Characterization of Fusarium and Neocosmospora Species Associated With Crown Rot and Stem Canker of Pistachio Rootstocks in California

Identification and Pathogenicity of Fusarium Species Associated with Young Vine Decline in California

Grapevine trunk diseases are caused by a broad diversity of fungal taxa that have serious impacts on the worldwide viticulture industry due to significant reductions in vineyards yield and lifespan. Field surveys carried out from 2018 to 2022 in California nurseries and young vineyards revealed a high incidence of Fusarium. Since Fusarium species are important pathogens of other perennial crops, the present study aimed to identify and determine the pathogenicity of the Fusarium species on grapevines. Morphology of the fungal colonies coupled with multilocus phylogenetic analyses using nucleotide sequences of the translation elongation factor 1-alpha (tef1) and the RNA polymerase II second largest subunit (rpb2) genes revealed the occurrence of 10 species clustering in six species complexes, namely F. fujikuroi (FFSC), F. oxysporum (FOSC), F. solani (FSSC), F. sambucinum (FSAMSC), F. incarnatum-equiseti (FIESC), and F. tricinctum (FTSC) species complexes. The species F. annulatum (FFSC) was the most prevalent in samples from both symptomatic young vineyards (73.5% incidence) and nursery propagation material (62.5% incidence). Pathogenicity of the 10 most frequent species was confirmed by fulfilling Koch's postulates on living woody tissue of 1103 Paulsen rootstocks. Our results suggest that Fusarium spp. are involved in the development of young vine decline, probably as opportunistic pathogens when grapevines are under stress conditions.

Identification and pathogenicity of Fusarium species associated with wilting and crown rot in almond (Prunus dulcis)

Severe Fusarium wilt and crown root symptoms were observed in almond orchards in Portugal. The present study elucidates the etiology of the disease through molecular, phenotypic, and pathogenic characterization. Three Fusarium isolates from Portugal were tested and 12 Fusarium isolates from almond from Spain were included for comparative purposes. Their identity was inferred by phylogenetic analysis combining tef1 and rpb2 sequences. The Portuguese isolates were identified as Fusarium oxysporum sensu stricto (s.s.), and the Spanish isolates as Fusarium nirenbergiae, F. oxysporum (s.s.), Fusarium proliferatum, Fusarium redolens (s.s.), Fusarium sambucinum (s.s.), and Fusarium sp. Fungal colonies and conidia were characterized on potato dextrose agar (PDA) and on Synthetischer Nährstoffarmer agar, respectively. The colonies had a variable morphology and their color ranged from white to pale violet. Typical Fusarium micro- and macroconidia were characterized. Temperature effect on mycelial growth was evaluated on PDA from 5 to 35 °C, with optimal growth temperature ranging between 16.8 and 26.4 °C. The pathogenicity of F. oxysporum was demonstrated by inoculating almond plants ('Lauranne') grafted on GF-677 or Rootpac 20 rootstocks. A significant reduction in plant growth, wilting, and xylem discoloration was observed, with Rootpac 20 being more susceptible than GF-677. Infections were also reproduced using naturally infested soils. Almond plants ('Lauranne') were inoculated with isolates of all Fusarium species, with F. redolens from Spain and F. oxysporum from Portugal being the most aggressive.

Trans-kingdom fungal pathogens infecting both plants and humans, and the problem of azole fungicide resistance

Azole antifungals are abundantly used in the environment and play an important role in managing fungal diseases in clinics. Due to the widespread use, azole resistance is an emerging global problem for all applications in several fungal species, including trans-kingdom pathogens, capable of infecting plants and humans. Azoles used in agriculture and clinics share the mode of action and facilitating cross-resistance development. The extensive use of azoles in the environment, e.g., for plant protection and wood preservation, contributes to the spread of resistant populations and challenges using these antifungals in medical treatments. The target of azoles is the cytochrome p450 lanosterol 14-α demethylase encoded by the CYP51 (called also as ERG11 in the case of yeasts) gene. Resistance mechanisms involve mainly the mutations in the coding region in the CYP51 gene, resulting in the inadequate binding of azoles to the encoded Cyp51 protein, or mutations in the promoter region causing overexpression of the protein. The World Health Organization (WHO) has issued the first fungal priority pathogens list (FPPL) to raise awareness of the risk of fungal infections and the increasingly rapid spread of antifungal resistance. Here, we review the main issues about the azole antifungal resistance of trans-kingdom pathogenic fungi with the ability to cause serious human infections and included in the WHO FPPL. Methods for the identification of these species and detection of resistance are summarized, highlighting the importance of these issues to apply the proper treatment.

Metabolomic and microbiomic insights into color changes during the sweating process in Dipsacus asper

Sweating is one of the most important primary processing methods of Chinese medicinal materials. Dipsacus asper is a typical representative of sweating treatment that is recommended by the Chinese Pharmacopoeia. The color change of the fracture surface of the root is the prominent feature of sweating treatment. However, few studies have focused on the mechanism of color change during sweating treatment. In this study, widely targeted metabolomics and ITS high-throughput sequencing technologies were applied to detect metabolites and microbial structure and diversity in the root of D. asper during sweating treatment. A total of 667 metabolites, including 36 downregulated and 78 upregulated metabolites, were identified in D. asper following sweating treatment. The significantly differential metabolites were divided into 12 classes, including terpenoids and phenolic acids. Moreover, all the differential terpenoids were upregulated and 20 phenolic acids showed a significant change after sweating treatment. In addition, microbial community diversity and richness increased following sweating treatment. The composition of microbial communities revealed that the relative abundances of Ascomycota and Basidiomycota significantly changed after sweating treatment. Correlation analysis revealed that Ascomycota (Fusarium sp., Macrophomina sp., Ilyonectria sp., Memnoniella sp., Penicillium sp., Cyphellophora sp., Neocosmospora sp., unclassified_f_Nectriaceae, and unclassified_o_Saccharomycetales) and Basidiomycota (Armillaria sp.) were associated with the content of terpenoids (6-deoxycatalpol and laciniatoside III) and phenolic acids (3-(4-hydroxyphenyl)-propionic acid, ethyl caffeate, 4-O-glucosyl-4-hydroxybenzoic acid, 2-acetyl-3-hydroxyphenyl-1-O-glucoside, 4-O-glucosyl-3,4-dihydroxybenzyl alcohol, 3-O-feruloylquinic acid, 3,4-O-dicaffeoylquinic acid methyl ester, O-anisic acid, and coniferyl alcohol). We speculate that the Ascomycota and Basidiomycota affect the content of terpenoids and phenolic acids, resulting in color change during sweating treatment in D. asper. This study provides a foundation for analyzing the mechanism involved in the processing of Chinese medicinal materials.

New Species of Neocosmospora (Ascomycota) from China as Evidenced by Morphological and Molecular Data

Species of Neocosmospora are commonly found in soil, plant debris, and living woody or herbaceous substrates and occasionally found in water and air. Some species are reported as saprobes, endophytes, opportunistic pathogens of plants and animals, or producers of bioactive natural products, cytotoxic compounds, and industrial enzymes. To reveal the species diversity of Neocosmospora, specimens from different provinces of China were investigated. Five new species, Neocosmospora anhuiensis, N. aurantia, N. dimorpha, N. galbana, and N. maoershanica, were introduced based on morphological characteristics and DNA sequence analyses of combined calmodulin (CAM), the internal transcribed spacer (ITS), the second largest subunit of RNA polymerase II (RPB2), and the translation elongation factor 1-α (TEF1) regions. Differences between these new species and their close relatives are compared in detail.

Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding

Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen-one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms.

Armeria maritima (Mill.) Willd. Flower Hydromethanolic Extract for Cucurbitaceae Fungal Diseases Control

The cliff rose (Armeria maritima), like other halophytes, has a phenolics-based antioxidant system that allows it to grow in saline habitats. Provided that antioxidant properties are usually accompanied by antimicrobial activity, in this study we investigated the phytochemicals present in a hydromethanolic extract of A. maritima flowers and explored its antifungal potential. The main phytocompounds, identified by gas chromatography-mass spectrometry, were: hexadecanoic acid, octadecanoic acid, 9-octadecenoic acid, 3-(3,4-dihydroxy-phenyl)-acrylic acid ethyl ester, and benzeneacetaldehyde. The antifungal activity of the extract and its main constituents-alone and in combination with chitosan oligomers-was tested against six pathogenic taxa associated with soil-borne diseases of plant hosts in the family Cucurbitaceae: Fusarium equiseti, F. oxysporum f. sp. niveum, Macrophomina phaseolina, Neocosmospora falciformis, N. keratoplastica, and Sclerotinia sclerotiorum. In in vitro tests, EC₉₀ effective concentrations in the 166-865 μg·mL^-1 range were obtained for the chitosan oligomers-A. maritima extract conjugate complexes, lower than those obtained for fosetyl-Al and azoxystrobin synthetic fungicides tested for comparison purposes, and even outperforming mancozeb against F. equiseti. In ex situ tests against S. sclerotiorum conducted on artificially inoculated cucumber slices, full protection was achieved at a dose of 250 μg·mL^-1. Thus, the reported results support the valorization of A. maritima as a source of biorationals for Cucurbitaceae pathogens protection, suitable for both organic and conventional agriculture.

Neocosmospora caricae sp. nov. and N. metavorans, two new stem and trunk canker pathogens on Ficus carica in Iran

During 2018–2021, a survey was conducted in rainfed fig (Ficus carica L.) orchards throughout the Fars Province of Iran to investigate the occurrence of canker diseases, and to identify the causal organisms. Morphological and cultural characteristics, as well as multilocus phylogenetic analyses of the internal transcribed spacer (ITS) region of rDNA, RNA polymerase II second largest subunit (RPB2), and the translation elongation factor 1-alpha (TEF1), revealed that the recovered isolates from the infected fig trees clustered in clade 3 of Neocosmospora (Nectriaceae), including N. metavorans, and a new taxon described here as N. caricae sp. nov. Neocosmospora caricae is characterised by falcate, multiseptate, gently dorsoventrally curved macroconidia with poorly developed foot-shaped basal cells, ovoid, aseptate microconidia that cluster in false heads, and abundant terminal or intercalary chlamydospores. Pathogenicity tests indicated that isolates of both Neocosmospora species were pathogenic, causing stem canker and wood discolouration on fig saplings of “Sabz” and “Shah Anjeer” cultivars. The present study adds to existing knowledge on the aetiology of fig stem and trunk canker, and may provide essential information for developing effective integrated management strategies against canker diseases affecting fig orchards in Iran.

Fungi Occurrence in Ready-to-Eat Hazelnuts (Corylus avellana) From Different Boreal Hemisphere Areas

The present study evaluated the fungal contamination of ready-to-eat dried hazelnuts considering for the first time the application of the same condition drying process of several hazelnut cultivars from different boreal hemisphere areas. Fifty lots of hazelnuts (Corylus avellana), belonging to eight cultivars from seven regions in four countries, were analyzed for fungal microbiota, describing both load levels and species diversity. For this purpose, a polyphasic approach consisting of morphological examination (optical and scanning electron microscope observation) and molecular characterization [PCR-DGGE analysis and sequence analyses of the internal transcribed spacer (ITS)] was performed. The results show that different fungal populations occur in dried hazelnuts regardless of their geographical area of production. Although some varieties appear to be relatively less susceptible, species related to Aspergillus, such as A. commune and A. ochraceus, Penicillium, including P. commune, P. solitum, and P. expansum, and Rhizopus, for instance, R. stolonifer and R. oryzae, have generally been found. A related character “hazelnut cultivar—fungi” was found for species related to the genera Trichoderma and Fusarium, including F. oxyxporum, F. solani, and F. falciforme. All 14 species found are known to host pathogenic strains. Therefore, their presence in a ready-to-eat product, such as dried hazelnuts, can pose a real danger to the consumer. Based on these considerations, the development of new protective strategies seems highly desirable. The species-level description of the contaminating fungal community acquired through this study is the starting point for the development of tailor-made protective biotechnologies.

Detection and Characterization of Stressed Sweet Cherry Tissues Using Machine Learning

Recent technological developments in the primary sector and machine learning algorithms allow the combined application of many promising solutions in precision agriculture. For example, the YOLOv5 (You Only Look Once) and ResNet Deep Learning architecture provide high-precision real-time identifications of objects. The advent of datasets from different perspectives provides multiple benefits, such as spheric view of objects, increased information, and inference results from multiple objects detection per image. However, it also raises crucial obstacles such as total identifications (ground truths) and processing concerns that can lead to devastating consequences, including false-positive detections with other erroneous conclusions or even the inability to extract results. This paper introduces experimental results from the machine learning algorithm (Yolov5) on a novel dataset based on perennial fruit crops, such as sweet cherries, aiming to enhance precision agriculture resiliency. Detection is oriented on two points of interest: (a) Infected leaves and (b) Infected branches. It is noteworthy that infected leaves or branches indicate stress, which may be due to either a stress/disease (e.g., Armillaria for sweet cherries trees, etc.) or other factors (e.g., water shortage, etc). Correspondingly, the foliage of a tree shows symptoms, while this indicates the stages of the disease.

First Report of Collar Rot in Purple Passion Fruit (Passiflora edulis) Caused by Neocosmospora solani in Yunnan province, China

Purple passion fruit (Passiflora edulis Sims) is a perennial climbing vine native to South America that is grown worldwide as an edible tropical fruit with excellent nutritional value and high economic value (Zibadi et al. 2007). With the increasing expansion of the plantation area in China, considerable economic loss caused by collar rot has attracted wide attention. From 2018-2020, collar rot resulted in the death of many plants of P. edulis 'Mantianxing', a commercial cultivar in China, in southwest China's Yunnan province. The disease spread quickly, and field incidence reached more than 50%. Stem rot symptoms were observed at the base of the stem, about 5-10 cm from the ground, resulting in wilting, defoliation, and death of plants. Representative symptomatic samples were collected from the base of five plants, surface disinfested for 30 seconds with 75% ethanol and 15 min with 10% hypochlorite, washed three times with sterile distilled water, then transferred to potato dextrose agar (PDA) dishes. After 2 days in the dark at 28℃, emerging fungal colonies were purified on new PDA dishes cultured at 28℃ for 7 days. The mycelia were flocculent. The color of the surface and the reverse colony was white and cream, respectively. On synthetic nutrient agar (SNA) medium, microconidia were oval, ellipsoidal or reniform, 0- or 1-septate, and 6.7-23.1 μm in length (n>30); macroconidia were straight to slightly curved, 3- or 5-septate, and 30.8-53.9 μm in length (n>30). Genomic DNA, extracted from six isolates, was amplified with three pairs of primers, ITS1 and ITS4 (White et al. 1990) , EF1-728F and EF1-986R (Carbone and Kohn 1999), and fRPB2-5F and fRPB2-7cR (Liu et al. 1999). The amplicons from all six isolates were sequenced and identical sequences obtained. The sequence of one representative isolate was uploaded to NCBI (National Center for Biotechnology Information) and analyzed with BLASTn in the Fusarium MLST database (https://fusarium.mycobank.org). The sequence of the internal transcribed spacer 1 (ITS1) region (GenBank MN944550) showed 99.1% (449/453 bp) identity to Fusarium solani strain NRRL 53667 (syn: Neocosmospora solani, GenBank MH582405). The sequence of the translation elongation factor-1 (EF-1) gene (GenBank MN938933) showed 97.8% identity (263/269 bp) to F. solani strain NRRL 32828 (GenBank DQ247135). The sequence of the second largest subunit of RNA polymerase Ⅱ (RPB2) gene (GenBank MW002686) showed 98.7% identity (810/821 bp) to F. solani strain NRRL 43441 (GenBank MH582407). Based on a multilocus phylogenetic analysis of the ITS1, EF-1 and RPB2 sequences, coupled with the morphological characteristics, the isolate (designated as NsPed1) was considered to be Neocosmospora solani (syn: Fusarium solani) (Crespo et al. 2019). Subsequently, three-month-old healthy seedlings and 45-day-old cuttings of P. edulis 'Mantianxing' plants were inoculated with the isolate NsPed1 to test its pathogenicity. Stems were wounded, approximately 1-2 mm deep, in the collar region of plants at 2 cm above the soil. A disk (9 mm in diameter) of NsPed1-colonized PDA was placed on the wound. Sterile PDA served as controls. All plants were kept in a growth chamber with 28-30°C, 60% relative humidity, and 16/8-h light/dark photoperiod. Fifteen plants were used for each treatment and replicated three times. Two weeks after inoculation, the stems of the inoculated plants turned brown with a lesion, 2-5 cm in length, and the leaves wilted. These symptoms were similar to those of the diseased plants in the field. The control plants were asymptomatic. N. solani NsPed1 was re-isolated from the infected plants, satisfying Koch's postulates. Taken together, N. solani NsPed1 was identified as the causal pathogen of collar rot in P. edulis 'Mantianxing'. Knowledge of the causal organism of collar rot in purple passion fruit will lead to improved measures to prevent and control the disease in China and other countries.

First Report of Stem Canker of Almond Trees Caused by Fusarium solani in Greece

Almond (Prunus dulcis) is an important crop for Greece grown on 15.130 ha in 2019. In September 2019, a severe stem canker disease was observed in 6-year-old trees of cv Marta grafted on the rootstock 'F675C14', in a new almond grove of cvs Marta, Soleta, Antonela, Belona and Laurete, in Vlachiana, Heraklion, Crete, Greece. Only cv Marta trees were affected. Diseased trees exhibited cankers on trunks and branches with pale yellow to red-colored gum excreting from cankers, yellowing, leaf fall, twig and branch dieback, bark and wood tissue discoloration. Severely affected trees were killed. A Fusarium-like fungus was consistently isolated from symptomatic wood tissue previously surface-disinfested with 95% ethanol, on acidified potato dextrose agar (APDA). Emerging colonies were transferred to new PDA and the growth rate of the fungus was 7.86 mm/day at 24 °C in the dark. The abundant aerial mycelium was initially white, turning into pale orange in the centre after 7 days of growth on PDA. Microscopic observations revealed hyaline conidiophores measuring 26.74 ± 20.44 μm in length, developing microconidia 5.00 to 9.50 × 2.50 to 4.75 μm (average 6.64 × 3.50 μm) and macroconidia 10.00 to 23.25 × 3.75 to 5.50 μm (average 16.42 × 4.50 μm) in size. DNA from one representative single-spore isolate (code KOUB.AM.VR1) was extracted and the internal transcribed spacer region (ITS) of ribosomal DNA and translation elongation factor 1-alpha (EF 1-a) genes were amplified using the primer pairs ITS1/ITS4 (White et al. 1990) and EF1-F/EF2-R (O'Donnell et al. 1998), respectively. The PCR products were sequenced and deposited in GenBank (accession Nos. MW547397 and MW554492). Based on morphological characteristics (Leslie and Summerell 2006) and a BLAST search with 100.00% and 99.38% identity to published F. solani ITS and EF 1-a sequences in GenBank (KX034335.1, DQ247636.1) the fungus was identified as F. solani. Eight 3-year-old almond trees of cv. Marta were artificially inoculated in March 2020 by making a 6.0-mm-diameter hole into the trunk, inserting a 6-mm-diameter mycelial disc taken from a 10-day-old PDA culture, sealing the hole with cellophane membrane and covering with adhesive paper tape. Another eight trees of the same cultivar were mock-inoculated with sterilized PDA discs and served as controls. Potted trees were kept under ambient conditions. One month post inoculation, yellow gum was evident excreting around the inoculation point in F. solani-treated trees but not in the controls. Seven months post inoculation, longitudinal and transverse sections of inoculated trunks revealed internal and external symptoms similar to those observed under natural infection conditions and F. solani was steadily re-isolated from symptomatic wood tissue and identified by colony morphology. Neither symptoms nor positive isolations were observed in control trunks. Pathogenicity tests were repeated twice. Fusarium solani has been reported as the causal agent of stem canker or wood decay diseases in several woody hosts including bitternut hickory, black walnut, mulberry and pistachio trees (Crespo et al. 2019; Markakis et al. 2017; Park and Juzwik 2012; Tisserat 1987). To the best of our knowledge, this is the first worldwide report of stem canker caused by F. solani on almond tree. This disease could potentially be an increasing problem in almond growing areas and result in severe crop losses. Hence, effective management practices should be investigated and applied.

Macrophomina Crown and Root Rot of Pistachio in California

In this study, declining pistachio rootstocks were detected in newly planted commercial pistachio orchards in Kern County, California. Symptoms were characterized by wilted foliage combined with crown rot in the rootstock. From diseased trees, 42 isolates were obtained, and all had similar cultural and morphological characteristics of Macrophomina phaseolina. Analyses of nucleotide sequences of three gene fragments, the internal transcribed spacer region (ITS1-5.8S-ITS2), partial sequences of β-tubulin, and translation elongation factor 1-α (TEF1) confirmed this identification, and 20 representative isolates are presented in the phylogenetic study. Testing of Koch's postulates showed that M. phaseolina, when inoculated to stems and roots of the pistachio rootstocks using mycelial plugs or a microsclerotial suspension, is indeed pathogenic to this host. The widely used clonal University of California Berkeley I (UCBI) rootstock appeared highly susceptible to M. phaseolina, suggesting that this pathogen is an emerging threat to the production of pistachio in California. This study confirmed the association of M. phaseolina with the decline of pistachio trees and represents the first description of this fungus as a crown rot-causing agent of pistachio in California.