Identification and Characterization of Diaporthe ambigua, D. australafricana, D. novem, and D. rudis Causing a Postharvest Fruit Rot in Kiwifruit

Diaporthe Species on Palms: Molecular Re-Assessment and Species Boundaries Delimitation in the D. arecae Species Complex

Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phylogenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes' (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae, D. chiangmaiensis and D. smilacicola. These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indistinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae. Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe.

Neofusicoccum actinidiae and Neofusicoccum guttata, Two New Species Causing Kiwifruit Rot in China

Kiwi is a popular fruit consumed worldwide. A number of fungal pathogens have been reported to cause postharvest rot of kiwifruit, and Botryosphaeriaceae species are the major causal agents of the disease. In this study, 18 isolates belonging to the genus Neofusicoccum (family Botryosphaeriaceae) were isolated from 247 symptomatic kiwifruits of the cultivars Jinyan, Jintao, and Jinkui collected from orchards in Hubei and Jiangxi provinces, China. Among the isolates, three grouped with various known Neofusicoccum parvum isolates, whereas the remaining 15 formed two independent clades. On the basis of further phylogenetic analyses with concatenated sequences of ITS and three genes encoding translation elongation factor 1-alpha (TEF), β-tubulin (TUB), and DNA-dependent RNA polymerase II subunit (RPB2), as well as morphological characteristics, two new species, N. actinidiae and N. guttata, were proposed. Their pathogenicity to kiwi, apple, and citrus fruits was also confirmed.

Activity of the botanical compound thymol against kiwifruit rot caused by Fusarium tricinctum and the underlying mechanisms

BACKGROUND

Kiwifruit rot is an important disease caused by different fungal pathogens, which can lead to huge economic loss in the kiwifruit industry. The aims of this study were to discover an effective botanical compound that significantly inhibits the pathogens causing kiwifruit rot, evaluate its control efficacy against this disease, and reveal the underlying mechanisms.

RESULTS

A strain of Fusarium tricinctum (GF-1), isolated from diseased kiwifruit, could cause fruit rot in both Actinidia chinensis var. chinensis and Actinidia chinensis var. deliciosa. Different botanical chemicals were used for antifungal activity test against GF-1 and thymol was the most effective one with a 50% effective concentration (EC₅₀ ) of 30.98 mg L^-1 . The minimal inhibitory concentration (MIC) of thymol against GF-1 was 90 mg L^-1 . Control efficacy of thymol against kiwifruit rot was evaluated and the results indicated that thymol could effectively decrease the occurrence and spread of kiwifruit rot. The mechanisms underlying the antifungal activity of thymol against F. tricinctum were investigated, and it showed that thymol could significantly damage the ultrastructure, destroy the plasma membrane integrity, and instantaneously increase energy metabolisms of F. tricinctum. Further investigations indicated that thymol could extend shelf life of kiwifruit by increasing their storability.

CONCLUSION

Thymol can effectively inhibit F. tricinctum that is one of the causal agents of kiwifruit rot. Multiple modes of action are involved in the antifungal activity. The results of this study indicate that thymol can be a promising botanical fungicide to control kiwifruit rot and provide useful references for thymol application in agriculture system. © 2023 Society of Chemical Industry.

The antifungal activity and mechanism of silver nanoparticles against four pathogens causing kiwifruit post-harvest rot

Post-harvest rot causes enormous economic loss to the global kiwifruit industry. Currently, there are no effective fungicides to combat the disease. It is unclear whether silver nanoparticles (AgNPs) are effective in controlling post-harvest rot and, if so, what the underlying antifungal mechanism is. Our results indicated that 75 ppm AgNPs effectively inhibited the mycelial growth and spore germination of four kiwifruit rot pathogens: Alternaria alternata, Pestalotiopsis microspora, Diaporthe actinidiae, and Botryosphaeria dothidea. Additionally, AgNPs increased the permeability of mycelium’s cell membrane, indicating the leakage of intracellular substance. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations revealed that AgNPs induced pathogen hypha shrinkage and distortion, as well as vacuolation in hypha cells, implying that AgNPs caused cellular and organelle structural degradation. The transcriptome sequencing of mycelium treated with AgNPs (24 h / 48 h) was performed on the Illumina Hiseq 4000 sequencing (RNA-Seq) platform. For the time points of 24 h and 48 h, AgNPs treatment resulted in 1,178 and 1,461 differentially expressed genes (DEGs) of A. alternata, 517 and 91 DEGs of P. microspora, 1,287 and 65 DEGs of D. actinidiae, 239 and 55 DEGs of B. dothidea, respectively. The DEGs were found to be involved in “catalytic activity,” “small molecule binding,” “metal ion binding,” “transporter activity,” “cellular component organization,” “protein metabolic process,” “carbohydrate metabolic process,” and “establishment of localization.” Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis also revealed that “carbohydrate metabolism,” “amino acid metabolism,” “energy metabolism,” and “xenobiotics biodegradation and metabolism” of “metabolism processes” were the most highly enriched pathways for these DEGs in four pathogens, with “cellular processes” being particularly enriched for B. dothidea. Furthermore, quantitative polymerase chain reactions (qPCRs) were used to validate the RNA-seq results. It was also confirmed that AgNPs could significantly reduce the symptoms of kiwifruit rot without leaving any Ag⁺ residue on the peel and flesh of kiwifruit. Our findings contributed to a better understanding of the antifungal effect and molecular mechanisms of AgNPs against pathogens causing kiwifruit post-harvest rot, as well as a new perspective on the application of this novel antifungal alternative to fruit disease control.

Diversity of Botryosphaeriaceae and Diaporthe Species Associated with Postharvest Apple Fruit Decay in Serbia

Family Botryosphaeriaceae and the genus Diaporthe (family Diaporthaceae) represent diverse groups of plant pathogens, which include causal agents of leaf spot, shoot blight, branch and stem cankers, dieback, and pre- and postharvest apple fruit decay. Apple fruit with symptoms of light to dark brown decay were collected during and after harvest from 2016 to 2018. Thirty selected isolates, on which pathogenicity was confirmed, were identified and characterized based on multilocus phylogeny and morphology. Five species from the family Botryosphaeriaceae and two from the genus Diaporthe (fam. Diaporthaceae) were discovered. The most commonly isolated was Diplodia seriata followed by Botryosphaeria dothidea. In this work, Diaporthe rudis is described as a new postharvest pathogen of apple fruit. Diplodia bulgarica, Diplodia sapinea, Neofusicoccum yunnanense, and Diaporthe eres are initially described as postharvest apple and D. sapinea as postharvest quince and medlar fruit pathogens in Serbia. Because species of the family Botryosphaeriaceae and the genus Diaporthe are known to cause other diseases on their hosts, have an endophytic nature, and have a wide host range, findings from this study imply that they may become a new challenge for successful fruit production.

Diaporthe sapindicola sp. nov. Causes Leaf Spots of Sapindus mukorossi in China

Sapindus mukorossi Gaertn. (Sapindaceae), or soapberry, is an important biodiesel tree in southern China. In recent years, leaf spot disease on soapberry has been observed frequently in a soapberry germplasm repository in Jianning County, Sanming City, Fujian province, China. The symptoms initially appeared as irregular, small, yellow spots, and the centers of the lesions became dark brown with time. Three fungal isolates from lesions were collected. Koch's postulates were performed, and their pathogenicity was confirmed. Morphologically, α-conidia from diseased tissues were single-celled, hyaline, smooth, clavate or ellipsoidal, and biguttulate, measuring 6.2 to 7.2 × 2.3 to 2.7 μm. In addition, the three isolates in this study developed three types (α, β, and γ) of conidia on potato dextrose agar, and their morphological characteristics matched those of Diaporthe. A phylogenetic analysis based on internal transcribed spacer, TEF, TUB, HIS, and CAL sequence data determined that the three isolates are a new species of Diaporthe. Based on both morphological and phylogenetic analyses, the causal fungus, Diaporthe sapindicola sp. nov., was described and illustrated.

Characterization of Botrytis cinerea and B. prunorum From Healthy Floral Structures and Decayed 'Hayward' Kiwifruit During Post-Harvest Storage

Gray mold is the primary postharvest disease of 'Hayward' kiwifruit (Actinidia deliciosa) in Chile, with a prevalence of 33.1% in 2016 and 7.1% in 2017. Gray mold develops during postharvest storage, which is characterized by a soft, light to brown watery decay that is caused by Botrytis cinerea and B. prunorum. However, there is no information on the role of B. prunorum during the development and storage of kiwifruit in Chile. For this purpose, asymptomatic flowers and receptacles were collected throughout fruit development and harvest from five orchards over two seasons in the Central Valley of Chile. Additionally, diseased kiwifruits were selected after storage for 100 days at 0°C and 2 days at 20°C. Colonies of Botrytis sp. with high and low conidial production were consistently obtained from apparently healthy petals, sepals, receptacles, and styles and diseased kiwifruit. Morphological and phylogenetic analysis of three partial gene sequences encoding glyceraldehyde-3-phosphate dehydrogenase, heat shock protein 60, and DNA-dependent RNA polymerase subunit II were able to identify and separate B. cinerea and B. prunorum species. Consistently, B. cinerea was predominantly isolated from all floral parts and fruit in apparently healthy tissue and diseased kiwifruit. During full bloom, the highest colonization by B. cinerea and B. prunorum was obtained from petals, followed by sepals. In storage, both Botrytis species were isolated from the diseased fruit (n = 644), of which 6.8% (n = 44) were identified as B. prunorum. All Botrytis isolates grew from 0°C to 30°C in vitro and were pathogenic on kiwifruit leaves and fruit. Notably, B. cinerea isolates were always more virulent than B. prunorum isolates. This study confirms the presence of B. cinerea and B. prunorum colonizing apparently healthy flowers and floral parts in fruit and causing gray mold during kiwifruit storage in Chile. Therefore, B. prunorum plays a secondary role in the epidemiology of gray mold developing in kiwifruit during cold storage.

Molecular Phylogenetic Diversity and Biological Characterization of Diaporthe Species Associated with Leaf Spots of Camellia sinensis in Taiwan

Camellia sinensis is one of the major crops grown in Taiwan and has been widely cultivated around the island. Tea leaves are prone to various fungal infections, and leaf spot is considered one of the major diseases in Taiwan tea fields. As part of a survey on fungal species causing leaf spots on tea leaves in Taiwan, 19 fungal strains morphologically similar to the genus Diaporthe were collected. ITS (internal transcribed spacer), tef1-α (translation elongation factor 1-α), tub2 (beta-tubulin), and cal (calmodulin) gene regions were used to construct phylogenetic trees and determine the evolutionary relationships among the collected strains. In total, six Diaporthe species, including one new species, Diaporthe hsinchuensis, were identified as linked with leaf spot of C. sinensis in Taiwan based on both phenotypic characters and phylogeny. These species were further characterized in terms of their pathogenicity, temperature, and pH requirements under laboratory conditions. Diaporthe tulliensis, D. passiflorae, and D. perseae were isolated from C. sinensis for the first time. Furthermore, pathogenicity tests revealed that, with wound inoculation, only D. hongkongensis was pathogenic on tea leaves. This investigation delivers the first assessment of Diaporthe taxa related to leaf spots on tea in Taiwan.

Eco-friendly management of postharvest fungal decays in kiwifruit

Kiwifruit is purchased by consumers worldwide and is increasing in demand. Unfortunately, kiwifruit is susceptible to postharvest decay caused by a variety of fungal pathogens, including Botrytis cinerea, Penicillium expansum, Alternaria alternata, Botryosphaeria dothidea, and Diaporthe spp. Among these pathogens, B. cinerea is the most prevalent and devastating. Infections by these fungal pathogens result in a deterioration in fruit quality and a reduction in marketable yield. Eco-friendly methods to control kiwifruit postharvest decay have been explored as alternatives to the use of synthetic fungicides. In this review, we provide an overview and discuss the virulence and pathogenesis of fungi that are causal agents of kiwifruit decay, especially B. cinerea, including recent molecular and genomic studies. Advances in pre- and postharvest measures for postharvest decay management, including biological control, physical applications, the use of natural compounds and plant hormones, and the use of combined methods, are also reviewed. Eco-friendly control measures are a critical component of an integrated management approach for sustainable production of kiwifruit. The need for further research on the use of microbial consortia for the management of postharvest diseases of kiwifruit is also discussed.

Diaporthe taoicola and D. siamensis, Two New Records on Citrus sinensis in China

Two Diaporthe species isolated from fruit of Citrus sinensis in China were characterized based on morphology and multilocus phylogeny of ITS, tef1, and tub2 gene sequences. The phylogeny indicated that the two species match Diaporthe taoicola and D. siamensis. A critical examination of phenotypic characteristics confirmed the phylogenetic results. Diaporthe taoicola was morphologically characterized by producing Alpha conidia with tapering toward both ends. Meanwhile, D. siamensis produced cylindrical or ellipsoidal Alpha conidia with two oil drops. Pathogenicity tests revealed that both species were pathogenic to fruit of C. sinensis. To our knowledge, the two species were firstly reported on Citrus sinensis in China.

Identification and Pathogenicity of Diplodia, Neofusicoccum, Cadophora, and Diaporthe Species Associated with Cordon Dieback in Kiwifruit cultivar Hayward in Central Chile

Dieback symptoms associated with fungal trunk pathogens cause significant economic losses for farmers of kiwifruit and other woody fruit trees worldwide. This study represents the first attempt to identify and characterize the fungal trunk pathogens associated with cordon dieback disease of kiwifruit in central Chile. Field surveys were conducted throughout the main kiwifruit-growing regions in central Chile to determine the incidence and characterize the fungal trunk pathogens associated with cordon dieback of kiwifruit cultivar Hayward through morphological, molecular, and pathogenicity studies. A total of 250 cordon samples were collected and isolations were performed on 2% acidified potato dextrose agar (APDA) plus antibiotics and Igepal. The incidence of kiwifruit cordon dieback ranged between 5% and 85% in all surveyed areas in central Chile. A total of 246 isolates were isolated and identified using culture and morphological features belonging to three fungal taxa: Diaporthaceae spp. (Diaporthe ambigua and D. australafricana; n = 133 isolates); Botryosphaeriaceae spp. (Diplodia seriata and Neofusicoccum parvum; n = 89 isolates); and Ploettnerulaceae spp. (Cadophora luteo-olivacea and C. malorum; n = 24 isolates). These were identified using phylogenetics studies of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) of the rDNA, part of the β-tubulin gene (tub2), and part of the translation elongation factor 1-α gene (tef1-α). Isolates of N. parvum and D. seriata were the most virulent, causing internal brown lesions and dieback symptoms in attached green shoots, attached lignified canes, and young inoculated kiwifruits. This report is the first to describe D. seriata and C. luteo-olivacea associated with kiwifruit cordon dieback in Chile. It presents the first description of N. parvum causing kiwifruit dieback worldwide.

Diaporthe species causing stem gray blight of red-fleshed dragon fruit (Hylocereus polyrhizus) in Malaysia

This study aimed to characterize the new fungal disease on the stem of red-fleshed dragon fruit (Hylocereus polyrhizus) in Malaysia, which is known as gray blight through morphological, molecular and pathogenicity analyses. Nine fungal isolates were isolated from nine blighted stems of H. polyrhizus. Based on morphological characteristics, DNA sequences and phylogeny (ITS, TEF1-α, and β-tubulin), the fungal isolates were identified as Diaporthe arecae, D. eugeniae, D. hongkongensis, D. phaseolorum, and D. tectonendophytica. Six isolates recovered from the Cameron Highlands, Pahang belonged to D. eugeniae (DF1 and DF3), D. hongkongensis (DF9), D. phaseolorum (DF2 and DF12), and D. tectonendophytica (DF7), whereas three isolates from Bukit Kor, Terengganu were recognized as D. arecae (DFP3), D. eugeniae (DFP4), and D. tectonendophytica (DFP2). Diaporthe eugeniae and D. tectonendophytica were found in both Pahang and Terengganu, D. phaseolorum and D. hongkongensis in Pahang, whereas D. arecae only in Terengganu. The role of the Diaporthe isolates in causing stem gray blight of H. polyrhizus was confirmed. To date, only D. phaseolorum has been previously reported on Hylocereus undatus. This is the first report on D. arecae, D. eugeniae, D. hongkongensis, D. phaseolorum, and D. tectonendophytica causing stem gray blight of H. polyrhizus worldwide.

High-Quality Genome Resource of the Pathogen of Diaporthe (Phomopsis) phragmitis Causing Kiwifruit Soft Rot

Diaporthe spp. are critical plant pathogens that cause wood cankers, wilt, dieback, and fruit rot in a wide variety of economic plant hosts and are regarded as one of the most acute threats faced by the kiwifruit industry worldwide. Diaporthe phragmitis NJD1 is a highly pathogenic isolate of soft rot of kiwifruit. Here, we present a high-quality genome-wide sequence of D. phragmitis NJD1 that was assembled into 28 contigs containing a total size of 58.33 Mb and N₅₀ length of 3.55 Mb. These results lay a solid foundation for understanding host-pathogen interaction and improving disease management strategies.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Diaporthe nebulae sp. nov. and First Report of D. cynaroidis D. novem, and D. serafiniae on Grapevines in South Africa

Diaporthe species cause Phomopsis cane and leaf spot as well as Phomopsis dieback on grapevines. Symptoms of Phomopsis dieback have increasingly been observed over the past few years. In order to assess the current status of Diaporthe on grapevines in the Western Cape Province of South Africa, isolations were made from dormant grafted nursery vines, dormant rootstock canes, and dying or dead spurs of field vines. Cultures identified as Diaporthe based on morphological features were further identified to species level by sequencing the internal transcribed spacers (ITS) 1 and 2 and 5.8S rRNA and, for a representative subsample of isolates, the partial beta-tubulin (tub2) and translation elongation factor 1-alpha (EF1-α) genes. Phylogenetic analysis of the combined ITS, tub2, and EF1-α data revealed nine Diaporthe species associated with grapevines during this survey. One of these represents a new species, D. nebulae sp. nov., and three other species, namely D. novem, D. cynaroidis, and D. serafiniae, are reported on grapevines in South Africa for the first time. Species-specific primers were designed for PCR identification of D. ampelina, D. ambigua, and D. foeniculina. Pathogenicity studies conducted on detached grapevine shoots indicated D. ampelina, D. novem, and D. nebulae sp. nov. as the most virulent species.

Emerging citrus diseases in Europe caused by species of Diaporthe

Species of Diaporthe are considered important plant pathogens, saprobes, and endophytes on a wide range of plant hosts. Several species are well-known on citrus, either as agents of pre- or post-harvest infections, such as dieback, melanose and stem-end rot on fruit. In this study we explored the occurrence, diversity and pathogenicity of Diaporthe species associated with Citrus and allied genera in European orchards, nurseries, and gardens. Surveys were carried out during 2015 and 2016 in Greece, Italy, Malta, Portugal, and Spain. A total of 79 Diaporthe strains were isolated from symptomatic twigs, branches and trunks. A multi-locus phylogeny was established based on five genomic loci (ITS, tef1, cal, his3 and tub2), and the morphological characters of the isolates determined. Preliminary pathogenicity tests were performed on lemon, lime, and orange plants with representative isolates. The most commonly isolated species were D. foeniculina and D. baccae, while only four isolates of D. novem were collected. Two new Diaporthe species, described here as D. limonicola and D. melitensis spp. nov. were found associated with a new devastating dieback disease of lemon plants. Furthermore, one cluster of sterile Diaporthe isolates was renamed as D. infertilis. Pathogenicity tests revealed most of the Citrus species as susceptible to D. baccae, D. foeniculina, and D. novem. Moreover, D. limonicola and D. melitensis caused serious cankers affecting all the Citrus species tested. This study is the first report of D. baccae and D. novem on citrus in Europe, and the first detection of a new Diaporthe canker disease of citrus in Europe. However, no isolates of D. citri were found. The study improves our understanding of the species associated with several disease symptoms on citrus plants, and provides useful information for effective disease management.