We explore the combined use of two beneficial fungal isolates, Trichoderma gamsii T6085 (Tg) and Clonostachys rosea IK726 (Cr), to enhance Fusarium head blight (FHB) management by biological control. We found no evidence for mycoparasitism or inhibition via diffusible metabolites, but Tg volatiles inhibited Cr growth slightly. Although Cr reduced Tg spore germination and mycelial growth in liquid culture, this effect seemed absent in planta. The BCAs differently modulated defence-related (DR) genes when colonizing roots or spikes. At seven days post-inoculation (dpi), root-applied Cr, alone and co-inoculated, induced a minor upregulation of PR1. In leaves, a systemic signalling response by root inoculation was detected. In spikes, Pal1, PR1, and Lox1 were upregulated by Cr alone and co-inoculated at 96 hours post-inoculation (hpi). However, Lox1 activation was enhanced by co-inoculation. On spikes inoculated with Fg, the BCAs revealed different patterns of DR gene modulation indicating involvement of different biocontrol mechanisms. In detail, Pgip2 was primarily upregulated at 24 hpi in co-inoculated spikes whereas at 72 hpi activation of DR genes was observed only with Tg. Notably, the disease incidence was reduced by 93 % by co-inoculation. In addition, the inoculum potential of F. graminearum on straw was reduced by all BCAs treatments, with ≥ 96 % reduction of perithecia after six months incubation. Our results show the potential of combining Tg and Cr as a more effective and stable FHB management strategy, than by treatments with the individual strains.

Abstract Small cereals such as wheat, barley, and oat are staple food that directly (food) and indirectly (feed) sustain large populations globally. However, their production is increasingly threatened by both abiotic and biotic stresses. Biotic stresses, primarily caused by plant pathogen such as fungi, bacteria, oomycota and viruses are responsible for nearly half of the annual crop losses. Many plant pathogens produce mycotoxins, which contaminate crops and pose significant risks affecting human health. Fusarium spp., particularly those associated with Fusarium head blight (FHB) on cereal, are mycotoxin producers. The economic and health impacts of FHB make it a critical area of research. Although several strategies exist to control FHB, none can fully eradicate the disease. Challenges include pathogen resistance to chemical fungicides and regulatory restriction on genetically modified organisms (GMOs). Biological control offers a sustainable alternative, utilizing living organism to counteract pathogens. Here we explore the mechanisms of biological control based on complex molecular patterns involved during the three-way interaction between plant, pathogen and biocontrol agent. We analyze the FHB pathosystem and associated BCAs from multiple perspectives, providing a comprehensive insight to BCAs efficacy. Information © The Authors 2025

Coffee leaf rust (CLR) is caused by the biotrophic pathogenic fungus Hemileia vastatrix. Despite being the most researched coffee disease, mysteries still exist relating to its epidemiology and biology. The objective of this work is to highlight past and present events concerning this prominent coffee disease. We start with an historical overview of the homeland of Coffea arabica, the Afromontane forest of south-west Ethiopia, and then follow its journey across the globe linked to colonial trade and power struggles. We report the relevance of CLR to coffee production today, with a focus on the Americas and summarize unproven hypotheses in relation to the cause of recent epidemics. We present an original hypothesis concerning the first major outbreak occurring in 1869 in Ceylon (Sri Lanka), based on geopolitical connections to global trade. We review old and new options for management of the disease. The likelihood of a yet undetected alternate host of H. vastatrix is also considered as an additional piece of the epidemiological puzzle. Finally, we reflect on the interactions between H. vastatrix and a changing climate. By better understanding past events, linked to CLR, we may be better prepared for future outbreaks.

Continuous pesticide usage has negative impacts on people and ecosystems associated with coffee farms. Alternative plant protection strategies can be implemented that are sustainable for both the environment and the coffee farmer. In this review, new genomic techniques (NGTs) such as RNAi (RNA interference, using spray-induced gene silencing - SIGS) are presented as a possible novel strategy to manage Coffea arabica pests and diseases. Exploitation of the coffee agroforestry system (AFS) is presented as another strategy, offering both plant protection and ecosystem restoration functions. Interactions within a coffee-AFS were found to both hinder and bolster the development of some coffee pests and diseases. Biological control represents a third strategy that has been examined to-date to combat important coffee pests and diseases (i.e., American leaf spot, black coffee twig borer, coffee berry borer, coffee berry disease, coffee leaf miner, coffee leaf rust, coffee wilt disease and green coffee scale). The astute use of RNAi, AFS and/or biological control have the potential to provide alternatives to conventional pesticides for future sustainable coffee production. However, these approaches must be compatible with the coffee farmers' local needs and accessibility and bolstered through nationwide support by advisory services and coffee authorities.

Many Fusarium species cause serious diseases for cereal cultivation. These include Fusarium head blight and crown rot on wheat and bakanae disease on rice. These represent a major concern both in terms of food security and food safety. The latter is connected with the risk of mycotoxin contamination of grains. Biological control has proven its potential for controlling head blight and crown rot diseases of cereals caused by Fusarium species in a number of studies, and indeed several commercial products are under development. We review current knowledge of the mechanisms underlying biological control with a focus on fungal biocontrol agents, and also include challenges related to co-occurrence of Fusarium species. Several of the established biological control mechanisms (antibiosis, competition, hyperparasitism and induced resistance) can act simultaneously, thus resulting in disease control and, consequently, reduction of mycotoxin contamination. We also review the biological roles of some of the many mycotoxins produced by Fusarium species, and the mechanisms by which they are detoxified by cereal enzymes or by other fungi and how biological control agents (BCAs) can stimulate their degradation. Finally, the effect of biocontrol agents on the resident microbiota, as well as the effect of the resident microbiota on the performances of BCAs, are discussed. New perspectives on the use of biocontrol agents for the management of Fusarium diseases on cereals.

Oat (Avena sativa) is susceptible to Fusarium head blight (FHB). The quality of oat grain is threatened by the accumulation of mycotoxins, particularly the trichothecene deoxynivalenol (DON), which also acts as a virulence factor for the main pathogen Fusarium graminearum. The plant can defend itself, e.g., by DON detoxification by UGT-glycosyltransferases (UTGs) and accumulation of PR-proteins, even though these mechanisms do not deliver effective levels of resistance. We studied the ability of the fungal biocontrol agent (BCA) Clonostachys rosea to reduce FHB and mycotoxin accumulation. Greenhouse trials showed that C. rosea-inoculation of oat spikelets at anthesis 3 days prior to F. graminearum inoculation reduced both the amount of Fusarium DNA (79%) and DON level (80%) in mature oat kernels substantially. DON applied to C. rosea-treated spikelets resulted in higher conversion of DON to DON-3-Glc than in mock treated plants. Moreover, there was a significant enhancement of expression of two oat UGT-glycosyltransferase genes in C. rosea-treated oat. In addition, C. rosea treatment activated expression of genes encoding four PR-proteins and a WRKY23-like transcription factor, suggesting that C. rosea may induce resistance in oat. Thus, C. rosea IK726 has strong potential to be used as a BCA against FHB in oat as it inhibits F. graminearum infection effectively, whilst detoxifying DON mycotoxin rapidly.

EDITORIAL article Front. Microbiol., 10 May 2023Sec. Microbe and Virus Interactions with Plants Volume 14 - 2023 | https://doi.org/10.3389/fmicb.2023.1203870

Specialised metabolites produced during plant-fungal associations often define how symbiosis between the plant and the fungus proceeds. They also play a role in the establishment of additional interactions between the symbionts and other organisms present in the niche. However, specialised metabolism and its products are sometimes overlooked when studying plant-microbe interactions. This limits our understanding of the specific symbiotic associations and potentially future perspectives of their application in agriculture. In this study, we used the interaction between the root endophyte Serendipita indica and tomato (Solanum lycopersicum) plants to explore how specialised metabolism of the host plant is regulated upon a mutualistic symbiotic association. To do so, tomato seedlings were inoculated with S. indica chlamydospores and subjected to RNAseq analysis. Gene expression of the main tomato specialised metabolism pathways was compared between roots and leaves of endophyte-colonised plants and tissues of endophyte-free plants. S. indica colonisation resulted in a strong transcriptional response in the leaves of colonised plants. Furthermore, the presence of the fungus in plant roots appears to induce expression of genes involved in the biosynthesis of lignin-derived compounds, polyacetylenes, and specific terpenes in both roots and leaves, whereas pathways producing glycoalkaloids and flavonoids were expressed in lower or basal levels.

The enigmatic endophytic fungi are beginning to reveal their secrets. Like pathogens, they can manipulate the host for their own benefit to create their own optimal habitat. Some endophytic manipulations induce resistance or otherwise outcompete pathogens and can thus be exploited for biological control. Like pathogens and other symbionts, endophytes produce effector proteins and other molecules, ranging from specialised metabolites, phytohormones and microRNAs, to manipulate their hosts and other microorganisms they meet. There is a continuum from endophyte to pathogen: some organisms can infest or cause disease in some hosts, but not in others. Molecular genetics approaches coupled with functional characterisation have demonstrated their worth for understanding the biological phenomena underlying endophytic fungal interactions.

Plant diseases represent a major constraint on agricultural production. Finding sustainable novel means for their control is an important challenge. The ever-increasing knowledge and understanding of plant-microbe interactions has led to several ingenious transgenic approaches to combat disease. The first transgenic disease-resistant plants expressed single or a few stacked genes encoding antimicrobial proteins. Whereas the first attempts were disappointing in the field, several examples from recent field studies are promising and some of these use ingenious designer approaches. Less progress has been made with antimicrobial metabolites where the challenges lie in obtaining biosynthetic genes and in coordinating their expression. The increased understanding of the processes regulating plant defence (plant immunity) and modes of action of pathogen effector proteins have also led to novel strategies for designing resistant plants. The most promising of these is host-induced gene silencing that targets specific pathogens, either the effectors or, preferably, essential housekeeping genes. With these approaches, and several maverick examples of "genes pulled out of a hat," the technical effort in designing resistant plants is finally paying off. The prospects are good, biologically speaking, but can industry deliver? There is still an issue of public acceptance of genetic engineering of crop plants, especially in Europe; so whilst considerable strategic and practical progress has been made over the last decade, vanishingly few products have been adopted by agriculture. Some of these have been in use for over two decades. As yet, all are against viral diseases and not against diseases caused by microorganisms.

Oat is susceptible to several Fusarium species that cause contamination with different trichothecene mycotoxins. The molecular mechanisms behind Fusarium resistance in oat have yet to be elucidated. In the present work, we identified and characterised two oat UDP-glucosyltransferases orthologous to barley HvUGT13248. Overexpression of the latter in wheat had been shown previously to increase resistance to deoxynivalenol (DON) and nivalenol (NIV) and to decrease disease the severity of both Fusarium head blight and Fusarium crown rot. Both oat genes are highly inducible by the application of DON and during infection with Fusarium graminearum. Heterologous expression of these genes in a toxin-sensitive strain of Saccharomyces cerevisiae conferred high levels of resistance to DON, NIV and HT-2 toxins, but not C4-acetylated trichothecenes (T-2, diacetoxyscirpenol). Recombinant enzymes AsUGT1 and AsUGT2 expressed in Escherichia coli rapidly lost activity upon purification, but the treatment of whole cells with the toxin clearly demonstrated the ability to convert DON into DON-3-O-glucoside. The two UGTs could therefore play an important role in counteracting the Fusarium virulence factor DON in oat.

Aqueous extracts of Cinnamomum zeylanicum , Capsicum annuum and Azadirachta indica were tested for efficacy for management of Pseudocercospora fijiensis in banana ( Musa spp.) when applied as foliar sprays. Extracts of C. annuum and A. indica demonstrated fungicidal effects in vitro, without showing phytotoxic effects. The two extracts protected tissue culture banana plantlets of cultivar Musakala to a similar degree as the traditional fungicide difenoconazole. Extracts of A. indica and C. annuum (0.3 g/ml) reduced Black Sigatoka severity by 69.3% and 65.6%, respectively, and were thus comparable to the fungicide difenoconazole (72.7%). Soil drenching of the extracts did not significantly reduce Black Sigatoka severity. In planta effects of the extracts mainly consisted of delayed symptom appearance and reduced lesion number. Symptom development was dependent on extract concentration and days between extract application and inoculation. Effect of the tested extracts on height of plants and new leaves was not significant. Collectively, our data suggest that A. indica and C. annuum have interesting and unique properties as plant protection agents against Pseudocercospora fijiensis , but further research is needed to investigate their efficacy.

The fungal endophyte Penicillium olsonii ML37 is a biocontrol agent of Fusarium head blight in wheat (caused by Fusarium graminearum), which has shown a limited direct inhibition of fungal growth in vitro. We used RNA-seq and LC-MS/MS analyses to elucidate metabolic interactions of the three-way system Penicillium–wheat–Fusarium in greenhouse experiments. We demonstrated that P. olsonii ML37 colonises wheat spikes and transiently activates plant defence mechanisms, as pretreated spikes show a faster and stronger expression of the defence metabolism during the first 24 h after pathogen inoculation. This effect was transient and the expression of the same genes was lower in the pathogen-infected spikes than in those infected by P. olsonii alone. This response to the endophyte includes the transcriptional activation of several WRKY transcription factors. This early activation is associated with a reduction in FHB symptoms and significantly lower levels of the F. graminearum metabolites 15-acetyl-DON and culmorin. An increase in the Penicillium-associated metabolite asperphanamate confirms colonisation by the endophyte. Our results suggest that the mode of action used by P. olsonii ML37 is via a local defence activation in wheat spikes, and that this fungus has potential as a novel biological alternative in wheat disease control.

Physiological adaption primarily occurs through biochemical changes brought about by de novo transcription and resultant protein accumulation. The application of molecular technologies has provided much new information about the transcripts and the encoded proteins which accumulate as a response to different forms of environmental stress. The defense mechanisms which actually arrest pathogen penetration or development include the hypersensitive response, physical barriers, antimicrobial proteins and metabolites. The activation of defense responses by pathogens apparently utilizes essentially the same types of intracellular signal transduction pathway as used in other perception-response systems described for eukaryotes. The specific components of the induced defenses do not all accumulate in the same tissues relative to the attacking microorganism. The cloning and characterization of race-specific resistance genes has had high priority in plant pathology research for a number of years since race specificity represents a simple difference between the states of health and disease.

The global sustainability agenda is increasing the demand for reduction in inputs into agricultural production while maintaining profitable yield of quality products. Plant diseases are a major constraint for both yield and product quality, but often tools for their control are ineffective or lacking. Biological control using antagonistic microorganisms has long been a subject of research resulting in a wide range of products that are now available and marketed in specific territories around the world. These preparations are often niche products with narrow uses. The research effort is intense both to develop new biological control agents (BCAs) and to obtain knowledge of the mechanisms underlying biological disease control. The prospects for biological control are promising. As a minimum, BCAs supplement other sustainable disease management practices such as disease resistance, and present opportunities for controlling diseases for which other approaches are ineffective or unavailable. We can realistically expect increasing use of BCAs to control crop diseases in ways that will benefit the environment. This review paper arose from a webinar held by the British Society for Plant Pathology as part of the International Year of Plant Heath (IYPH2020), at which many of the 300 participants posed or discussed interesting questions. This review is based on that input and the panel members at the webinar are all included as co-authors in this review.

Ustilaginoidea virens, causing rice false smut (RFS) is an economically important ascomycetous fungal pathogen distributed in rice-growing regions worldwide. Here, we identified a novel transcription factor UvCGBP1 (Cutinase G-box binding protein) from this fungus, which is unique to ascomycetes. Deletion of UvCGBP1 affected development and virulence of U. virens. A total of 865 downstream target genes of UvCGBP1 was identified using ChIP-seq and the most significant KEGG enriched functional pathway was the MAPK signaling pathway. Approximately 36% of target genes contain the AGGGG (G-box) motif in their promoter. Among the targets, deletion of UvCGBP1 affected transcriptional and translational levels of UvPmk1 and UvSlt2, both of which were important in virulence. ChIP-qPCR, yeast one-hybrid and EMSA confirmed that UvCGBP1 can bind the promoter of UvPmk1 or UvSlt2. Overexpression of UvPmk1 in the ∆UvCGBP1-33 mutant restored partially its virulence and hyphae growth, indicating that UvCGBP1 could function via the MAPK pathway to regulate fungal virulence. Taken together, this study uncovered a novel regulatory mechanism of fungal virulence linking the MAPK pathway mediated by a G-box binding transcription factor, UvCGBP1.

Plants in nature are subject to constant attack by plant pathogenic microbes. In this chapter, the authors focus on the inducible biochemical mechanisms underlying resistance and the limited knowledge of the means by which plants regulate these responses to pathogens. They discuss the main strategies used to obtain this knowledge. Peroxidases are believed to be responsible for the extracellular polymerization of the monomers to give lignin and suberin, as well as to other cell wall components such as polysaccharides and possibly cell wall proteins. Various classes of defense-related compounds, the isoflavonoid, furanocoumarin, and related phytoalexins, the stilb-une phytoalexins and lignin, as well as the signal molecule salicyclic acid are all synthesized through this pathway, as are anthocyanin pigments and other compounds of unknown function. The shotgun approach for studying induced gene expression utilizes cDNA libraries to obtain clones representing transcripts which accumulate in tissue responding to the pathogen.

Interactions between plant-associated fungi and their hosts are characterized by a continuous crosstalk of chemical molecules. Specialized metabolites are often produced during these associations and play important roles in the symbiosis between the plant and the fungus, as well as in the establishment of additional interactions between the symbionts and other organisms present in the niche. Serendipita indica, a root endophytic fungus from the phylum Basidiomycota, is able to colonize a wide range of plant species, conferring many benefits to its hosts. The genome of S. indica possesses only few genes predicted to be involved in specialized metabolite biosynthesis, including a putative terpenoid synthase gene (SiTPS). In our experimental setup, SiTPS expression was upregulated when the fungus colonized tomato roots compared to its expression in fungal biomass growing on synthetic medium. Heterologous expression of SiTPS in Escherichia coli showed that the produced protein catalyzes the synthesis of a few sesquiterpenoids, with the alcohol viridiflorol being the main product. To investigate the role of SiTPS in the plant-endophyte interaction, an SiTPS-over-expressing mutant line was created and assessed for its ability to colonize tomato roots. Although overexpression of SiTPS did not lead to improved fungal colonization ability, an in vitro growth-inhibition assay showed that viridiflorol has antifungal properties. Addition of viridiflorol to the culture medium inhibited the germination of spores from a phytopathogenic fungus, indicating that SiTPS and its products could provide S. indica with a competitive advantage over other plant-associated fungi during root colonization.