Sclerotinia sclerotiorum (Lib.) de Bary: biology and molecular traits of a cosmopolitan pathogen

Enhancement of the biocontrol mechanisms of Trichoderma longibrachiatum combined with different supplements for controlling Sclerotinia sclerotiorum in Phaseolus vulgaris

The fungus Sclerotinia sclerotiorum is a highly destructive soil-borne pathogen that causes a significant threat to common bean production regions worldwide. In this study, Trichoderma longibrachiatum was mixed separately with various supplements to promote its efficiency in controlling S. sclerotiorum in common beans. The results indicated that the filtrate of T. longibrachiatum blended with potassium tartrate was the most efficient inhibitor of the growth and sclerotia formation of the pathogen. The same mixture also caused enormous morphological deterioration to the mycelia and sclerotia as observed using scanning electron microscopy. The FTIR spectra showed remarkable changes in vibrations related to the functional groups of all treatments. SDS-PAGE fingerprints and SCoT markers were used to determine the differences between treatments. In the greenhouse experiment, the rate of surviving plants in the treatment of T. longibrachiatum combined with potassium tartrate, thiamine, niacin, and a mixture of micronutrients was much higher than in the control groups after 30 days. The treatment of T. longibrachiatum mixed with potassium tartrate resulted in the highest levels of total phenolics, polyphenoloxidase activity, and peroxidase activity in the leaves of common beans. Furthermore, the same treatment displayed a higher number of surviving common bean plants under field conditions after 30, 45, and 60 days in soil naturally infested with the pathogen while also improving plant growth parameters. This study provides valuable insights into the effective biocontrol of S. sclerotiorum using T. longibrachiatum, in combination with various supplements, and highlights the potential for successful application of this strategy in common beans.

Trans-Kingdom sRNA Silencing in Sclerotinia sclerotiorum for Crop Fungal Disease Management

Sclerotinia sclerotiorum is a globally widespread and vast destructive plant pathogenic fungus that causes significant yield losses in crops. Due to the lack of effective resistant germplasm resources, the control of diseases caused by S. sclerotiorum largely relies on chemical fungicides. However, excessive use of these chemicals not only causes environmental concerns but also leads to the increased development of resistance in S. sclerotiorum. In contrast, trans-kingdom sRNA silencing-based technologies, such as host-induced gene silencing (HIGS) and spray-induced gene silencing (SIGS), offer novel, effective, and environmentally friendly methods for the management of S. sclerotiorum infection. This review summarizes recent advances in the identification of S. sclerotiorum pathogenic genes, target gene selection, categories, and application of trans-kingdom RNA interference (RNAi) technologies targeting this pathogen. Although some challenges, including off-target effects and the efficiency of external sRNA uptake, exist, recent findings have proposed solutions for further improvement. Combined with the latest developments in CRISPR/Cas gene editing and other technologies, trans-kingdom RNAi has significant potential to become a crucial tool in the control of sclerotinia stem rot (SSR), mitigating the impact of S. sclerotiorum on crop production.

Unraveling the Antagonistic Potential of Trichoderma for Combating Sclerotinia Rot of Mustard

Identification of a sustainable alternative for the restricted range of current antifungal agents is one of decisive objective in modern agriculture. Consequently, extensive global research are been ongoing for unraveling the eco-friendly and effective bio agents that will be capable of controlling pathogens. This study explores the efficacy of Trichoderma isolates in combating Sclerotinia rot in mustard, primarily caused by Sclerotinia sclerotiorum. In this study, 12 Trichoderma isolates (designated as PBTMSR) were isolated using baiting technique from mustard rhizospheric soil as potential biocontrol agents and their cultural, morphological, molecular characteristics were studied along with in vitro and in field antagonistic potential assessment for selecting most promising isolates for the management of this disease. Cultural, biochemical characterization of all the isolates confirmed that the all the isolates belonged to Trichoderma spp. and among these, 06 isolates namely PBTMSR4, 5, 6, 8, 9 and 10 were found most promising in their antagonistic potential against the test pathogen under in vitro conditions and were selected and evaluated under both artificial and natural epiphytotic field conditions for the management of Sclerotinia stem rot of mustard. Among Trichoderma isolate PBTMSR4 showed maximum reduction in Sclerotinia rot incidence (70.0% and 50.73%) with followed by PBTMSR8 (60.0% & 42.15%) under artificial and natural field conditions, respectively. The highest yield was with PBTMSR4 (23.70 q/ha) followed by PBTMSR8 (23.11 q/ha) as compared to check (21.48 q/ha) under natural field conditions. These two Trichoderma isolates namely, PBTMSR4 (OR351298) and PBTMSR8 (OR355825) were identified as Trichoderma afroharzianum and Trichoderma lixii respectively. The findings have practical implications for agriculture, suggesting a sustainable biocontrol strategy that can enhance crop resilience and can also contribute to integrated pest management practices.

A Hypovirulence-Associated Partitivirus and Re-Examination of Horizontal Gene Transfer Between Partitiviruses and Cellular Organisms

Previous research has unearthed the integration of the coat protein (CP) gene from alphapartitivirus into plant genomes. Nevertheless, the prevalence of this horizontal gene transfer (HGT) between partitiviruses and cellular organisms remains an enigma. In our investigation, we discovered a novel partitivirus, designated Sclerotinia sclerotiorum alphapartitivirus 1 (SsAPV1), from a hypovirulent strain of Sclerotinia sclerotiorum. Intriguingly, we traced homologs of the SsAPV1 CP to plant genomes, including Helianthus annuus. To delve deeper, we employed the CP and RNA-dependent RNA polymerase (RdRP) sequences of partitiviruses as "bait" to search the NCBI database for similar sequences. Our search unveiled a widespread occurrence of HGT between viruses from all five genera within the family Partitiviridae and other cellular organisms. Notably, numerous CP-like and RdRP-like genes were identified in the genomes of plants, protozoa, animals, fungi, and even, for the first time, in an archaeon. The majority of CP and RdRP genes were integrated into plant and insect genomes, respectively. Furthermore, we detected DNA fragments originating from the SsAPV1 RNA genome in some subcultures of virus-infected strains. It suggested that SsAPV1 RdRP may possesses reverse transcriptase activity, facilitating the integration of viral genes into cellular organism genomes, and this function requires further confirmation. Our study not only offers a hypovirulence-associated partitivirus with implications for fungal disease control but also sheds light on the extensive integration events between partitiviruses and cellular organisms and enhances our comprehension of the origins, evolution, and ecology of partitiviruses, as well as the genome evolution of cellular organisms.

In vitro biocontrol potential of plant extract-based formulation against infection structures of Phytophthora infestans along with lower non-target effects

Late blight, caused by Phytophthora infestans, is among the most destructive diseases affecting tomatoes and potatoes. The use of synthetic fungicides is becoming increasingly restricted due to the banning of several active ingredients for environmental and health reasons. Moreover, the rise of fungicide-resistant strains is compromising their effectiveness. Solutions for sustainable crop protection are thus urgently needed. Biocontrol products based on plant extracts appear to be a promising solution. This study aimed to evaluate in vitro inhibitory potential of a plant extract-based biocontrol product on the different stages of P. infestans lifecycle, including mycelial development and, formation and germination of infection structures (sporangia and zoospores). Non-target effects were also assessed using four fungi, three of which were isolated from the phyllosphere, and two ubiquitous bacteria. For this purpose, the formulated product (FV) and the plant extract at different concentrations (PE and CPE) were tested through bioassays. The results show that the mycelial growth of Phytophthora infestans was completely inhibited by the FV and less affected by the CPE. Infection structures were more sensitive to PE than mycelia, although FV was consistently the most effective inhibitor. Interestingly, at non-inhibitory doses, zoospore germination exhibited disturbances, such as an increase in abnormal germination phenotypes. Overall, PE showed significant inhibitory potential against the oomycete. FV exhibited a strong impact on mycelium, sporangia, and zoospores at very low concentrations (0.01-0.05%), suggesting an optimized inhibitory effect of PE. Non-target effects of FV on fungal and bacterial growth were observed only at concentrations substantially higher than those required to inhibit P. infestans in vitro. This study highlights the strong efficacy of the plant extract-based biocontrol product against the target oomycete, with minimal impact on non-target microorganisms. These findings support its potential as a promising anti-Phytophthora agent within integrated late blight management strategies.

Ornithine enhances common bean growth and defense against white mold disease via interfering with SsOAH and diminishing the biosynthesis of oxalic acid in Sclerotinia sclerotiorum

The necrotrophic fungal phytopathogen, Sclerotinia sclerotiorum (Lib.) de Bary, employs a multilayered strategy to infect a wide range of host plants. The current study proposed the diamine L-ornithine, a non-proteinogenic amino acid that promotes the synthesis of other essential amino acids, as an alternative management strategy to boost the molecular, physiological, and biochemical responses of common bean (Phaseolus vulgaris L.) against white mold disease caused by S. sclerotiorum. In vitro experiments showed that L-ornithine significantly inhibited the mycelial growth of S. sclerotiorum in a dose-dependent manner. Moreover, it markedly diminished the white mold severity under greenhouse conditions. Moreover, L-ornithine stimulated the growth of treated plants suggesting that the tested concentration of L-ornithine has no phytotoxicity on treated plants. Additionally, L-ornithine enhanced the non-enzymatic antioxidants (total soluble phenolics and flavonoids), the enzymatic antioxidants (CAT, POX, and PPO), and upregulated the gene expression of three antioxidant-associated genes (PvCAT1, PvSOD, and PvGR). Moreover, in silico analysis showed that the genome of S. sclerotiorum possesses a putative oxaloacetate acetylhydrolase (SsOAH) protein that is highly similar in its functional analysis, conserved domains, and topology with OAH from Aspergillus fijiensis (AfOAH) and Penicillium lagena (PlOAH). Interestingly, the addition of L-ornithine to the potato dextrose broth (PDB) medium significantly down-regulated the gene expression of SsOAH in the mycelium of S. sclerotiorum. Likewise, exogenous application of L-ornithine significantly down-regulated the gene expression of SsOAH in the fungal mycelia collected from treated plants. Finally, L-ornithine application significantly diminished the secretion of oxalic acid in the PDB medium as well as infected leaves. Collectively, L-ornithine plays a pivotal role in maintaining the redox status, in addition to boosting the defense responses of infected plants. The current study provides insights that may lead to innovative eco-friendly approaches for controlling white mold disease and mitigating its impact on common bean cultivation particularly, and other crops in general.

Effects of High Tunnel Soil Solarization on Sclerotinia sclerotiorum in the Temperate Climate of Central Kentucky

Diseases caused by Sclerotinia spp. can affect a wide range of plants, including vegetables, with yield losses ranging from 10 to 50%. Sclerotinia diseases can be especially problematic in high tunnels in which high-value vegetable crops are planted in early spring to extend the growing season, achieve earlier harvest, and bring higher profits. Fungicide applications and crop rotations are limited because of product application restrictions and constraints on time, crop resistance, and profitability. Soil solarization is a cultural management method that uses transparent polyethylene to raise soil temperatures via solar irradiation to kill pathogens, pests, and weeds. A 2-year study was conducted in a Kentucky high tunnel to determine the maximum temperature potential of solarization at various soil depths at different durations during different seasons and to identify temperatures at which S. sclerotiorum sclerotia lose viability. The experiment included solarization treatments of 2, 4, and 6 weeks and a nonsolarized control implemented in spring, summer, and fall. Sclerotia and temperature data loggers were buried at 5.1-, 10.2-, and 15.2-cm soil depths. The number of hours at which soil temperatures reached ≥40°C was greatest in summer in both years, followed by fall, and then spring. The highest average daily maximum soil temperature reached was 48.9°C, which occurred during the summer 6-week solarization in Year 1. The viability of buried sclerotia was overall lower in solarized treatments compared with nonsolarized treatments in both years. In general, the 2-week solarization treatment had a significantly higher percentage of sclerotial germination than the 4-week and 6-week treatments, which were not significantly different from one another. The viability of sclerotia was progressively higher with burial depth. In both years, sclerotial germination was significantly lower in summer compared with spring and fall.

Exploring the interaction between endornavirus and Sclerotinia sclerotiorum: mechanisms of phytopathogenic fungal virulence and antivirus

Hypovirulence-associated mycoviruses have the potential as biocontrol agents for plant fungal disease management, and exploration of the interactions between these mycoviruses and phytopathogenic fungi can provide opportunities to elucidate the underlying mechanisms of hypovirulence and antiviruses. We previously found that Sclerotinia sclerotiorum endornavirus 3 (SsEV3), belonging to the genus Betaendornavirus within the family Endornaviridae, confers hypovirulence on the phytopathogenic fungus Sclerotinia sclerotiorum, but the underlying mechanisms remains unclear. In this study, we found that the SsEV3-infected strain produced fewer sclerotia, failed to form infection cushions on plant hosts, exhibited increased cell vacuolation, and was more sensitive to abiotic stresses. SsEV3 infection evoked transcriptional rewiring in S. sclerotiorum, affecting genes related to virulence factors for pathogenicity and RNAi pathway for antiviruses. An unknown biological function of gene Sssnf1 was downregulated following SsEV3 infection. Deletion of Sssnf1 impaired infection cushion formation and decreased virulence of S. sclerotiorum. Five key RNAi-related genes were significantly upregulated, and deletion of Ssdcl2 contributed to SsEV3 accumulation. Additionally, we identified a hypothetical protein encoded by Sshp1 that directly interacts with the RNA-dependent RNA polymerase (RdRp) domain encoded by SsEV3. Although the deletion mutants of Sshp1 exhibited normal colony morphology, they showed higher SsEV3 accumulation and reduced resistance to reactive oxygen species, indicating that this gene, similar to RNAi-related genes, plays an antiviral role in response to SsEV3 infection and may represent a new antivirus factor. Therefore, examination of the interaction between endornavirus and S. sclerotiorum provides new insights into the mechanisms of antivirus and virulence in phytopathogenic fungi.IMPORTANCEHypovirulence-associated mycoviruses have emerged as promising biocontrol agents, and studying their interactions with phytopathogenic fungi helps uncover mechanisms of fungal pathogenesis and antiviral defense. This study provides critical insights into the interaction between Sclerotinia sclerotiorum and its hypovirulence-associated endornavirus, SsEV3, elucidating the molecular mechanisms underlying mycovirus-induced changes in fungal virulence and antivirus defense. SsEV3 infection not only impairs fungal virulence traits, including infection cushion formation and sclerotial production but also triggers host antiviral responses involving typical RNA interference pathways. New virulence factors, such as Sssnf1, and antiviral factors, such as Sshp1, were identified based on the established interaction system between S. sclerotiorum and endornavirus. These findings deepen our understanding of fungus-mycovirus interactions, highlighting the role of SsEV3 in reducing the virulence of S. sclerotiorum, and facilitating the development of mycovirus-based biological control strategies.

RNA interference-mediated targeting of monooxygenase SsMNO1 for controlling Sclerotinia stem rot caused by Sclerotinia sclerotiorum

BACKGROUND

Sclerotinia sclerotiorum is a devastating fungal pathogen that poses a threat to a variety of economically important crops. Owing to the lack of highly resistant cultivars and the prolonged survival of sclerotia, effective control of Sclerotinia diseases remains challenging. RNA interference (RNAi) agents targeting essential active transcripts of genes associated with the development and virulence of pathogens are a valuable and promising disease control method.

RESULTS

Our finding suggested that a flavin adenine dinucleotide (FAD)-dependent monooxygenase gene SsMNO1 plays pivotal roles in the hyphal growth, sclerotial development, and virulence of S. sclerotiorum, rendering it a potential target for RNAi-mediated management of S. sclerotiorum. The external application of double-stranded RNA (dsRNA) targeting SsMNO1 inhibited sclerotial development in artificial media and plant tissues. Furthermore, dsRNA significantly reduced the hyphal virulence of S. sclerotiorum in host plants by interfering with SsMNO1 expression. The inhibitory activity persisted for over 1 week on the surface of Brassica napus. Artificial small interfering RNA (siRNA) targeting SsMNO1 also exhibited inhibitory effects. Transgenic Arabidopsis thaliana plants expressing SsMNO1 hairpin RNAi constructs showed increased resistance to S. sclerotiorum infection. Notably, the total RNA extracts from SsMNO1-RNAi plants also reduced the hyphal virulence in Brassica napus.

CONCLUSIONS

Therefore, RNAi agents targeting SsMNO1 have dual effects on sclerotial development and hyphal virulence, rendering it an ideal target for controlling diseases caused by S. sclerotiorum. © 2024 Society of Chemical Industry.

SsNEP2 Plays a Role in the Interaction Between Sclerotinia sclerotiorum and Coniothyrium minitans

Sclerotinia sclerotiorum, a fungal pathogen that is spread worldwide and causes serious diseases on crops, can be parasitized specifically by the mycoparasite Coniothyrium minitans. SsNEP2, encoding a necrosis-inducing protein in S. sclerotiorum, was previously inferred to play a role in the virulence to host plants. In this study, silencing of SsNEP2 in S. sclerotiorum had no significant (p < 0.01) influence on mycelial morphology, while overexpression led to lower mycelial growth and more branches. When amended with the fermentation broth of the SsNEP2 silencing mutants, conidial germination of C. minitans was promoted, while conidial production decreased. When parasitized by C. minitans, enhanced resistance of the SsNEP2 silencing mutants and weaker resistance of the overexpressed transformants were observed compared to the wild-type S. sclerotiorum strain 1980. In addition, the expression of SsNEP2 in C. minitans enhanced mycelial parasitism on S. sclerotiorum and restored the effect of silencing SsNEP2 in S. sclerotiorum on mycoparasitism. Thus, we highlight the role of SsNEP2 as a PAMP-like protein in the mycoparasitism between C. minitans and its host fungus S. sclerotiorum. SsNEP2 can be used to promote the biological potential of C. minitans.

Genome-wide identification and characterization of transcription factors involved in defense responses against Sclerotinia sclerotiorum in Brassica juncea

Sclerotinia sclerotiorum could cause significant yield losses of up to 70% in rapeseed cultivation. Nevertheless, the availability of immune or highly resistant germplasm and mechanisms to combat S. sclerotiorum, particularly in B. juncea, remains insufficient. Transcription factors (TFs) are recognized for their critical role in plant defense against S. sclerotiorum. In the present study, a total of 4807 TFs from 48 families were expressed and identified at 12, 24, and 36 h after inoculation (HAI) in two B. juncea lines: G21-912, exhibiting higher S. sclerotiorum resistance (HR), and G21-853, displaying lower S. sclerotiorum resistance (LR). The number of differentially expressed TFs (DETs) between the HR and the LR lines peaked at 24 HAI, with 202 upregulated and 105 downregulated TFs. Through expression and subcellular localization analyses, three candidate DETs, namely BjuA037408 (ETHYLENE RESPONSIVE FACTOR 59, ERF59), BjuB028842 (RELATED TO ABI3/VP1 1, RAV1), and BjuA016484 (WRKY25), were identified as the primary TFs in defense against S. sclerotiorum inoculation. The expression of these three genes was validated in the double haploid lines of BC3 (the third backcrossing generation) derived from the HR×LR cross. This study serves as a valuable case study for the characterization of TFs associated with defense mechanisms against S. sclerotiorum in B. juncea. The confirmed resistant B. juncea line of HR, along with the three key DETs, is expected to significantly contribute to future breeding efforts aimed at developing Sclerotinia-resistant varieties.

The glutathione S-transferase BnGSTU12 enhances the resistance of Brassica napus to Sclerotinia sclerotiorum through reactive oxygen species homeostasis and jasmonic acid signaling

Sclerotinia sclerotiorum is a severe disease that affects rapeseed (Brassica napus), resulting in significant yield losses. In previous study, we identified the candidate GLUTATHIONE S-TRANSFERASE (GST) gene, BnGSTU12, associated with sclerotiorum stem resistance and the expression levels of BnGSTU12 in resistant lines were higher than that in susceptible lines. We analyzed the function of the BnGSTU12 during S. sclerotiorum infection in this study. BnGSTU12 expression was induced by S. sclerotiorum, with a strong increase 24 h after onset of infection. Transgenic functional analysis indicated that overexpression of BnGSTU12 in Arabidopsis thaliana and B. napus enhanced resistance to S. sclerotiorum, whereas BnGSTU12 silencing decreased S. sclerotiorum resistance. The inoculated BnGSTU12-OE A. thaliana and B. napus plants showed higher antioxidant enzyme activity and lower H2O2 contents than the wild type. As BnGSTU12 was rapidly induced by the phytohormones salicylic acid (SA), ethylene, and methyl jasmonate (MeJA), we investigated the involvement of the JA and SA pathways in GSTU12-mediated S. sclerotiorum resistance. JA content was higher in infected BnGSTU12-OE plants than in the wild type, whereas their SA contents were comparable. In addition, the expression levels of JASMONATE RESISTANT (JAR) involved in JA-Ile biosynthesis and those of JA-responsive genes were higher, the expression of JAZ gene repressing JA signaling was less in OE plants than WT after 12 and 24 h inoculation with S. sclerotiorum. Our results show that BnGSTU12 enhances resistance to S. sclerotiorum through ROS homeostasis and JA signaling.

Biocontrol Potential of Rhizospheric Bacillus Strains Against Sclerotinia minor Jagger Causing Lettuce Drop

Phytopathogenic Sclerotinia minor Jagger causes lettuce drop, a destructive soil-borne disease. As potential biocontrol agents for this disease, 2 of 31 bacterial strains isolated from soil samples from fields containing S. minor Jagger were identified using in vitro antagonistic assays against S. minor Jagger. Bioactivity experiments showed that Bac20 had higher inhibitory activity against S. minor Jagger than Bac45. Based on 16S rRNA sequences and phylogenetic analysis of a combination of sequences from gyrA, rpoB, purH, polC, and groEL, Bac20 and Bac45 were identified as Bacillus velezensis and Bacillus subtilis, respectively. Lipopeptide compounds produced by each strain were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. Both strains produced three types of lipopeptides, namely surfactins, iturins, and fengycins, whereas Bac20 showed the strongest intensity in its production of iturins, more than that of Bac45. Bac20 inhibited oxalic acid formation in early-stage lettuce leaves infected with S. minor Jagger, delaying pathogen infestation. Greenhouse experiments for controlling lettuce drop demonstrated that inoculation with Bac20 controlled lettuce drop by 71.7%. In conclusion, this study revealed that B. velezensis Bac20 has high potential for use as a biocontrol agent for controlling the lettuce drop caused by S. minor Jagger.

Efficacy of Trichoderma longibrachiatum SC5 Fermentation Filtrate in Inhibiting the Sclerotinia sclerotiorum Growth and Development in Sunflower

Sclerotinia sclerotiorum is a destructive pathogen responsible for sunflower sclerotinia rot, resulting in substantial yield and economic losses worldwide. Trichoderma species have demonstrated the capacity to inhibit plant pathogen growth through the production of secondary metabolites. However, there are fewer recent studies focusing on the application of Trichoderma metabolites in inhibiting S. sclerotiorum growth and development and controlling sunflower sclerotinia rot disease. Our results showed that five Trichoderma strains (SC5, T6, TN, P6, and TS3) exhibited mycelial growth inhibition higher than 60% in dual culture assays out of the 11 tested strains. The Trichoderma SC5 fermentation filtrate exhibited superior efficacy compared to other strains, achieving a 94.65% inhibition rate of mycelial growth on S. sclerotiorum, 96% inhibition of myceliogenic germination of sclerotia, and 81.05% reduction in the oxalic acid content of S. sclerotiorum, while significantly increasing the cell membrane permeability. In addition, the Trichoderma SC5 fermentation filtrate significantly decreased the activities of polygalacturonase and pectin methyl-galacturonic enzymes and even caused S. sclerotiorum hyphae to swell, branch, twist, lyse, and inhibited the production and development of sclerotia. Moreover, the Trichoderma SC5 fermentation filtrate downregulated genes expression that associated with the growth and infection of S. sclerotiorum. The control efficacies of the protective and curative activities of the Trichoderma SC5 fermentation filtrate were 95.45% and 75.36%, respectively, on detached sunflower leaves at a concentration of 8 mg/mL. Finally, the Trichoderma SC5 was identified as Trichoderma longibrachiatum through morphological and phylogenetic analysis. Our research indicates that the T. longibrachiatum SC5 can be considered a promising biological control candidate against S. sclerotiorum and controlling the sunflower sclerotinia rot disease, both in vitro and in vivo.

White Mold: A Global Threat to Crops and Key Strategies for Its Sustainable Management

White mold, caused by the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, is a significant biotic stress impacting horticultural and field crops worldwide. This disease causes plants to wilt and ultimately die, resulting in considerable yield losses. This monocyclic disease progresses through a single infection cycle involving basal infections from myceliogenically germinated sclerotia or aerial infections initiated by ascospores from carpogenically germinated sclerotia. The pathogen has a homothallic mating system with a weak population structure. Relatively cool temperatures and extended wetness are typical conditions for spreading the disease. Each stage of infection triggers a cascade of molecular and physiological events that underpin defense responses against S. sclerotiorum. Molecular markers can help rapid diagnosis of this disease in plants. Effective management strategies encompass altering the crop microclimate, applying fungicides, reducing inoculum sources, and developing resistant plant varieties. Integrated approaches combining those strategies often yield the best results. This review discusses the latest insights into the biology, epidemiology, infection mechanisms, and early detection of white mold. This review also aims to provide comprehensive guidelines for sustainable management of this destructive disease while reducing the use of excessive pesticides in crop fields.

Comparative transcriptome analysis in two contrasting genotypes for Sclerotinia sclerotiorum resistance in sunflower

Sclerotinia sclerotiorum as a necrotrophic fungus causes the devastating diseases in many important oilseed crops worldwide. The preferred strategy for controlling S. sclerotiorum is to develop resistant varieties, but the molecular mechanisms underlying S. sclerotiorum resistance remain poorly defined in sunflower (Helianthus annuus). Here, a comparative transcriptomic analysis was performed in leaves of two contrasting sunflower genotypes, disease susceptible (DS) B728 and disease resistant (DR) C6 after S. sclerotiorum inoculation. At 24 h post-inoculation, the DR genotype exhibited no visible growth of the hyphae as well as greater activity of superoxide dismutase activity (SOD), peroxidase (POD), catalase (CAT), glutathione-S-transferase (GST), ascorbate peroxidase (APX) and monodehydroascorbate reductase (MDAR) than DS genotype. A total of 10151 and 7439 differentially expressed genes (DEGs) were detected in DS and DR genotypes, respectively. Most of DEGs were enriched in cell wall organisation, protein kinase activity, hormone, transcription factor activities, redox homeostasis, immune response, and secondary metabolism. Differential expression of genes involved in expansins, pectate lyase activities, ethylene biosynthesis and signaling and antioxidant activity after S. sclerotiorum infection could potentially be responsible for the differential resistance among two genotypes. In summary, these finding provide additional insights into the potential molecular mechanisms of S. sclerotiorum's defense response and facilitate the breeding of Sclerotinia-resistant sunflower varieties.

Isothermal Detection Methods for Fungal Pathogens in Closed Environment Agriculture

Closed environment agriculture (CEA) is rapidly gaining traction as a sustainable option to meet global food demands while mitigating the impacts of climate change. Fungal pathogens represent a significant threat to crop productivity in CEA, where the controlled conditions can inadvertently foster their growth. Historically, the detection of pathogens has largely relied on the manual observation of signs and symptoms of disease in the crops. These approaches are challenging at large scale, time consuming, and often too late to limit crop loss. The emergence of fungicide resistance further complicates management strategies, necessitating the development of more effective diagnostic tools. Recent advancements in technology, particularly in molecular and isothermal diagnostics, offer promising tools for the early detection and management of fungal pathogens. Innovative detection methods have the potential to provide real-time results and enhance pathogen management in CEA systems. This review explores isothermal amplification and other new technologies in detection of fungal pathogens that occur in CEA.

The Good, the Bad, and the Fungus: Insights into the Relationship Between Plants, Fungi, and Oomycetes in Hydroponics

Hydroponic systems are examples of controlled environment agriculture (CEA) and present a promising alternative to traditional farming methods by increasing productivity, profitability, and sustainability. In hydroponic systems, crops are grown in the absence of soil and thus lack the native soil microbial community. This review focuses on fungi and oomycetes, both beneficial and pathogenic, that can colonize crops and persist in hydroponic systems. The symptomatology and mechanisms of pathogenesis for Botrytis, Colletotrichum, Fulvia, Fusarium, Phytophthora, Pythium, and Sclerotinia are explored for phytopathogenic fungi that target floral organs, leaves, roots, and vasculature of economically important hydroponic crops. Additionally, this review thoroughly explores the use of plant growth-promoting fungi (PGPF) to combat phytopathogens and increase hydroponic crop productivity; details of PGP strategies and mechanisms are discussed. The benefits of Aspergillus, Penicillium, Taloromyces, and Trichoderma to hydroponics systems are explored in detail. The culmination of these areas of research serves to improve the current understanding of the role of beneficial and pathogenic fungi, specifically in the hydroponic microbiome.

Baseline sensitivity and physiological characteristics of natural product hinokitiol against Sclerotinia sclerotiorum

BACKGROUND

Sclerotinia sclerotiorum, a pathogenic fungus of oilseed rape, poses a severe threat to the oilseed rapeseed industry. In this study, we evaluated the potential of the natural compound hinokitiol against S. sclerotiorum by determining its biological activity and physiological characteristics.

RESULTS

Our results showed that hinokitiol strongly inhibited the hyphae expansion of S. sclerotiorum, and its effective concentration of hyphae growing inhibition by 50% (EC50) against 103 S. sclerotiorum strains varied from 0.36 to 3.45 μg/mL, with an average of 1.23 μg/mL. Hinokitiol possessed better protective efficacy than therapeutic effects, and it exhibited no cross-resistance between carbendazim. After treatment with hinokitiol, many vesicular protrusions developed on the mycelium with rough surface and thickened cell wall. Moreover, the cell membrane permeability and glycerol content increased, while the oxalic acid declined after hinokitiol treatment. In addition, hinokitiol induced membrane lipid peroxidation and improved the production of reactive oxygen species (ROS) in S. sclerotiorum. Importantly, real-time quantitative polymerase chain reaction showed that cell wall and ROS synthesis-related genes were significantly up-regulated after hinokitiol treatment.

CONCLUSION

This study revealed that hinokitiol has good biological activity against S. sclerotiorum and could be considered as an alternative bio-fungicide for the resistance management in controlling sclerotinia stem rot infected by S. sclerotiorum. These investigations provided new insights into understanding the toxic action of hinokitiol against pathogenic fungi. © 2024 Society of Chemical Industry.

Global mRNA profiling reveals the effect of boron as a crop protection tool against Sclerotinia sclerotiorum

Sclerotinia sclerotiorum, the causal agent of white mould, is a necrotrophic fungal pathogen responsible for extensive crop loss. Current control options rely heavily on the application of chemical fungicides that are becoming less effective and may lead to the development of fungal resistance. In the current study, we used a foliar application of boron to protect Brassica napus (canola) from S. sclerotiorum infection using whole-plant infection assays. Application of boron to aerial surfaces of the canola plant reduced the number of S. sclerotiorum-forming lesions by 87 % compared to an untreated control. Dual RNA sequencing revealed the effect of boron on both the host plant and fungal pathogen during the infection process. Differential gene expression analysis and gene ontology term enrichment further revealed the mode of action of a foliar boron spray at the mRNA level. A single foliar application of boron primed the plant defence response through the induction of genes associated with systemic acquired resistance while an application of boron followed by S. sclerotiorum infection-induced genes associated with defence response-related cellular signalling cascades. Additionally, in S. sclerotiorum inoculated on boron-treated B. napus, we uncovered gene activity in response to salicylic acid breakdown, consistent with salicylic acid-dependent systemic acquired resistance induction within the host plant. Taken together, this study demonstrates that a foliar application of boron results in priming of the B. napus plant defence response, likely through systemic acquired resistance, thereby contributing to increased tolerance to S. sclerotiorum infection.

Genetic diversity and virulence variability of Sclerotinia sclerotiorum in Eastern and Northeastern India

Sclerotinia sclerotiorum, the necrotrophic cosmopolitan fungus, has become an emerging and re-emerging pathogen in the subtropical regions. Genetic diversity of 36 isolates of the fungus isolated from infected samples collected from the eastern and North eastern states was carried out using UP-PCR and SSR. Virulence variability was analysed based on four different measures. Among the eight UP-PCR primers and various combinations used, L-21, 3-2 and AA2M2-AS4 generated maximum number of fingerprints (13, 13 and 12, respectively) ranging from 100bp to 1kb. The isolates exhibited varied level of aggressiveness; majority (77.78%) were moderately virulent, 8.33% (22.22% of Assam and 6.67% of West Bengal) isolates were highly virulent, and 13.89% were less virulent. Several amplification products viz., 500bp generated by AA2M2-AS4, 150bp by AA2M2-L-21 and 100bp by L-21-3-2 were positively correlated with disease severity grading at 5% level of significance, whereas, 600bp band generated by AA2M2-3-2 was correlated at 1% level of significance. This indicates presence of these bands in highly virulent isolates. Out of the eight SSR primers, TATG9 did not generate any amplification and the isolates were divided into two major groups; the group II contained single isolate from Nagaland (NG4) indicating it to be genetically diverse from rest of the isolates. The subgroup A of the major group I was the largest and most diverse group with 11 members indicating genetic admixture within different geographic populations with different levels of similarity (70-100%). Genetic diversity based on SSR banding pattern showed highest value of Nei's gene diversity and Shannon's index of diversity (%pb = 61.11; h = 0.219; I = 0.330) for the Nagaland population with 9 members followed by West Bengal population with 15 members. Nei's genetic distance of all the tested populations was low, ranging from 0.0014 to 0.2350; however, genetic identity was high ranging from 0.7905 to 0.9986. The findings suggest that the pathogen populations of eastern and North eastern region were predominantly clonal with some evidence of infrequent out crossing.

A novel protein elicitor (Cs08297) from Ciboria shiraiana enhances plant disease resistance

Ciboria shiraiana is a necrotrophic fungus that causes mulberry sclerotinia disease resulting in huge economic losses in agriculture. During infection, the fungus uses immunity elicitors to induce plant tissue necrosis that could facilitate its colonization on plants. However, the key elicitors and immune mechanisms remain unclear in C. shiraiana. Herein, a novel elicitor Cs08297 secreted by C. shiraiana was identified, and it was found to target the apoplast in plants to induce cell death. Cs08297 is a cysteine-rich protein unique to C. shiraiana, and cysteine residues in Cs08297 were crucial for its ability to induce cell death. Cs08297 induced a series of defence responses in Nicotiana benthamiana, including the burst of reactive oxygen species (ROS), callose deposition, and activation of defence-related genes. Cs08297 induced-cell death was mediated by leucine-rich repeat (LRR) receptor-like kinases BAK1 and SOBIR1. Purified His-tagged Cs08297-thioredoxin fusion protein triggered cell death in different plants and enhanced plant resistance to diseases. Cs08297 was necessary for sclerotial development, oxidative-stress adaptation, and cell wall integrity but negatively regulated virulence of C. shiraiana. In conclusion, our results revealed that Cs08297 is a novel fungal elicitor in fungi inducing plant immunity. Furthermore, its potential to enhance plant resistance provides a new target to control agricultural diseases biologically.

The TOR signalling pathway in fungal phytopathogens: A target for plant disease control

Plant diseases caused by fungal phytopathogens have led to significant economic losses in agriculture worldwide. The management of fungal diseases is mainly dependent on the application of fungicides, which are not suitable for sustainable agriculture, human health, and environmental safety. Thus, it is necessary to develop novel targets and green strategies to mitigate the losses caused by these pathogens. The target of rapamycin (TOR) complexes and key components of the TOR signalling pathway are evolutionally conserved in pathogens and closely related to the vegetative growth and pathogenicity. As indicated in recent systems, chemical, genetic, and genomic studies on the TOR signalling pathway, phytopathogens with TOR dysfunctions show severe growth defects and nonpathogenicity, which makes the TOR signalling pathway to be developed into an ideal candidate target for controlling plant disease. In this review, we comprehensively discuss the current knowledge on components of the TOR signalling pathway in microorganisms and the diverse roles of various plant TOR in response to plant pathogens. Furthermore, we analyse a range of disease management strategies that rely on the TOR signalling pathway, including genetic modification technologies and chemical controls. In the future, disease control strategies based on the TOR signalling network are expected to become a highly effective weapon for crop protection.

An effector essential for virulence of necrotrophic fungi targets plant HIRs to inhibit host immunity

Phytopathogens often secrete effectors to enhance their infection of plants. In the case of Sclerotinia sclerotiorum, a necrotrophic phytopathogen, a secreted protein named SsPEIE1 (Sclerotinia sclerotiorum Plant Early Immunosuppressive Effector 1) plays a crucial role in its virulence. During the early stages of infection, SsPEIE1 is significantly up-regulated. Additionally, transgenic plants expressing SsPEIE1 exhibit increased susceptibility to different phytopathogens. Further investigations revealed that SsPEIE1 interacts with a plasma membrane protein known as hypersensitive induced reaction (HIR) that dampens immune responses. SsPEIE1 is required for S. sclerotiorum virulence on wild-type Arabidopsis but not on Arabidopsis hir4 mutants. Moreover, Arabidopsis hir2 and hir4 mutants exhibit suppressed pathogen-associated molecular pattern-triggered reactive oxygen species (ROS) bursts and salicylic acid (SA)-associated immune gene induction, all of which are phenocopied by the SsPEIE1 transgenic plants. We find that the oligomerization of AtHIR4 is essential for its role in mediating immunity, and that SsPEIE1 inhibits its oligomerization through competitively binding to AtHIR4. Remarkably, both Arabidopsis and rapeseed plants overexpress AtHIR4 display significantly increased resistance to S. sclerotiorum. In summary, these results demonstrate that SsPEIE1 inhibits AtHIR4 oligomerization-mediated immune responses by interacting with the key immune factor AtHIR4, thereby promoting S. sclerotiorum infection.

Selenium in soil enhances resistance of oilseed rape to Sclerotinia sclerotiorum by optimizing the plant microbiome

Plants can recruit beneficial microbes to enhance their ability to resist disease. It is well established that selenium is beneficial in plant growth, but its role in mediating microbial disease resistance remains poorly understood. Here, we investigated the correlation between selenium, oilseed rape rhizosphere microbes, and Sclerotinia sclerotiorum. Soil application of 0.5 and 1.0 mg kg-1 selenium [selenate Na2SeO4, Se(VI) or selenite Na2SeO3, Se(IV)] significantly increased the resistance of oilseed rape to Sclerotinia sclerotiorum compared with no selenium application, with a disease inhibition rate higher than 20% in Se(VI)0.5, Se(IV)0.5 and Se(IV)1.0 mg kg-1 treatments. The disease resistance of oilseed rape was related to the presence of rhizosphere microorganisms and beneficial bacteria isolated from the rhizosphere inhibited Sclerotinia stem rot. Burkholderia cepacia and the synthetic community consisting of Bacillus altitudinis, Bacillus megaterium, Bacillus cereus, Bacillus subtilis, Bacillus velezensis, Burkholderia cepacia, and Flavobacterium anhui enhanced plant disease resistance through transcriptional regulation and activation of plant-induced systemic resistance. In addition, inoculation of isolated bacteria optimized the bacterial community structure of leaves and enriched beneficial microorganisms such as Bacillus, Pseudomonas, and Sphingomonas. Bacillus isolated from the leaves were sprayed on detached leaves, and it also performed a significant inhibition effect on Sclerotinia sclerotiorum. Overall, our results indicate that selenium improves plant rhizosphere microorganisms and increase resistance to Sclerotinia sclerotiorum in oilseed rape.

Mycologists and Virologists Align: Proposing Botrytis cinerea for Global Mycovirus Studies

Mycoviruses are highly genetically diverse and can significantly change their fungal host's phenotype, yet they are generally under-described in genotypic and biological studies. We propose Botrytis cinerea as a model mycovirus system in which to develop a deeper understanding of mycovirus epidemiology including diversity, impact, and the associated cellular biology of the host and virus interaction. Over 100 mycoviruses have been described in this fungal host. B. cinerea is an ideal model fungus for mycovirology as it has highly tractable characteristics-it is easy to culture, has a worldwide distribution, infects a wide range of host plants, can be transformed and gene-edited, and has an existing depth of biological resources including annotated genomes, transcriptomes, and isolates with gene knockouts. Focusing on a model system for mycoviruses will enable the research community to address deep research questions that cannot be answered in a non-systematic manner. Since B. cinerea is a major plant pathogen, new insights may have immediate utility as well as creating new knowledge that complements and extends the knowledge of mycovirus interactions in other fungi, alone or with their respective plant hosts. In this review, we set out some of the critical steps required to develop B. cinerea as a model mycovirus system and how this may be used in the future.

Innovative sustainable bioreactor-in-a-granule formulation of Trichoderma asperelloides

The advancement of fungal biocontrol agents depends on replacing cereal grains with low-cost agro-industrial byproducts for their economical mass production and development of stable formulations. We propose an innovative approach to develop a rice flour-based formulation of the beneficial biocontrol agent Trichoderma asperelloides CMAA1584 designed to simulate a micro-bioreactor within the concept of full biorefinery process, affording in situ conidiation, extended shelf-life, and effective control of Sclerotinia sclerotiorum, a devastating pathogen of several dicot agricultural crops worldwide. Rice flour is an inexpensive and underexplored byproduct derived from broken rice after milling, capable of sustaining high yields of conidial production through our optimized fermentation-formulation route. Conidial yield was mainly influenced by nitrogen content (0.1% w/w) added to the rice meal coupled with the fermentor type. Hydrolyzed yeast was the best nitrogen source yielding 2.6 × 109 colony-forming units (CFU)/g within 14 days. Subsequently, GControl, GLecithin, GBreak-Thru, GBentonite, and GOrganic compost+Break-Thru formulations were obtained by extrusion followed by air-drying and further assessed for their potential to induce secondary sporulation in situ, storage stability, and efficacy against Sclerotinia. GControl, GBreak-Thru, GBentonite, and GOrganic compost+Break-Thru stood out with the highest number of CFU after sporulation upon re-hydration on water-agar medium. Shelf-life of formulations GControl and GBentonite remained consistent for > 3 months at ambient temperature, while in GBentonite and GOrganic compost+Break-Thru formulations remained viable for 24 months during refrigerated storage. Formulations exhibited similar efficacy in suppressing the myceliogenic germination of Sclerotinia irrespective of their concentration tested (5 × 104 to 5 × 106 CFU/g of soil), resulting in 79.2 to 93.7% relative inhibition. Noteworthily, all 24-month-old formulations kept under cold storage successfully suppressed sclerotia. This work provides an environmentally friendly bioprocess method using rice flour as the main feedstock to develop waste-free granular formulations of Trichoderma conidia that are effective in suppressing Sclerotinia while also improving biopesticide shelf-life. KEY POINTS: • Innovative "bioreactor-in-a-granule" system for T. asperelloides is devised. • Dry granules of aerial conidia remain highly viable for 24 months at 4 °C. • Effective control of white-mold sclerotia via soil application of Trichoderma-based granules.

Predicted multispecies unintended effects from outdoor genome editing

CRISPR/Cas9, a potent genetic engineering tool widely adopted in agriculture, is capable of introducing new characteristics into plants on a large scale and without conventional breeding methods. Despite its remarkable efficiency, concerns have arisen regarding unintended consequences in uncontrolled environments. Our aim was to assess potential activity in organisms that could be exposed to genome editing in uncontrolled environments. We developed three scenarios, using irrigation, fumigation and fertilization as delivery methods, based on outdoor uses in agriculture, namely pest and disease control. Using publicly available software (Cas-OFFinder, NCBI Genome Data Viewer and STRING), off-target effects were predicted in multiple species commonly found in the agroecosystem, including humans (16 of 38 (42 %) sampled). Metabolic enrichment analysis (gene IDs), by connecting off-target genes into a physiological network, predicted effects on the development of nervous and respiratory systems. Our findings emphasize the importance of exercising caution when considering the use of this genome editing in uncontrolled environments. Unintended genomic alterations may occur in unintended organisms, underscoring the significance of understanding potential hazards and implementing safety measures to protect human health and the environment.

Fusiform nanoparticle boosts efficient genetic transformation in Sclerotinia sclerotiorum

BACKGROUND

Sclerotinia sclerotiorum is a highly destructive phytopathogenic fungus that poses a significant threat to a wide array of crops. The current constraints in genetic manipulation techniques impede a thorough comprehension of its pathogenic mechanisms and the development of effective control strategies.

RESULTS

Herein, we present a highly efficient genetic transformation system for S. sclerotiorum, leveraging the use of fusiform nanoparticles, which are synthesized with FeCl3 and 2,6-diaminopyrimidine (DAP). These nanoparticles, with an average longitude length of 59.00 nm and a positively charged surface, facilitate the direct delivery of exogenous DNA into the mycelial cells of S. sclerotiorum, as well as successful integration with stable expression. Notably, this system circumvents fungal protoplast preparation and tedious recovery processes, streamlining the transformation process considerably. Furthermore, we successfully employed this system to generate S. sclerotiorum strains with silenced oxaloacetate acetylhydrolase-encoding gene Ss-oah1.

CONCLUSIONS

Our findings demonstrate the feasibility of using nanoparticle-mediated delivery as a rapid and reliable tool for genetic modification in S. sclerotiorum. Given its simplicity and high efficiency, it has the potential to significantly propel genetic research in filamentous fungi, offering new avenues for elucidating the intricacies of pathogenicity and developing innovative disease management strategies.

Genetic diversity and genome-wide association study of partial resistance to Sclerotinia stem rot in a Canadian soybean germplasm panel

KEY MESSAGE

Developing genetically resistant soybean cultivars is key in controlling the destructive Sclerotinia Stem Rot (SSR) disease. Here, a GWAS study in Canadian soybeans identified potential marker-trait associations and candidate genes, paving the way for more efficient breeding methods for SSR. Sclerotinia stem rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is one of the most important diseases leading to significant soybean yield losses in Canada and worldwide. Developing soybean cultivars that are genetically resistant to the disease is the most inexpensive and reliable method to control the disease. However, breeding for resistance is hampered by the highly complex nature of genetic resistance to SSR in soybean. This study sought to understand the genetic basis underlying SSR resistance particularly in soybean grown in Canada. Consequently, a panel of 193 genotypes was assembled based on maturity group and genetic diversity as representative of Canadian soybean cultivars. Plants were inoculated and screened for SSR resistance in controlled environments, where variation for SSR phenotypic response was observed. The panel was also genotyped via genotyping-by-sequencing and the resulting genotypic data were imputed using BEAGLE v5 leading to a catalogue of 417 K SNPs. Through genome-wide association analyses (GWAS) using FarmCPU method with threshold of FDR-adjusted p-values < 0.1, we identified significant SNPs on chromosomes 2 and 9 with allele effects of 16.1 and 14.3, respectively. Further analysis identified three potential candidate genes linked to SSR disease resistance within a 100 Kb window surrounding each of the peak SNPs. Our results will be important in developing molecular markers that can speed up the breeding for SSR resistance in Canadian grown soybean.

High-Resolution Disease Phenotyping Reveals Distinct Resistance Mechanisms of Tomato Crop Wild Relatives against Sclerotinia sclerotiorum

Besides the well-understood qualitative disease resistance, plants possess a more complex quantitative form of resistance: quantitative disease resistance (QDR). QDR is commonly defined as a partial but more durable form of resistance and, therefore, might display a valuable target for resistance breeding. The characterization of QDR phenotypes, especially of wild crop relatives, displays a bottleneck in deciphering QDR's genomic and regulatory background. Moreover, the relationship between QDR parameters, such as infection frequency, lag-phase duration, and lesion growth rate, remains elusive. High hurdles for applying modern phenotyping technology, such as the low availability of phenotyping facilities or complex data analysis, further dampen progress in understanding QDR. Here, we applied a low-cost (<1.000 €) phenotyping system to measure lesion growth dynamics of wild tomato species (e.g., Solanum pennellii or Solanum pimpinellifolium). We provide insight into QDR diversity of wild populations and derive specific QDR mechanisms and their cross-talk. We show how temporally continuous observations are required to dissect end-point severity into functional resistance mechanisms. The results of our study show how QDR can be maintained by facilitating different defense mechanisms during host-parasite interaction and that the capacity of the QDR toolbox highly depends on the host's genetic context. We anticipate that the present findings display a valuable resource for more targeted functional characterization of the processes involved in QDR. Moreover, we show how modest phenotyping technology can be leveraged to help answer highly relevant biological questions.

Establishment of an Infection System for Gentian (Gentiana spp.) Sclerotial Flower Blight Disease

Gentians (Gentiana spp.) as floriculture crops are constantly exposed to several fungal and viral pathogens in the field. Among the fungal diseases afflicting gentian production, gentian sclerotial flower blight caused by Ciborinia gentianae incurs economic losses, as it affects flowers before and after harvest. Currently, preventive measures for this disease are limited, and no resistant cultivars have been reported. This is partly because of the lack of a reliable infection system that could promote research on this plant-fungus interaction. In this study, Gentiana plant tissue culture material was inoculated with C. gentianae culture filtrate. We successfully demonstrated non-ascospore-mediated infection of C. gentianae. Inoculation of individual hyphal structures present in the culture filtrate suggested that sclerotial primordia are the main agents of this infection. Interestingly, our results indicated that primary infection of C. gentianae occurs in petals rather than leaves, which enables systemic infection and therefore mirrors the fungus's infection strategy observed in the field. Moreover, we showed that (i) non-ascospore hyphal structures can also cause disease in flowers grown in the field, and (ii) ascosporic infection can also be observed using the in vitro system, opening possibilities for both practical and basic research aimed to combat gentian sclerotial flower blight disease.

Effective, Consistent, and Rapid Noncontact Application Methods for Seedling Basal Stem Infection by Sclerotinia sclerotiorum

Sclerotinia sclerotiorum (Lib.) de Bary, an economically devastating soilborne fungal pathogen known to cause disease across a wide range of plants, produces long-term inoculum called sclerotia that can germinate either carpogenically by ascospores infecting aboveground plant parts or myceliogenically to infect stem base and roots. Typically, for research purposes, S. sclerotiorum diseases are initiated by direct contact methods, using S. sclerotiorum mycelium agar plugs wrapped around the stem or sclerotia placed directly beneath root mass. However, reproducible noncontact methods leading to basal stem infection are not currently available. Therefore, the objective of this study was to develop effective noncontact protocols that consistently generate basal plant stem infection from S. sclerotiorum in the soil. Using three host plant species (canola, lupin, and lettuce), we determined two methods that reliably produced basal stem infection. The first method, where mycelial agar plugs were positioned just below the soil surface at a distance of 5 mm from each seedling, led to 100% infection in all plants. The second method used pathogen-infested soil by mixing the soil with dry inoculum in the form of a powder prepared from mycelium-colonized organic substrates. Four substrates consistently produced 100% seedling infection at 4 days after inoculation (DAI): wheat bran, wheat grain, red rice, and hulled millet. In contrast, chia, canary, sesame, and ryegrass seed substrates resulted in less than 50% seedling infection at 10 DAI, and infection levels did not progress further. The two soil inoculation methods outlined in this study will enhance future research on the progression of S. sclerotiorum diseases, with the potential to screen disease-resistant host genotypes to basal S. sclerotiorum infection and, in particular, to test the effectiveness of soil applications of fungicides or biocontrol agents against S. sclerotiorum basal infection.

Overexpression of AcWRKY31 Increases Sensitivity to Salt and Drought and Improves Tolerance to Mealybugs in Pineapple

Pineapple is a globally significant tropical fruit, but its cultivation faces numerous challenges due to abiotic and biotic stresses, affecting its quality and quantity. WRKY transcription factors are known regulators of stress responses, however, their specific functions in pineapple are not fully understood. This study investigates the role of AcWRKY31 by overexpressing it in pineapple and Arabidopsis. Transgenic pineapple lines were obtained using Agrobacterium-mediated transformation methods and abiotic and biotic stress treatments. Transgenic AcWRKY31-OE pineapple plants showed an increased sensitivity to salt and drought stress and an increased resistance to biotic stress from pineapple mealybugs compared to that of WT plants. Similar experiments in AcWRKY31-OE, AtWRKY53-OE, and the Arabidopsis Atwrky53 mutant were performed and consistently confirmed these findings. A comparative transcriptomic analysis revealed 5357 upregulated genes in AcWRKY31-OE pineapple, with 30 genes related to disease and pathogen response. Notably, 18 of these genes contained a W-box sequence in their promoter region. A KEGG analysis of RNA-Seq data showed that upregulated DEG genes are mostly involved in translation, protein kinases, peptidases and inhibitors, membrane trafficking, folding, sorting, and degradation, while the downregulated genes are involved in metabolism, protein families, signaling, and cellular processes. RT-qPCR assays of selected genes confirmed the transcriptomic results. In summary, the AcWRKY31 gene is promising for the improvement of stress responses in pineapple, and it could be a valuable tool for plant breeders to develop stress-tolerant crops in the future.

Biocontrol Methods for the Management of Sclerotinia sclerotiorum in Legumes: A Review

Sclerotinia sclerotiorum is an economically damaging fungal pathogen that causes Sclerotinia stem rot in legumes, producing enormous yield losses. This pathogen is difficult to control due to its wide host spectrum and ability to produce sclerotia, which are resistant bodies that can remain active for long periods under harsh environmental conditions. Here, the biocontrol methods for the management of S. sclerotiorum in legumes are reviewed. Bacillus strains, which synthesized lipopeptides and volatile organic compounds, showed high efficacies in soybean plants, whereas the highest efficacies for the control of the pathogen in alfalfa and common bean were observed when using Coniothyrium minitans and Streptomyces spp., respectively. The biocontrol efficacies in fields were under 65%, highlighting the lack of strategies to achieve a complete control. Overall, although most studies involved extensive screenings using different biocontrol agent concentrations and application conditions, there is a lack of knowledge regarding the specific antifungal mechanisms, which limits the optimization of the reported methods.

Integrated Assays of Genome-Wide Association Study, Multi-Omics Co-Localization, and Machine Learning Associated Calcium Signaling Genes with Oilseed Rape Resistance to Sclerotinia sclerotiorum

Sclerotinia sclerotiorum (Ss) is one of the most devastating fungal pathogens, causing huge yield loss in multiple economically important crops including oilseed rape. Plant resistance to Ss pertains to quantitative disease resistance (QDR) controlled by multiple minor genes. Genome-wide identification of genes involved in QDR to Ss is yet to be conducted. In this study, we integrated several assays including genome-wide association study (GWAS), multi-omics co-localization, and machine learning prediction to identify, on a genome-wide scale, genes involved in the oilseed rape QDR to Ss. Employing GWAS and multi-omics co-localization, we identified seven resistance-associated loci (RALs) associated with oilseed rape resistance to Ss. Furthermore, we developed a machine learning algorithm and named it Integrative Multi-Omics Analysis and Machine Learning for Target Gene Prediction (iMAP), which integrates multi-omics data to rapidly predict disease resistance-related genes within a broad chromosomal region. Through iMAP based on the identified RALs, we revealed multiple calcium signaling genes related to the QDR to Ss. Population-level analysis of selective sweeps and haplotypes of variants confirmed the positive selection of the predicted calcium signaling genes during evolution. Overall, this study has developed an algorithm that integrates multi-omics data and machine learning methods, providing a powerful tool for predicting target genes associated with specific traits. Furthermore, it makes a basis for further understanding the role and mechanisms of calcium signaling genes in the QDR to Ss.

Recent advances in virulence of a broad host range plant pathogen Sclerotinia sclerotiorum: a mini-review

Sclerotinia sclerotiorum is a typical necrotrophic plant pathogenic fungus, which has a wide host range and can cause a variety of diseases, leading to serious loss of agricultural production around the world. It is difficult to control and completely eliminate the characteristics, chemical control methods is not ideal. Therefore, it is very important to know the pathogenic mechanism of S. sclerotiorum for improving host living environment, relieving agricultural pressure and promoting economic development. In this paper, the life cycle of S. sclerotiorum is introduced to understand the whole process of S. sclerotiorum infection. Through the analysis of the pathogenic mechanism, this paper summarized the reported content, mainly focused on the oxalic acid, cell wall degrading enzyme and effector protein in the process of infection and its mechanism. Besides, recent studies reported virulence-related genes in S. sclerotiorum have been summarized in the paper. According to analysis, those genes were related to the growth and development of the hypha and appressorium, the signaling and regulatory factors of S. sclerotiorum and so on, to further influence the ability to infect the host critically. The application of host-induced gene silencing (HIGS)is considered as a potential effective tool to control various fungi in crops, which provides an important reference for the study of pathogenesis and green control of S. sclerotiorum.

In silico analysis of fungal prion-like proteins for elucidating their role in plant-fungi interactions

Prion-like proteins (PrLPs) have emerged as beneficial molecules with implications in adaptive responses. These proteins possess a conserved prion-like domain (PrLD) which is an intrinsically disordered region capable of adopting different conformations upon perceiving external stimuli. Owing to changes in protein conformation, functional characteristics of proteins harboring PrLDs get altered thereby, providing a unique mode of protein-based regulation. Since PrLPs are ubiquitous in nature and involved in diverse functions, through this study, we aim to explore the role of such domains in yet another important physiological process viz. plant-microbe interactions to get insights into the mechanisms dictating cross-kingdom interactions. We have evaluated the presence and functions of PrLPs in 18 different plant-associated fungi of agricultural importance to unravel their role in plant-microbe interactions. Of the 241,997 proteins scanned, 3,820 (~ 1.6%) were identified as putative PrLPs with pathogenic fungi showing significantly higher PrLP density than their beneficial counterparts. Further, through GO enrichment analysis, we could predict several PrLPs from pathogenic fungi to be involved in virulence and formation of stress granules. Notably, PrLPs involved in (retro)transposition were observed exclusively in pathogenic fungi. We even analyzed publicly available data for the expression alterations of fungal PrLPs upon their interaction with their respective hosts which revealed perturbation in the levels of some PrLP-encoding genes during interactions with plants. Overall, our work sheds light into the probable role of prion-like candidates in plant-fungi interaction, particularly in context of pathogenesis, paving way for more focused studies for validating their role.

Facilitation of Sclerotinia sclerotiorum infestation by aphid feeding behaviour is not affected by aphid resistance in oilseed rape

The relation between aphids and Sclerotinia stem rot (SSR) in oilseed rape is rarely examined because they are often studied alone. We have observed a significant correlation between the number of aphids and the occurrence of SSR in our field studies. Electropenetrography (EPG) was used to evaluate the effects of Brevicoryne brassicae (Linnaeus) on two oilseed rape cultivars while acquiring, vectoring and inoculating of Sclerotinia sclerotiorum Lib. (de Bary) ascospores. The results demonstrated that aphid feeding followed by the application of an ascospore suspension significantly increased S. sclerotiorum incidence. Aphids were capable of adhering to ascospores and carrying them to healthy plants, thereby causing diseases. The results of the EPG analysis indicated that aphid feeding behaviour was significantly altered in all leaf tissue levels following infection with S. sclerotiorum. Aphids initiated their first puncture significantly sooner than the control group, began probing mesophyll cells earlier, significantly increased the frequency of both short probes and intracellular punctures and had a significantly shorter pathway duration. On infected aphid-susceptible cultivars, aphids secreted more saliva but had reduced ingestion compared with aphids feeding on non-infected oilseed rape. In addition, ascospores can affect aphid feeding behaviour by adhering to aphids. Aphids carrying ascospores punctured cells earlier, with a significant increase in the frequency and duration of short probes and cell punctures, shortened pathway durations, increased salivation and reduced ingestion compared with aphids not carrying ascospores. On aphid-susceptible cultivars, aphids carrying ascospores delayed puncture onset, but on resistant cultivars, puncture onset was shortened. There is a correlation between aphids and S. sclerotiorum. The impact of S. sclerotiorum on aphid feeding behaviour is directional, favouring the spread of the fungus. This promotion does not appear to be altered by the aphid resistance of the cultivar.

A review on mechanisms and prospects of endophytic bacteria in biocontrol of plant pathogenic fungi and their plant growth-promoting activities

Endophytic bacteria, living inside plants, are competent plant colonizers, capable of enhancing immune responses in plants and establishing a symbiotic relationship with them. Endophytic bacteria are able to control phytopathogenic fungi while exhibiting plant growth-promoting activity. Here, we discussed the mechanisms of phytopathogenic fungi control and plant growth-promoting actions discovered in some major groups of beneficial endophytic bacteria such as Bacillus, Paenibacillus, and Pseudomonas. Most of the studied strains in these genera were isolated from the rhizosphere and soils, and a more extensive study of these endophytic bacteria is needed. It is essential to understand the underlying biocontrol and plant growth-promoting mechanisms and to develop an effective screening approach for selecting potential endophytic bacteria for various applications. We have suggested a screening strategy to identify potentially useful endophytic bacteria based on mechanistic phenomena. The discovery of endophytic bacteria with useful biocontrol and plant growth-promoting characteristics is essential for developing sustainable agriculture.

Natural variation in BnaA07.MKK9 confers resistance to Sclerotinia stem rot in oilseed rape

Sclerotinia stem rot (SSR), caused by the necrotrophic fungus Sclerotinia sclerotiorum, is one of the most devastating diseases for several major oil-producing crops. Despite its impact, the genetic basis of SSR resistance in plants remains poorly understood. Here, through a genome-wide association study, we identify a key gene, BnaA07. MKK9, that encodes a mitogen-activated protein kinase kinase that confers SSR resistance in oilseed rape. Our functional analyses reveal that BnaA07.MKK9 interacts with BnaC03.MPK3 and BnaC03.MPK6 and phosphorylates them at the TEY activation motif, triggering a signaling cascade that initiates biosynthesis of ethylene, camalexin, and indole glucosinolates, and promotes accumulation of H2O2 and the hypersensitive response, ultimately conferring resistance. Furthermore, variations in the coding sequence of BnaA07.MKK9 alter its kinase activity and improve SSR resistance by ~30% in cultivars carrying the advantageous haplotype. These findings enhance our understanding of SSR resistance and may help engineer novel diversity for future breeding of oilseed rape.

Sclerotia degradation by Trichoderma-mycoparasitic; an effective and sustainable trend in the drop lettuce disease control caused by Sclerotinia sclerotiorum

Controlling the hazard of sclerotia produced by the Sclerotinia sclerotiorum is very complex, and it is urgent to adopt an effective method that is harmonious environmentally to control the disease. Among the six isolates isolated from the rhizosphere of lettuce, the isolate HZA84 demonstrated a high activity in its antagonism towards Sclerotinia sclerotiorum in vitro, and produces siderophore. By amplification of internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF1-α), and RNA polymerase II subunit (RPB2) genes, the isolate HZA84 was identified as Trichoderma asperellum, which was confirmed by analysis of phylogenetic tree. The Scanning electron microscope monitoring detected that the isolate HZA84 spread over the sclerotial surface, thus, damaging, decomposing, and distorting the globular cells of the outer cortex of the sclerotia. The Real-time polymerase chain reaction (RT-qPCR) analysis disclosed the overexpression of two genes (chit33 and chit37) encoding the endochitinase in addition to one gene (prb1) encoding the proteinase during 4 and 8 days of the parasitism behavior of isolate HZA84 on the sclerotia surface. These enzymes aligned together in the sclerotia destruction by hyperparasitism. On the other hand, the pots trial revealed that spraying of isolate HZA84 reduced the drop disease symptoms of lettuce. The disease severity was decreased by 19.33 and the biocontrol efficiency was increased by 80.67% within the fourth week of inoculation. These findings magnify the unique role of Trichoderma in disrupting the development of plant diseases in sustainable ways.

Double-Stranded RNA Targeting White Mold Sclerotinia sclerotiorum Argonaute 2 for Disease Control via Spray-Induced Gene Silencing

Sclerotinia sclerotiorum, the causal agent of white mold infection, is a cosmopolitan fungal pathogen that causes major yield losses in many economically important crops. Spray-induced gene silencing has recently been shown to be a promising alternative method for controlling plant diseases. Based on our prior research, we focused on developing a spray-induced gene silencing approach to control white mold by silencing S. sclerotiorum argonaute 2 (SsAgo2), a crucial part of the fungal small RNA pathway. We compared the lesion size as a result of targeting each ∼500-bp segment of SsAgo2 from the 5' to the 3' end and found that targeting the PIWI/RNaseH domain of SsAgo2 is most effective. External application of double-stranded RNA (dsRNA)-suppressed white mold infection using either in vitro or in vivo transcripts was determined at the rate of 800 ng/0.2 cm2 area with a downregulation of SsAgo2 from infected leaf tissue confirmed by RT-qPCR. Furthermore, magnesium/iron-layered double hydroxide nanosheets loaded with in vitro- and in vivo-transcribed dsRNA segments significantly reduced the rate of S. sclerotiorum lesion expansion. In vivo-produced dsRNA targeting the PIWI/RNaseH domain of the SsAgo2 transcript showed increased efficacy in reducing the white mold symptoms of S. sclerotiorum when combined with layered double hydroxide nanosheets. This approach is promising to produce a large scale of dsRNA that can be deployed as an environmentally friendly fungicide to manage white mold infections in the field.

Variation in Pathogenicity and Subsequent Production of Sclerotia of Sclerotinia sclerotiorum Isolates in Different Cover Crops, Flower Strips, and Weeds

Cover crops and flower strips are used in agricultural fields as part of integrated pest management strategies. However, their potential as secondary hosts of soilborne pathogens such as Sclerotinia sclerotiorum in oilseed rape cultivation is not fully comprehended. In the current study, we evaluated the effect of pathogen virulence on the development of Sclerotinia stem/leaf rot and sclerotia production in 33 plant species from 11 botanical families using two S. sclerotiorum isolates. Furthermore, the effect of sclerotial size on carpogenic germination was studied. Results showed that the pathogen's virulence significantly affected the occurrence and development of Sclerotinia stem/leaf rot and the subsequent production of sclerotia. Among all plant species tested, 26 were more susceptible to the highly aggressive S. sclerotiorum isolate, which produced more and bigger sclerotia in 17 species than the less aggressive isolate. Moreover, a stronger positive correlation was found between the relative lesion length of plants inoculated with the highly aggressive isolate and the number of sclerotia produced by this isolate (Spearman's rank correlation coefficient [rs] = 0.572; P = 0.004). Additionally, we found that larger and heavier sclerotia produced stipes and apothecia earlier and at a greater rate than smaller ones. The heavyweight class had the highest carpogenic germination rate (82.4%), followed by the average (67.2%) and lightweight classes (59.5%). Our findings highlight the need for further investigation into the potential risks associated with cover crops, weeds, and flower strips as secondary hosts of soilborne pathogens in agricultural fields.

Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens

The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.

Genome-wide identification of the ICS family genes and its role in resistance to Plasmodiophora brassicae in Brassica napus L

The isochorismate synthase (ICS) proteins are essential regulators of salicylic acid (SA) synthesis, which has been reported to regulate resistance to biotic and abiotic stresses in plants. Clubroot caused by Plasmodiophora brassicae is a common disease that threatens the yield and quality of Oilseed rape (Brassica napus L.). Exogenous application of salicylic acid reduced the incidence of clubroot in oilseed rape. However, the potential importance of the ICS genes family in B. napus and its diploid progenitors has been unclear. Here, we identified 16, 9, and 10 ICS genes in the allotetraploid B. napus, diploid ancestor Brassica rapa and Brassica oleracea, respectively. These ICS genes were classified into three subfamilies (I-III), and member of the same subfamilies showed relatively conserved gene structures, motifs, and protein domains. Furthermore, many hormone-response and stress-related promoter cis-acting elements were observed in the BnaICS genes. Exogenous application of SA delayed the growth of clubroot galls, and the expression of BnaICS genes was significantly different compared to the control groups. Protein-protein interaction analysis identified 58 proteins involved in the regulation of ICS in response to P. brassicae in B. napus. These results provide new clues for understanding the resistance mechanism to P. brassicae.

Genome-Wide Identification and Multi-Stress Response Analysis of the DABB-Type Protein-Encoding Genes in Brassica napus

The DABB proteins, which are characterized by stress-responsive dimeric A/B barrel domains, have multiple functions in plant biology. In Arabidopsis thaliana, these proteins play a crucial role in defending against various pathogenic fungi. However, the specific roles of DABB proteins in Brassica napus remain elusive. In this study, 16 DABB encoding genes were identified, distributed across 10 chromosomes of the B. napus genome, which were classified into 5 branches based on phylogenetic analysis. Genes within the same branch exhibited similar structural domains, conserved motifs, and three-dimensional structures, indicative of the conservation of BnaDABB genes (BnaDABBs). Furthermore, the enrichment of numerous cis-acting elements in hormone induction and light response were revealed in the promoters of BnaDABBs. Expression pattern analysis demonstrated the involvement of BnaDABBs, not only in the organ development of B. napus but also in response to abiotic stresses and Sclerotinia sclerotiorum infection. Altogether, these findings imply the significant impacts of BnaDABBs on plant growth and development, as well as stress responses.

Recent Advances of Oxalate Decarboxylase: Biochemical Characteristics, Catalysis Mechanisms, and Gene Expression and Regulation

Oxalate decarboxylase (OXDC) is a typical Mn2+/Mn3+ dependent metal enzyme and splits oxalate to formate and CO2 without any organic cofactors. Fungi and bacteria are the main organisms expressing the OXDC gene, but with a significantly different mechanism of gene expression and regulation. Many articles reported its potential applications in the clinical treatment of hyperoxaluria, low-oxalate food processing, degradation of oxalate salt deposits, oxalate acid diagnostics, biocontrol, biodemulsifier, and electrochemical oxidation. However, some questions still remain to be clarified about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II)/Mn(III), the nature of dioxygen involved in the catalytic mechanism, and how OXDC acquires Mn(II) /Mn(III). This review mainly summarizes its biochemical and structure characteristics, gene expression and regulation, and catalysis mechanism. We also deep-mined oxalate decarboxylase gene data from National Center for Biotechnology Information to give some insights to explore new OXDC with diverse biochemical properties.

4-Hydroxybenzoic Acid-Based Hydrazide-Hydrazones as Potent Growth Inhibition Agents of Laccase-Producing Phytopathogenic Fungi That Are Useful in the Protection of Oilseed Crops

The research on new compounds against plant pathogens is still socially and economically important. It results from the increasing resistance of pests to plant protection products and the need to maintain high yields of crops, particularly oilseed crops used to manufacture edible and industrial oils and biofuels. We tested thirty-five semi-synthetic hydrazide-hydrazones with aromatic fragments of natural origin against phytopathogenic laccase-producing fungi such as Botrytis cinerea, Sclerotinia sclerotiorum, and Cerrena unicolor. Among the investigated molecules previously identified as potent laccase inhibitors were also strong antifungal agents against the fungal species tested. The highest antifungal activity showed derivatives of 4-hydroxybenzoic acid and salicylic aldehydes with 3-tert-butyl, phenyl, or isopropyl substituents. S. sclerotiorum appeared to be the most susceptible to the tested compounds, with the lowest IC50 values between 0.5 and 1.8 µg/mL. We applied two variants of phytotoxicity tests for representative crop seeds and selected hydrazide-hydrazones. Most tested molecules show no or low phytotoxic effect for flax and sunflower seeds. Moreover, a positive impact on seed germination infected with fungi was observed. With the potential for application, the cytotoxicity of the hydrazide-hydrazones of choice toward MCF-10A and BALB/3T3 cell lines was lower than that of the azoxystrobin fungicide tested.