Circumscription of the anthracnose pathogens Colletotrichum lindemuthianum and C. nigrum

Morphological and transcriptional analysis of Colletotrichum lindemuthianum race 7 during early stages of infection in common bean

The infection process of the hemibiotrophic fungus Colletotrichum lindemuthianum has been independently studied at the microscopic and genomic levels. However, the relationship between the morphological changes and the pathogenicity mechanisms of the fungus at the early stages of the infection remains uncharacterized. Therefore, this study attempts to bridge this gap by integrating microscopic and transcriptional approaches to understand the infection process of C. lindemuthianum. Fungal structures were followed by fluorescence microscopy for 120 hours. Simultaneously, the transcriptomic profile was made using RNAseq. Morphological characterization shows that appressoria, infective vesicles, and secondary hypha formation occur before 72 hours. Additionally, we assembled 38,206 transcripts with lengths between 201 and 3,548 bp. The secretome annotation revealed the expression of 1,204 CAZymes, of which 17 exhibited secretion domains and were identified as chitinases and β-1,3-glucanases, 27 were effector candidates, and 30 were transport proteins mostly associated with ABC-type. Finally, we confirmed the presence and expression of CAC1 role during the appressoria formation of Clr7. This result represents the first report of adenylate cyclase expression evaluated under three different approaches. In conclusion, C. lindemuthianum colonizes the host through different infection structures complemented with the expression of multiple enzymes, where CAC1 favors disease development.

Identification and Genetic Diversity Analysis of the Pathogen of Anthracnose of Pepper in Guizhou

Anthracnose of pepper is a significant disease caused by Colletotrichum spp. In 2017 and 2021, 296 isolates were obtained from 69 disease samples. Through morphological analysis, pathogenicity detection, and polygenic phylogenetic analysis, the above strains were attributed to 10 species: C. scovillei, C. fructicola, C. karstii, C. truncatum, C. gloeosporioides, C. kahawae, C. boninense, C. nymphaeae, C. plurivorum, and C. nigrum. C. scovillei had the most strains (150), accounting for 51.02% of the total isolates; C. fructicola came in second (72 isolates), accounting for 24.49%. Regarding regional distribution, Zunyi City has the highest concentration of strains-92 strains total, or 34.18%-across seven species. Notably, this investigation showed that C. nymphaeae infected pepper fruit for the first time in China. Genetic diversity analysis showed that C. fructicola could be divided into seven haplotypes, and the population in each region had apparent genetic differentiation. However, the genetic distance between each population was not significantly related to geographical distance. Neutral detection and nucleotide mismatch analysis showed that C. fructicola might have undergone population expansion.

Morphological, Pathological and Genetic Diversity of the Colletotrichum Species, Pathogenic on Solanaceous Vegetable Crops in Bulgaria

Colletotrichum species are among the most devastating plant pathogens in a wide range of hosts. Their accurate identification requires a polyphasic approach, including geographical, ecological, morphological, and genetic data. Solanaceous crops are of significant economic importance for Bulgarian agriculture. Colletotrichum-associated diseases pose a serious threat to the yield and quality of production but are still largely unexplored. The aim of this study was to identify and characterize 26 pathogenic Colletotrichum isolates that threaten solanaceous crops based on morphological, pathogenic, and molecular data. DNA barcodes enabled the discrimination of three main taxonomic groups: C. acutatum, C. gloeosporioides, and C. coccodes. Three different species of acutatum complex (C. nymphaeae, C. godetiae, and C. salicis) and C. cigarro of the gloeosporioides complex were associated with fruit anthracnose in peppers and tomatoes. The C. coccodes group was divided in two clades: C. nigrum, isolated predominantly from fruits, and C. coccodes, isolated mainly from roots. Only C. salicis and C. cigarro produced sexual morphs. The species C. godetiae, C. salicis, and C. cigarro have not previously been reported in Bulgaria. Our results enrich the knowledge of the biodiversity and specific features of Colletotrichum species, which are pathogenic to solanaceous hosts, and may serve as a scientific platform for efficient disease control and resistance breeding.

Phylogeny and pathogenicity of Colletotrichum lindemuthianum causing anthracnose of Phaseolus vulgaris cv. Bhaderwah-Rajmash from northern Himalayas, India

With an annual loss of up to 100%, anthracnose caused by Colletotrichum is one of the most devastating diseases of common beans (Phaseolus vulgaris L.). Due to few distinctive morphological characters, Colletotrichum species are frequently misidentified. In India, several Colletotrichum species have been reported as pathogens of Phaseolus species, but none had previously been validated by means of molecular tools. In this study, we studied Colletotrichum strains from common beans cv. Bhaderwah-Rajmash from the northern Himalayas of India based on both morphological and DNA sequence data of six loci, namely ITS, gapdh, chs-1, his3, act, tub2. The strains were identified as C. lindemuthianum that belongs to the C. orbiculare species complex. Representative C. lindemuthianum strains tested on Phaseolus vulgaris cv. Bhaderwah-Rajmash were pathogenic and exhibited variation in symptomology and disease progression. By identifying the causal agent, we provided substantial information to develop the best control strategies for anthracnose of Phaseolus vulgaris from the northern Himalayas of India.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03216-0.

Endophytic Colletotrichum Species from Aquatic Plants in Southwest China

Colletotrichum species are plant pathogens, saprobes, and endophytes in many economically important hosts. Many studies have investigated the diversity and pathogenicity of Colletotrichum species in common ornamentals, fruits, and vegetables. However, Colletotrichum species occurring in aquatic plants are not well known. During the investigation of the diversity of endophytic fungi in aquatic plants in southwest China, 66 Colletotrichum isolates were obtained from aquatic plants there, and 26 of them were selected for sequencing and analyses of actin (ACT), chitin synthase (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the internal transcribed spacer (ITS) region, and β-tubulin (TUB2) genomic regions. Based on morphological characterization and multi-locus phylogenetic analyses, 13 Colletotrichum species were recognized, namely, C. baiyuense sp. nov., C. casaense sp. nov., C. demersi sp. nov., C. dianense sp. nov., C. fructicola, C. garzense sp. nov., C. jiangxiense, C. karstii, C. philoxeroidis sp. nov., C. spicati sp. nov., C. tengchongense sp. nov., C. vulgaris sp. nov., C. wuxuhaiense sp. nov. Two species complexes, the C. boninense species complex and C. gloeosporioides species complex, were found to be associated with aquatic plants. Pathogenicity tests revealed a broad diversity in pathogenicity and aggressiveness among the eight new Colletotrichum species.

First report of quinoa anthracnose caused by Colletotrichum nigrum and C. truncatum in the United States

Quinoa (Chenopodium quinoa Willd.) is increasingly produced outside its native Andean range. In September 2019, stem lesions were observed on all six plants of quinoa accessions PI 510547 (25% severity) and PI 596293 (75% severity) in a demonstration plot in Ames, IA. Lesions were bleached, silvery-white to dark gray, slightly sunken, oval to linear with slightly tapered tips and contained setose acervuli. Fungi were isolated from both accessions following disinfestation with 70% ethanol and plating onto ½ acidified potato dextrose agar (APDA) and V8 medium. Isolates were examined morphologically. On V8 medium, isolate CQ1 produced sparse, flat, gray mycelia with profuse sclerotia and hyaline, aseptate, cylindrical conidia (n= 50, mean: 21.0 (range: 19.2-24) by 4.3 (2.4-4.8) µm); isolate CQ2 produced fluffy, gray to dark gray mycelia with profuse sclerotia and acervuli and hyaline, aseptate, falcate conidia (n =50, 26.8 (24-31.2) by 2.4 µm). Direct hyphal PCR was used to amplify ITS (ITS1/ITS4), ACT (ACT-512F/ACT-783R), GAPDH (GDF1/GDR1), CHS-1 (CHS-79F/CHS-234R), and TUB2 (T1/Bt-2b, CQ1 only) (Fu et al. 2019, Liu et al. 2013), and products were sequenced bidirectionally (MT772082-3, MT786524-30). A maximum likelihood tree was generated in MEGA X (Kumar et al. 2018) from a multiple sequence alignment of vouchered CBS isolates (Liu et al. 2013) and CQ1 was identified as Colletotrichum nigrum. CQ2 sequences showed 99-100% similarity to Colletotrichum truncatum sequences in Genbank (MN581860, MK675238, MF682518, MK118057). Koch's postulates were completed once with two isolates of each species grown on V8 medium under 12 hours of near UV light for two weeks. Greenhouse conditions were a 12 hr day/night cycle and temperature range of 26-30° C. Approximately 5 mL of mycelium on agar medium was sterilely removed and macerated in 6 mL of sterile distilled water. Non-inoculated medium was macerated in sterile water as a control. Forty-day old quinoa PI 634920 were inoculated by making three, 2-3 mm incisions between the cotyledons and first true leaves with a sterile razor blade. Next, 500 µL of slurry was placed on 2.54 cm2 of sterile cheesecloth and placed against the wound and wrapped with Parafilm. Six plants were inoculated per isolate and control. After two weeks, sunken, bleached to tan areas extended past wound sites of inoculated plants. No discoloration or sunken tissue was observed on control plants. Plants were tented with plastic film for one week. Acervuli were observed on C. truncatum- and C. nigrum-inoculated stems, and sclerotia were observed on C. nigrum-inoculated stems. Stems were surface disinfested with 10% bleach and plated onto ½ APDA. Colony morphologies of isolated fungi matched those of original inoculum for inoculated plants. Colletotrichum spp. were never isolated from control plants. When stems were inoculated, approximately 100 µL of slurry was also placed on 3-5 detached quinoa leaves in Petri dishes with moistened blotter paper and incubated for 48 hours at 25° C. Brownish, circular lesions developed on leaves inoculated with either species, but no lesions developed on control-slurry leaves. Colletotrichum spp. cause disease in quinoa relatives including spinach (Kurt 2015), beets (Gourley 1966) and amaranth (Wu 2001). This is the first description of Colletotrichum spp. causing stem lesions on quinoa in the United States. This disease may emerge in new quinoa production regions and may cause yield losses due to lodging.

The Colletotrichum dracaenophilum, C. magnum and C. orchidearum species complexes

Although Glomerella glycines, Colletotrichum magnum and C. orchidearum are known as causal agents of anthracnose of soybean, Cucurbitaceae and Orchidaceae, respectively, their taxonomy remains unresolved. In preliminary analyses based on ITS, strains of these species appear basal in Colletotrichum phylogenies, clustering close to C. cliviae, C. brevisporum and other recently described species from tropical or subtropical regions. Phylogenetic analyses (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 102 strains previously identified as Ga. glycines, C. magnum and C. orchidearum as well as other related strains from different culture collections and studies placed these taxa in three species complexes, and distinguished at least 24 species, including 11 new species. In this study, C. magnum, C. orchidearum and C. piperis were epitypified and their taxonomy resolved, while C. cliviicola was proposed as a new name for C. cliviae. Furthermore, a sexual morph was observed for C. yunnanense, while C. brevisporum, C. cliviicola and C. tropicicola were reported from new hosts or countries. Regarding their conidial morphology, species in the C. dracaenophilum, C. magnum and C. orchidearum species complexes are reminiscent of C. gloeosporioides or C. boninense s. lat., and were likely to be confused with them in the past.

Genera of phytopathogenic fungi: GOPHY 1

Genera of Phytopathogenic Fungi (GOPHY) is introduced as a new series of publications in order to provide a stable platform for the taxonomy of phytopathogenic fungi. This first paper focuses on 21 genera of phytopathogenic fungi: Bipolaris, Boeremia, Calonectria, Ceratocystis, Cladosporium, Colletotrichum, Coniella, Curvularia, Monilinia, Neofabraea, Neofusicoccum, Pilidium, Pleiochaeta, Plenodomus, Protostegia, Pseudopyricularia, Puccinia, Saccharata, Thyrostroma, Venturia and Wilsonomyces. For each genus, a morphological description and information about its pathology, distribution, hosts and disease symptoms are provided. In addition, this information is linked to primary and secondary DNA barcodes of the presently accepted species, and relevant literature. Moreover, several novelties are introduced, i.e. new genera, species and combinations, and neo-, lecto- and epitypes designated to provide a stable taxonomy. This first paper includes one new genus, 26 new species, ten new combinations, and four typifications of older names.

Chilli Anthracnose: The Epidemiology and Management

Indian cuisine is renowned and celebrated throughout the world for its spicy treat to the tongue. The flavor and aroma of the food generated due to the use of spices creates an indelible experience. Among the commonly utilized spices to stimulate the taste buds in Indian food, whole or powdered chilli constitutes an inevitable position. Besides being a vital ingredient of of Indian food, chilli occupy an important position as an economic commodity, a major share in Indian economy. Chilli also has uncountable benefits to human health. Fresh green chilli fruits contain more Vitamin C than found in citrus fruits, while red chilli fruits have more Vitamin A content than as found in carrots. The active component of the spice, Capsaicin possesses the antioxidant, anti-mutagenic, anti-carcinogenic and immunosuppressive activities having ability to inhibit bacterial growth and platelet aggregation. Though introduced by the Portuguese in the Seventeenth century, India has been one of the major producers and exporters of this crop. During 2010-2011, India was the leading exporter and producer of chilli in the world, but recently due to a decline in chilli production, it stands at third position in terms of its production. The decline in chilli production has been attributed to the diseases linked with crop like anthracnose or fruit rot causing the major share of crop loss. The disease causes severe damage to both mature fruits in the field as well as during their storage under favorable conditions, which amplifies the loss in yield and overall production of the crop. This review gives an account of the loss in production and yield procured in chili cultivation due to anthracnose disease in Indian sub-continent, with emphasis given to the sustainable management strategies against the conventionally recommended control for the disease. Also, the review highlights the various pathogenic species of Colletotrichum spp, the causal agent of the disease, associated with the host crop in the country. The information in the review will prove of immense importance for the groups targeting the problem, for giving a collective information on various aspects of the epidemiology and management of the disease.

Unravelling Colletotrichum species associated with Camellia: employing ApMat and GS loci to resolve species in the C. gloeosporioides complex

We investigated the phylogenetic diversity of 144 Colletotrichum isolates associated with symptomatic and asymptomatic tissues of Camellia sinensis and other Camellia spp. from seven provinces in China (Fujian, Guizhou, Henan, Jiangxi, Sichuan, Yunnan, Zhejiang), and seven isolates obtained from other countries, including Indonesia, UK, and the USA. Based on multi-locus (ACT, ApMat, CAL, GAPDH, GS, ITS, TUB2) phylogenetic analyses and phenotypic characters, 11 species were distinguished, including nine well-characterised species (C. alienum, C. boninense, C. camelliae, C. cliviae, C. fioriniae, C. fructicola, C. gloeosporioides, C. karstii, C. sia-mense), and two novel species (C. henanense and C. jiangxiense). Of these, C. camelliae proved to be the most dominant and probably host specific taxon occurring on Camellia. An epitype is also designated for the latter species in this study. Colletotrichum jiangxiense is shown to be phylogenetically closely related to the coffee berry pathogen C. kahawae subsp. kahawae. Pathogenicity tests and the pairwise homoplasy index test suggest that C. jiangxiense and C. kahawae subsp. kahawae are two independent species. This study represents the first report of C. alienum and C. cliviae occurring on Camellia sinensis. In addition, our study demonstrated that the combined use of the loci ApMat and GS in a phylogenetic analysis is able to resolve all currently accepted species in the C. gloeosporioides species complex.

The Colletotrichum destructivum species complex - hemibiotrophic pathogens of forage and field crops

Colletotrichum destructivum is an important plant pathogen, mainly of forage and grain legumes including clover, alfalfa, cowpea and lentil, but has also been reported as an anthracnose pathogen of many other plants worldwide. Several Colletotrichum isolates, previously reported as closely related to C. destructivum, are known to establish hemibiotrophic infections in different hosts. The inconsistent application of names to those isolates based on outdated species concepts has caused much taxonomic confusion, particularly in the plant pathology literature. A multilocus DNA sequence analysis (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 83 isolates of C. destructivum and related species revealed 16 clades that are recognised as separate species in the C. destructivum complex, which includes C. destructivum, C. fuscum, C. higginsianum, C. lini and C. tabacum. Each of these species is lecto-, epi- or neotypified in this study. Additionally, eight species, namely C. americae-borealis, C. antirrhinicola, C. bryoniicola, C. lentis, C. ocimi, C. pisicola, C. utrechtense and C. vignae are newly described.

The Colletotrichum gigasporum species complex

In a preliminary analysis, 21 Colletotrichum strains with large conidia preserved in the CBS culture collection clustered with a recently described species, C. gigasporum, forming a clade distinct from other currently known Colletotrichum species complexes. Multi-locus phylogenetic analyses (ITS, ACT, TUB2, CHS-1, GAPDH) as well as each of the single-locus analyses resolved seven distinct species, one of them being C. gigasporum. Colletotrichum gigasporum and its close allies thus constitute a previously unknown species complex with shared morphological features. Five of the seven species accepted in the C. gigasporum species complex are described here as novel species, namely C. arxii, C. magnisporum, C. pseudomajus, C. radicis and C. vietnamense. A species represented by a single sterile strain, namely CBS 159.50, was not described as novel species, and is treated as Colletotrichum sp. CBS 159.50. Furthermore, C. thailandicum is reduced to synonymy with C. gigasporum.

Colletotrichum caudatum s.l. is a species complex

Colletotrichum caudatum sensu lato is a widespread fungal pathogen of warm-season grasses. The fungus is easily differentiated from other Colletotrichum species through the presence of a unique filiform appendage at the apex of the conidium. Multi-locus phylogenetic analysis of four DNA sequence markers from 21 isolates of C. caudatum s.l. from six grass hosts recovered the morphospecies as a well-supported monophyletic group. Although closely related to other Colletotrichum species pathogenic to warm-season grasses (e.g. C. sublineola, C. falcatum, C. navitas, C. graminicola), the sister taxon placement of C. caudatum remained unclear. Four major subgroups and three monotypic lineages were identified from the C. caudatum s.l. isolates. Despite the presence of localized, taxon-specific incongruence between gene trees and evidence for recombination in the dataset, application of genealogical concordance species recognition criteria diagnosed the four subgroups as phylogenetic species. Traditional morphology-based species concept defines C. caudatum as one species with a broad host range; however, multi-locus phylogenetic analyses refuted this model. Instead, isolates from different hosts were mainly segregated into different lineages. In particular, isolates from the type locale and host (USA, Sorghastrum nutans) collected within a 400 km radius were divided into three distinct species that corresponded with the three sampling sites. These data established that traditional morphological and ecological features are not informative for recognition of taxa within C. caudatum s.l., although there is some evidence that some species may be host specific. To stabilize the application of the name C. caudatum, DNA sequence data from the lectotype was generated, an epitype strain consistent with the type was designated and illustrated, and an emended description of C. caudatum sensu stricto is provided. Colletotrichum alcornii, C. baltimorense, C. somersetense, and C. zoysiae are described as new morphologically cryptic species related to C. caudatum s.s.

Characterization of Glomerella strains recovered from anthracnose lesions on common bean plants in Brazil

Anthracnose caused by Colletotrichum lindemuthianum is an important disease of common bean, resulting in major economic losses worldwide. Genetic diversity of the C. lindemuthianum population contributes to its ability to adapt rapidly to new sources of host resistance. The origin of this diversity is unknown, but sexual recombination, via the Glomerella teleomorph, is one possibility. This study tested the hypothesis that Glomerella strains that are frequently recovered from bean anthracnose lesions represent the teleomorph of C. lindemuthianum. A large collection of Glomerella isolates could be separated into two groups based on phylogenetic analysis, morphology, and pathogenicity to beans. Both groups were unrelated to C. lindemuthianum. One group clustered with the C. gloeosporioides species complex and produced mild symptoms on bean tissues. The other group, which belonged to a clade that included the cucurbit anthracnose pathogen C. magna, caused no symptoms. Individual ascospores recovered from Glomerella perithecia gave rise to either fertile (perithecial) or infertile (conidial) colonies. Some pairings of perithecial and conidial strains resulted in induced homothallism in the conidial partner, while others led to apparent heterothallic matings. Pairings involving two perithecial, or two conidial, colonies produced neither outcome. Conidia efficiently formed conidial anastomosis tubes (CATs), but ascospores never formed CATs. The Glomerella strains formed appressoria and hyphae on the plant surface, but did not penetrate or form infection structures within the tissues. Their behavior was similar whether the beans were susceptible or resistant to anthracnose. These same Glomerella strains produced thick intracellular hyphae, and eventually acervuli, if host cell death was induced. When Glomerella was co-inoculated with C. lindemuthianum, it readily invaded anthracnose lesions. Thus, the hypothesis was not supported: Glomerella strains from anthracnose lesions do not represent the teleomorphic phase of C. lindemuthianum, and instead appear to be bean epiphytes that opportunistically invade and sporulate in the lesions.