Early Season Symptoms on Stem, Inflorescences and Flowers of Grapevine Associated with Botryosphaeriaceae Species

A comparison of microbiota isolation methods reveals habitat preferences for fermentative yeasts and plant pathogenic fungi in the grape berry

The methodologies for profiling the grape berry microbiota have exponentially evolved in the past 25 years. Recently, concerns arose regarding the homogeneity in the protocols of grape harvesting, sequencing and bioinformatic analyses, but the bias introduced by the microbiota isolation method is still unexplored. This study followed a simple approach of comparing two most used methods of microbiota collection from grape berries (washing vs crushing), hypothesizing a significant impact in the outcome of the microbiota profiles analyzed by NGS metabarcoding. Experiments conducted in fruits of three cultivars of the Douro wine region showed that only 52 % of OTUs were common to both surface and juice microbiota, suggesting specific microbial niches. Thirteen fungal genera were abundantly detected in the fruit surface, including Alternaria, Aureobasidium, Cladosporium, Didymella and Bipolaris. Fermentative yeasts including Meyerozyma and Saccharomyces cerevisiae were exclusively detected in the juice, together with several Penicillium species. Distinct habitat preferences of species within the genera Alternaria, Sporobolomyces and Rhodotorula were also revealed. The study showed that the microbiota isolation method is crucial in the detection of certain plant pathogenic/saprophytic fungi and yeasts with biotechnological and oenological interest, adding novelty to the globally accepted assumption that S. cerevisiae in musts originates primarily from the cellar.

Diplodia seriata Biocontrol Is Altered via Temperature and the Control of Bacteria

Grapevine trunk diseases (GTDs) attack the vine's wood, devastating vineyards worldwide. Chile is the world's fourth-largest wine exporter, and Cabernet Sauvignon is one of the most economically important red wine varieties. Botryosphaeria dieback is an important GTD, and Diplodia seriata is one of the main pathogenic species. Biocontrol studies of these pathogens are commonly carried out at different incubation times but at a single temperature. This study aimed to evaluate the biocontrol effect of Chilean PGPB and grapevine endophytic bacteria against D. seriata at different temperatures. We analyzed the biocontrol effect of Pseudomonas sp. GcR15a, Pseudomonas sp. AMCR2b and Rhodococcus sp. PU4, with three D. seriata isolates (PUCV 2120, PUCV 2142 and PUCV 2183) at 8, 22 and 35 °C. Two dual-culture antagonism methods (agar plug diffusion and double plate) were used to evaluate the in vitro effect, and an in vivo test was performed with Cabernet Sauvignon cuttings. In vitro, the greatest inhibitions were obtained using the agar plug diffusion method and at a temperature of 8 °C, where Rhodococcus sp. PU4 obtains a 65% control (average) and Pseudomonas sp. GcR15a a 57% average. At 22 °C, only strains of Pseudomonas sp. show control. At 35 °C, one Pseudomonas strain shows the highest control (38%), on average, similar to tebuconazole (33%), and then Rhodococcus sp. (30%). In vivo, a biocontrol effect is observed against two D. seriata isolates, while the PUCV 2142 proves to be more resistant to control. The biocontrol ability at low temperatures is promising for effective control in the field, where infections occur primarily in winter.

Exploring Factors Conditioning the Expression of Botryosphaeria Dieback in Grapevine for Integrated Management of the Disease

Species from the Botryosphaeriaceae family are the causal agents of Botryosphaeria dieback (BD), a worldwide grapevine trunk disease. Because of their lifestyle and their adaptation to a wide range of temperatures, these fungi constitute a serious threat to vineyards and viticulture, especially in the actual context of climate change. Grapevine plants from both nurseries and vineyards are very susceptible to infections by botryosphaeriaceous fungi due to several cuts and wounds made during their propagation process and their entire life cycle, respectively. When decline becomes chronic or apoplectic, it reduces the longevity of the vineyard and affects the quality of the wine, leading to huge economic losses. Given the environmental impact of fungicides, and their short period of effectiveness in protecting pruning wounds, alternative strategies are being developed to fight BD fungal pathogens and limit their propagation. Among them, biological control has been recognized as a promising and sustainable alternative. However, there is still no effective strategy for combating this complex disease, conditioned by both fungal life traits and host tolerance traits, in relationships with the whole microbiome/microbiota. To provide sound guidance for an effective and sustainable integrated management of BD, by combining the limitation of infection risk, tolerant grapevine cultivars, and biological control, this review explores some of the factors conditioning the expression of BD in grapevine. Among them, the lifestyle of BD-associated pathogens, their pathogenicity factors, the cultivar traits of tolerance or susceptibility, and the biocontrol potential of Bacillus spp. and Trichoderma spp. are discussed.

Neofusicoccum actinidiae and Neofusicoccum guttata, Two New Species Causing Kiwifruit Rot in China

Kiwi is a popular fruit consumed worldwide. A number of fungal pathogens have been reported to cause postharvest rot of kiwifruit, and Botryosphaeriaceae species are the major causal agents of the disease. In this study, 18 isolates belonging to the genus Neofusicoccum (family Botryosphaeriaceae) were isolated from 247 symptomatic kiwifruits of the cultivars Jinyan, Jintao, and Jinkui collected from orchards in Hubei and Jiangxi provinces, China. Among the isolates, three grouped with various known Neofusicoccum parvum isolates, whereas the remaining 15 formed two independent clades. On the basis of further phylogenetic analyses with concatenated sequences of ITS and three genes encoding translation elongation factor 1-alpha (TEF), β-tubulin (TUB), and DNA-dependent RNA polymerase II subunit (RPB2), as well as morphological characteristics, two new species, N. actinidiae and N. guttata, were proposed. Their pathogenicity to kiwi, apple, and citrus fruits was also confirmed.

Differential carbohydrate-active enzymes and secondary metabolite production by the grapevine trunk pathogen Neofusicoccum parvum Bt-67 grown on host and non-host biomass

Neofusicoccum parvum is one of the most aggressive Botryosphaeriaceae species associated with grapevine trunk diseases. This species may secrete enzymes capable of overcoming the plant barriers, leading to wood colonization. In addition to their roles in pathogenicity, there is an interest in taking advantage of N. parvum carbohydrate-active enzymes (CAZymes), related to plant cell wall degradation, for lignocellulose biorefining. Furthermore, N. parvum produces toxic secondary metabolites that may contribute to its virulence. In order to increase knowledge on the mechanisms underlying pathogenicity and virulence, as well as the exploration of its metabolism and CAZymes for lignocellulose biorefining, we evaluated the N. parvum strain Bt-67 capacity in producing lignocellulolytic enzymes and secondary metabolites when grown in vitro with two lignocellulosic biomasses: grapevine canes (GP) and wheat straw (WS). For this purpose, a multiphasic study combining enzymology, transcriptomic, and metabolomic analyses was performed. Enzyme assays showed higher xylanase, xylosidase, arabinofuranosidase, and glucosidase activities when the fungus was grown with WS. Fourier transform infrared (FTIR) spectroscopy confirmed the lignocellulosic biomass degradation caused by the secreted enzymes. Transcriptomics indicated that the N. parvum Bt-67 gene expression profiles in the presence of both biomasses were similar. In total, 134 genes coding CAZymes were up-regulated, where 94 of them were expressed in both biomass growth conditions. Lytic polysaccharide monooxygenases (LPMOs), glucosidases, and endoglucanases were the most represented CAZymes and correlated with the enzymatic activities obtained. The secondary metabolite production, analyzed by high-performance liquid chromatography-ultraviolet/visible spectophotometry-mass spectrometry (HPLC-UV/Vis-MS), was variable depending on the carbon source. The diversity of differentially produced metabolites was higher when N. parvum Bt-67 was grown with GP. Overall, these results provide insight into the influence of lignocellulosic biomass on virulence factor expressions. Moreover, this study opens the possibility of optimizing the enzyme production from N. parvum with potential use for lignocellulose biorefining.

Higher Virulence of Diplodia seriata Isolates on Vines of cv. Cabernet Sauvignon Associated with 10-Year-Old Wood Compared to Young Tissue

Botryosphaeria dieback (BD) occurs in young and old plants. In the field, the prevalence and severity of the disease increase proportionally with the age of vineyards. Among the pathogens that cause BD, Diplodia seriata is the most prevalent species in Chile and other countries with a Mediterranean climate. To date, no information is available on the susceptibility of adult wood to infection by this pathogen since most of the pathogenicity tests have been carried out on 1- or 2-year-old shoots or detached canes. Therefore, a pathogenicity test was carried out on plants under field conditions, with inoculations in 1-year-old shoots and 2- and 10-year-old wood in grapevine cv. Cabernet Sauvignon. A pathogenicity test was carried out with two isolates of D. seriata. The results for the plants show that D. seriata was significantly more aggressive on the 10-year-old than on the one- or two-year-old tissue, where the lesions were 4.3 and 2.3 cm on average, respectively. These results were compared with the lesions obtained from two-year-old canes after the isolates were activated in grape berries. Also, the Chilean isolates of D. seriata were compared phylogenetically with those from other countries, and no major differences were found between them. Our results are consistent with the damage observed in the field, contributing to the knowledge of the epidemiology of this disease in Mediterranean climates. In the future, the effect observed in cv. Cabernet Sauvignon with D. seriata on virulence at different tissue ages should be tested for other BD-causing agents and wine varieties.

Prevalence, Identity, Pathogenicity, and Infection Dynamics of Botryosphaeriaceae Causing Avocado Branch Canker in California

Botryosphaeria branch canker and dieback of avocado (Persea americana Mill.) has expanded in avocado-growing areas in recent years. Twenty-one avocado groves in the major producing regions of California were surveyed in 2018 and 2019. Monthly inoculations of wounded, green, and lignified branches of 'Hass' and 'Lamb Hass' were conducted. Botryosphaeriaceae were the predominant fungi recovered from cankered tissues collected across the surveyed traditional and high-density orchards and caused symptoms on all six sampled cultivars. These fungi were also recovered in asymptomatic twigs and other organs and thus exist as a potential reservoir for future infections. Molecular analyses of 173 isolates showed that Neofusicoccum luteum had the greatest incidences across sites and cultivars, with 83 and 29% recovered from Hass and Lamb Hass, respectively. Pathogenicity tests on excised (Hass, GEM, and Hass mutants) and attached shoots from potted (Hass) and mature avocado trees (Hass and Lamb Hass) showed that all species were pathogenic on wounded, green, and mature branches of the specified cultivars. Monthly inoculations of wounded, green, and lignified branches of Hass and Lamb Hass showed that both stem types were susceptible throughout the inoculation periods, regardless of the avocado phenological stage. In temperature-dependent growth and infection studies, growth of three points could vary during the growing season. Botryosphaeriaceae grown was higher between 20 and 30°C, but only Lasiodiplodia theobromae significantly grew and caused external lesions at 35°C. Lasiodiplodia theobromae also grew more on perseitol-amended media, all indicating its adaptation to warmer temperatures and capacity in metabolizing the avocado-produced sugar. Overall, this study extended our knowledge of the prevalence, identity, and pathogenicity of Botryosphaeriaceae on avocado cultivars, which will be useful to tailor management strategies.

Botryosphaeriaceae gene machinery: Correlation between diversity and virulence

The Botryosphaeriaceae family comprises numerous fungal pathogens capable of causing economically meaningful diseases in a wide range of crops. Many of its members can live as endophytes and turn into aggressive pathogens following the onset of environmental stress events. Their ability to cause disease may rely on the production of a broad set of effectors, such as cell wall-degrading enzymes, secondary metabolites, and peptidases. Here, we conducted comparative analyses of 41 genomes representing six Botryosphaeriaceae genera to provide insights into the genetic features linked to pathogenicity and virulence. We show that these Botryosphaeriaceae genomes possess a large diversity of carbohydrate-active enzymes (CAZymes; 128 families) and peptidases (45 families). Botryosphaeria, Neofusicoccum, and Lasiodiplodia presented the highest number of genes encoding CAZymes involved in the degradation of the plant cell wall components. The genus Botryosphaeria also exhibited the highest abundance of secreted CAZymes and peptidases. Generally, the secondary metabolites gene cluster profile was consistent in the Botryosphaeriaceae family, except for Diplodia and Neoscytalidium. At the strain level, Neofusicoccum parvum NpBt67 stood out among all the Botryosphaeriaceae genomes, presenting a higher number of secretome constituents. In contrast, the Diplodia strains showed the lowest richness of the pathogenicity- and virulence-related genes, which may correlate with their low virulence reported in previous studies. Overall, these results contribute to a better understanding of the mechanisms underlying pathogenicity and virulence in remarkable Botryosphaeriaceae species. Our results also support that Botryosphaeriaceae species could be used as an interesting biotechnological tool for lignocellulose fractionation and bioeconomy.

Response of Different Grapevine Cultivars to Infection by Lasiodiplodia theobromae and Lasiodiplodia mediterranea

Botryosphaeria dieback is a grapevine trunk disease that affects all viticulture regions of the world. Species of the genus Lasiodiplodia have been reported as pathogenic toward grapevine in several growing regions and have also been previously reported from Portuguese vineyards. Species in this genus, particularly Lasiodiplodia theobromae, have been reported in previous studies to be more aggressive than other Botryosphaeriaceae species most commonly associated with Botryosphaeria dieback. The aim of this study was to assess the response of some of the more representative cultivars planted throughout Portuguese vineyards, 'Touriga Nacional,' 'Touriga Franca,' 'Alvarinho,' 'Aragonez' (= 'Tempranillo'), and 'Cabernet Sauvignon,' by performing artificial inoculations with Lasiodiplodia spp. collected in different geographic locations worldwide. Two experiments, one that involved inoculating 2-year-old grapevines kept in greenhouse-controlled conditions with six isolates of L. theobromae and one isolate of L. mediterranea and one that involved inoculating 7-year-old field-grown grapevines with two isolates of L. theobromae, were conducted twice. We assessed the response of the cultivars by evaluating the length of lesions caused by the isolates 5 months after inoculation. The results showed that all isolates studied were able to infect the annual shoots because they were always reisolated and produced internal wood discoloration. Significant differences were found for all isolate-cultivar combinations. In both experiments, Touriga Nacional showed the largest lesions and while Aragonez recorded the smallest lesions of the cultivars inoculated with Lasiodiplodia spp. In general, Portuguese isolates were more aggressive than those from Peru, which were mildly aggressive. These results are a first insight into the response of selected Portuguese cultivars to Lasiodiplodia species, which are present in Portugal but not commonly associated with Botryosphaeria dieback. This research contributes to our knowledge of the impact that Botryosphaeria dieback causal agents have on crucial national cultivars, which may help winegrowers not only manage current cultural practices but also optimize decision making when planning new vineyards.

Combining an HA + Cu (II) Site-Targeted Copper-Based Product with a Pruning Wound Protection Program to Prevent Infection with Lasiodiplodia spp. in Grapevine

The genus Lasiodiplodia has been reported from several grape growing regions and is considered as one of the fastest wood colonizers, causing Botryosphaeria dieback. The aim of this study was to (i) evaluate the efficacy of Esquive®, a biocontrol agent, on vineyard pruning wound protection, applied single or, in a combined protection strategy with a new site-targeted copper-based treatment (LC2017), and (ii) compare their efficacy with chemical protection provided by the commercially available product, Tessior®. For two seasons, protectants were applied onto pruning wounds, while LC2017 was applied throughout the season according to the manufacturer's instructions. Pruning wounds of two different cultivars were inoculated with three isolates of Lasiodiplodia spp. Efficacy of the wound protectants, varied between both years of the assay and according to the cultivar studied but were able to control the pathogen to some extent. The application of LC2017 did not show clear evidence of improving the control obtained by the sole application of the other products tested. Nevertheless, LC2017 showed a fungistatic effect against Lasiodiplodia spp., in vitro, and has previously shown an elicitor effect against grapevine trunk diseases. Therefore, this combination of two protection strategies may constitute a promising long-term approach to mitigate the impact of Botryosphaeria dieback.