biofumigation was used with Trichoderma spp. root treatments. The effect of white mustard residues and chemical fumigation on populations of D. torresensis propagules in soil was inconsistent, possibly because of varying pretreatment inoculum levels. CONCLUSION Biofumigation with white mustard plants has potential for improving control of black-foot disease in grapevines. This control strategy can reduce soil inoculum levels and protect young plants from infection, providing grape growers and nursery propagators with more tools for developing integrated and sustainable control systems. © 2018 Society of Chemical Industry.

[Aims] The study aimed to assess comparatively the accuracy and efficiency of three culture media protocols for estimating black-foot disease pathogens populations in soils and to examine how shifts in the abundance and composition of black-foot pathogens correspond to changes in specific soil properties. [Methods] Firstly, culture media were compared by evaluating the mycelial growth of selected black-foot pathogens and by estimating the population of Dactylonectria torresensis from artificially infested soils. Secondly, the most efficient culture medium was selected for estimating the viable propagules of black-foot disease pathogens in eight naturally infested soils. An analysis of the soil physicochemical properties was conducted. Data were statistically analyzed in order to explore possible relationships between the studied variables. [Results] Glucose-Faba Bean Rose Bengal Agar (GFBRBA) was selected as the most efficient culture medium. All naturally infested soils tested positive for the presence of black-foot pathogens. D. torresensis was the most frequently isolated species, followed by Dactylonectria alcacerensis and Ilyonectria liriodendri. A positive relationship between calcium carbonate and the Colony-Forming Units (CFUs) level of black-foot pathogens in soil was obtained. [Conclusions] In this study, we provide an early, specific, and accurate detection of viable propagules of black-foot pathogens in soil, which is critical to understand the ecology of these fungi and to design effective management strategie, The research was funded by CAR (Government of La Rioja, Spain), under the project “Characterization, epidemiology and control of fungal trunk pathogens of grapevine in La Rioja” (project number R-03-16). We thank “Instituto Navarro de Tecnologías e Infraestructuras Agroalimentarias” (INTIA), Spain, which collected the soil samples from the field in Olite for further use in the experiment. We thank P. Yécora and M. Andrés for technical assistance. David Gramaje was supported by the DOC-INIA program from the National Institute for Agronomic Research (INIA), co-funded by the European Social Fund. Carmen Berlanas was supported by the FPI-INIA program from the INIA. Beatriz López was supported by the PhD program from the Government of La Rioja.

Juglans regia L. (English walnut) trees with cankers and dieback symptoms were observed in two regions in the Czech Republic. Isolations were made from diseased branches. In total, 138 fungal isolates representing 10 fungal species were obtained from wood samples and identified based on morphological characteristics and molecular methods: Cadophora novi-eboraci, Cadophora spadicis, Cryptovalsa ampelina, Diaporthe eres, Diplodia seriata, Dothiorella omnivora, Eutypa lata, Eutypella sp., Peroneutypa scoparia, and Phaeoacremonium sicilianum. Pathogenicity tests conducted under field conditions with all species using the mycelium-plug method indicated that Eutypa lata and Cadophora spp. were highly virulent to woody stems of walnut. This is the first study to detect and identify fungal trunk pathogens associated with diseased walnut trees in Europe., Ministerstvo Školství, Mládeže a Tělovýchovy Grant/Award Number: CZ.02.1.01/0.0/0.0/16_025/0007314 Technologická Agentura České Republiky Grant/Award Number: TJ02000096

Two hundred and twenty-five Diaporthe isolates were collected from 2005 to 2019 in almond orchards showing twig cankers and shoot blight symptoms in five different regions across Spain. Multilocus DNA sequence analysis with five loci (ITS, tub, tef-1α, cal and his), allowed the identification of four known Diaporthe species, namely: D. amygdali, D. eres, D. foeniculina and D. phaseolorum. Moreover, a novel phylogenetic species, D. mediterranea, was described. Diaporthe amygdali was the most prevalent species, due to the largest number of isolates (85.3%) obtained from all sampled regions. The second most frequent species was D. foeniculina (10.2%), followed by D. mediterranea (3.6%), D. eres and D. phaseolorum, each with only one isolate. Pathogenicity tests were performed using one-year-old almond twigs cv. Vayro and representative isolates of the different species. Except for D. foeniculina and D. phaseolorum, all Diaporthe species were able to cause lesions significantly different from those developed on the uninoculated controls. Diaporthe mediterranea caused the most severe symptoms. These results confirm D. amygdali as a key pathogen of almonds in Spain. Moreover, the new species, D. mediterranea, should also be considered as a potential important causal agent of twig cankers and shoot blight on this crop., Research funded by the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), grants RTA2017-00009-C04-01, -02, -03 and -04 and with matching funds from the European Regional Development Fund (ERDF). G. Elena and C. Agustí-Brisach were supported by the Spanish post-doctoral grants “Juan de la Cierva-Formación” and “Juan de la Cierva-Incorporación”, respectively. J. Luque and X. Miarnau were partially supported by the CERCA program, Generalitat de Catalunya. D. Gramaje was supported by the Ramón y Cajal program, Spanish Government (RYC-2017-23098).