Colletotrichum species associated with sugarcane red rot in Brazil

Sugarcane is a widely cultivated crop in Brazil and in many parts of the world. However, the red rot causes huge losses due to the reduction of sucrose and deterioration of the juice. The aim of this study was to identify Colletotrichum species associated with the red rot through polyphasic approaches; which included phylogenetic, morpho-cultural analyzes and pathogenicity tests. Nine isolates from the states of Alagoas and two from São Paulo, Brazil, were preliminary analyzed with the glyceraldehyde-3 phosphate dehydrogenase gene (GAPDH), as an initial measure for species diversity. Later on, the representative isolates of each species were sequenced with the β-tubulin (TUB2) gene, calmodulin (CAL), DNA lyase (APN2/MAT IGS) and the ITS-rDNA region. Morphocultural characterization was performed by evaluating the mycelial growth rate (MGR), colony appearance and the shape and size of 50 conidia and appressoria. For the pathogenicity test asymptomatic leaves and stalks of sugarcane were tested with and without injuries. Phylogenetic analysis associated with morphocultural characteristics and the pathogenicity test of the eleven isolates revealed three Colletotrichum species: Colletotrichum falcatum (8 isolates), Colletotrichum siamense (1 isolate) and Colletotrichum plurivorum (2 isolates) causing the red rot disease in sugar cane. All species were pathogenic in wounded leaves and stalks, being C. falcatum the one causing the largest lesions (1.12 cm) in leaves and C. plurivorum in stalks (0.67 cm). Therefore, this study confirms the association of C. falcatum as a sugarcane pathogen and records for the first time worldwide the occurrence of C. siamense and C. plurivorum associated with this host.     

Colletotrichum species associated with cassava anthracnose in China

Anthracnose caused by Colletotrichum (CAD) is an economically important disease of cassava; however, research on its species diversity and geographical distribution of Colletotrichum in China remains limited. In this study, we investigated the phylogenetic diversity of Colletotrichum isolates associated with symptomatic leaf tissues of cassava from Guangxi and Yunnan provinces in China and aimed to confirm their identification using advanced techniques. Based on multi‐locus phylogenetic analyses and phenotypic characteristics, we identified four species from the isolates, comprising C. plurivorum, C. karstii, C. fructicola and C. siamense, and we found variation in degrees of virulence among the species and between cassava varieties. Our results are the first to report these species from cassava, and they provide a basis for the development of management strategies for CAD in cassava.     

虎耳草炭疽病病原菌鉴定

【目的】从虎耳草炭疽病病斑分离病原菌,并对病原菌进行鉴定。【方法】采用柯赫氏法则对从病斑组织块分离的病原菌进行验证,通过形态学结合多基因分子系统学方法对病原菌进行鉴定。【结果】从虎耳草炭疽病病斑分离到2株菌株(菌株号:LPSU 20120244、LPSU 20120251)。2株菌株孢子均无色,无隔,直、圆柱状,菌株LPSU 20120244孢子(11-25)μm×(5-9)μm,菌株LPSU 20120251孢子(15-25)μm×(5-7)μm。多基因分子系统树中,2株菌株分别与喀斯特炭疽菌(Colletotrichum karstii Y.L.Yang,Zuo Y.Liu,K.D.HydeL.Cai)和江西炭疽菌(C.jiangxiense F.LiuL.Cai)模式菌株聚为一支,支持率均为100%。【结论】形态学及多基因分子系统学分析表明菌株LPSU 20120244为喀斯特炭疽菌,菌株LPSU 20120251为江西炭疽菌。     

Elucidating the Colletotrichum spp. diversity responsible for papaya anthracnose in Brazil

Papaya (Carica papaya L.) is among the most important tropical fruits produced in Brazil and is grown in nearly every state. However, several diseases can affect papaya production. Anthracnose stands out among these diseases due to high postharvest yield losses. Previous studies identified Colletotrichum magna (invalid name) and Colletotrichum gloeosporioides causing anthracnose of papaya in Brazil, but species identification was inadequate due to reliance on nuclear ribosomal internal transcribed space (nrITS) and glutamine synthetase (GS) sequences. Thus, the diversity of Colletotrichum spp. causing papaya anthracnose in Brazil may be underestimated. The present study aims to identify the Colletotrichum species associated with papaya anthracnose in Brazil based on broad geographical sampling and multilocus phylogenetic analysis, as well as to assess the prevalence and aggressiveness of the species found. Here, we report C. chrysophilum, C. fructicola, C. gloeosporioides, C. karsti, C. okinawense, C. plurivorum, C. queenslandicum, C. siamense, C. theobromicola, Colletotrichum truncatum causing papaya anthracnose in Brazil. We are also synonymizing Colletotrichum corchorum-capsularis under C. truncatum. Colletotrichum okinawense was the most prevalent species in general and in most sampled locations, and with C. truncatum represents the most aggressive species.     

Why species delimitation matters for fungal ecology: Colletotrichum diversity on wild and cultivated cashew in Brazil

Anthracnose is one of the most important plant diseases globally, occurring on a wide range of cultivated and wild host species. This study aimed to identify the Colletotrichum species associated with cashew anthracnose in Brazil, determine their phylogenetic relationships and geographical distribution, and provide some insight into the factors that may be influencing community composition. Colletotrichum isolates collected from symptomatic leaves, stems, inflorescences, and fruit of cultivated and wild cashew, across four Brazilian biomes, were identified as Colletotrichum chrysophilum, Colletotrichum fragariae, Colletotrichum fructicola, Colletotrichum gloeosporioides sensu stricto, Colletotrichum queenslandicum, Colletotrichum siamense and Colletotrichum tropicale. Colletotrichum siamense was the most dominant species. The greatest species richness was associated with cultivated cashew; leaves harbored more species than the other organs; the Atlantic Forest encompassed more species than the other biomes; and Pernambuco was the most species-rich location. However, accounting for the relative abundance of Colletotrichum species and differences in sample size across strata, the interpretation of which community is most diverse depends on how species are delimited. The present study provides valuable information about the Colletotrichum/cashew pathosystem, sheds light on the causal agents identification,and highlights the impact that species delimitation can have on ecological studies of fungi.     

Morphological and molecular identification of Colletotrichum species associated with cassava anthracnose in Thailand

The objective of this study was to identify the causal agent of anthracnose disease of cassava in Thailand. The study was carried out by collecting cassava samples with anthracnose symptoms from various planting areas including 10 districts of eight provinces in Thailand. One hundred and thirty‐six Colletotrichum samples were isolated from cassava anthracnose lesions on leaves, petioles and stems. Thirty‐eight single‐spore isolates were subsequently obtained and cultured on half potato dextrose agar for morphological and molecular characterizations. All 38 isolates were pathogenic with varying degrees of virulence when tested on detached leaves of Kasetsart 50, a susceptible cassava cultivar. Based on their growth habit, colony morphology, conidial morphology and the internal transcribed spacer sequences similarity to that of Colletotrichum accessions in the GenBank, one isolate was identified as C. capsici, one as C. lindemuthianum, two as C. aeschynomene, four as C. boninense and 28 C. gloeosporioides species complex. Geographically, the cosmopolitan C. gloeosporioides species complex was found in all regions, but other species were found only in particular regions. This is, so far, the first report of Colletotrichum complex species associated with cassava anthracnose in Thailand.     

Pythium and Phytopythium species associated with weeds collected in vegetable production fields in Brazil

This study aimed to identify Pythium and Phytopythium species from weeds collected in vegetable fields and test their pathogenicity. Weeds with symptoms of damping-off, root rot or wilt were sampled in the Brazilian states of Ceará, Goiás and Pernambuco, as well as in the Distrito Federal, for isolation and identification of the causal agents. Once isolated, colonies with typical Pythium and Phytopythium characteristics grew in selective V8 medium. Procedures for species identification included morphology and amplification of the ITS and Cox II regions, which were compared with other accessions available at GenBank. The phylogenetic relationships among the isolates and pathogenicity to their original hosts were evaluated. Six Pythium species were identified: P. aphanidermatum, P. oopapillum, P. orthogonon, P. ultimum var. ultimum, P. myriotylum and P. sylvaticum, and two species of Phytopythium, Phy. chamaehyphon and Phy. oedochilum. In the pathogenicity tests, the 10 weed hosts showed symptoms of damping-off or root rot after inoculation, with exception of Portulaca oleraceae in which none of the isolates was pathogenic. Therefore, common weeds in vegetable fields areas can host different Pythium and Phytopythium species and play an important role in the epidemiology of vegetable diseases, in particular on pathogen survival and population increase.     

Infra-specific diversity of Colletotrichum truncatum associated with chilli anthracnose in India based on microsatellite marker analysis

Colletotrichum truncatum is a fungal species associated with anthracnose disease in many economically important crops within the plant families Fabaceae and Solanaceae. Understanding the degree of genetic diversity within C. truncatum population will provide insights into the ability of this species to evolve in response to environmental conditions, and thus be helpful in designing effective control strategies for this pathogen. In this study, microsatellite markers from 27 loci were used to investigate the genetic diversity and population structure among 99 isolates of C. truncatum from India. All the loci (100%) were polymorphic and a total of 140 different alleles were amplified. Six distinct groups were obtained based on unweighted pair group method with arithmetical average cluster analysis. The isolates belonging to Group V showed the highest level of genetic diversity and a broad host range. Analysis of molecular variance analysis showed that the variation occurs mostly within groups. Microsatellite markers-based genetic diversity estimation revealed high diversity among C. truncatum isolates from India.     

Soybean anthracnose caused by Colletotrichum species: Current status and future prospects

Soybean (Glycine max) is one of the most important cultivated plants worldwide as a source of protein‐rich foods and animal feeds. Anthracnose, caused by different lineages of the hemibiotrophic fungus Colletotrichum, is one of the main limiting factors to soybean production. Losses due to anthracnose have been neglected, but their impact may threaten up to 50% of the grain production.TaxonomyWhile C. truncatum is considered the main species associated with soybean anthracnose, recently other species have been reported as pathogenic on this host. Until now, it has not been clear whether the association of new Colletotrichum species with the disease is related to emerging species or whether it is due to the undergoing changes in the taxonomy of the genus.Disease symptomsTypical anthracnose symptoms are pre‐ and postemergence damping‐off; dark, depressed, and irregular spots on cotyledons, stems, petioles, and pods; and necrotic laminar veins on leaves that can result in premature defoliation. Symptoms may evolve to pod rot, immature opening of pods, and premature germination of grains.ChallengesAs accurate species identification of the causal agent is decisive for disease control and prevention, in this work we review the taxonomic designation of Colletotrichum isolated from soybean to understand which lineages are pathogenic on this host. We also present a comprehensive literature review of soybean anthracnose, focusing on distribution, symptomatology, epidemiology, disease management, identification, and diagnosis. We consider the knowledge emerging from population studies and comparative genomics of Colletotrichum spp. associated with soybean providing future perspectives in the identification of molecular factors involved in the pathogenicity process.Useful websiteUpdates on Colletotrichum can be found at http://www.colletotrichum.org/.All available Colletotrichum genomes on GenBank can be viewed at http://www.colletotrichum.org/genomics/.     

Detection and molecular characterization of carbendazim-resistant Colletotrichum truncatum Isolates causing anthracnose of soybean in Thailand

A loss of fungicide efficacy, particularly for carbendazim, was noted in soybean fields in Thailand and was considered to be due to the development of Colletotrichum truncatum resistance. The carbendazim sensitivity of C. truncatum populations isolated from various soybean fields in Thailand was thus evaluated with in vitro sensitivity assays and molecular characterization of mutations in the sequences of the ß₂-tubulin (TUB2) gene that confer carbendazim resistance in the pathogen. Among 52 isolates, 46 isolates were classified as highly resistant (HR) to carbendazim (EC₅₀ > 1,000 µg/ml). All HR isolates grew on PDA amended with carbendazim at 1,000 µg/ml. Six isolates were classified as carbendazim sensitive (S) (EC₅₀ < 1 µg/ml). Mycelial growth on PDA amended with 1 µg/ml carbendazim was inhibited by over 50% compared with growth on PDA alone. When a partial TUB2 gene from the isolates was amplified and analysed using predicted amino acid sequences, an alteration from glutamic acid to alanine at codon 198 (E198A) was found in 45 HR isolates for which the EC₅₀ was higher than 2000 µg/ml. This mutation resulted from a nucleotide substitution from adenine to cytosine (GA G → GC G). The other HR isolate, CtPhS_1, with EC₅₀ of 1,127 µg/ml, had an alteration at codon 200 (F200Y) (TT C → TA C).     

Molecular systematics in the genus Mucor with special regards to species encountered in cheese

The genus Mucor, a member of the order Mucorales, comprises different species encountered in cheeses. Although fungi play a fundamental role in cheese manufacturing and ripening, the taxonomy of many fungal species found in cheese is poorly defined; indeed, this is the case for Mucor spp. In the present study, we assessed the phylogenetic relationships among 70 Mucor strains, including 36 cheese isolates, by using a five gene phylogenetic approach combined with morphological analyses. Overall, at least six species of Mucor were identified among the cheese isolates including a possible new taxon. The present study also suggests that the genus Mucor comprises undescribed taxa and needs to be properly defined.     

Unravelling Diaporthe species associated with Camellia

The genus Diaporthe (syn. Phomopsis) comprises important pathogens, endophytes or saprobes with diverse host associations and worldwide distribution. Phomopsis theae is the first and hitherto the only recorded Diaporthe species on Camellia in China. The aim of this study was to investigate the Diaporthe species associated with symptomatic and asymptomatic tissues of Camellia spp. from several provinces in China. Eighty-three strains were isolated in the present study. Based on the multi-locus (ITS, HIS, TEF1, TUB) phylogenetic analyses and phenotypic characters, four novel species (D. apiculata Y.H. Gao & L. Cai, D. compacta Y.H. Gao & L. Cai, D. oraccinii Y.H. Gao & L. Cai, D. penetriteum Y.H. Gao & L. Cai), and three known species (D. discoidispora, D. hongkongensis, D. ueckerae) were identified. Five strains were assigned to D. amygdali species complex and 17 strains to D. eres species complex respectively, but they could not be further identified to species level using current multi-locus phylogenetic analysis and morphological characters. Of the identified species, D. compacta and D. discoidispora are only known as endophytes. Diaporthe hongkongensis is the dominant species on Camellia, accounting for 53.3% of the frequency of occurrence. Diaporthe lithocarpus is synonymized with D. hongkongensis; D. miriciae is synonymized with D. ueckerae. Our study revealed a high diversity of undescribed Diaporthe species on Camellia.     

The distinctive population structure of Colletotrichum species associated with olive anthracnose in the Algarve region of Portugal reflects a host–pathogen diversity hot spot

Anthracnose ( Colletotrichum spp.) is an important disease of olive fruits. Diversity and biogeographic relationships of the olive anthracnose pathogens in the Algarve (Portugal) were investigated, along with host association patterns and disease levels during 2004–2007, to test the hypothesis that this region is a host–pathogen diversity hot spot. Diverse Colletotrichum acutatum and Colletotrichum gloeosporioides populations were identified based on rRNA-internal transcribed spacer and partial β-tubulin 2 gene sequences of 95 isolates. Spatial and temporal variations in the occurrence of the eight genetic entities of the pathogens were linked to olive biogeography. Disease occurrence patterns suggest that C. acutatum populations are more stable pathogens, while C. gloeosporioides populations appear to be more influenced by favourable conditions. Three unique C. acutatum populations were identified, but none of the eight populations were dominant, with the most frequent type representing only 27%. Thus, the population structure of olive anthracnose pathogens in the Algarve is distinct from other parts of Portugal and other world locations, where only one or two genetic entities are dominant. This pattern and level of genetic diversity in a restricted area, where oleaster (wild olive tree), ancient landraces and modern cultivars of olive occur in close proximity, suggests the Algarve as a centre of diversity of the anthracnose pathogens and corroborates recent work suggesting western Mediterranean as an important centre of olive diversity and domestication.     

Identification and Characterization of Colletotrichum spp. affecting Fruit after Harvest in Brazil

Colletotrichum spp. cause anthracnose in various fruits post‐harvest and are a particularly important problem in tropical and subtropical fruits. The disease in fruits of avocado, guava, papaya, mango and passion fruit has been reported to be caused by C. gloeosporioides, and in banana by C. musae. In subtropical and temperate crops such apple, grape, peach and kiwi, the disease is caused by C. acutatum. The variation in pathogenic, morphological, cultural and molecular characteristics of Brazilian isolates of Colletotrichum acutatum Simmonds and isolates from post‐harvest decays of avocado, banana, guava, papaya, mango and passion fruit was evaluated. The fruits were inoculated with mycelium of C. acutatum, Colletotrichum spp. and C. musae on a disc of potato dextrose agar. The morphological, cultural and molecular characteristics studied were conidia morphology, colony growth at different temperatures, colony coloration and PCR with primers CaInt2 and ITS4 for C. acutatum and CgInt and ITS4 for C. gloeosporioides. C. acutatum was pathogenic to avocado, guava, papaya, mango and passion fruit, but it was not pathogenic to banana. The morphological, cultural and molecular studies indicated that the avocado, papaya, mango and passion fruit isolates were C. gloeosporioides. The natural guava isolate was identified as C. acutatum, which had not been found previously to produce anthracnose symptoms on guava in Brazil.     

A new Rhizopogon species associated with Pinus amamiana in Japan

Pinus amamiana is an endangered Pinus species found only on Yakushima Island and Tanegashima Island, Japan. We surveyed remaining P. amamiana forests and found some sporocarps of Rhizopogon (Boletales), many species of which exhibit strict host specificity to a narrow range of Pinaceae trees and play critical roles in host establishment. Based on morphological characteristics and molecular phylogeny, here we describe Rhizopogon yakushimensis sp. nov. This new species belongs to a new clade, phylogenetically related to the subgenera Versicolores and Rhizopogon. We also confirmed its ectomycorrhizal association with P. amamiana by comparing rDNA ITS sequences between the sporocarps and ectomycorrhizal root tips.