Characterization of Colletotrichum Species Causing Bitter Rot of Apple in Kentucky Orchards

The MdVQ37-MdWRKY100 complex regulates salicylic acid content and MdRPM1 expression to modulate resistance to Glomerella leaf spot in apples

Glomerella leaf spot (GLS), caused by the fungus Colletotrichum fructicola, is considered one of the most destructive diseases affecting apples. The VQ-WRKY complex plays a crucial role in the response of plants to biotic stresses. However, our understanding of the defensive role of the VQ-WRKY complex on woody plants, particularly apples, under biotic stress, remains limited. In this study, we elucidated the molecular mechanisms underlying the defensive role of the apple MdVQ37-MdWRKY100 module in response to GLS infection. The overexpression of MdWRKY100 enhanced resistance to C. fructicola, whereas MdWRKY100 RNA interference in apple plants reduced resistance to C. fructicola by affecting salicylic acid (SA) content and the expression level of the CC-NBS-LRR resistance gene MdRPM1. DAP-seq, Y1H, EMSA, and RT-qPCR assays indicated that MdWRKY100 inhibited the expression of MdWRKY17, a positive regulatory factor gene of SA degradation, upregulated the expression of MdPAL1, a key enzyme gene of SA biosynthesis, and promoted MdRPM1 expression by directly binding to their promotors. Transient overexpression and silencing experiments showed that MdPAL1 and MdRPM1 positively regulated GLS resistance in apples. Furthermore, the overexpression of MdVQ37 increased the susceptibility to C. fructicola by reducing the SA content and expression level of MdRPM1. Additionally, MdVQ37 interacted with MdWRKY100, which repressed the transcriptional activity of MdWRKY100. In summary, these results revealed the molecular mechanism through which the apple MdVQ37-MdWRKY100 module responds to GLS infection by regulating SA content and MdRPM1 expression, providing novel insights into the involvement of the VQ-WRKY complex in plant pathogen defence responses.

New Species-Specific Real-Time PCR Assays for Colletotrichum Species Causing Bitter Rot of Apple

Bitter rot of apple is an economically important worldwide disease caused by different Colletotrichum species, depending on many factors such as climate, geography, other hosts, and crop management practices. Culture, morphology, and single-locus sequencing-based methods for identifying the Colletotrichum species are severely limited in effectiveness, while the multilocus sequence typing methods available for delineating species are costly, time-intensive, and require high expertise. We developed species-specific hydrolysis probe real-time PCR assays for the following nine Colletotrichum species causing bitter rot in the Mid-Atlantic U.S.A.: C. fructicola, C. chrysophilum, C. noveboracense, C. gloeosporioides s.s., C. henanense, C. siamense and C. theobromicola from the C. gloeosporioides species complex, and C. fioriniae and C. nymphaeae from the C. acutatum species complex. After searching 14 gene regions, we designed primers and probes in 5 of them for the nine target species. Four primer-probe set pairs were able to be duplexed. Sensitivity tests showed as little as 0.5 pg DNA were detectable. These real-time PCR assays will provide rapid and reliable identification of these key Colletotrichum species and will be critically important for studies aiming to elucidate their biology, epidemiology, and management on apples as the number one produced and consumed tree fruit in the U.S.A.

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.

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.

Fungal Endophytes: Discovering What Lies within Some of Canada's Oldest and Most Resilient Grapevines

Plant diseases and pests reduce crop yields, accounting for global crop losses of 30% to 50%. In conventional agricultural production systems, these losses are typically controlled by applying chemical pesticides. However, public pressure is mounting to curtail agrochemical use. In this context, employing beneficial endophytic microorganisms is an increasingly attractive alternative to the use of conventional chemical pesticides in agriculture. A multitude of fungal endophytes are naturally present in plants, producing enzymes, small peptides, and secondary metabolites due to their bioactivity, which can protect hosts from pathogens, pests, and abiotic stresses. The use of beneficial endophytic microorganisms in agriculture is an increasingly attractive alternative to conventional pesticides. The aim of this study was to characterize fungal endophytes isolated from apparently healthy, feral wine grapes in eastern Canada that have grown without agrochemical inputs for decades. Host plants ranged from unknown seedlings to long-lost cultivars not widely propagated since the 1800s. HPLC-MS was used to identify unique endophyte-derived chemical compounds in the host plants, while dual-culture competition assays showed a range in endophytes' ability to suppress the mycelial growth of Botrytis, which is typically controlled in viticulture with pesticides. Twelve of the most promising fungal endophytes isolated were identified using multilocus sequencing and morphology, while DNA barcoding was employed to identify some of their host vines. These fungal endophyte isolates, which consisted of both known and putative novel strains, belonged to seven genera in six families and five orders of Ascomycota. Exploring the fungal endophytes in these specimens may yield clues to the vines' survival and lead to the discovery of novel biocontrol agents.

Characterization and evaluation of Bacillus subtilis GYUN-2311 as a biocontrol agent against Colletotrichum spp. on apple and hot pepper in Korea

Crop plants are vulnerable to a variety of diseases, including anthracnose, caused by various species of Colletotrichum fungi that damages major crops, including apples and hot peppers. The use of chemical fungicides for pathogen control may lead to environmental pollution and disease resistance. Therefore, we conducted this research to develop a Bacillus subtilis-based biological control agent (BCA). B. subtilis GYUN-2311 (GYUN-2311), isolated from the rhizosphere soil of an apple orchard, exhibited antagonistic activity against a total of 12 fungal pathogens, including eight Colletotrichum species. The volatile organic compounds (VOCs) and culture filtrate (CF) from GYUN-2311 displayed antifungal activity against all 12 pathogens, with 81% control efficiency against Fusarium oxysporum for VOCs and 81.4% control efficacy against Botryosphaeria dothidea for CF. CF also inhibited germination and appressorium formation in Colletotrichum siamense and C. acutatum. The CF from GYUN-2311 showed antifungal activity against all 12 pathogens in different media, particularly in LB medium. It also exhibited plant growth-promoting (PGP) activity, lytic enzyme activity, siderophore production, and the ability to solubilize insoluble phosphate. In trials on apples and hot peppers, GYUN-2311 effectively controlled disease, with 75 and 70% control efficacies against C. siamense in wounded and unwounded apples, respectively. Similarly, the control efficacy of hot pepper against C. acutatum in wounded inoculation was 72%. Combined application of GYUN-2311 and chemical suppressed hot pepper anthracnose to a larger extent than other treatments, such as chemical control, pyraclostrobin, TK®, GYUN-2311 and cross-spraying of chemical and GYUN-2311 under field conditions. The genome analysis of GYUN-2311 identified a circular chromosome comprising 4,043 predicted protein-coding sequences (CDSs) and 4,096,969 bp. B. subtilis SRCM104005 was the strain with the highest average nucleotide identity (ANI) to GYUN-2311. AntiSMASH analysis identified secondary metabolite biosynthetic genes, such as subtilomycin, bacillaene, fengycin, bacillibactin, pulcherriminic acid, subtilosin A, and bacilysin, whereas BAGEL analysis confirmed the presence of competence (ComX). Six secondary metabolite biosynthetic genes were induced during dual culture in the presence of C. siamense. These findings demonstrate the biological control potential of GYUN-2311 against apple and hot pepper anthracnose.

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.

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.

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.

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.

Identification and Fungicide Sensitivity of Colletotrichum spp. from Apple Flowers and Fruitlets in Brazil

Glomerella leaf spot (GLS) and bitter rot (BR), caused by Colletotrichum spp., are major diseases on apple in southern Brazil. Among integrated pest management tools for disease management in commercial orchards, fungicides remain an important component. This study aimed to identify Colletotrichum spp. from cultivar Eva in Paraná state orchards; evaluate their in vitro sensitivity to cyprodinil, tebuconazole, iprodione, and fluazinam; and determine the baseline in vitro sensitivity of these isolates to benzovindiflupyr and natamycin. Most isolates belonged to Colletotrichum melonis and C. nymphaeae of the C. acutatum species complex. The two species varied in sensitivity to fluazinam and tebuconazole, but no variability was found for any other fungicide. The lowest 50% effective concentration (EC₅₀) values of Colletotrichum spp. were observed for cyprodinil (mean EC₅₀ < 0.02) and benzovindiflupyr (mean EC₅₀ < 0.05); EC₅₀ values were intermediate for fluazinam (mean EC₅₀ < 0.33) and tebuconazole (mean EC₅₀ < 0.14), and they were highest for natamycin (mean EC₅₀ < 5.56) and iprodione (mean EC₅₀ > 12). Cyprodinil and fluazinam are registered for use in Brazil for apple disease management but not specifically for GLS and BR. Tebuconazole is one of the few products registered for Colletotrichum spp. control in apples. In conclusion, flowers and fruitlets can serve as sources of inoculum for GLS and BR disease; C. acutatum was the predominant species complex in these tissues; cyprodinil and fluazinam applications may suppress GLS and BR; and benzovindiflupyr and natamycin warrant further investigation for GLS and BR disease control of apple due to comparably high in vitro sensitivity.

Molecular Characterization and Fungicide Sensitivity of Jujube Pathogens Colletotrichum gloeosporioides Sensu Stricto and Colletotrichum nymphaeae in South Korea

Jujube (Ziziphus jujuba) is cultivated across South Korea because of its medicinal and economic value. It is used as a sweetener in jam, tea, and snacks and a garnish in many cuisines. Anthracnose caused by Colletotrichum spp. accounts for huge economic losses for jujube growers. In 2019 and 2020, severe anthracnose was observed in the jujube-growing areas of South Korea. The infected fruit displayed small, water-soaked, sunken, circular spots. Infected fruit were collected from different commercial orchards of Boeungun and Gyeongsan regions of South Korea, and putative causal agents were isolated on potato dextrose agar. Based on the morphological and molecular characteristics, the fungal isolates were identified as Colletotrichum gloeosporioides sensu stricto and C. nymphaeae. The pathogenicity of these isolates was confirmed by inoculating a conidial suspension (1 × 10⁶ conidia ml^-1) on healthy fruit. The in vitro sensitivity of the fungal isolates to tebuconazole, carbendazim, and azoxystrobin was also tested. All isolates showed high sensitivity to azoxystrobin in terms of mycelial growth inhibition (half maximal effective concentration value of 0.01 to 0.6 µg/ml). To the best of our knowledge, this is also the first report of jujube anthracnose caused by C. nymphaeae in South Korea.

The velvet proteins CsVosA and CsVelB coordinate growth, cell wall integrity, sporulation, conidial viability and pathogenicity in the rubber anthracnose fungus Colletotrichum siamense

Colletotrichum siamense, a member of Colletotrichum gloeosporioides complex species, is the primary pathogen causing rubber anthracnose, which leads to significant economic loss in natural rubber production. Velvet family proteins are fungal-specific proteins and play an essential role in regulating development and secondary metabolism. In this study, we characterized two velvet proteins CsVosA and CsVelB in C. siamense as the orthologs of VosA and VelB in Aspergillus nidulans. CsVosA is located in the nucleus, and CsVelB displays a localization in both the nucleus and the cytoplasm. Deleting CsvosA or CsvelB results in a slow growth rate, and the CsvelB-knockout mutants also exhibit low mycelial density. CsVosA and CsVelB are involved in regulating chitin metabolism and distribution, leading to the variation in the cell wall integrity of C. siamense. Furthermore, disruption of CsvosA or CsvelB can decrease conidial production and viability, and the ΔCsvosA and ΔCsvelB mutants also lose the ability to produce fruiting bodies. Pathogenicity assays show that deleting CsvosA or CsvelB can lower the virulence, and the two velvet genes are essential for the full virulence of C. siamense. Based on the results of the yeast two-hybrid analysis and bimolecular fluorescence complementation assays, CsVosA can interact with CsVelB and form the complex CsVosA-CsVelB in the conidia of C. siamense, which may play essential roles in maintaining the cell wall integrity and conidial viability. In addition, CsVelB is also involved in regulating melanin production of C. siamense. In conclusion, CsVosA and CsVelB regulate vegetative growth, cell wall integrity, asexual/sexual sporulation, conidial viability and virulence in C. siamense.

Biocontrol potential of Trichoderma harzianum CGMCC20739 (Tha739) against postharvest bitter rot of apples

This study investigated the biocontrol ability of Trichoderma harzianum CGMCC20739 (Tha739) against apple bitter rot caused by Colletotrichum gloeosporioides. In vitro tests, Tha739 inhibited the mycelial growth of C. gloeosporioides. Microscopic observation showed that Tha739 grew in parallel with, coiled around, and deformed the hyphae of C. gloeosporioides. Tha739-derived metabolites decreased the conidia production of C. gloeosporioides. In vivo tests, the lesion diameters of wounded apples treated with Tha739 1 h before C. gloeosporioides were lower than those of wounded apples treated with Tha739 after pathogen inoculation. In addition, compared with the apples inoculated with C. gloeosporioides only, the disease index of unwounded apples inoculated with Tha739 and C. gloeosporioides decreased by 2.17-fold. Furthermore, compared with the control, the total soluble solid contents of apples treated with Tha739 were 9.02 % and 1.54 % higher at 1 and 3 d, respectively. The titratable acidity contents of apples treated with Tha739 were 10.02 % and 14.58 % higher than those in the control at 1 and 3 d after treatment, respectively. The soluble sugar content and weight loss in Tha739 treatment group and control were not significantly different. The results showed that Tha739 could control apple bitter rot and maintain the nutritional quality of the fruit. Thus, T. harzianum Tha739 is a potentially biocontrol agent for harvested apples.

Pest categorisation of Colletotrichum aenigma, C. alienum, C. perseae, C. siamense and C. theobromicola

The EFSA Plant Health Panel performed a pest categorisation of Colletotrichum aenigma, C. alienum, C. perseae, C. siamense and C. theobromicola, five clearly defined fungi of the C. gloeosporioides complex causing anthracnose. The pathogens are widely distributed in at least three continents. C. aenigma and C. siamense are reported from Italy and C. alienum from Portugal, including the Madeira Islands, with a restricted distribution. C. perseae and C. theobromicola are not known to be present in the EU. However, there is uncertainty on the status of the pathogens worldwide and in the EU because of the taxonomic re-evaluation of the genus Colletotrichum and the lack of specific surveys. The pathogens are not included in Commission Implementing Regulation (EU) 2019/2072 and there are no reports of interceptions in the EU. With the exception of C. perseae, which has a very limited number of hosts, the other four Colletotrichum species have relatively wide host ranges. Therefore, this pest categorisation focused on those hosts for which there is robust evidence that the pathogens were formally identified by a combination of morphology, pathogenicity and multilocus sequence analysis. Host plants for planting and fresh fruits are the main entry pathways into the EU. Host availability and climate suitability factors occurring in some parts of the EU are favourable for the establishment of the pathogens. No yield losses have been reported so far in the EU but in non-EU areas of their current distribution, the pathogens have a direct impact on cultivated hosts that are also relevant for the EU. Phytosanitary measures are available to prevent the further introduction and spread of C. aenigma, C. alienum and C. siamense into the EU as well as the introduction and spread of C. perseae and C. theobromicola. C. aenigma, C. alienum, C. perseae, C. siamense and C. theobromicola satisfy the criteria that are within the remit of EFSA to assess for these species to be regarded as potential Union quarantine pests.

Diversity of Colletotrichum Species Causing Apple Bitter Rot and Glomerella Leaf Spot in China

Bitter rot and Glomerella leaf spot (GLS) of apples, caused by Colletotrichum species, are major diseases of apples around the world. A total of 98 isolates were obtained from apple fruits with bitter rot, and 53 isolates were obtained from leaves with leaf spot in the primary apple production regions in China. These isolates were characterized morphologically, and five gene regions (ITS, ACT, GAPDH, CHS-1 and TUB2) were sequenced for each isolate. A phylogenetic analysis, combined with a comparison of the morphological, cultural and pathogenic characters, sorted bitter rot isolates into six species: C. alienum, C. fructicola, C. gloeosporioides sensu stricto, C. nymphaeae, C. siamense and one new species, C. orientalis Dandan Fu & G.Y. Sun. Among these, C. siamense was the predominant pathogen associated with bitter rot. Isolates from leaf spot were identified as two species, C. aenigma and C. fructicola. This is the first report of C. orientalis as an apple bitter rot pathogen worldwide, and the results provide important insights into the diversity of Colletotrichum species in China.

Characterization of Colletotrichum Isolates Causing Colletotrichum Dieback of Citrus in California

Dieback caused by Colletotrichum spp. is an emerging disease in California citrus groves. A large-scale survey with emphasis on seasonal variations of latent infections was conducted throughout citrus orchards in Fresno, Kern, and Tulare counties in 2019 and 2020. Latent infections on citrus leaves and twigs varied markedly between years. Isolates of Colletotrichum spp. were obtained from asymptomatic tissue, and two groups were formed based on colony and spore morphology. The morphological groups were further identified based on multigene sequence analysis using the DNA regions ITS1-5.8S-ITS2, TUB2, and GAPDH. Results revealed that isolates belong to two phylogenetic species, C. gloeosporioides and C. karstii, being C. karstii more frequently isolated. Representative isolates of each species were further selected and characterized based on the response of physiological variables to temperature. Both species had similar optimum growth temperatures but differed in maximum growth rates, with C. gloeosporioides exhibiting a greater growth rate than that of C. karstii on media. Pathogenicity tests on citrus trees demonstrated the ability of C. gloeosporioides and C. karstii to cause lesions on twigs and no differences in aggressiveness. A fungicide screening performed in this study determined that the DMI fungicides were the most effective in reducing the mycelial growth of C. gloeosporioides and C. karstii. The QoI fungicides showed a remarkably inhibitory impact on spore germination of both species. On average, C. karstii was more sensitive to the DMI fungicides than C. gloeosporioides. The findings of this study provide new information to understand the Colletotrichum dieback of citrus.

A Novel Heptasegmented Positive-Sense Single-Stranded RNA Virus from the Phytopathogenic Fungus Colletotrichum fructicola

In this study, a novel positive-sense single-stranded RNA (+ssRNA) mycovirus, tentatively named Colletotrichum fructicola RNA virus 1 (CfRV1), was identified in the phytopathogenic fungus Colletotrichum fructicola. CfRV1 has seven genomic components, encoding seven proteins from open reading frames (ORFs) flanked by highly conserved untranslated regions (UTRs). Proteins encoded by ORFs 1, 2, 3, 5, and 6 are more similar to the putative RNA-dependent RNA polymerase (RdRp), hypothetical protein (P2), methyltransferase, and two hypothetical proteins of Hadaka virus 1 (HadV1), a capsidless 10- or 11-segmented +ssRNA virus, while proteins encoded by ORFs 4 and 7 showed no detectable similarity to any known proteins. Notably, proteins encoded by ORFs 1 to 3 also share considerably high similarity with the corresponding proteins of polymycoviruses. Phylogenetic analysis conducted based on the amino acid sequence of CfRV1 RdRp and related viruses placed CfRV1 and HadV1 together in the same clade, close to polymycoviruses and astroviruses. CfRV1-infected C. fructicola strains demonstrate a moderately attenuated growth rate and virulence compared to uninfected isolates. CfRV1 is capsidless and potentially encapsulated in vesicles inside fungal cells, as revealed by transmission electron microscopy. CfRV1 and HadV1 are +ssRNA mycoviruses closely related to polymycoviruses and astroviruses, represent a new linkage between +ssRNA viruses and the intermediate double-stranded RNA (dsRNA) polymycoviruses, and expand our understanding of virus diversity, taxonomy, evolution, and biological traits. IMPORTANCE A scenario proposing that dsRNA viruses evolved from +ssRNA viruses is still considered controversial due to intergroup knowledge gaps in virus diversity. Recently, polymycoviruses and hadakaviruses were found as intermediate dsRNA and +ssRNA stages, respectively, between +ssRNA and dsRNA viruses. Here, we identified a novel +ssRNA mycovirus, Colletotrichum fructicola RNA virus 1 (CfRV1), isolated from Colletotrichum fructicola in China. CfRV1 is phylogenetically related to the 10- or 11-segmented Hadaka virus 1 (HadV1) but consists of only seven genomic segments encoding two novel proteins. CfRV1 is naked and may be encapsulated in vesicles inside fungal cells, representing a potential novel lifestyle for multisegmented RNA viruses. CfRV1 and HadV1 are intermediate +ssRNA mycoviruses in the linkage between +ssRNA viruses and the intermediate dsRNA polymycoviruses and expand our understanding of virus diversity, taxonomy, and evolution.

Multilocus Phylogenetic Analyses of Colletotrichum gloeosporioides Species Complex Causing Crown Rot on Strawberry in Florida

Colletotrichum gloeosporioides is the causal agent of Colletotrichum crown rot of strawberry in the southern United States. Recent multigene studies defined C. gloeosporioides as a complex species comprised of 37 species. In our study, we phylogenetically characterized C. gloeosporioides isolates from strawberry and other noncultivated plants around strawberry fields. One hundred fifteen strawberry isolates and 38 isolates from noncultivated hosts were sequenced for five genomic regions: internal transcribed spacer, actin, calmodulin, chitin synthase, and glyceraldehyde-3-phosphate dehydrogenase. Phylogenetic analysis using the maximum likelihood and Bayesian inference methods, based on partition-specific models, revealed that most of the isolates in Florida (86%) were closely related to C. siamense, whereas 14 isolates were closely related to C. theobromicola (syn. C. fragariae), four isolates were C. fructicola, and three isolates were C. clidemiae. However, only the first three species were pathogenic to strawberry. Morphological characteristics evaluated show that mycelial growth of all species is approximately 5 mm/day, but colony morphology varies by species and incubation conditions. In vitro mating of the isolates demonstrated that C. fructicola is homothallic whereas C. siamense and C. theobromicola isolates are heterothallic. The biological importance of these different Colletotrichum species is currently being investigated to determine whether different management strategies are needed in strawberry production fields.

Comparative transcriptome analysis reveals significant differences in gene expression between pathogens of apple Glomerella leaf spot and apple bitter rot

Background

Apple Glomerella leaf spot (GLS) and apple bitter rot (ABR) are two devastating foliar and fruit diseases on apples. The different symptoms of GLS and ABR could be related to different transcriptome patterns. Thus, the objectives of this study were to compare the transcriptome profiles of Colletotrichum gloeosporioides species complex isolates GC20190701, FL180903, and FL180906, the pathogen of GLS and ABR, and to evaluate the involvement of the genes on pathogenicity.

Results

A relatively large difference was discovered between the GLS-isolate GC20190701 and ABR-isolates FL180903, FL180906, and quite many differential expression genes associated with pathogenicity were revealed. The DEGs between the GLS- and ABR-isolate were significantly enriched in GO terms of secondary metabolites, however, the categories of degradation of various cell wall components did not. Many genes associated with secondary metabolism were revealed. A total of 17 Cytochrome P450s (CYP), 11 of which were up-regulated while six were down-regulated, and five up-regulated methyltransferase genes were discovered. The genes associated with the secretion of extracellular enzymes and melanin accumulation were up-regulated. Four genes associated with the degradation of the host cell wall, three genes involved in the degradation of cellulose, and one gene involved in the degradation of xylan were revealed and all up-regulated. In addition, genes involved in melanin syntheses, such as tyrosinase and glucosyltransferase, were highly up-regulated.

Conclusions

The penetration ability, pathogenicity of GLS-isolate was greater than that of ABR-isolate, which might indicate that GLS-isolate originated from ABR-isolates by mutation. These results contributed to highlighting the importance to investigate such DEGs between GLS- and ABR-isolate in depth.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08493-w.

Colletotrichum Species Associated with Peaches in China

Colletotrichum is regarded as one of the 10 most important genera of plant pathogens in the world. It causes diseases in a wide range of economically important plants, including peaches. China is the largest producer of peaches in the world but little is known about the Colletotrichum spp. affecting the crop. In 2017 and 2018, a total of 286 Colletotrichum isolates were isolated from symptomatic fruit and leaves in 11 peach production provinces of China. Based on multilocus phylogenetic analyses (ITS, ACT, CAL, CHS-1, GAPDH, TUB2, and HIS3) and morphological characterization, the isolates were identified to be C. nymphaeae, C. fioriniae, and C. godetiae of the C. acutatum species complex, C. fructicola and C. siamense of the C. gloeosporioides species complex, C. karsti of the C. boninense species complex, and one newly identified species, C. folicola sp. nov. This study is the first report of C. karsti and C. godetiae in peaches, and the first report of C. nymphaeae, C. fioriniae, C. fructicola, and C. siamense in peaches in China. C. nymphaeae is the most prevalent species of Colletotrichum in peaches in China, which may be the result of fungicide selection. Pathogenicity tests revealed that all species found in this study were pathogenic on both the leaves and fruit of peaches, except for C. folicola, which only infected the leaves. The present study substantially improves our understanding of the causal agents of anthracnose on peaches in China.

Sensitivity to fungicides in isolates of Colletotrichum gloeosporioides and C. acutatum species complexes and efficacy against anthracnose diseases

Colletotrichum species cause diseases on many plants and are among the 'top 10' fungal plant pathogens. Species of the C. gloeosporioides and C. acutatum complexes are particularly important because they infect temperate fruit crops, but their control relies largely on chemical fungicides. In this study, differences in intrinsic fungicide sensitivity were determined in vitro using isolates of the C. gloeosporioides sp. complex (C. fructicola, C. siamense, and C. tropicale) and the C. acutatum sp. complex (C. fioriniae and C. nymphaeae), which had never been exposed to fungicides. Mycelial growth of all isolates was sensitive to the QoI azoxystrobin, the SDHI benzovindiflupyr, and the new DMI fungicide mefentrifluconazole. The isolates of C. nymphaeae were highly sensitive to the phenylpyrrole fungicide fludioxonil. The isolates of C. gloeosporioides sp. complex were sensitive to the bis-guanidine fungicide iminoctadine-albesilate, whereas those of C. acutatum sp. complex were inherently insensitive. These results are valuable when sensitivity of field populations is monitored in resistance management. Although SDHI fungicides are largely not effective against diseases caused by Colletotrichum species, benzovindiflupyr controlled anthracnose disease of various crops such as kidney bean, garland chrysanthemum, and strawberry, caused by C. lindemuthianum, C. chrysanthemi, and C. siamense, respectively, demonstrating this fungicide to be unique among SDHIs and having a broad control spectrum against anthracnose. To help understanding the reason for differential activity of benzovindiflupyr and boscalid, sdhB gene sequences were analyzed but those of C. lindemuthianum, C. chrysanthemi, and C. scovillei revealed no known mutations reported to be responsible for SDHI resistance in other fungi, indicating that other mechanism(s) than target-site modification may be involved in differential sensitivity to benzovindiflupyr and boscalid, found in Colletotrichum species.

Sustainable Apple Disease Management in China: Challenges and Future Directions for a Transforming Industry

Apple trees are grown worldwide, and consuming fresh apple fruit is associated with many health benefits. China produces about half of the world's apple supply. However, apple growing in China differs sharply from that in western countries in terms of the prevalent diseases and corresponding management strategies. For instance, family-owned small-scale orchards dominate China's apple industry, and manual bagging of fruit has been a long-standing practice for controlling fruit diseases. In recent years, rural labor shortages have been increasingly challenging the traditional production system, and China's apple industry is experiencing a rapid transition to much larger-scale enterprises featuring high-density orchards with advanced automation and mechanization. Associated with this transition are new challenges and grower demands that are changing the face of apple disease management. This Feature Article summarizes the ongoing transformation of China's apple industry in the context of sustainable disease management.

Transcriptome Analysis of the Molecular Patterns of Pear Plants Infected by Two Colletotrichum fructicola Pathogenic Strains Causing Contrasting Sets of Leaf Symptoms

Colletotrichum fructicola infects pear leaves, resulting in two major symptoms: tiny black spots (TS) followed by severe early defoliation and big necrotic lesions (BnL) without apparent damage depending on the pathotypes. How the same fungal species causes different symptoms remains unclear. To understand the molecular mechanism underlying the resulting diseases and the diverse symptoms, two C. fructicola pathogenetic strains (PAFQ31 and PAFQ32 responsible for TS and BnL symptoms, respectively) were inoculated on Pyrus pyrifolia leaves and subjected to transcriptome sequencing at the quiescent stage (QS) and necrotrophic stage (NS), respectively. In planta, the genes involved in the salicylic acid (SA) signaling pathway were upregulated at the NS caused by the infection of each strain. In contrast, the ethylene (ET), abscisic acid (ABA), and jasmonic acid (JA) signaling pathways were specifically related to the TS symptoms caused by the infection of strain PAFQ31, corresponding to the yellowish and early defoliation symptoms triggered by the strain infection. Correspondingly, SA was accumulated in similar levels in the leaves infected by each strain at NS, but JA was significantly higher in the PAFQ31-infected as measured using high-performance liquid chromatography. Weighted gene co-expression network analysis also reveals specific genes, pathways, phytohormones, and transcription factors (TFs) associated with the PAFQ31-associated early defoliation. Taken together, these data suggest that specific metabolic pathways were regulated in P. pyrifolia in response to the infection of two C. fructicola pathotypes resulting in the diverse symptoms: JA, ET, and ABA accumulated in the PAFQ31-infected leaves, which negatively affected the chlorophyll metabolism and photosynthesis pathways while positively affecting the expression of senescence-associated TFs and genes, resulted in leaf yellowing and defoliation; whereas SA inhibited JA-induced gene expression in the PAFQ32-infected leaves, which led to hypersensitive response-like reaction and BnL symptoms.

Fungicide Sensitivity of Colletotrichum Species Causing Bitter Rot of Apple in the Mid-Atlantic U.S.A

Apple growers in the Mid-Atlantic region of the U.S.A. have reported increased losses to bitter rot of apple. We tested the hypothesis that this increase is because the Colletotrichum population has developed resistance to commonly used single-mode-of-action (single-MoA) fungicides. We screened 220 Colletotrichum isolates obtained from 38 apple orchards in the Mid-Atlantic region for resistance to 11 fungicides in Fungicide Resistance Action Committee (FRAC) groups 1, 7, 9, 11, 12, and 29. Eleven (5%) of these isolates were resistant to FRAC group 1 with confirmed β-tubulin E198A mutations, and two (<1%) were also resistant to FRAC group 11 with confirmed cytochrome-b G143A mutations. Such low frequencies of resistant isolates indicate that fungicide resistance is unlikely to be the cause of any regional increase in bitter rot. A subsample of isolates was subsequently tested in vitro for sensitivity to every single-MoA fungicide registered for apple in the Mid-Atlantic U.S.A. (22 fungicides; FRAC groups 1, 3, 7, 9, 11, 12, and 29), and 13 fungicides were tested in field trials. These fungicides varied widely in efficacy both within and between FRAC groups. Comparisons of results from our in vitro tests with results from our field trials and other field trials conducted across the eastern U.S.A. suggested that EC₂₅ values (concentrations that reduce growth by 25%) are better predictors of fungicide efficacy in normal field conditions than EC₅₀ values. We present these results as a guideline for choosing single-MoA fungicides for bitter rot control in the Mid-Atlantic U.S.A.

Recent advances and future perspective of essential oils in control Colletotrichum spp.: A sustainable alternative in postharvest treatment of fruits

The world population growth has raised concerns about food security. Agricultural systems are asked to satisfy a growing demand for food with increasingly limited resources, and simultaneously still must reduce the impacts on the environment. This scenario encourages the search for safe and sustainable production strategies. Reducing losses in the production process can be one of the main ways to guarantee food safety. In fruticulture, it is estimated that more than 50% of the production can be lost between harvest and the final consumer due to postharvest diseases caused by phytopathogenic fungi. The fungi of the genus Colletotrichum are opportunistic and are associated with several diseases, being the anthracnose the most relevant in terms of the quality and yield losses in fruit species around worldwide. To control these diseases, the use of synthetic fungicides has been the main instrument utilized, however, because of their phytotoxicity to human health, the environment, and strong selection pressure imposed by continuous applications, the fungicides have caused resistance in the pathogen populations. So reducing the excessive application of these products is indispensable for human health and for sustainable Agriculture. Towards this purpose, research has been carried out to identify the phytopathological potentiality of essential oils (EOs) extracted from plants. Therefore, this review aims to contribute to the formation of knowledge bases, about the discoveries, recent advances, and the use of EOs as a strategy to alternatively control fungal disease caused by Colletotrichum spp. in postharvest fruits. Here, we provide valuable information exploring the application potential of essential oils as commercially useful biorational pesticides for food preservation, contributing to sustainable production and global food security.

Colletotrichum fioriniae and Colletotrichum godetiae Causing Postharvest Bitter Rot of Apple in South Tyrol (Northern Italy)

South Tyrol (northern Italy) harbors one of the largest interconnected apple farming areas in Europe, contributing approximately 10% to the apple production of the European Union. Despite the availability of sophisticated storage facilities, postharvest diseases occur, one of which is bitter rot of apple. In Europe, this postharvest disease is mainly caused by the Colletotrichum acutatum species complex. This study aimed to characterize the Colletotrichum spp. isolated from decayed apple fruit collected in 2018 and 2019 in South Tyrol. The characterization of Colletotrichum spp. was accomplished based on multilocus DNA sequences of four different genomic regions-actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone H3 (HIS3), and the internal transcribed spacer (ITS) region-as well as morphological and pathogenicity assessment. A phylogenetic analysis based on multilocus DNA sequences showed that the isolates obtained from apples with symptoms of bitter rot belonged to the species Colletotrichum godetiae and Colletotrichum fioriniae, which are part of the Colletotrichum acutatum species complex. A third species isolated from apples belonging to the same species complex, Colletotrichum salicis, was described in this area. Moreover, the Colletotrichum isolates found in this study proved to be virulent on Cripps Pink, Golden Delicious, and Roho 3615/Evelina. To the best of our knowledge, C. godetiae and C. fioriniae have so far never been mentioned as postharvest pathogens of apple in Italy, although the reanalysis of samples collected in the past indicates that these pathogens have been occurring in Italy for at least a decade. So far, bitter rot seems to play a minor role as a postharvest disease in South Tyrol, but it was disproportionately represented on a few scab-resistant apple cultivars, which are increasingly planted in organically managed orchards. Considering that the expansion of organic apple production and the conversion to new potentially Colletotrichum-susceptible cultivars will continue, the present study represents an important contribution toward a better understanding of bitter rot in this geographic area.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Variations in the Community Structure of Fungal Microbiota Associated with Apple Fruit Shaped by Fruit Bagging-Based Practice

The various fungal communities that adhere to apple fruit are influenced by agricultural practices. However, the effects of fruit bagging-based management practice on the fungal microbiota are still unknown, and little is known about the fungal communities of bagged apple fruit. We conducted a study using apple fruit grown in a conventionally managed orchard where pesticide use is an indispensable practice. Fungal communities were collected from the calyx-end and peel tissues of bagged and unbagged fruit and characterized using barcode-type next-generation sequencing. Fruit bagging had a stronger effect on fungal richness, abundance, and diversity of the fungal microbiota in comparison to non-bagging. In addition, bagging also impacted the compositional variation of the fungal communities inhabiting each fruit part. We observed that fruit bagging had a tendency to maintain ecological equilibrium since Ascomycota and Basidiomycota were more distributed in bagged fruit than in unbagged fruit. These fungal communities consist of beneficial fungi rather than potentially harmful fungi. Approximately 50 dominant taxa were detected in bagged fruit, for example, beneficial genera such as Articulospora, Bullera, Cryptococcus, Dioszegia, Erythrobasidium, and Sporobolomyces, as well as pathogenic genera such as Aureobasidium and Taphrina. These results suggested that fruit bagging could significantly increase fungal richness and promote healthy fungal communities, especially the harmless fungal communities, which might be helpful for protecting fruit from the effects of pathogens. This study provides a foundation for understanding the impacts of bagging-based practice on the associated fungal microbiota.

Use of Telomere Fingerprinting to Identify Clonal Lineages of Colletotrichum fioriniae in Kentucky Mixed-Fruit Orchards

Multiple species in the fungal genus Colletotrichum cause anthracnose fruit rot diseases that are responsible for major yield losses of as much as 100%. Individual species of Colletotrichum typically have broad host ranges and can infect multiple fruit species. Colletotrichum fioriniae causes anthracnose fruit rots of apples, blueberries, and strawberries in Kentucky orchards where these fruits grow in close proximity. This raises the possibility of cross-infection, which may have significant management implications. The potential occurrence of cross-infection was investigated by using telomere fingerprinting to identify C. fioriniae clones in several mixed-fruit orchards. Telomere fingerprints were highly polymorphic among a test group of C. fioriniae strains and effectively defined clonal lineages. Fingerprints were compared among apple, blueberry, and strawberry isolates of C. fioriniae from three different orchards and similarity matrices were calculated to build phylograms for each orchard group. Multiple clonal lineages of C. fioriniae were identified within each orchard on the same fruit host. Related lineages were found among isolates from different hosts, but the results did not provide direct evidence for cross-infection of different fruit species by the same clones. Recovery of the same clonal lineages within orchards across multiple years suggested that local dispersal was important in pathogen population structure and that C. fioriniae strains persisted within orchards over time. Isolates from blueberry were less diverse than isolates from apple, perhaps related to more intensive anthracnose management protocols on apple versus blueberry. Telomere fingerprinting is a valuable tool for understanding population dynamics of Colletotrichum fruit rot fungi.

Bitter Rot of Apple in the Mid-Atlantic United States: Causal Species and Evaluation of the Impacts of Regional Weather Patterns and Cultivar Susceptibility

Apple growers in the Mid-Atlantic region of the United States have been reporting an increase in losses to bitter rot of apple and are requesting up-to-date management recommendations. Management is complicated by variations in apple cultivar susceptibility, temperature, rainfall, and biology of the Colletotrichum spp. that cause bitter rot. Over 500 apple fruit with bitter rot were obtained from 38 orchards across the Mid-Atlantic and the causal species were identified as Colletotrichum fioriniae and C. nymphaeae of the C. acutatum species complex and C. chrysophilum, C. noveboracense, C. siamense, C. fructicola, C. henanense, and C. gloeosporioides sensu stricto of the C. gloeosporioides species complex, the latter two being first reports. Species with faster in vitro growth rates at higher temperatures were more abundant in warmer regions of the Mid-Atlantic, while those with slower growth rates at higher temperatures were more abundant in cooler regions. Regional bloom dates are earlier and weather data show a gradual warming trend that likely influenced but was not necessarily the main cause of the recent increase in bitter rot in the region. A grower survey of apple cultivar susceptibility showed high variation, with the increase in acres planted to the highly susceptible cultivar Honeycrisp broadly corresponding to the increase in reports of bitter rot. These results form a basis for future studies on the biology and ecology of the Colletotrichum spp. responsible, and suggest that integrated bitter rot management must begin with selection of less-susceptible apple cultivars.

Diversity and Cross-Infection Potential of Colletotrichum Causing Fruit Rots in Mixed-Fruit Orchards in Kentucky

Fungi in the genus Colletotrichum cause apple, blueberry, and strawberry fruit rots, which can result in significant losses. Accurate identification is important because species differ in aggressiveness, fungicide sensitivity, and other factors affecting management. Multiple Colletotrichum species can cause similar symptoms on the same host, and more than one fruit type can be infected by a single Colletotrichum species. Mixed-fruit orchards may facilitate cross-infection, with significant management implications. Colletotrichum isolates from small fruits in Kentucky orchards were characterized and compared with apple isolates via a combination of morphotyping, sequencing of voucher loci and whole genomes, and cross-inoculation assays. Seven morphotypes representing two species complexes (C. acutatum and C. gloeosporioides) were identified. Morphotypes corresponded with phylogenetic species C. fioriniae, C. fructicola, C. nymphaeae, and C. siamense, identified by TUB2 or GAPDH barcodes. Phylogenetic trees built from nine single-gene sequences matched barcoding results with one exception, later determined to belong to an undescribed species. Comparison of single-gene trees with representative whole genome sequences revealed that CHS and ApMat were the most informative for diagnosis of fruit rot species and individual morphotypes within the C. acutatum or C. gloeosporioides complexes, respectively. All blueberry isolates belonged to C. fioriniae, and most strawberry isolates were C. nymphaeae, with a few C. siamense and C. fioriniae also recovered. All three species cause fruit rot on apples in Kentucky. Cross-inoculation assays on detached apple, blueberry, and strawberry fruits showed that all species were pathogenic on all three hosts but with species-specific differences in aggressiveness.

Quantification of Colletotrichum fioriniae in Orchards and Deciduous Forests Indicates It Is Primarily a Leaf Endophyte

Colletotrichum fioriniae of the C. acutatum species complex is an important hemibiotrophic pathogen of vegetables and fruits in temperate regions worldwide. In apple, it is one of the primary species responsible for bitter rot disease. Understanding the disease cycle is complicated because many broadleaf plants can be hosts of C. fioriniae. By detecting and quantifying rain-splashed C. acutatum species complex conidia in more than 500 samples from heavily bitter-rot-infected apple orchards and nearby forested woodlots over two summers, we show that conidial quantities were higher in the woodlots than in the orchards. Testing of more than 1,000 surface-disinfected leaves of apple and 24 different forest plant species showed that overall C. fioriniae was an abundant leaf endophyte, with high variation in leaf colonization area. Endophytic isolates from leaves were pathogenic on apples, and multilocus sequence analysis showed 100% identity between most isolates from leaves and diseased fruits. Apple leaves endophytically infected with C. fioriniae were present in a conventionally managed orchard and abundant in an untreated orchard. These lines of evidence, in the context of previously published research, lead us to hypothesize that the main ecological role of C. fioriniae is that of a leaf endophyte, which we present as a generalized C. fioriniae infection cycle that provides an updated framework for its integrated management in agricultural systems.

Diversity, Pathogenicity, and Fungicide Sensitivity of Colletotrichum Species Associated with Apple Anthracnose in South Korea

Apple fruits with anthracnose symptoms were collected from commercial apple orchards in different regions of the Republic of Korea, and isolations were made on potato dextrose agar to isolate the causal agents. The fungal isolates were identified based on their morphological characteristics, growth rates, and multigene sequences. Nine isolates were identified via phylogenetic analysis: three Colletotrichum fructicola, two C. fioriniae, one C. gloeosporioides sensu stricto (s.s.), two C. nymphaeae, and one C. siamense isolates. The pathogenicity of the Colletotrichum isolates was tested using detached apple fruits under laboratory conditions. This study also reidentified six Colletotrichum isolates responsible for apple anthracnose, which were deposited in the Korean Agricultural Culture Collection. Among the six isolates, three were identified as C. siamense (deposited as C. gloeosporioides s.s.), and three were C. nymphaeae (deposited as C. acutatum s.s.). All the Colletotrichum species identified in this study were highly sensitive to tebuconazole in terms of inhibition of mycelial growth (EC₅₀ value of 0.12 to 2.1 μg/ml).

Managing Colletotrichum on Fruit Crops: A "Complex" Challenge

The fungal genus Colletotrichum includes numerous important plant pathogenic species and species complexes that infect a wide variety of hosts. Its taxonomy is particularly complex because species' phenotypes and genotypes are difficult to differentiate. Two notable complexes, C. acutatum and C. gloeosporioides, are known for infecting temperate fruit crops worldwide. Even species within these complexes vary in traits such as tissue specificity, aggressiveness, geographic distribution, and fungicide sensitivity. With few effective chemicals available to control these pathogens, and the persistent threat of fungicide resistance, there is a need for greater understanding of this destructive genus and the methods that can be used for disease management. This review summarizes current research on diseases caused by Colletotrichum spp. on major fruit crops in the United States, focusing on the taxonomy of species involved, disease management strategies, and future management outlook.

Identification and characterization of Colletotrichum species causing apple bitter rot in New York and description of C. noveboracense sp. nov

Apple bitter rot caused by Colletotrichum species is a growing problem worldwide. Colletotrichum spp. are economically important but taxonomically un-resolved. Identification of Colletotrichum spp. is critical due to potential species-level differences in pathogenicity-related characteristics. A 400-isolate collection from New York apple orchards were morphologically assorted to two groups, C. acutatum species complex (CASC) and C. gloeosporioides species complex (CGSC). A sub-sample of 44 representative isolates, spanning the geographical distribution and apple varieties, were assigned to species based on multi-locus phylogenetic analyses of nrITS, GAPDH and TUB2 for CASC, and ITS, GAPDH, CAL, ACT, TUB2, APN2, ApMat and GS genes for CGSC. The dominant species was C. fioriniae, followed by C. chrysophilum and a novel species, C. noveboracense, described in this study. This study represents the first report of C. chrysophilum and C. noveboracense as pathogens of apple. We assessed the enzyme activity and fungicide sensitivity for isolates identified in New York. All isolates showed amylolytic, cellulolytic and lipolytic, but not proteolytic activity. C. chrysophilum showed the highest cellulase and the lowest lipase activity, while C. noveboracense had the highest amylase activity. Fungicide assays showed that C. fioriniae was sensitive to benzovindiflupyr and thiabendazole, while C. chrysophilum and C. noveboracense were sensitive to fludioxonil, pyraclostrobin and difenoconazole. All species were pathogenic on apple fruit with varying lesion sizes. Our findings of differing pathogenicity-related characteristics among the three species demonstrate the importance of accurate species identification for any downstream investigations of Colletotrichum spp. in major apple growing regions.

Characterization and Fungicide Sensitivity of Colletotrichum Species Causing Strawberry Anthracnose in Eastern China

Strawberry anthracnose caused by Colletotrichum spp. is one of the most serious diseases in the strawberry fields of China. In total, 196 isolates of Colletotrichum were obtained from leaves, stolons, and crowns of strawberry plants with anthracnose symptoms in eastern China and were characterized based on morphology, internal transcribed spacer (ITS), and β-tubulin (TUB2) gene sequences. All 196 isolates were identified as the Colletotrichum gloeosporioides species complex. In total, 62 strains were further identified at the species level by phylogenetic analyses of multilocus sequences of ITS, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), Apn2-Mat1-2 intergenic spacer and partial mating type (ApMat), calmodulin (CAL), and TUB2. Three species from the C. gloeosporioides species complex were identified: Colletotrichum siamense, C. fructicola, and C. aenigma. Isolates of C. siamense were tolerant to high temperatures, with a significantly larger colony diameter than the other two species when grown above 36°C. The inoculation of strawberry plants confirmed the pathogenicity of all three species. C. siamense isolates resulted in the highest disease severity. The in vitro sensitivities of C. siamense and C. fructicola isolates to azoxystrobin and three demethylation-inhibitor (DMI) fungicides (difenoconazole, tebuconazole, and prochloraz) were determined. Both species were sensitive to DMI fungicides but not to azoxystrobin. C. siamense isolates were more sensitive to prochloraz, while C. fructicola isolates were more sensitive to difenoconazole and tebuconazole. The present study provides valuable information for the effective management of strawberry anthracnose.

Characterization of Colletotrichum ocimi Population Associated with Black Spot of Sweet Basil (Ocimum basilicum) in Northern Italy

Black spot is a major foliar disease of sweet basil (Ocimum basilicum) present in a typical cultivation area of northern Italy, including the Liguria and southern Piedmont regions, where this aromatic herb is an economically important crop. In this study, 15 Colletotrichum isolates obtained from sweet basil plants with symptoms of black spot sampled in this area were characterized morphologically and by nuclear DNA analysis using internal transcribed spacers (ITS) and intervening 5.8S nrDNA as well as part of the β-tubulin gene (TUB2) regions as barcode markers. Analysis revealed all but one isolate belonged to the recently described species C. ocimi of the C. destructivum species complex. Only one isolate was identified as C. destructivum sensu stricto (s.s.). In pathogenicity tests on sweet basil, both C. ocimi and C. destructivum s.s. isolates incited typical symptoms of black spot, showing that although C. ocimi prevails in this basil production area, it is not the sole causal agent of black spot in northern Italy. While no other hosts of C. ocimi are known worldwide, the close related species C. destructivum has a broad host range, suggesting a speciation process of C. ocimi within this species complex driven by adaptation to the host.

Paralogous CYP51 Genes of Colletotrichum spp. Mediate Differential Sensitivity to Sterol Demethylation Inhibitors

Colletotrichum spp. isolates contain two paralogous CYP51 genes that encode sterol 14-demethylase enzymes; however, their role in sensitivity to demethylation inhibitor (DMI) fungicides is yet to be determined. In this study, each of the two genes from Colletotrichum fioriniae and C. nymphaeae was able to rescue the function of CYP51 in the yeast Saccharomyces cerevisiae, demonstrating their independent function. Deletion of CYP51A led to increased sensitivity to propiconazole, diniconazole, prothioconazole, cyproconazole, epoxiconazole, flutriafol, prochloraz, and difenoconazole in C. fioriniae, and to the same fungicides and tebuconazole in C. nymphaeae, with the exception of prochloraz. Deletion of CYP51B in C. fioriniae and CYP51B in C. nymphaeae made mutants increasingly sensitive to five of nine DMI fungicides tested. The results suggest species-specific, differential binding of DMI fungicides onto the two CYP51 enzymes. Pairing DMIs with different effects on CYP51A and -B deletion mutants resulted in synergistic effects, as determined in mycelial growth inhibition experiments. Deletion mutants showed no fitness penalty in terms of mycelial growth, sporulation, and virulence. Our study elucidates the effect of CYP51A and CYP51B of Colletotrichum spp. on DMI sensitivity, suggesting that using a mixture of DMIs may improve the efficacy for anthracnose management.

Etiology of Cyclocarya paliurus Anthracnose in Jiangsu Province, China

Cyclocarya paliurus is an extremely valuable and multifunctional tree species whose leaves have traditionally been used in used in medicine or as a medicinal tea in China. In recent years, anthracnose has been frequently observed on young leaves of C. paliurus in several nurseries located in Jiangsu Province, resulting in great yield and quality losses. To date, no information is available about the prevalence of C. paliurus anthracnose in China. The main purpose of the present study was to characterize the etiology of C. paliurus anthracnose. Phylogenetic analysis of the eight-loci concatenated dataset revealed that all 44 single-spore Colletotrichum isolates belonged to three species in the Colletotrichum gloeosporioides species complex, namely, Colletotrichum aenigma, Colletotrichum fructicola, and C. gloeosporioides sensu stricto. Phenotypic features, including the colony appearance and the morphology of conidia, appressoria, and ascospores, were consistent with the phylogenetic grouping. Virulence tests validated that the three Colletotrichum species could cause typical symptoms of anthracnose on C. paliurus leaves, similar to those observed in the field. The optimum mycelial growth temperature ranged from 25 to 30°C for all representative isolates, while C. gloeosporioides s. s. isolates exhibited greater tolerance to high temperature (40°C). Fungicide sensitivity assays indicated that all three Colletotrichum species were sensitive to tetramycin, which may be a potential alternative for the management of C. paliurus anthracnose. To our knowledge, this study provides the first report of C. aenigma, C. fructicola, and C. gloeosporioides s. s. causing C. paliurus anthracnose in China as well as in the world.

Characterization of Colletotrichum Species Causing Anthracnose of Pomegranate in the Southeastern United States

Anthracnose fruit rot and leaf blight caused by Colletotrichum species are important diseases of pomegranate in the southeastern United States. In this study, 26 isolates from pomegranate were identified based on pathological and molecular characterization. Isolates were identified to species based on multilocus sequence analysis with the internal transcribed spacer region, glyceraldehyde-3-phosphate dehydrogenase, β-tubulin, and chitin synthase genomic genes. Pomegranate isolates grouped within the C. acutatum and C. gloeosporioides species complexes, with more than 73% belonging to the latter group. Three species were identified within the C. acutatum species complex (C. nymphaeae [n = 5], C. fioriniae [n = 1], and C. simmondsii [n = 1]), and three other species were identified within the C. gloeosporioides species complex (C. theobromicola [n = 11], C. siamense [n = 6], and C. gloeosporioides [n = 2]). Inoculations of pomegranate fruit showed that isolates from the C. acutatum species complex were more aggressive than isolates from the C. gloeosporioides species complex. Interestingly, opposite results were observed when leaves of rooted pomegranate cuttings were inoculated. In addition, Colletotrichum isolates from pomegranate, strawberry, blueberry, mango, and citrus were cross-pathogenic when inoculated to fruit. This is the first study identifying six different species of Colletotrichum causing pomegranate leaf blight and fruit anthracnose in the southeastern United States and the potential cross-pathogenic capability of pomegranate isolates to other commercially important crops.

Sensitivity of the Colletotrichum acutatum Species Complex From Apple Trees in Brazil to Dithiocarbamates, Methyl Benzimidazole Carbamates, and Quinone Outside Inhibitor Fungicides

Glomerella leaf spot (GLS) and bitter rot (BR) on apples are often caused by Colletotrichum acutatum in Paraná State, Brazil. GLS control is difficult because of its rapid development, with an incubation period of only 2 days under favorable conditions. Therefore, producers use successive fungicide applications every season; however, failure to control GLS has been commonly reported. The objectives of this study were to determine the sensitivity of isolates of the C. acutatum species complex obtained from apple orchards in Brazil to mancozeb, thiophanate-methyl, and azoxystrobin fungicides. Isolates from the different parts of the plant (leaves, flowers, buds, and twigs) and cultivars (Gala and Eva) showed different levels of sensitivity to mancozeb, thiophanate-methyl, and azoxystrobin. For mancozeb, the frequencies of isolates were 25% highly resistant, 50% low-resistance, and 25% sensitive. For thiophanate-methyl, the frequencies of isolates were 72.2% highly resistant, 11.1% resistant, and 16.7% moderately resistant. For azoxystrobin, the frequencies of isolates were 11.1% highly resistant, 5.6% resistant, and 83.3% sensitive. Interestingly, no mutations in the β-tubulin and cytochrome b genes were observed in any of the isolates resistant to thiophanate-methyl and azoxystrobin fungicides.

MdWRKY100 encodes a group I WRKY transcription factor in Malus domestica that positively regulates resistance to Colletotrichum gloeosporioides infection

Apple (Malus domestica) is an important fruit worldwide; however, the development of the apple industry is limited by fungal disease. Apple bitter rot caused by the pathogen Colletotrichum gloeosporioides is one of the most devastating apple diseases, leading to large-scale losses in apple quality and production. WRKY transcription factors have important functions in the regulation of biotic and abiotic stresses. However, their biological and molecular functions in non-model plants, including apple, remain poorly understood. Here, we isolated MdWRKY100 from 'Hanfu' apple. The MdWRKY100 protein fused to green fluorescent protein localized to the nucleus, and MdWRKY100 in yeast cells displayed transcriptional activation activity, which is consistent with the function of a transcription factor. Additionally, several putative cis-acting elements involved in abiotic stress responsiveness were also identified in the MdWRKY100 promoter. Transcriptional analysis revealed that MdWRKY100 was expressed ubiquitously in all examined apple organs. Overexpression in apple increased resistance to Colletotrichum gloeosporioides, while RNAi silencing transgenic plants were more sensitive to Colletotrichum gloeosporioides. Collectively, our data demonstrate that MdWRKY100 is a positive regulator of Colletotrichum gloeosporioides resistance in apple.

Anthracnose Fruit and Root Necrosis of Strawberry Are Caused by a Dominant Species Within the Colletotrichum acutatum Species Complex in the United States

Strawberry anthracnose fruit rot and root necrosis, caused by Colletotrichum acutatum, are primary limiting factors in fruit production fields in the United States. Recent research focusing on the phenotypic and genetic characteristics of this species has shed light on the diversity of the C. acutatum species complex. In this study, we performed multilocus sequence analysis of four genetic loci to characterize 217 C. acutatum isolates collected over a 23-year period from symptomatic plant tissues of strawberry from six different states. The results revealed two Colletotrichum spp. (C. nymphaeae and C. fioriniae), with 97.7% of the isolate collection (212 of 217) belonging to C. nymphaeae as a dominant clonal linage, regardless of the isolation source. No correlation between species groups and geographical origins of the isolates was observed. Further sequence comparison between historical and contemporary isolates showed the same populations being widely distributed throughout the strawberry nurseries and production fields in the United States and Canada. Subsequently, a subset of 12 isolates representing different quinone-outside inhibitor fungicide resistance profiles from root or fruit tissue of strawberry was selected for comparison of pathogenicity on strawberry. In this test, isolates of different resistance groups or different isolation sources exhibited a similar degree of aggressiveness and caused indistinguishable symptoms on strawberry crowns (P = 0.9555 and 0.7873, respectively) and fruit (P = 0.1638 and 0.1141, respectively), although a significant difference among individual isolates was observed in detached-fruit assays (P = 0.0123). Separate pathogenicity tests using isolates of the two species revealed C. nymphaeae being more aggressive than C. fioriniae in infecting strawberry roots and crowns (P = 0.0073). Therefore, given the occurrence and pathogenicity of C. nymphaeae, this species is likely the sole cause responsible for strawberry anthracnose in the United States.

Diversity in species composition and fungicide resistance profiles in Colletotrichum isolates from apples

Outbreaks of bitter rot were observed in three commercial apple orchards in Illinois despite best management efforts during the 2018 production season. Three isolates from symptomatic fruit from these orchards and two isolates from an orchard in South Carolina were identified to the species level using morphological tools and calmodulin, glyceraldehyde-3-phosphate dehydrogenase, and beta-tubulin gene sequences. The isolates from Illinois were identified as Colletotrichum siamense of the Colletotrichum gloeosporioides species complex and the ones from South Carolina as Colletotrichum fioriniae and Colletotrichum fructicola of the Colletotrichum acutatum and the C. gloeosporioides species complex, respectively. Two of the three C. siamense isolates from Illinois were resistant to azoxystrobin and thiophanate-methyl as determined in mycelial growth tests in vitro. EC₅₀ values were >100 μg/ml for both fungicides. One isolate was only resistant to azoxystrobin. None of the isolates from South Carolina was resistant to either of the two compounds. All five isolates were sensitive to fludioxonil (EC₅₀ values <0.1 μg/ml), propiconazole (EC₅₀ values ranged from 0.15 to 0.36 μg/ml), and benzovindiflupyr (EC₅₀ values ranged from <0.1 to 0.33 μg/ml). Resistance in C. siamense to azoxystrobin and thiophanate-methyl was confirmed in detached fruit studies using apples treated with label rates of registered product. Resistance to thiophanate-methyl in C. siamense was based on E198A mutation in b-tubulin gene, whereas resistance to azoxystrobin was based on G143A in cytochrome b (CYTB). One isolate resistant to azoxystrobin possessed no amino acid variation in CYTB. This study shows that quinone outside inhibitor fungicide resistance in Colletotrichum from apple has emerged and is being selected for in Illinois apple orchards by current spray strategies. Resistance monitoring may alert growers to potential threats, but the employment of molecular tools based on current knowledge of resistance mechanisms will provide incomplete results.

Colletotrichum acutatum and C. gloeosporioides Species Complexes Associated with Apple in Brazil

Glomerella leaf spot (GLS) is an apple disease that concerns growers due to the increases in severity over the years and the difficulties in control. Species within the Colletotrichum acutatum and C. gloeosporioides species complexes cause GLS, but the proportion of species within each complex in Brazilian apple orchards is not known. The objectives of this study were to identify isolates of Colletotrichum causing GLS on apple orchards in the main Brazilian producing regions to the species level. Two hundred and seven isolates were obtained in orchards in São Paulo (SP), Parana (PR), Santa Catarina (SC), and Rio Grande do Sul (RS) states. Genomic DNA was extracted, and the ITS, GAPDH, CHS-1, and TUB2 genes were amplified and sequenced. The phylogenetic trees were generated using a concatenated alignment. One hundred and fourteen isolates were identified as belonging to the C. acutatum species complex (Cac) and 93 to the C. gloeosporioides species complex (Cgc). Five phylogenetic species were identified: C. melonis (1.9%), C. nymphaeae (47.4%), C. paranaense (2.4%), C. limetticola (3.4%), and C. fructicola (44.9%). In SC, Cgc predominates, but in the states of SP, PR, and RS, Cac was predominant. This is the first report of C. limetticola from apple.

Characterization and Fungicide Sensitivity of Colletotrichum spp. from Different Hosts in Shandong, China

Anthracnose, caused by Colletotrichum species, can severely infect the fruits and leaves of more than 30 plants and thus results in great yield and quality losses. To identify the major Colletotrichum species infecting walnut fruits, strawberry leaves, grape fruits, and tea leaves in Shandong Province, China, 101 strains were collected and isolated. The morphological characteristics of all isolates were observed, and multilocus phylogenetic analyses (ITS, GAPDH, ACT, TUB2, CAL, CHS-1, and HIS3) were conducted on the representative isolates. The strains were identified as five Colletotrichum species, namely, C. gloeosporioides sensu stricto, C. fructicola, C. camelliae, C. acutatum sensu stricto, and C. viniferum. Among them, C. viniferum was reported for the first time from walnut fruits and strawberry leaves in Shandong Province, China. Corresponding leaves or fruits were used as a model to clarify the pathogenicity of these isolates. The results showed that C. fructicola obtained from strawberry leaves was more aggressive than C. viniferum. All of the isolates obtained from various hosts were highly sensitive to pyraclostrobin, difenoconazole, fludioxonil, tebuconazole, pyrisoxazole, and tetramycin in terms of mycelial growth inhibition (EC₅₀ values of 0.07 to 1.63 mg/liter). The fastest mycelial growth was observed in the temperature range of 25-28°C for all isolates. In addition, anthracnose symptoms occur frequently under these conditions. Overall, this study can improve the understanding of Colletotrichum species causing anthracnose in walnut fruits, strawberry leaves, grape fruits, and tea leaves and can provide a solid foundation for the effective control of this disease in different hosts.

Identification and Characterization of Colletotrichum Species Associated with Bitter Rot Disease of Apple in South Korea

Bitter rot caused by Colletotrichum species is a common fruit rotting disease of apple and one of the economically important disease in worldwide. In 2015 and 2016, distinct symptoms of bitter rot disease were observed in apple orchards in five regions of South Korea. In the present study, infected apples from these regions were utilized to obtain eighteen isolates of Colletotrichum spp. These isolates were identified and characterized according to their morphological characteristics and nucleotide sequence data of internal transcribed spacer regions and glyceraldehyde-3-phosphate-dehydrogenase. Molecular analyses suggested that the isolates of Colletotrichum causing the bitter rot disease in South Korea belong to 4 species: C. siamense; C. fructicola; C. fioriniae and C. nymphaeae. C. siamense and C. fructicola belonged to Musae Clade of C. gloeosporioides complex species while C. fioriniae and C. nymphaeae belonged to the Clade 3 and Clade 2 of C. acutatum complex species, respectively. Additionally, we also found that the isolates of C. gloeosporioides species-complex were more aggressive than those in the C. acutatum species complex via pathogenicity tests. Taken together, our results suggest that accurate identification of Colletotrichum spp. within each species complex is required for management of bitter rot disease on apple fruit in South Korea.