Colletotrichum - current status and future directions

Evaluation of sterols as markers of fungal spoilage in red pepper powder

Red pepper powder (RPP) made from ground dried red pepper (Capsicum annuum L.) is prone to adulteration with fungal-spoiled RPP to gain unfair profits in Korea. This study aimed to investigate the effects of fungal infection on the ergosterol and phytosterol content of RPP and evaluate the potential of the sterol content as a marker for identifying fungal-spoiled RPP. Ergosterol was detected only in fungal-spoiled RPP and not in unspoiled RPP [ Collapse

Key Words

• Adulteration
• Alternaria alternata
• Colletotrichum acutatum
• Ergosterol
• Fungal spoilage
• Phytosterols

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MESH Headings

• Capsicum/microbiology
• Capsicum/chemistry
• Food Contamination/analysis
• Fungi/metabolism
• Fungi/isolation & purification
• Sterols/analysis
• Powders/chemistry
• Biomarkers/analysis
• Phytosterols/analysis
• Ergosterol/analysis

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Affiliation(s)

Eunji Choi Department of Food and Nutrition, Sookmyung Women's University, Seoul 04310, South Korea.
Hyang Sook Chun Department of Food Science & Technology, Chung-Ang University, Anseong 17546, South Korea.
Joong-Hyuck Auh Department of Food Science & Technology, Chung-Ang University, Anseong 17546, South Korea.
Sangdoo Ahn Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea.
Byung Hee Kim Department of Food and Nutrition, Sookmyung Women's University, Seoul 04310, South Korea.

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Transcription Factor CgSte12 Regulates Pathogenicity by Affecting Appressorium Structural Development in the Anthracnose-Causing Fungus Colletotrichum gloeosporioides

Colletotrichum gloeosporioides is the causal agent of poplar anthracnose, which induces major economic losses and adversely affects the ecosystem services of poplar forests. The appressorium serves as a penetration structure for many pathogenic fungi, including C. gloeosporioides. The production of mucilage and the formation of penetration pegs are critically important for the appressorium-mediated penetration of host tissues. We previously found that CgPmk1 is a key protein involved in appressorium formation, penetration, and pathogenicity. Although CgSte12, which is a transcription factor that functions downstream of CgPmk1, regulates the formation of penetration pegs, its role in C. gloeosporioides appressorium development and pathogenicity has not been elucidated. Here, we developed C. gloeosporioides CgSTE12 mutants and characterized the molecular and cellular functions of CgSTE12. The results showed that mycelial growth and morphology were not affected in the CgSTE12 knockout mutants, which produced normal melanized appressoria. However, these mutants had less mucilage secreted around the appressoria, impaired appressorial cone formation, and the inability to form penetration pores and pegs, which ultimately led to a significant loss of pathogenicity. Our comparative transcriptome analysis revealed that CgSte12 controls the expression of genes involved in appressorium development and function, including genes encoding cutinases, NADPH oxidase, spermine biosynthesis-related proteins, ceramide biosynthesis-related proteins, fatty acid metabolism-related proteins, and glycerophospholipid metabolism-related proteins. Overall, our findings indicate that CgSte12 is a critical regulator of appressorium development and affects C. gloeosporioides pathogenicity by modulating the structural integrity of appressoria.

Fungicide resistance in Colletotrichum fructicola and Colletotrichum siamense causing peach anthracnose in China

Peach is one of the popular and economically important fruit crops in China. Peach cultivation is hampered due to attacks of anthracnose disease, causing significant economic losses. Colletotrichum fructicola and Colletotrichum siamense belong to the Colletotrichum gloeosporioides species complex and are considered major pathogens of peach anthracnose. Application of different groups of fungicides is a routine approach for controlling this disease. However, fungicide resistance is a significant drawback in managing peach anthracnose nowadays. In this study, 39 isolates of C. fructicola and 41 isolates of C. siamense were collected from different locations in various provinces in China. The sensitivity of C. fructicola and C. siamense to some commonly used fungicides, i.e., carbendazim, iprodione, fluopyram, and propiconazole, was determined. All the isolates of C. fructicola collected from Guangdong province showed high resistance to carbendazim, whereas isolates collected from Guizhou province were sensitive. In C. siamense, isolates collected from Hebei province showed moderate resistance, while those from Shandong province were sensitive to carbendazim. On the other hand, all the isolates of C. fructicola and C. siamense showed high resistance to the dicarboximide (DCF) fungicide iprodione and succinate dehydrogenase inhibitor (SDHI) fungicide fluopyram. However, they are all sensitive to the demethylation inhibitor (DMI) fungicide propiconazole. Positive cross-resistance was observed between carbendazim and benomyl as they are members of the same methyl benzimidazole carbamate (MBC) group. While no correlation of sensitivity was observed between different groups of fungicides. No significant differences were found in each fitness parameter between carbendazim-resistant and sensitive isolates in both species. Molecular characterization of the β-tubulin 2 (TUB2) gene revealed that in C. fructicola, the E198A point mutation was the determinant for the high resistance to carbendazim, while the F200Y point mutation was linked with the moderate resistance to carbendazim in C. siamense. Based on the results of this study, DMI fungicides, e.g., propiconazole or prochloraz could be used to control peach anthracnose, especially at locations where the pathogens have already developed the resistance to carbendazim and other fungicides.

Exhaustive identification and characterization of Colletotrichum siamense and Colletotrichum fructicola as causative agents of circular leaf spot disease of rubber tree (Hevea brasiliensis) in India

The rubber tree (Hevea brasiliensis) is one of the major domesticated crops planted commercially for the production of natural rubber (NR) worldwide. In recent years, rubber trees in the Southern states of India and other rubber-producing countries have experienced a severe leaf spot disease, characterized by the appearance of several brown circular spots in the initial stage, which later spread all over the lamina of fully matured leaves, leading to yellowing and defoliation. The causal organism of this Circular Leaf Spot (CLS) disease has not been conclusively identified in any previous studies. In this study, we collected infected leaf samples from various locations in the South Indian states. We aimed to identify the actual fungal pathogen that causes the CLS disease on rubber trees. Based on the morphological and molecular analysis of the most frequently isolated fungi from infected leaf samples were identified as Colletotrichum siamense and Colletotrichum fructicola. Pathogenicity tests also confirmed the involvement of isolated Colletotrichum spp. in the development of CLS disease. These findings provide valuable insights into understanding the CLS disease and its impact on rubber cultivation. To our knowledge, it is the first report of C. siamense and C. fructicola associated with CLS disease of rubber trees in India.

Exploring the Global Trends of Bacillus, Trichoderma and Entomopathogenic Fungi for Pathogen and Pest Control in Chili Cultivation

Chili, renowned globally and deeply ingrained in various cultures. Regrettably, the onset of diseases instigated by pests and pathogens has inflicted substantial losses on chili crops, with some farms experiencing complete production decimation. Challenges confronting chili cultivation include threats from pathogenic microbes like Xanthomonas, Fusarium, Phytophthora, Verticillium, Rhizoctonia, Colletotrichium and Viruses, alongside pests such as whiteflies, mites, thrips, aphids, and fruit flies. While conventional farming practices often resort to chemical pesticides to combat these challenges, their utilization poses substantial risks to both human health and the environment. In response to this pressing issue, this review aims to evaluate the potential of microbe-based biological control as eco-friendly alternatives to chemical pesticides for chili cultivation. Biocontrol agents such as Bacillus spp., Trichoderma spp., and entomopathogenic fungi present safer and more environmentally sustainable alternatives to chemical pesticides. However, despite the recognised potential of biocontrol agents, research on their efficacy in controlling the array of pests and pathogens affecting chili farming remains limited. This review addresses this gap by evaluating the efficiency of biocontrol agents, drawing insights from existing studies conducted in other crop systems, regarding pest and pathogen management. Notably, an analysis of Scopus publications revealed fewer than 30 publications in 2023 focused on these three microbial agents. Intriguingly, India, as the world's largest chili producer, leads in the number of publications concerning Bacillus spp., Trichoderma spp., and entomopathogenic fungi in chili cultivation. Further research on microbial agents is imperative to mitigate infections and reduce reliance on chemical pesticides for sustainable chili production.

Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species

The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country.

CfHMG Differentially Regulates the Sexual Development and Pathogenicity of Colletotrichum fructicola Plus and Minus Strains

Colletotrichum fructicola shows morphological and genetic differences in plus and minus strains. However, the mechanism of the differentiation between two types of strains is still largely unclear. Our early transcriptome analysis revealed that CfHMG expression differed in plus and minus strains. To define the functions of the CfHMG gene, we constructed gene deletion mutants by homologous recombination. We found that a CfHMG deletion mutant of the minus strain, CfHMG-M, could lead to a reduction in perithecium sizes and densities on media and sterile perithecium formation compared with the minus wild type (WT), whereas there was no effect for the plus mutant CfHMG-P. In co-cultures between CfHMG-P and minus WT, CfHMG-M and plus WT, or CfHMG-P and CfHMG-M, the quantities of perithecia were all reduced significantly. When conidial suspensions were inoculated on non-wounded apple fruit, it was found that the virulence of the minus mutant decreased significantly but not for the plus one. Further, we found that the virulence decrease in minus mutants was caused by a decrease in the conidium germination rate. Our results indicate that CfHMG of C. fructicola plays an important role in the mating line formation between the plus and minus strain for both strains and differentially regulates the perithecium size, density, fertilization, and virulence of the minus strain. The results are significant for further detecting the differentiated mechanisms between the plus and minus strains in Colletotrichum fungi.

What are the 100 most cited fungal genera?

The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.

Diversity of Colletotrichum species associated with anthracnose on Euonymus japonicus and their sensitivity to fungicides

As an evergreen shrub, Euonymus japonicus plays a crucial role in urban landscape construction, and its growth is affected by severe foliar anthracnose caused by Colletotrichum spp. However, the biodiversity of Colletotrichum species associated with anthracnose on E. japonicus remains undetermined. This study involved a two-year collection of E. japonicus leaf samples with typical anthracnose symptoms from 9 districts in Beijing, China. A total of 194 Colletotrichum isolates were obtained, and eight Colletotrichum species were subsequently identified using morphological characteristics and molecular identification with the ACT, GADPH, CHS, TUB2, and CAL genes, as well as the rDNA-ITS region. These species included Colletotrichum aenigma, C. fructicola, C. gloeosporioides, C. grossum, C. hebeiense, C. karstii, C. siamense, and C. theobromicola with C. siamense being the most prevalent (57%), followed by C. aenigma and C. theobromicola. Furthermore, C. fructicola, C. grossum and C. hebeiense are reported for the first time as causal agents of anthracnose on E. japonicus worldwide, and C. karstii is newly reported to be associated with E. japonicus anthracnose in China. Pathogenicity tests revealed that all tested isolates exhibited pathogenicity in the presence of wounds, emphasizing the need to avoid artificial or mechanical wounds to prevent infection in E. japonicus management. The EC50 values of five fungicides, namely difenoconazole, flusilazole, tebuconazole, hexaconazole, and prochloraz, were found to be less than 10 mg/L, indicating their strong potential for application. Notably, the EC50 of prochloraz was less than 0.05 mg/L for C. theobromicola. These findings offer valuable insights for the management of anthracnose on E. japonicus.

Discovery of a Biocontrol Strain Trichaptum laricinum: Its Metabolites and Antifungal Activity against Pathogenic Fungus Colletotrichum anthrisci

Finding safe and environmentally friendly fungicides is one of the important strategies in modern pesticide research and development. In this work, the antipathogenic effects of the fungus Trichaptum laricinum against the anthracnose pathogen Colletotrichum anthrisci were studied. The EtOAc extract of T. laricinum showed remarkable antifungal activity against C. anthrisci with an inhibition rate of 50% at 256 μg/mL. Bioguided isolation of the cultural broth of T. laricinum produced four new drimane sesquiterpenes, trichalarins A-D (1-4), and six other metabolites (5-10). Their structures were established by extensive spectroscopic methods, quantum chemical calculations, and single-crystal X-ray diffraction. All compounds exhibited antifungal activity against C. anthrisci with minimum inhibitory concentrations (MICs) of 8-64 μg/mL in vitro. Further in vivo assay suggested that compounds 2, 6, and 9 could significantly inhibit C. anthrisci growth in avocado fruit with inhibition rates close to 80% at the concentration of 256 μg/mL, while compounds 2 and 6 had an inhibition rate over 90% at the concentration of 512 μg/mL. The EtOAc extract of T. laricinum had no inhibitory effect on Pinus massoniana seed germination and growth at the concentration of 2 mg/mL, showing good environmental friendliness. Thus, the fungus T. laricinum could be considered as an ideal biocontrol strain, and its metabolites provided a diverse material basis for the antibiotic agents.

Chitosan and Chitooligosaccharides: Antifungal Potential and Structural Insights

Chitosan is a cationic polysaccharide derived from chitin deacetylation. This polysaccharide and its oligosaccharides have many biological activities and can be used in several fields due to their favorable characteristics, such as biodegradability, biocompatibility, and nontoxicity. This review aims to explore the antifungal potential of chitosan and chitooligosaccharides along with the conditions used for the activity and mechanisms of action they use to kill fungal cells. The sources, chemical properties, and applications of chitosan and chitooligosaccharides are discussed in this review. It also addresses the threat fungi pose to human health and crop production and how these saccharides have proven to be effective against these microorganisms. The cellular processes triggered by chitosan and chitooligosaccharides in fungal cells, and prospects for their use as potential antifungal agents are also examined.

The CfKOB1 gene related to cell apoptosis is required for pathogenicity and involved in mycovirus-induced hypovirulence in Colletotrichum fructicola

Colletotrichum fructicola is a globally significant phytopathogenic fungus. Mycovirus-induced hypovirulence has great potential for biological control and study of fungal pathogenic mechanisms. We previously reported that the mycovirus Colletotrichum alienum partitivirus 1 (CaPV1) is associated with the hypovirulence of C. fructicola, and the present study aimed to further investigate a host factor and its roles in mycovirus-induced hypovirulence. A gene named CfKOB1, which encodes putative protein homologous to the β-subunit of voltage-gated potassium channels and aldo-keto reductase, is downregulated upon CaPV1 infection and significantly upregulated during the early infection phase of Nicotiana benthamiana by C. fructicola. Deleting the CfKOB1 gene resulted in diminished vegetative growth, decreased production of asexual spores, hindered appressorium formation, reduced virulence, and altered tolerance to abiotic stresses. Transcriptome analysis revealed that CfKOB1 regulates many metabolic pathways as well as the cell cycle and apoptosis. Furthermore, enhanced apoptosis was observed in the ΔCfKOB1 mutants. Viral RNA accumulation was significantly increased in the CfKOB1 deletion mutant. Additionally, our findings demonstrated that CaPV1 infection in the WT strain also induced cell apoptosis. Collectively, these results highlight the diverse biological roles of the CfKOB1 gene in the fungus C. fructicola, while it also participates in mycovirus-induced hypovirulence by regulating apoptosis.

Identifying and Controlling Anthracnose Caused by Colletotrichum Taxa of Welsh Onion in Sanxing, Taiwan

Leaves of Welsh onion (Allium fistulosum) are subject to various fungal diseases such as anthracnose (Colletotrichum species) and Stemphylium leaf blight (Stemphylium vesicarium). These diseases are the main biotic limitations to Welsh onion production in northern Taiwan. From 2018 to 2020, anthracnose symptoms were observed throughout Welsh onion fields in northern Taiwan, mainly the Sanxing area. In total, 33 strains of Colletotrichum species were isolated from diseased leaves, and major causative agents were identified based on a multilocus phylogenetic analysis using four genomic regions (act, tub2, gapdh, and internal transcribed spacer). Based on this phylogeny, Colletotrichum species causing anthracnose of Welsh onion were identified as C. spaethianum (C. spaethianum species complex) and C. circinans (C. dematium species complex) in the Sanxing area, northern Taiwan. To determine and compare the pathogenicity of each species, representative fungal strains of each species were inoculated on the cultivar 'Siao-Lyu' by spraying spore suspension onto the leaf surface. Welsh onion plants were susceptible to both species, but disease incidence and severity were higher in C. spaethianum. In total, 31 fungicides were tested to determine their efficacy in reducing mycelial growth and conidial germination of representative strains of C. spaethianum and C. circinans under laboratory conditions. Five fungicides-fluazinam, metiram, mancozeb, thiram, and dithianon-effectively reduced mycelial growth and spore germination in both C. spaethianum and C. circinans. In contrast, difenoconazole and trifloxystrobin + tebuconazole, which are commonly used in Welsh onion production in northern Taiwan, mainly the Sanxing area, were ineffective. These results serve as valuable insights for growers, enabling them to identify and address the emergence of anthracnose caused by C. spaethianum and C. circinans of Welsh onion, employing fungicides with diverse modes of action. The findings of this study support sustainable management of anthracnose in Sanxing, northern Taiwan, although further field tests of the fungicides are warranted.

The Need and Opportunity to Update the Inventory of Plant Pathogenic Fungi and Oomycetes in Mexico

Mexico generates specific phytosanitary regulations for each product and origin to prevent the entry of quarantine pests and/or delay their spread within the national territory, including fungi and oomycetes. Phytosanitary regulations are established based on available information on the presence or absence of these pathogens in the country; however, the compilation and precise analysis of reports is a challenging task due to many publications lacking scientific rigor in determining the presence of a taxon of phytosanitary interest in the country. This review evaluated various studies reporting the presence of plant pathogenic fungi and oomycetes in Mexico and concluded that some lists of diseases and phytopathogenic organisms lack technical-scientific basis. Thus, it highlights the need and presents an excellent opportunity to establish a National Collection of Fungal Cultures and a National Herbarium for obligate parasites, as well as to generate a National Database of Phytopathogenic Fungi and Oomycetes present in Mexico, supported by the combination of morphological, molecular, epidemiological, pathogenicity, symptom, and micrograph data. If realized, this would have a direct impact on many future applications related to various topics, including quarantines, risk analysis, biodiversity studies, and monitoring of fungicide resistance, among others.

Identification and Characterization of Colletotrichum truncatum and C. destructivum Causing Stem Rot of White Clover in China

White clover (Trifolium repens L.) is an excellent quality forage legume species with superior planting efficiency, which reduces the cost of artificial weeding and nitrogen fertilizer inputs, and has feeding and economic value. However, from June to September 2022, severe stem rot affected the yield and quality of white clover crops in Harbin, Heilongjiang Province, China. The aim of this study was to identify the causative agents of the disease. Overall, Colletotrichum truncatum (6 isolates) and C. destructivum (10 isolates) were obtained from rotten white clover stems and identified based on morpho-molecular characteristics and phylogenetic analyses. Pathogenicity tests of the isolates revealed that C. destructivum had a higher pathogenicity to white clover than C. truncatum. In addition, all isolates were highly pathogenic to broad bean, fodder soybean, soybean, pak choi, and chickpea, were pathogenic to mint, and did not infect corn, wheat, or cilantro. C. destructivum and C. truncatum isolates were very sensitive to tebuconazole and pyraclostrobin, with EC50 values of 0.54 to 0.70 μg/ml and 0.42 to 0.62 μg/ml, respectively, efficacies ranging between 93.2 to 94.9% and 90.2 to 95.2% at 600 μg/ml and 450 μg/ml, respectively, and EC90 values of 1.88 to 13.36 μg/ml and 1.32 to 23.39 μg/ml, respectively. Therefore, intercropping of host and nonhost plants and chemicals can be considered to control stem rot in white clover. These results provide a basis for controlling C. destructivum and C. truncatum in white clover in China.

Development of a TaqMan Real-Time PCR for Early and Accurate Detection of Anthracnose Pathogen Colletotrichum siamense in Pachira glabra

Anthracnose, caused by Colletotrichum siamense, is a destructive disease of Pachira glabra in southern China. Early and proper monitoring and quantification of C. siamense is of importance for disease control. A calmodulin (CAL) gene-based TaqMan real-time PCR assay was developed for efficient detection and quantification of C. siamense, which reliably detected as low as 5 pg of genomic DNA and 12.8 fg (5800 copies) of target DNA. This method could specifically recognize all tested C. siamense isolates, while no amplification was observed in other closely related Colletotrichum species. The assay could still detect C. siamense in plant mixes, of which only 0.01% of the tissue was infected. A dynamic change in the amount of C. siamense population was observed during infection, suggesting that this real-time PCR assay can be used to monitor the fungal growth progression in the whole disease process. Moreover, the method enabled the detection of C. siamense in naturally infected and symptomless leaves of P. glabra trees in fields. Taken together, this specific TaqMan real-time PCR provides a rapid and accurate method for detection and quantification of C. siamense colonization in P. glabra, and will be useful for prediction of the disease to reduce the epidemic risk.

The microbiome dynamics and interaction of endosymbiotic Symbiodiniaceae and fungi are associated with thermal bleaching susceptibility of coral holobionts

The thermal bleaching percentage of coral holobionts shows interspecific differences under heat-stress conditions, which are closely related to the coral-associated microbiome. However, the ecological effects of community dynamics and interactions between Symbiodiniaceae and fungi on coral thermal bleaching susceptibility remain unclear. In this study, we analyzed the diversity, community structure, functions, and potential interaction of Symbiodiniaceae and fungi among 18 coral species from a high thermal bleaching risk atoll using next-generation sequencing. The results showed that heat-tolerant C3u sub-clade and Durusdinium dominated the Symbiodiniaceae community of corals and that there were no core amplicon sequence variants in the coral-associated fungal community. Fungal richness and the abundance of confirmed functional animal-plant pathogens were significantly positively correlated with the coral thermal bleaching percentage. Fungal indicators, including Didymellaceae, Chaetomiaceae, Schizophyllum, and Colletotrichum, were identified in corals. Each coral species had a complex Symbiodiniaceae-fungi interaction network (SFIN), which was driven by the dominant Symbiodiniaceae sub-clades. The SFINs of coral holobionts with low thermal bleaching susceptibility exhibited low complexity and high betweenness centrality. These results indicate that the extra heat tolerance of coral in Huangyan Island may be linked to the high abundance of heat-tolerant Symbiodiniaceae. Fungal communities have high interspecific flexibility, and the increase of fungal diversity and pathogen abundance was correlated with higher thermal bleaching susceptibility of corals. Moreover, fungal indicators were associated with the degrees of coral thermal bleaching susceptibility, including both high and intermediate levels. The topological properties of SFINs suggest that heat-tolerant coral have limited fungal parasitism and strong microbial network resilience.IMPORTANCEGlobal warming and enhanced marine heatwaves have led to a rapid decline in coral reef ecosystems worldwide. Several studies have focused on the impact of coral-associated microbiomes on thermal bleaching susceptibility in corals; however, the ecological functions and interactions between Symbiodiniaceae and fungi remain unclear. We investigated the microbiome dynamics and potential interactions of Symbiodiniaceae and fungi among 18 coral species in Huangyan Island. Our study found that the Symbiodiniaceae community of corals was mainly composed of heat-tolerant C3u sub-clade and Durusdinium. The increase in fungal diversity and pathogen abundance has close associations with higher coral thermal bleaching susceptibility. We first constructed an interaction network between Symbiodiniaceae and fungi in corals, which indicated that restricting fungal parasitism and strong interaction network resilience would promote heat acclimatization of corals. Accordingly, this study provides insights into the role of microorganisms and their interaction as drivers of interspecific differences in coral thermal bleaching.

Guanosine-specific single-stranded ribonuclease effectors of a phytopathogenic fungus potentiate host immune responses

Plants activate immunity upon recognition of pathogen-associated molecular patterns. Although phytopathogens have evolved a set of effector proteins to counteract plant immunity, some effectors are perceived by hosts and induce immune responses. Here, we show that two secreted ribonuclease effectors, SRN1 and SRN2, encoded in a phytopathogenic fungus, Colletotrichum orbiculare, induce cell death in a signal peptide- and catalytic residue-dependent manner, when transiently expressed in Nicotiana benthamiana. The pervasive presence of SRN genes across Colletotrichum species suggested the conserved roles. Using a transient gene expression system in cucumber (Cucumis sativus), an original host of C. orbiculare, we show that SRN1 and SRN2 potentiate host pattern-triggered immunity responses. Consistent with this, C. orbiculare SRN1 and SRN2 deletion mutants exhibited increased virulence on the host. In vitro analysis revealed that SRN1 specifically cleaves single-stranded RNAs at guanosine, leaving a 3'-end phosphate. Importantly, the potentiation of C. sativus responses by SRN1 and SRN2, present in the apoplast, depends on ribonuclease catalytic residues. We propose that the pathogen-derived apoplastic guanosine-specific single-stranded endoribonucleases lead to immunity potentiation in plants.

Genome comparisons reveal accessory genes crucial for the evolution of apple Glomerella leaf spot pathogenicity in Colletotrichum fungi

Apple Glomerella leaf spot (GLS) is an emerging fungal disease caused by Colletotrichum fructicola and other Colletotrichum species. These species are polyphyletic and it is currently unknown how these pathogens convergently evolved to infect apple. We generated chromosome-level genome assemblies of a GLS-adapted isolate and a non-adapted isolate in C. fructicola using long-read sequencing. Additionally, we resequenced 17 C. fructicola and C. aenigma isolates varying in GLS pathogenicity using short-read sequencing. Genome comparisons revealed a conserved bipartite genome architecture involving minichromosomes (accessory chromosomes) shared by C. fructicola and other closely related species within the C. gloeosporioides species complex. Moreover, two repeat-rich genomic regions (1.61 Mb in total) were specifically conserved among GLS-pathogenic isolates in C. fructicola and C. aenigma. Single-gene deletion of 10 accessory genes within the GLS-specific regions of C. fructicola identified three that were essential for GLS pathogenicity. These genes encoded a putative non-ribosomal peptide synthetase, a flavin-binding monooxygenase and a small protein with unknown function. These results highlight the crucial role accessory genes play in the evolution of Colletotrichum pathogenicity and imply the significance of an unidentified secondary metabolite in GLS pathogenesis.

Identification and Fungicide Screening of Fungal Species Associated with Walnut Anthracnose in Shaanxi and Liaoning Provinces, China

Walnut is cultivated around the world for its precious woody nut and edible oil. Recently, walnut infected by Colletotrichum spp. resulted in a great yield and quality loss. In August and September 2014, walnut fruits with anthracnose were sampled from two commercial orchards in Shaanxi and Liaoning provinces, and five representative isolates were used in this study. To identify the pathogen properly, four genes per region (internal transcribed spacer, glyceraldehyde-3-phosphate dehydrogenase, actin, and chitin synthase) were sequenced and used in phylogenetic studies. Based on multilocus phylogenetic analysis, five isolates clustered with Colletotrichum fioriniae, including its ex-type, with 100% bootstrap support. The results of multilocus phylogenetic analyses, morphology, and pathogenicity confirmed that C. fioriniae was one of the walnut anthracnose pathogens in China. All 13 fungicides tested inhibited mycelial growth and spore germination. Flusilazole, fluazinam, prochloraz, and pyraclostrobin showed the strongest suppressive effects on the mycelial growth than the others, the average EC50 values ranged from 0.09 to 0.40 μg/ml, and there was not any significant difference (P < 0.05). Pyraclostrobin, thiram, and azoxystrobin were the most effective fungicides on spore germination (P < 0.05), and the EC50 values ranged from 0.01 to 0.44 μg/ml. Pyraclostrobin, azoxystrobin, fluazinam, flusilazole, mancozeb, thiram, and prochloraz exhibited a good control effect on walnut anthracnose caused by C. fioriniae, and preventive activities were greater than curative activities. Pyraclostrobin at 250 a.i. μg/ml and fluazinam at 500 a.i. μg/ml provided the highest preventive and curative efficacy, and the values ranged from 81.3 to 82.2% and from 72.9 to 73.6%, respectively. As a consequence, mancozeb and thiram could be used at the preinfection stage, and pyraclostrobin, azoxystrobin, flusilazole, fluazinam, and prochloraz could be used at the early stage for effective prevention and control of walnut anthracnose caused by C. fioriniae. The results will provide more significant instructions for controlling the disease effectively in northern China.

Comparative Transcriptomics Analysis Reveals the Differences in Transcription between Resistant and Susceptible Pepper (Capsicum annuum L.) Varieties in Response to Anthracnose

Pepper (Capsicum annuum L.) is a herbaceous plant species in the family Solanaceae. Capsicum anthracnose is caused by the genus Colletotrichum. spp., which decreases pepper production by about 50% each year due to anthracnose. In this study, we evaluated the resistance of red ripe fruits from 17 pepper varieties against anthracnose fungus Colletotrichum capsici. We assessed the size of the lesion diameter and conducted significance analysis to identify the resistant variety of B158 and susceptible variety of B161. We selected a resistant cultivar B158 and a susceptible cultivar B161 of pepper and used a transcription to investigate the molecular mechanisms underlying the plant's resistance to C. capsici, of which little is known. The inoculated fruit from these two varieties were used for the comparative transcription analysis, which revealed the anthracnose-induced differential transcription in the resistant and susceptible pepper samples. In the environment of an anthrax infection, we found that there were more differentially expressed genes in resistant varieties compared to susceptible varieties. Moreover, the response to stimulus and stress ability was stronger in the KANG. The transcription analysis revealed the activation of plant hormone signaling pathways, phenylpropanoid synthesis, and metabolic processes in the defense response of peppers against anthracnose. In addition, ARR-B, AP2-EREBP, bHLH, WRKY, and NAC are associated with disease resistance to anthracnose. Notably, WRKY and NAC were found to have a potentially positive regulatory role in the defense response against anthracnose. These findings contribute to a more comprehensive understanding of the resistance mechanisms of red pepper fruit to anthracnose infection, providing valuable molecular insights for further research on the resistance mechanisms and genetic regulations during this developmental stage of pepper.

A novel partitivirus conferring hypovirulence by affecting vesicle transport in the fungus Colletotrichum

Colletotrichum spp. are economically important phytopathogenic fungi that cause anthracnose in a variety of plant species worldwide. Hypovirulence-associated mycoviruses provide new options for the biological control of plant fungal diseases. Here, we found a novel partitivirus from Colletotrichum alienum and named it Colletotrichum alienum partitivirus 1 (CaPV1). CaPV1 contained two dsRNA segments encoding an RNA-dependent RNA polymerase and a capsid protein and was classified under the genus Gammapartitivirus of the family Partitiviridae. CaPV1 significantly decreased host virulence, mycelial growth, appressorial development, and appressorium turgor but increased conidial production with abnormal morphology. In addition, CaPV1 could be successfully transfected into other Colletotrichum species, including C. fructicola, C. spaethianum, and C. gloeosporioides, and caused hypovirulence, indicating the broad application potential of this virus. CaPV1 caused significant transcriptional rewiring of the host fungus C. alienum. Notably, some genes related to vesicle transport in the CaPV1-infected strain were downregulated, consistent with the impaired endocytosis pathway in this fungus. When the Rab gene CaRab7, which is associated with endocytosis in vesicle transport, was knocked out, the virulence of the mutants was reduced. Overall, our findings demonstrated that CaPV1 has the potential to control anthracnose caused by Colletotrichum, and the mechanism by which Colletotrichum induces hypovirulence is caused by affecting vesicle transport.IMPORTANCEColletotrichum is a kind of economically important phytopathogenic fungi that cause anthracnose disease in a variety of plant species worldwide. We found a novel mycovirus of the Gammapartitivirus genus and Partitiviridae family from the phytopathogenic fungus Colletotrichum alienum and named it CaPV1. This study revealed that CaPV1 infection significantly decreased host virulence and fitness by affecting mycelial growth, appressorial development, and appressorium turgor. In addition, CaPV1 could also infect other Colletotrichum species, including C. fructicola, C. spaethianum, and C. gloeosporioides, by viral particle transfection and resulting in hypovirulence of these Colletotrichum species. Transcriptomic analysis showed that CaPV1 caused significant transcriptional rewiring of the host fungus C. alienum, especially the genes involved in vesicle transport. Moreover, endocytosis and gene knockout assays demonstrated that the mechanism underlying CaPV1-induced hypovirulence is, at least in part, caused by affecting the vesicle transport of the host fungus. This study provided insights into the mechanisms underlying the pathogenesis of Colletotrichum species and mycovirus-fungus interactions, linking the role of mycovirus and fungus vesicle transport systems in shaping fungal pathogenicity.

What's in my Pot? Six Colletotrichum Species Causing Anthracnose in Brazilian Pecan Orchards

Pecan (Carya illinoinensis) is one important exotic forest crop cultivated in South America, specifically in Brazil, Uruguay, and Argentina. However, diseases such as anthracnose, favored by high humidity conditions and high summer temperatures, make its cultivation difficult, causing important loss to pecan farmers. This study used morphological and molecular approaches to identify the Colletotrichum species causing anthracnose in pecan plantations in Southern Brazil. The isolates obtained from pecan fruits with anthracnose symptoms were grouped through quantitative morphological characteristics into three distinct morphotypes. Molecular analysis of nuclear genes allowed the identification of six species of Colletotrichum causing anthracnose in pecan: C. nymphaeae, C. fioriniae, C. gloeosporioides, C. siamense, C. kahawae, and C. karsti. Three of these species are reported for the first time as causal agents of anthracnose in pecan. Therefore, these results provide an important basis for the adoption and/or development of anthracnose management strategies in pecan orchards cultivated in southern Brazil and neighboring countries.

Re-identification of Colletotrichum gloeosporioides Species Complex Isolates in Korea and Their Host Plants

The Colletotrichum gloeosporioides species complex includes many phytopathogenic species, causing anthracnose disease on a wide range of host plants and appearing to be globally distributed. Seventy-one Colletotrichum isolates in the complex from different plants and geographic regions in Korea were preserved in the Korean Agricultural Culture Collection (KACC). Most of them had been identified based on hosts and morphological features, this could lead to inaccurate species names. Therefore, the KACC isolates were re-identified using DNA sequence analyses of six loci, comprising internal transcribed spacer, gapdh, chs-1, his3, act, and tub2 in this study. Based on the combined phylogenetic analysis, KACC strains were assigned to 12 known species and three new species candidates. The detected species are C. siamense (n = 20), C. fructicola (n = 19), C. gloeosporioides (n = 9), C. aenigma (n = 5), C. camelliae (n = 3), C. temperatum (n = 3), C. musae (n = 2), C. theobromicola (n = 2), C. viniferum (n = 2), C. alatae (n = 1), C. jiangxiense (n = 1), and C. yulongense (n = 1). Of these, C. jiangxiense, C. temperatum, C. theobromicola and C. yulongense are unrecorded species in Korea. Host plant comparisons showed that 27 fungus-host associations are newly reported in the country. However, plant-fungus interactions need to be investigated by pathogenicity tests.

Evolutionary history of the cytochrome P450s from Colletotrichum species and prediction of their putative functional roles during host-pathogen interactions

The genomes of species belonging to the genus Colletotrichum harbor a substantial number of cytochrome P450 monooxygenases (CYPs) encoded by a broad diversity of gene families. However, the biological role of their CYP complement (CYPome) has not been elucidated. Here, we investigated the putative evolutionary scenarios that occurred during the evolution of the CYPome belonging to the Colletotrichum Graminicola species complex (s.c.) and their biological implications. The study revealed that most of the CYPome gene families belonging to the Graminicola s.c. experienced gene contractions. The reductive evolution resulted in species restricted CYPs are predominant in each CYPome of members from the Graminicola s.c., whereas only 18 families are absolutely conserved among these species. However, members of CYP families displayed a notably different phylogenetic relationship at the tertiary structure level, suggesting a putative convergent evolution scenario. Most of the CYP enzymes of the Graminicola s.c. share redundant functions in secondary metabolite biosynthesis and xenobiotic metabolism. Hence, this current work suggests that the presence of a broad CYPome in the genus Colletotrichum plays a critical role in the optimization of the colonization capability and virulence.

Colletotrichum nanjingense sp. nov. and C. gloeosporioides s.s. Causing Leaf Tip Blight on Jasminum mesnyi in Nanjing, Jiangsu, China

Jasminum mesnyi Hance is an important medicinal and ornamental plant. This species is native to South Central China and Vietnam and grows primarily in the subtropical biomes. In June 2022, 17 Colletotrichum strains were isolated from leaf tip blight on foliage of J. mesnyi in Nanjing, Jiangsu, China. Based on morphological characteristics and multilocus phylogenetic analyses of six genomic loci (ITS, CAL, ACT, TUB2, CHS-1, and GAPDH), a new species, namely, C. nanjingense, and a known species, namely, C. gloeosporioides s.s., were described and reported. Pathogenicity tests revealed that both species were pathogens causing leaf tip blight on J. mesnyi. The results provided necessary information for disease control and enhanced our understanding of the diversity of Colletotrichum species in China.

CFHTF2 Is Needed for Vegetative Growth, Conidial Morphogenesis and the Osmotic Stress Response in the Tea Plant Anthracnose (Colletotrichum fructicola)

Tea is an important cash crop worldwide, and its nutritional value has led to its high economic benefits. Tea anthracnose is a common disease of tea plants that seriously affects food safety and yield and has a far-reaching impact on the sustainable development of the tea industry. In this study, phenotypic analysis and pathogenicity analysis were performed on knockout and complement strains of HTF2-the transcriptional regulator of tea anthracnose homeobox-and the pathogenic mechanism of these strains was explored via RNA-seq. The MoHox1 gene sequence of the rice blast fungus was indexed, and the anthracnose genome was searched for CfHTF2. Evolutionary analysis recently reported the affinity of HTF2 for C. fructicola and C. higginsianum. The loss of CfHTF2 slowed the vegetative growth and spore-producing capacity of C. fructicola and weakened its resistance and pathogenesis to adverse conditions. The transcriptome sequencing of wild-type N425 and CfHTF2 deletion mutants was performed, and a total of 3144 differentially expressed genes (DEGs) were obtained, 1594 of which were upregulated and 1550 of which were downregulated. GO and KEGG enrichment analyses of DEGs mainly focused on signaling pathways such as the biosynthesis of secondary metabolites. In conclusion, this study lays a foundation for further study of the pathogenic mechanism of tea anthracnose and provides a molecular basis for the analysis of the pathogenic molecular mechanism of CfHTF2.

First Report of Colletotrichum fructicola, C. rhizophorae sp. nov. and C. thailandica sp. nov. on Mangrove in Thailand

Colletotrichum, a genus within the phylum Ascomycota (Fungi) and family Glomerellaceae are important plant pathogens globally. In this paper, we detail four Colletotrichum species found in mangrove ecosystems. Two new species, Colletotrichum rhizophorae and C. thailandica, and a new host record for Colletotrichum fructicola were identified in Thailand. Colletotrichum tropicale was collected from Taiwan's mangroves and is a new record for Rhizophora mucronata. These identifications were established through a combination of molecular analysis and morphological characteristics. This expanded dataset for Colletotrichum enhances our understanding of the genetic diversity within this genus and its associations with mangrove ecosystems. The findings outlined herein provide data on our exploration of mangrove pathogens in Asia.

Screening and characterization of biocontrol bacteria isolated from Ageratum conyzoides against Collectotrichum fructicola causing Chinese plum (Prunus salicina Lindl.) anthracnose

Chinese plum (Prunus salicina Lindl.) is a nutritionally and economically important stone fruit widely grown around the world. Anthracnose, caused by Collectotrichum spp., is one of the primary biotic stress factors limiting plum production. Medicinal plants may harbor rhizospheric or endophytic microorganisms that produce bioactive metabolites that can be used as anthracnose biocontrol agents. Here, 27 bacterial isolates from the medicinal plant A. conyzoides with diverse antagonistic activities against C. fructicola were screened. Based on morphological, physiological, biochemical, and molecular characterization, 25 of these isolates belong to different species of genus Bacillus, one to Pseudomonas monsensis, and one more to Microbacterium phyllosphaerae. Eight representative strains showed high biocontrol efficacy against plum anthracnose in a pot experiment. In addition, several Bacillus isolates showed a broad spectrum of inhibitory activity against a variety of fungal phytopathogens. Analysis of the volatile organic compound profile of these eight representative strains revealed a total of 47 compounds, most of which were ketones, while the others included alkanes, alkenes, alcohols, pyrazines, and phenols. Overall, this study confirmed the potential value of eight bacterial isolates for development as anthracnose biocontrol agents.

Blueberry floral probiotics: nectar microbes inhibit the growth of Colletotrichum pathogens

AIMS

To identify whether microorganisms isolated from blueberry flowers can inhibit the growth of Colletotrichum, an opportunistic plant pathogen that infects flowers and threatens yields, and to assess the impacts of floral microbes and Colletotrichum pathogens on artificial nectar sugars and honey bee consumption.

METHODS AND RESULTS

The growth inhibition of Colletotrichum (Colletotrichum acutatum, Colletotrichum fioriniae, and Colletotrichum gloeosporioides) was screened using both artificial nectar co-culture and dual culture plate assays. All candidate nectar microbes were screened for antagonism against a single C. acutatum isolate. Then, the top four candidate nectar microbes showing the strongest inhibition of C. acutatum (Neokomagataea thailandica, Neokomagataea tanensis, Metschnikowia rancensis, and Symmetrospora symmetrica) were evaluated for antagonism against three additional C. acutatum isolates, and single isolates of both C. fioriniae and C. gloeosporioides. In artificial nectar assays, single and three-species cultures inhibited the growth of two of four C. acutatum isolates by ca. 60%, but growth of other Colletotrichum species was not affected. In dual culture plate assays, inhibition was observed for all Colletotrichum species for at least three of four selected microbial antagonists (13%‒53%). Neither honey bee consumption of nectar nor nectar sugar concentrations were affected by any microbe or pathogen tested.

CONCLUSIONS

Selected floral microbes inhibited growth of all Colletotrichum species in vitro, although the degree of inhibition was specific to the assay and pathogen examined. In all microbial treatments, nectar sugars were preserved, and honey bee preference was not affected.

Study on the Antifungal Activity and Potential Mechanism of Natamycin against Colletotrichum fructicola

In this investigation, the antifungal activity, its influence on the quality of apples, and the molecular mechanism of natamycin against Colletotrichum fructicola were systematically explored. Our findings indicated that natamycin showed significant inhibition against C. fructicola. Moreover, it efficaciously maintained the apple quality by modulating the physicochemical index. Research on the antifungal mechanism showed that natamycin altered the mycelial microstructure, disrupted the plasma membrane integrality, and decreased the ergosterol content of C. fructicola. Interestingly, the exogenous addition of ergosterol weakened the antifungal activity of natamycin. Importantly, natamycin markedly inhibited the expression of Cyp51A and Cyp51B genes in C. fructicola, which was contrary to the results obtained after treatment with triazole fungicide flusilazole. All these results exhibited sufficient proof that natamycin had enormous potential to be conducive as a promising biopreservative against C. fructicola on apples, and these findings will advance our knowledge on the mechanism of natamycin against pathogenic fungi.

Efficient multiple gene knockout in Colletotrichum higginsianum via CRISPR/Cas9 ribonucleoprotein and URA3-based marker recycling

Colletotrichum higginsianum is a hemibiotrophic pathogen that causes anthracnose disease on crucifer hosts, including Arabidopsis thaliana. Despite the availability of genomic and transcriptomic information and the ability to transform both organisms, identifying C. higginsianum genes involved in virulence has been challenging due to recalcitrance to gene targeting and redundancy of virulence factors. To overcome these obstacles, we developed an efficient method for multiple gene disruption in C. higginsianum by combining CRISPR/Cas9 and a URA3-based marker recycling system. Our method significantly increased the efficiency of gene knockout via homologous recombination by introducing genomic DNA double-strand breaks. We demonstrated the applicability of the URA3-based marker recycling system for multiple gene targeting in the same strain. Using our technology, we successfully targeted two melanin biosynthesis genes, SCD1 and PKS1, which resulted in deficiency in melanization and loss of pathogenicity in the mutants. Our findings demonstrate the effectiveness of our methods in analysing virulence factors in C. higginsianum, thus accelerating research on plant-fungus interactions.

A Bitter, Complex Problem: Causal Colletotrichum Species in Virginia Orchards and Apple Fruit Susceptibility

Bitter rot, caused by Colletotrichum species, is one of the most devastating summer rot diseases affecting apple production in the Eastern United States. Given the differences in virulence and fungicide sensitivity levels between organisms belonging to the acutatum species complex (CASC) and the gloeosporioides species complex (CGSC), monitoring their diversity, geographic distribution, and frequency are essential for successful bitter rot management. In a 662-isolate collection from apple orchards in Virginia, isolates from CGSC were dominant (65.5%) in comparison to the CASC (34.5%). In a subsample of 82 representative isolates, using morphological and multilocus phylogenetic analyses, we identified C. fructicola (26.2%), C. chrysophilum (15.6%), C. siamense (0.8%), and C. theobromicola (0.8%) from CGSC and C. fioriniae (22.1%) and C. nymphaeae (1.6%) from CASC. The dominant species were C. fructicola, followed by C. fioriniae and C. chrysophilum. C. siamense followed by C. theobromicola developed the largest and deepest rot lesions on Honeycrisp fruit in our virulence tests. Detached fruit of nine apple cultivars and one wild accession (Malus sylvestris) were harvested early and late season and tested in controlled conditions for their susceptibility to C. fioriniae and C. chrysophilum. All cultivars were susceptible to both representative bitter rot species, with Honeycrisp fruit being the most susceptible and M. sylvestris, accession PI 369855, being the most resistant. We demonstrate that the frequency and prevalence of species in Colletotrichum complexes are highly variable in the Mid-Atlantic and provide region-specific data on apple cultivar susceptibility. Our findings are necessary for the successful management of bitter rot as an emerging and persistent problem in apple production both pre- and postharvest.

CfCpmd1 Regulates Pathogenicity and Sexual Development of Plus and Minus Strains in Colletotrichum fructicola Causing Glomerella Leaf Spot on Apple in China

Colletotrichum fructicola is a devastating fungal pathogen of diverse plants. Sexually compatible plus and minus strains occur in the same ascus. However, the differentiation mechanism of plus and minus strains remains poorly understood. Here, we characterized a novel Cys2-His2-containing transcription factor CfCpmd1. The plus CfCpmd1 deletion mutant (Δ+CfCpmd1) resulted in slow hyphal growth and a fluffy cotton-like colony, and the minus deletion mutant (Δ-CfCpmd1) exhibited characters similar to the wild type (WT). Δ+CfCpmd1 led to defective perithecial formation, whereas Δ-CfCpmd1 produced more and smaller perithecia. The normal mating line was developed by pairing cultures of Δ-CfCpmd1 and plus WT, whereas a weak line was observed between Δ+CfCpmd1 and minus WT. Conidial production was completely abolished in both plus and minus mutants. When inoculated on non-wounded apple leaves with mycelial plugs, Δ-CfCpmd1 was nonpathogenic because of failure to develop conidia and appressoria, while Δ+CfCpmd1 could infect apple leaves by appressoria differentiated directly from hyphal tips, even though no conidia formed. Collectively, our results demonstrate that CfCpmd1 of C. fructicola is an important gene related to plus and minus strain differentiation, which also affects hyphal growth, sporulation, appressorium formation, and pathogenicity.

Two new species of Colletotrichum (Glomerellaceae, Glomerellales) causing walnut anthracnose in Beijing

Colletotrichum species are plant pathogens, saprobes and endophytes on various plant hosts. It is regarded as one of the 10 most important genera of plant pathogens in the world. Walnut anthracnose is one of the most severe diseases affecting walnut productivity and quality in China. In this study, 162 isolates were obtained from 30 fruits and 65 leaf samples of walnut collected in Beijing, China. Based on morphological characteristics and DNA sequence analyses of the concatenated loci, namely internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), chitin synthase 1 (CHS-1) and beta-tubulin (TUB2), these isolates were identified as two novel species of Colletotrichum, i.e. C.juglandicola and C.peakense. Koch's postulates indicated that both C.juglandicola and C.peakense could cause anthracnose in walnut.

Genomic analysis of Colletotrichum camelliae responsible for tea brown blight disease

BACKGROUND

Colletotrichum camelliae, one of the most important phytopathogenic fungi infecting tea plants (Camellia sinensis), causes brown blight disease resulting in significant economic losses in yield of some sensitive cultivated tea varieties. To better understand its phytopathogenic mechanism, the genetic information is worth being resolved.

RESULTS

Here, a high-quality genomic sequence of C. camelliae (strain LT-3-1) was sequenced using PacBio RSII sequencing platform, one of the most advanced Three-generation sequencing platforms and assembled. The result showed that the fungal genomic sequence is 67.74 Mb in size (with the N50 contig 5.6 Mb in size) containing 14,849 putative genes, of which about 95.27% were annotated. The data revealed a large class of genomic clusters potentially related to fungal pathogenicity. Based on the Pathogen Host Interactions database, a total of 1698 genes (11.44% of the total ones) were annotated, containing 541 genes related to plant cell wall hydrolases which is remarkably higher than those of most species of Colletotrichum and others considered to be hemibiotrophic and necrotrophic fungi. It's likely that the increase in cell wall-degrading enzymes reflects a crucial adaptive characteristic for infecting tea plants.

CONCLUSION

Considering that C. camelliae has a specific host range and unique morphological and biological traits that distinguish it from other species of the genus Colletotrichum, characterization of the fungal genome will improve our understanding of the fungus and its phytopathogenic mechanism as well.

Diversity of Colletotrichum species associated with torch ginger anthracnose

Anthracnose caused by Colletotrichum species is one of the most important diseases of torch ginger. The disease leads to loss of aesthetic and commercial value of torch ginger stems. This study aimed to characterize Colletotrichum species associated with torch ginger anthracnose in the production areas of Pernambuco and Ceará. A total of 48 Colletotrichum isolates were identified using molecular techniques. Pathogenicity tests were performed on torch ginger with representative isolates. Phylogenetic analyses based on seven loci-DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locus MAT1-2-1 (APN2/MAT-IGS), calmodulin (CAL), intergenic spacer between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a hypothetical protein (GAP2-IGS), glutamine synthetase (GS), and β-tubulin (TUB2)-revealed that they belong to five known Colletotrichum species, namely, C. chrysophilum, C. fructicola, C. siamense, C. theobromicola, and C. tropicale, and three newly discovered species, described here as C. atlanticum, C. floscerae, and C. zingibericola. Of these, C. atlanticum was the most dominant. Pathogenicity assays showed that all isolates were pathogenic to torch ginger bracts. All species are reported for the first time associated with torch ginger in Brazil. The present study contributes to the current understanding of the diversity of Colletotrichum species associated with anthracnose on torch ginger and demonstrates the importance of accurate species identification for effective disease management strategies.

The evolution of mini-chromosomes in the fungal genus Colletotrichum

Anthracnose diseases caused by Colletotrichum species are among the most common fungal diseases. These symptoms typically manifest as dark, sunken lesions on leaves, stems, and fruit. In China, mango anthracnose seriously affects fruit yield and quality. Genome sequencing of several species shows the presence of mini-chromosomes. These are thought to contribute to virulence, but their formation and activity remain to be fully elucidated. Here, we assembled 17 Colletotrichum genomes (16 isolated from mango plus one from persimmon) through PacBio long-read sequencing. Half of the assembled scaffolds had telomeric repeats at both ends indicating full-length chromosomes. Based on comparative genomics analysis at interspecies and intraspecies levels, we identified extensive chromosomal rearrangements events. We analyzed mini-chromosomes of Colletotrichum spp. and found large variation among close relatives. In C. fructicola, homology between core chromosomes and mini-chromosomes suggested that some mini-chromosomes were generated by recombination of core chromosomes. In C. musae GZ23-3, we found 26 horizontally transferred genes arranged in clusters on mini-chromosomes. In C. asianum FJ11-1, several potential pathogenesis-related genes on mini-chromosomes were upregulated, especially in strains with highly pathogenic phenotypes. Mutants of these upregulated genes showed obvious defects in virulence. Our findings provide insights into the evolution and potential relationships to virulence associated with mini-chromosomes. IMPORTANCE Colletotrichum is a cosmopolitan fungal genus that seriously affects fruit yield and quality of many plant species. Mini-chromosomes have been found to be related to virulence in Colletotrichum. Further examination of mini-chromosomes can help us elucidate some pathogenic mechanisms of Colletotrichum. In this study, we generated novel assemblies of several Colletotrichum strains. Comparative genomic analyses within and between Colletotrichum species were conducted. We then identified mini-chromosomes in our sequenced strains systematically. The characteristics and generation of mini-chromosomes were investigated. Transcriptome analysis and gene knockout revealed pathogenesis-related genes located on mini-chromosomes of C. asianum FJ11-1. This study represents the most comprehensive investigation of chromosome evolution and potential pathogenicity of mini-chromosomes in the Colletotrichum genus.

Colletotrichum siamense, a Novel Causal Agent of Viburnum odoratissimum Leaf Blotch and Its Sensitivity to Fungicides

Viburnum odoratissimum Ker-Gawl is native to Asia and is usually used as a garden ornamental. In September 2022, a leaf blotch on V. odoratissimum was observed in Nanjing, Jiangsu, China. The disease causes the leaves of the plants to curl and dry up and defoliate early. It not only seriously affects the growth of the plants but also greatly reduces the ornamental value. The pathogenic fungus was isolated from the diseased leaves, and the fungus was identified to be Colletotrichum siamense based on morphological features and multilocus phylogenetic analyses of the internal transcribed spacer (ITS) region, actin (ACT), calmodulin (CAL), beta-tubulin 2 (TUB2), chitin synthase (CHS-1), Apn2-Mat1-2 intergenic spacer and partial mating type (ApMat), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes. Pathogenicity tests were performed by inoculating healthy leaves with conidia. C. siamense can grow at 15-35 °C, with an optimal growth temperature at 25-30 °C. The results of sensitivity to nine fungicides showed that C. siamense was the most sensitive to prochloraz in the concentration range of 0.01 μg/mL to 100 μg/mL. Therefore, spraying prochloraz before the optimum growth temperature of pathogenic fungus can achieve effective control. It provided useful information for future studies on the prevention and treatment strategies of C. siamense. This is the first report of leaf blotch caused by C. siamense on V. odoratissimum in China and worldwide.

Mango anthracnose disease: the current situation and direction for future research

Mango anthracnose disease (MAD) is a destructive disease of mangoes, with estimated yield losses of up to 100% in unmanaged plantations. Several strains that constitute Colletotrichum complexes are implicated in MAD worldwide. All mangoes grown for commercial purposes are susceptible, and a resistant cultivar for all strains is not presently available on the market. The infection can widely spread before being detected since the disease is invincible until after a protracted latent period. The detection of multiple strains of the pathogen in Mexico, Brazil, and China has prompted a significant increase in research on the disease. Synthetic pesticide application is the primary management technique used to manage the disease. However, newly observed declines in anthracnose susceptibility to many fungicides highlight the need for more environmentally friendly approaches. Recent progress in understanding the host range, molecular and phenotypic characterization, and susceptibility of the disease in several mango cultivars is discussed in this review. It provides updates on the mode of transmission, infection biology and contemporary management strategies. We suggest an integrated and ecologically sound approach to managing MAD.

Insights into Grape Ripe Rot: A Focus on the Colletotrichum gloeosporioides Species Complex and Its Management Strategies

Grape ripe rot, which is predominantly caused by the Colletotrichum species, presents a growing threat to global grape cultivation. This threat is amplified by the increasing populations of the Colletotrichum species in response to warmer climates. In this review, we investigate the wide-ranging spectrum of grape ripe rot, specifically highlighting the role and characteristics of the C. gloeosporioides species complex (CGSC). We incorporate this understanding as we explore the diverse symptoms that lead to infected grapevines, their intricate life cycle and epidemiology, and the escalating prevalence of C. viniferum in Asia and globally. Furthermore, we delve into numerous disease management strategies, both conventional and emerging, such as prevention and mitigation measures. These strategies include the examination of host resistances, beneficial cultivation practices, sanitation measures, microbiome health maintenance, fungicide choice and resistance, as well as integrated management approaches. This review seeks to enhance our understanding of this globally significant disease, aspiring to assist in the development and improvement of effective prevention and control strategies.

Genomic Resources of Four Colletotrichum Species (C. fioriniae, C. chrysophilum, C. noveboracense, and C. nupharicola) Threatening Commercial Apple Production in the Eastern United States

The genus Colletotrichum includes nine major clades with 252 species and 15 major phylogenetic lineages, also known as species complexes. Colletotrichum spp. are one of the top fungal plant pathogens causing anthracnose and pre- and postharvest fruit rots worldwide. Apple orchards are imperiled by devastating losses from apple bitter rot, ranging from 24 to 98%, which is a serious disease caused by several Colletotrichum species. Bitter rot is also a major postharvest rot disease, with C. fioriniae causing from 2 to 14% of unmarketable fruit in commercial apple storages. Dominant species causing apple bitter rot in the Mid-Atlantic United States are C. fioriniae from the Colletotrichum acutatum species complex and C. chrysophilum and C. noveboracense from the C. gloeosporioides species complex (CGSC). C. fioriniae is the dominant species causing apple bitter rot in the Northeastern and Mid-Atlantic states. C. chrysophilum was first identified on banana and cashew but has been recently found as the second most dominant species causing apple bitter rot in the Mid-Atlantic. As the third most dominant pathogen, C. noveboracense MB 836581 was identified as a novel species in the CGSC, causing apple bitter rot in the Mid-Atlantic. C. nupharicola is a sister group to C. fructicola and C. noveboracense, also causing bitter rot on apple. We deliver the resources of 10 new genomes, including two isolates of C. fioriniae, three isolates of C. chrysophilum, three isolates of C. noveboracense, and two isolates of C. nupharicola collected from apple fruit, yellow waterlily, and Juglans nigra. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Re-identification of Colletotrichum acutatum Species Complex in Korea and Their Host Plants

Colletotrichum acutatum species complex is one of the most important groups in the genus Colletotrichum with a high species diversity and a wide range of host plants. C. acutatum and related species have been collected from different plants and locations in Korea and deposited into the Korean Agricultural Culture Collection (KACC), National Institute of Agricultural Sciences since the 1990s. These fungal isolates were previously identified based mainly on morphological characteristics, and a limitation of molecular data was provided. To confirm the identification of species, 64 C. acutatum species complex isolates in KACC were used in this study for DNA sequence analyses of six loci: nuclear ribosomal internal transcribed spacers (ITS), betatubulin 2 (TUB2), histone-3 (HIS3), glyceraldehyde3-phosphate dehydrogenase (GAPDH), chitin synthase 1 (CHS-1), and actin (ACT). The molecular analysis revealed that they were identified in six different species of C. fioriniae (24 isolates), C. nymphaeae (21 isolates), C. scovillei (12 isolates), C. chrysanthemi (three isolates), C. lupini (two isolates), and C. godetiae (one isolate), and a novel species candidate. We compared the hosts of KACC isolates with "The List of Plant Diseases in Korea", previous reports in Korea and global reports and found that 23 combinations between hosts and pathogens could be newly reported in Korea after pathogenicity tests, and 12 of these have not been recorded in the world.

Probiotic Bacteria, Anaerobic Soil Disinfestation, and Mustard Cover Crop Biofumigation Suppress Soilborne Disease and Increase Yield of Strawberry in a Perennial Organic Production System

Black root rot complex and crown rot of strawberry caused by soilborne fungi limit sustainable strawberry production in the northeastern United States, especially in perennial systems, including matted row and plasticulture. As pathogen populations build up over time in the rhizosphere and infect the root system, feeder roots are pruned, which diminishes nutrient and water uptake and causes stunted plant growth or death. Alternative management options are needed for many organic and small growers who can't use chemical fumigants due to new regulations and potential health hazards. Strawberry plug plants were grown on beneficial microbe-inoculated or uninoculated planting mix followed by transplanting in fruiting field plots that either was biofumigated with mustard cover crop (MCC), anaerobically disinfested (ASD), or left untreated. Different combinations of plug plants and field plot treatments were used to determine the efficacy of individual treatments or synergistic effects from combination treatment. Plug plants were transplanted in pretreated plastic mulched raised beds and grown following a typical organically recommended production system. Plants grown on TerraGrow (TG)-inoculated planting mix showed enhanced plant vigor in the fruiting field compared with untreated plants. Weeds that grew through planting holes were significantly (P ≤ 0.045) suppressed in ASD plots compared with untreated plots in the first year. Plants treated with a combination treatment of TG and ASD had significantly higher fruit yield in both years (2019 and 2020), although the difference was greater in the second year. Plant vigor and survival in treated plots except MCC were also significantly higher in the second year compared with the untreated control. Suppression of pathogenic microbes and plant vigor improvement in treated plots appear to be the factors providing beneficial effects and higher net economic return. Taken together, our results suggest that a combination of beneficial microbes and ASD could be an alternative to synthetic fumigation in a perennial strawberry production system.

A highly stable chain-based EuIII metal-organic framework as a turn-on and blue-shift luminescent sensor for dipicolinic acid

The development of a rapid and selective method for the identification of dipicolinic acid (DPA), a specific biomarker in Bacillus anthracis spores, is of great importance for the avoidance of anthrax infection. Herein, a chain-based Eu^III metal-organic framework with the formula {[Eu₃(BTDB)₃(μ₃-OH)₃(H₂O)]·solvents}_n (JXUST-38, H₂BTDB = (benzo[c][1,2,5]thiadiazole-4,7-diyl)dibenzoic acid) was obtained using 2-fluorobenzoic acid as the pH regulator. JXUST-38 exhibits good chemical and thermal stability and can specifically recognize DPA in N,N-dimethylformamide solution through luminescence enhancement and blue-shift effects with a detection limit of 0.05 μM. Furthermore, the significant luminescence enhancement and blue shift under UV lamps are obviously observable by the naked eye. The luminescence sensing mechanism is attributed to absorbance-induced enhancement between JXUST-38 and DPA. Test paper and mixed-matrix membrane based on JXUST-38 are designed for DPA detection. In addition, the feasibility of using JXUST-38 in biosensing is discussed in detail.

Multi-Locus Phylogenetic Analysis Revealed the Association of Six Colletotrichum Species with Anthracnose Disease of Coffee (Coffea arabica L.) in Saudi Arabia

Several Colletotrichum species are able to cause anthracnose disease in coffee (Coffea arabica L.) and occur in all coffee production areas worldwide. A planned investigation of coffee plantations was carried out in Southwest Saudi Arabia in October, November, and December 2022. Various patterns of symptoms were observed in all 23 surveyed coffee plantations due to unknown causal agents. Isolation from symptomatic fresh samples was performed on a PDA medium supplemented with streptomycin sulfate (300 mg L^-1) and copper hydroxide (42.5 mg L^-1). Twenty-seven pure isolates of Colletotrichum-like fungi were obtained using a spore suspension method. The taxonomic placements of Colletotrichum-like fungi were performed based on the sequence dataset of multi-loci of internal transcribed spacer region rDNA (ITS), chitin synthase I (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), β-tubulin (TUB2), and partial mating type (Mat1-2) (ApMat) genes. The novel species are described in detail, including comprehensive morphological characteristics and colored illustrations. The pathogenicity of the isolated Colletotrichum species was assessed on detached coffee leaves as well as green and red fruit under laboratory conditions. The multi-locus phylogenetic analyses of the six-loci, ITS, ACT, CHS-1, TUB2, GAPDH and ApMat, revealed that 25 isolates were allocated within the C. gloeosporioides complex, while the remaining two isolates were assigned to the C. boninense complex. Six species were recognized, four of them, C. aeschynomenes, C. siamense, C. phyllanthi, and C. karstii, had been previously described. Based on molecular analyses and morphological examination comparisons, C. saudianum and C. coffeae-arabicae represent novel members within the C. gloeosporioides complex. Pathogenicity investigation confirmed that the Colletotrichum species could induce disease in coffee leaves as well as green and red fruits with variations. Based on the available literature and research, this is the first documentation for C. aeschynomenes, C. siamense, C. karstii, C. phyllanthi, C. saudianum, and C. coffeae-arabicae to cause anthracnose on coffee in Saudi Arabia.

Plant-Fungi Interactions: Where It Goes?

Fungi live different lifestyles-including pathogenic and symbiotic-by interacting with living plants. Recently, there has been a substantial increase in the study of phytopathogenic fungi and their interactions with plants. Symbiotic relationships with plants appear to be lagging behind, although progressive. Phytopathogenic fungi cause diseases in plants and put pressure on survival. Plants fight back against such pathogens through complicated self-defense mechanisms. However, phytopathogenic fungi develop virulent responses to overcome plant defense reactions, thus continuing their deteriorative impacts. Symbiotic relationships positively influence both plants and fungi. More interestingly, they also help plants protect themselves from pathogens. In light of the nonstop discovery of novel fungi and their strains, it is imperative to pay more attention to plant-fungi interactions. Both plants and fungi are responsive to environmental changes, therefore construction of their interaction effects has emerged as a new field of study. In this review, we first attempt to highlight the evolutionary aspect of plant-fungi interactions, then the mechanism of plants to avoid the negative impact of pathogenic fungi, and fungal strategies to overcome the plant defensive responses once they have been invaded, and finally the changes of such interactions under the different environmental conditions.

High Genetic Diversity and Structure of Colletotrichum gloeosporioides s.l. in the Archipelago of Lesser Antilles

Colletotrichum gloeosporioides is a species complex of agricultural importance as it causes anthracnose disease on many crop species worldwide, and strong impact regionally on Water Yam (Dioscorea alata) in the Caribbean. In this study, we conducted a genetic analysis of the fungi complex in three islands of the Lesser Antilles-Guadeloupe (Basse Terre, Grande Terre and Marie Galante), Martinique and Barbados. We specifically sampled yam fields and assessed the genetic diversity of strains with four microsatellite markers. We found a very high genetic diversity of all strains on each island, and intermediate to strong levels of genetic structure between islands. Migration rates were quite diverse either within (local dispersal) or between islands (long-distance dispersal), suggesting important roles of vegetation and climate as local barriers, and winds as an important factor in long-distance migration. Three distinct genetic clusters highlighted different species entities, though there was also evidence of frequent intermediates between two clusters, suggesting recurrent recombination between putative species. Together, these results demonstrated asymmetries in gene flow both between islands and clusters, and suggested the need for new approaches to anthracnose disease risk control at a regional level.

Uncovering Phytotoxic Compounds Produced by Colletotrichum spp. Involved in Legume Diseases Using an OSMAC-Metabolomics Approach

Different fungal species belonging to the Colletotrichum genus cause anthracnose disease in a range of major crops, resulting in huge economic losses worldwide. Typical symptoms include dark, sunken lesions on leaves, stems, or fruits. Colletotrichum spp. have synthesized, in vitro, a number of biologically active and structurally unusual metabolites that are involved in their host's infection process. In this study, we applied a one strain many compounds (OSMAC) approach, integrated with targeted and non-targeted metabolomics profiling, to shed light on the secondary phytotoxic metabolite panels produced by pathogenic isolates of Colletotrichum truncatum and Colletotrichum trifolii. The phytotoxicity of the fungal crude extracts was also assessed on their primary hosts and related legumes, and the results correlated with the metabolite profile that arose from the different cultural conditions. To the best of our knowledge, this is the first time that the OSMAC strategy integrated with metabolomics approaches has been applied to Colletotrichum species involved in legume diseases.

Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance

BACKGROUND

Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.