Alternaria spp.: from general saprophyte to specific parasite

Positive selection and functional diversification of transcription factor Cmr1 homologs in Alternaria

Transcription factor Cmr1 (Colletotrichum melanin regulation 1) and its homologs in several plant fungal pathogens are the regulators of the 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis pathway and have evolved functional diversification in morphology and pathogenicity. The fungal genus Alternaria comprises the group of "black fungi" that are rich in DHN-melanin in the primary cell wall and septa of the conidia. Some Alternaria species cause many economically important plant diseases worldwide. However, the evolution and function of Cmr1 homologs in Alternaria remain poorly understood. Here, we identified a total of forty-two Cmr1 homologs from forty-two Alternaria spp. and all contained one additional diverse fungal specific transcription factor motif. Phylogenetic analysis indicated the division of these homologs into five major clades and three branches. Dated phylogeny showed the A and D clades diverged latest and earliest, respectively. Molecular evolutionary analyses revealed that three amino acid sites of Cmr1 homologs in Alternaria were the targets of positive selection. Asmr1, the homolog of Cmr1 in the potato early blight pathogen, Alternaria solani was amplified and displayed the sequence conservation at the amino acid level in different A. solani isolates. Asmr1 was further confirmed to have the transcriptional activation activity and was upregulated during the early stage of potato infection. Deletion of asmr1 led to the decreased melanin content and pathogenicity, deformed conidial morphology, and responses to cell wall and fungicide stresses in A. solani. These results suggest positive selection and functional divergence have played a role in the evolution of Cmr1 homologs in Alternaria. KEY POINTS: • Cmr1 homologs were under positive selection in Alternaria species • Asmr1 is a functional transcription factor, involved in spore development, melanin biosynthesis, pathogenicity, and responses to cell wall and fungicide stresses in A. solani • Cmr1 might be used as a potential taxonomic marker of the genus Alternaria.

Alternaria solani effectors AsCEP19 and AsCEP20 reveal novel functions in pathogenicity and conidiogenesis

Previous work identified a pair of specific effectors AsCEP19 and AsCEP20 in Alternaria solani as contributors to the virulence of A. solani. Here, we constructed AsCEP19 and AsCEP20 deletion mutants in A. solani strain HWC168 to further reveal the effects of these genes on the biology and pathogenicity of A. solani. Deletion of AsCEP19 and AsCEP20 did not affect vegetative growth but did affect conidial maturation, with an increase in the percentage of abnormal conidia produced. Furthermore, we determined the expression patterns of genes involved in the conidiogenesis pathway and found that the regulatory gene abaA was significantly upregulated and chsA, a positive regulator for conidiation, was significantly downregulated in the mutant strains compared to the wild-type strain. These results suggest that AsCEP19 and AsCEP20 indirectly affect the conidial development and maturation of A. solani. Pathogenicity assays revealed significantly impaired virulence of ΔAsCEP19, ΔAsCEP20, and ΔAsCEP19 + AsCEP20 mutants on potato and tomato plants. Moreover, we performed localization assays with green fluorescent protein-tagged proteins in chili pepper leaves. We found that AsCEP19 can specifically localize to the chloroplasts of chili pepper epidermal cells, while AsCEP20 can localize to both chloroplasts and the plasma membrane. Weighted gene co-expression network analysis revealed enrichment of genes of this module in the photosynthesis pathway, with many hub genes associated with chloroplast structure and photosynthesis. These results suggest that chloroplasts are the targets for AsCEP19 and AsCEP20.

IMPORTANCE

Alternaria solani is an important necrotrophic pathogen causing potato early blight. Previous studies have provide preliminary evidence that specific effectors AsCEP19 and AsCEP20 contribute to virulence, but their respective functions, localization, and pathogenic mechanisms during the infection process of A. solani remain unclear. Here, we have systematically studied the specific effectors AsCEP19 and AsCEP20 for the first time, which are essential for conidial maturation. The deletion of AsCEP19 and AsCEP20 can significantly impair fungal pathogenicity. Additionally, we preliminarily revealed that AsCEP19 and AsCEP20 target the chloroplasts of host cells. Our findings further enhance our understanding of the molecular mechanisms underlying the virulence of necrotrophic pathogens.

A metagenomic survey of the fecal microbiome of the African savanna elephant (Loxodonta africana)

The African savanna elephant (Loxodonta africana) is the largest terrestrial animal on Earth and is found primarily in Southern and Eastern Africa. It is a hindgut, colonic fermenter and subsists on a diet of raw plant materials found in its grazing area. In this study the bacterial, archaeal and fungal populations of seven African savanna elephant fecal metagenomes were first characterized using amplicon sequencing. On the genus level it was observed that the p-1088-a5 gut group in the bacteriome, Methanocorpusulum and Methanobrevibacter in the archaeome and Alternaria, Aurobasidium, Didymella and Preussia in the mycome, predominated. Subsequently, metagenomic shotgun sequencing was employed to identify possible functional pathways and carbohydrate-active enzymes (CAZymes). Carbohydrate catabolic pathways represented the main degradation pathways, and the fecal metagenome was enriched in the glycohydroside (GH) class of CAZymes. Additionally, the top GH families identified - GH43, GH2, GH13 and GH3 - are known to be associated with cellulytic, hemicellulytic and pectolytic activities. Finally, the CAZymes families identified in the African savanna elephant were compared with those found in the Asian elephant and it was demonstrated that there is a unique repository of CAZymes that could be leveraged in the biotechnological context such as the degradation of lignocellulose for the production of second-generation biofuels and energy.

Distinct effects of phyllosphere and rhizosphere microbes on invader Ageratina adenophora during its early life stages

Microbes strongly affect invasive plant growth. However, how phyllosphere and rhizosphere soil microbes distinctively affect seedling mortality and growth of invaders across ontogeny under varying soil nutrient levels remains unclear. In this study, we used the invader Ageratina adenophora to evaluate these effects. We found that higher proportions of potential pathogens were detected in core microbial taxa in leaf litter than rhizosphere soil and thus leaf inoculation had more adverse effects on seed germination and seedling survival than soil inoculation. Microbial inoculation at different growth stages altered the microbial community and functions of seedlings, and earlier inoculation had a more adverse effect on seedling survival and growth. The soil nutrient level did not affect microbe-mediated seedling growth and the relative abundance of the microbial community and functions involved in seedling growth. The effects of some microbial genera on seedling survival are distinct from those on growth. Moreover, the A. adenophora seedling-killing effects of fungal strains isolated from dead seedlings by non-sterile leaf inoculation exhibited significant phylogenetic signals, by which strains of Allophoma and Alternaria generally caused high seedling mortality. Our study stresses the essential role of A. adenophora litter microbes in population establishment by regulating seedling density and growth.

Pollen products collected from honey bee hives experiencing minor stress have altered fungal communities and reduced antimicrobial properties

Fungi are increasingly recognized to play diverse roles within honey bee hives, acting as pathogens, mutualists, and commensals. Pollen products, essential for hive nutrition, host significant fungal communities with potential protective and nutritional benefits. In this study, we profile the fungal communities and antifungal properties of three pollen products from healthy and stressed hives: fresh pollen collected by forager bees from local plants; stored pollen packed into the comb inside the hive; and bee bread, which is stored pollen following anaerobic fermentation used for bee and larval nutrition. Using amplicon sequencing, we found significant differences in fungal community composition, with hive health and sample type accounting for 8.8% and 19.3% of variation in beta diversity, respectively. Pollen and bee bread extracts had species-specific antimicrobial activity and inhibited the fungal hive pathogens Ascosphaera apis, Aspergillus flavus, and Aspergillus fumigatus, and the bacterial hive pathogen Paenibacillus larvae. Activity was positively correlated with phenolic and antioxidant content and was diminished in stressed hives. The plant source of pollen determined by amplicon sequencing differed in stressed hives, suggesting altered foraging behaviour. These findings illustrate the complex interplay between honey bees, fungal communities, and hive products, which should be considered in hive management and conservation.

Two novel species and a new host record of Alternaria (Pleosporales, Pleosporaceae) from sunflower (Compositae) in Myanmar

Sunflower (Helianthusannuus L.) is a widely cultivated, fast-growing crop known for its seeds and oil, with substantial ecological and economic importance globally. However, it faces challenges from leaf diseases caused by Alternaria species, which threaten its yield. Three small-spored Alternaria species were isolated from leaf spot and blight symptoms on sunflower in Myanmar. All the species were determined based on morphological characterization and a multi-locus phylogenetic assessment of seven genes, including the internal transcribed spacer of rDNA region (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase second largest subunit (RPB2), translation elongation factor 1-α (TEF1), Alternaria major allergen gene (Alt a 1), endopolygalacturonase gene (EndoPG), and an anonymous gene region (OPA10-2). The results introduced two new Alternaria species, A.myanmarensis sp. nov. and A.yamethinensis sp. nov., and a known species of A.burnsii, firstly reported from sunflower.

Greenhouses represent an important evolutionary niche for Alternaria alternata

Alternaria alternata is a ubiquitous soil-borne fungus capable of causing diseases in a variety of plants and occasionally in humans. While populations of A. alternata from infected plants have received significant attention, relatively little is known about its soil populations, including its population genetic structure and antifungal susceptibilities. In addition, over the last two decades, greenhouses have become increasingly important for food and ornamental plant production throughout the world, but how greenhouses might impact microbial pathogens such as A. alternata populations remains largely unknown. Different from open crop fields, greenhouses are often more intensively cultivated, with each greenhouse being a relatively small and isolated space where temperature and humidity are higher than surrounding environments. Previous studies have shown that greenhouse populations of two common molds, Aspergillus fumigatus and A. alternata, within a small community in southwestern China were variably differentiated. However, the relative contribution of physical separation among local greenhouses to the large-scale population structure remains unknown. Here, we isolated strains of A. alternata from seven greenhouses in Shijiazhuang, northeast China. Their genetic diversity and triazole susceptibilities were analyzed and compared with each other and with 242 isolates from nine greenhouses in Kunming, southwest China. Results showed that the isolation of greenhouses located <1 km from each other locally contributed similarly to the overall genetic variation as that between the two distant geographic regions. In addition, our results indicate that greenhouses could be significant sources of triazole resistance, with greenhouses often differing in their frequencies of resistant strains to different triazoles.

IMPORTANCE

Greenhouses have become increasingly important for food production and food security. However, our understanding of how greenhouses may contribute to genetic variations in soil microbial populations is very limited. In this study, we obtained and analyzed soil populations of the cosmopolitan fungal pathogen Alternaria alternata in seven greenhouses in Shijiazhuang, northeast China. Our analyses revealed high proportions of isolates being resistant to agricultural triazole fungicides and medical triazole drugs, including cross-resistance to both groups of triazoles. In addition, we found that greenhouse populations of A. alternata located within a few kilometers showed similar levels of genetic differentiation as those separated by over 2,000 km between northeast and southwest China. Our study suggests that greenhouse populations of this and potentially other fungal pathogens represent an important ecological niche and an emerging threat to food security and human health.

Characterization of Alternaria blotch disease of apple in Himachal Pradesh, India: insights on morphology, pathogenicity, and molecular features

BACKGROUND

Alternaria blotch disease in Himachal Pradesh, India, caused by Alternaria spp., adversely affects apple cultivars, resulting in reduced fruit size and quality accompanied by premature leaf fall.

METHODS AND RESULTS

Sixteen Alternaria isolates from apple growing regions underwent comprehensive analysis including morphology, pathogenicity, and molecular characterization. Variations in conidiophore and conidia dimensions, shapes, and divisions were observed among isolates. Pathogenicity assays revealed differences in incubation periods, latent phases, and disease responses. Molecular characterization via nuclear ITS rDNA and RAPD analysis indicated 99-100% homology with Alternaria alternata, Alternaria mali, and other Alternaria spp., with a close phylogenetic relationship to Chinese isolates. Differentiation of isolates based on origin, cultural characteristics, and morphology was achieved using RAPD markers.

CONCLUSIONS

The study identifies diverse genotypes and morphotypes of Alternaria contributing to apple blotch disease in Himachal Pradesh. These findings highlight the complexity of the pathogenic environment and hold significant implications for disease management in apple orchards.

Expansion of the multi-locus gene alignment approach to improve identification of the fungal species Alternaria alternata

Alternaria alternata is part of a genus comprised of over 600 different species that occur all over the world and cause damage to humans, plants and thereby to the economy. Yet, even though some species are causing tremendous issues, the past years have shown that assigning newly found isolates to known species was rather inconsistent. Most identifications are usually done on the basis of spore morphology, chemotype and molecular markers. In this work we used strains isolated from the wild as well as commercial strains of the DSMZ (German collection of microorganisms and cell cultures) as a reference, to show, that the variation within the Alternaria alternata species is comparable to the variation between different species of the genus Alternaria in regards to spore morphology and chemotype. We compared the different methods of identification and discerned the concatenation of multiple molecular markers as the deciding factor for better identification. Up until this point, usually a concatenation of two or three traditional molecular markers was used. Some of those markers being stronger some weaker. We show that the concatenation of five molecular markers improves the likeliness of a correct assignment, thus a better distinction between the different Alternaria species.

Leaf surface microbiota transplantation confers resistance to coffee leaf rust in susceptible Coffea arabica

Coffee leaf rust, caused by the fungus Hemileia vastatrix, has become a major concern for coffee-producing countries. Additionally, there has been an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla, but the protection depended on the concentration of the microbiota. Certain fungi, such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora and Torula, and bacteria, such as Chryseobacterium, Sphingobium and especially Enterobacter, had their populations increased and this may be related to the antagonism seen against H. vastatrix. Interestingly, the relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplantation, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust, as well as help to optimize the development of biocontrol agents.

Integrated Analysis of Transcriptome and Metabolome Reveals Differential Responses to Alternaria brassicicola Infection in Cabbage (Brassica oleracea var. capitata)

Black spot, caused by Alternaria brassicicola (Ab), poses a serious threat to crucifer production, and knowledge of how plants respond to Ab infection is essential for black spot management. In the current study, combined transcriptomic and metabolic analysis was employed to investigate the response to Ab infection in two cabbage (Brassica oleracea var. capitata) genotypes, Bo257 (resistant to Ab) and Bo190 (susceptible to Ab). A total of 1100 and 7490 differentially expressed genes were identified in Bo257 (R_mock vs. R_Ab) and Bo190 (S_mock vs. S_Ab), respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that "metabolic pathways", "biosynthesis of secondary metabolites", and "glucosinolate biosynthesis" were the top three enriched KEGG pathways in Bo257, while "metabolic pathways", "biosynthesis of secondary metabolites", and "carbon metabolism" were the top three enriched KEGG pathways in Bo190. Further analysis showed that genes involved in extracellular reactive oxygen species (ROS) production, jasmonic acid signaling pathway, and indolic glucosinolate biosynthesis pathway were differentially expressed in response to Ab infection. Notably, when infected with Ab, genes involved in extracellular ROS production were largely unchanged in Bo257, whereas most of these genes were upregulated in Bo190. Metabolic profiling revealed 24 and 56 differentially accumulated metabolites in Bo257 and Bo190, respectively, with the majority being primary metabolites. Further analysis revealed that dramatic accumulation of succinate was observed in Bo257 and Bo190, which may provide energy for resistance responses against Ab infection via the tricarboxylic acid cycle pathway. Collectively, this study provides comprehensive insights into the Ab-cabbage interactions and helps uncover targets for breeding Ab-resistant varieties in cabbage.

Identifying key environmental factors to model Alt a 1 airborne allergen presence and variation

Fungal spores, commonly found in the atmosphere, can trigger important respiratory disorders. The glycoprotein Alt a 1 is the major allergen present in conidia of the genus Alternaria and has a high clinical relevance for people sensitized to fungi. Exposure to this allergen has been traditionally assessed by aerobiological spore counts, although this does not always offer an accurate estimate of airborne allergen load. This study aims to pinpoint the key factors that explain the presence and variation of Alt a 1 concentration in the atmosphere in order to establish exposure risk periods and improve forecasting models. Alternaria spores were sampled using a Hirst-type volumetric sampler over a five-year period. The allergenic fraction from the bioaerosol was collected using a low-volume cyclone sampler and Alt a 1 quantified by Enzyme-Linked ImmunoSorbent Assay. A cluster analysis was executed in order to group days with similar environmental features and then analyze days with the presence of the allergen in each of them. Subsequently, a quadratic discriminant analysis was performed to evaluate if the selected variables can predict days with high Alt a 1 load. The results indicate that higher temperatures and absolute humidity favor the presence of Alt a 1 in the atmosphere, while time of precipitation is related to days without allergen. Moreover, using the selected parameters, the quadratic discriminant analysis to predict days with allergen showed an accuracy rate between 67 % and 85 %. The mismatch between daily airborne concentration of Alternaria spores and allergen load can be explained by the greater contribution of medium-to-long distance transport of the allergen from the major emission sources as compared with spores. Results highlight the importance of conducting aeroallergen quantification studies together with spore counts to improve the forecasting models of allergy risk, especially for fungal spores.

Characterization of antifungal properties of avocado leaves and majagua flowers extracts and their potential application to control Alternaria alternata

Plant extracts are used as an alternative to a wide range of foods against different types of fungal pathogens. In the present study, the extracts of avocado leaves (Persea americana) and majagua flowers (Talipariti elatum) were tested according to their antifungal activity against different fungi. The most promising extracts were those of majagua flowers that were applied lyophilized and in aqueous extract, being very effective against Alternaria alternata and reaching a 50 % in vitro reduction. Antifungal properties were also evaluated during infection of apples by A. alternata. A decrease in infection progression was confirmed with up to a 30 % reduction in disease incidence and a 20 % reduction in disease severity. Majagua extracts were also tested combined with edible pectin coatings, greatly increasing their effectiveness up 60 % reduction. Thus, extracts of majagua could provide a feasible alternative to control fungal pathogens during postharvest.

Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato

Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.

Alternaria diseases on potato and tomato

Alternaria spp. cause different diseases in potato and tomato crops. Early blight caused by Alternaria solani and brown spot caused by Alternaria alternata are most common, but the disease complex is far more diverse. We first provide an overview of the Alternaria species infecting the two host plants to alleviate some of the confusion that arises from the taxonomic rearrangements in this fungal genus. Highlighting the diversity of Alternaria fungi on both solanaceous hosts, we review studies investigating the genetic diversity and genomes, before we present recent advances from studies elucidating host-pathogen interactions and fungicide resistances.

TAXONOMY

Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Pleosporales, Family Pleosporaceae, Genus Alternaria.

BIOLOGY AND HOST RANGE

Alternaria spp. adopt diverse lifestyles. We specifically review Alternaria spp. that cause disease in the two solanaceous crops potato (Solanum tuberosum) and tomato (Solanum lycopersicum). They are necrotrophic pathogens with no known sexual stage, despite some signatures of recombination.

DISEASE SYMPTOMS

Symptoms of the early blight/brown spot disease complex include foliar lesions that first present as brown spots, depending on the species with characteristic concentric rings, which eventually lead to severe defoliation and considerable yield loss.

CONTROL

Good field hygiene can keep the disease pressure low. Some potato and tomato cultivars show differences in susceptibility, but there are no fully resistant varieties known. Therefore, the main control mechanism is treatment with fungicides.

©Relationship between endophytic fungal diversity and colonization and soil factors of cultured blueberry roots in Guizhou Province, Southwest China

Dark septate endophytes (DSEs) inhabit plant roots and soil in ecosystems and host plants worldwide. DSE colonization is influenced by cultivars, soil factors, and specific habitat conditions. The regular diversity of DSEs in blueberries in Guizhou, China, is still unclear. In this study, four cultivars (Gardenblue, Powderblue, O'Neal, and Legacy) in three areas (Gaopo, Majiang, and Fenggang) in Guizhou were used to identify DSEs by morphological and molecular biological methods and to clarify the relationship between DSE diversity and DSE colonization and soil factors of cultivated blueberries in Guizhou. The DSEs isolated from cultivated blueberry roots in 3 areas in Guizhou Province were different, belonging to 17 genera, and the dominant genera were Penicillium, Phialocephala, and Thozetella. DSEs isolated from Majiang belonged to 12 genera and 16 species, those from Gaopo belonged to 7 genera and 15 species, and those from Fenggang belonged to 5 genera and 7 species. Among the different blueberry varieties, 11 genera were isolated from O'Neal, 12 genera were isolated from Powderblue, 11 genera were isolated from Legacy and 13 genera were isolated from Gardenblue. Coniochaeta is endemic to O'Neal, Chaetomium and Curvularia are endemic to Powderblue, and Thielavia is endemic to Legacy. Correlation analysis showed that DSE diversity was significantly correlated with DSE colonization and soil factors.

Isolation and Identification of Alternaria alternata from Potato Plants Affected by Leaf Spot Disease in Korea: Selection of Effective Fungicides

Brown leaf spot disease caused by Alternaria spp. is among the most common diseases of potato crops. Typical brown spot symptoms were observed in commercial potato-cultivation areas of northern Korea from June to August 2020-2021. In total, 68 isolates were collected, and based on sequence analysis of the internal transcribed spacer (ITS) region, the collected isolates were identified as Alternaria spp. (80.9%). Phylogenetic analysis revealed that a majority of these isolates clustered within a clade that included A. alternata. Additionally, the ITS region and rpb2 yielded the most informative sequences for the identification of A. alternata. Pathogenicity tests confirmed that the collected pathogens elicited symptoms identical to those observed in the field. In pathogenicity tests performed on seven commercial cultivars, the pathogens exhibited strong virulence in both wound and non-wound inoculations. Among the cultivars tested, Arirang-1ho, Arirang-2ho, and Golden Ball were resistant to the pathogens. Furthermore, among the fungicides tested in vitro, mancozeb and difenoconazole were found to be effective for inhibiting mycelial growth. In summary, our findings suggest that A. alternata plays a critical role in leaf disease in potato-growing regions and emphasise the necessity of continuous monitoring and management to protect against this disease in Korea.

Seven new species of Alternaria (Pleosporales, Pleosporaceae) associated with Chinese fir, based on morphological and molecular evidence

Chinese fir (Cunninghamialanceolata) is a special fast-growing commercial tree species in China and has significant ecological and economic value. However, it experienced damage from leaf blight caused by pathogenic fungi of the genus Alternaria. To determine the diversity of Alternaria species associated with leaf blight of Chinese fir in China, infected leaves were collected from five major cultivation provinces (Fujian, Henan, Hunan, Jiangsu and Shandong provinces). A total of 48 fungal strains of Alternaria were obtained. Comparison of morphology and phylogenetic analyses, based on nine loci (ITS, SSU, LSU, GAPDH, RPB2, TEF1, Alt a1, endoPG and OPA10-2) of the representative isolates as well as the pairwise homoplasy index tests, revealed that the fungal strains belonged to seven undescribed taxa of Alternaria, which are described here and named as Alternariacunninghamiicolasp. nov., A.dongshanqiaoensissp. nov., A.hunanensissp. nov., A.kunyuensissp. nov., А. longqiaoensissp. nov., A.shandongensissp. nov. and A.xinyangensissp. nov. In order to prove Koch's postulates, pathogenicity tests on detached Chinese fir leaves revealed significant pathogenicity amongst these species, of which A.hunanensis is the most pathogenic to Chinese fir. This study represents the first report of A.cunninghamiicola, A.dongshanqiaoensis, A.hunanensis, A.kunyuensis, A.longqiaoensis, A.shandongensis and A.xinyangensis causing leaf blight on Chinese fir. Knowledge obtained in this study enhanced our understanding of Alternaria species causing leaf blight on Chinese fir and was crucial for the disease management and the further studies in the future.

Saturated brine dissolution and liquid-liquid extraction combined with UPLC-MS/MS for the detection of typical Alternaria toxins in pear paste

BACKGROUND

Alternaria can infest pears to produce metabolites, which can contaminate pears and their processed products. Pear paste, one of the most important pear-based products, is popular among Chinese consumers especially for its cough relieving and phlegm removal properties. Although people are concerned about the risk of Alternaria toxins in many agro-foods and their products, little is known about the toxins in pear paste.

RESULTS

A method was developed for the determination of tenuazonic acid, alternariol, alternariol menomethyl ether, altenuene and tentoxin in pear paste by ultra-performance liquid chromatography tandem mass spectrometry with saturated sodium sulphate dissolution and acidified acetonitrile extraction. The mean recoveries of the five toxins were 75.3-113.8% with relative standard deviations of 2.8-12.2% at spiked levels of 1.0-100 μg kg-1 . Alternaria toxins were detected in 53 out of 76 samples, with a detection rate of 71.4%. Tenuazonic acid (67.1%), alternariol (35.5%), tentoxin (23.7%) and alternariol monomethyl ether (7.9%) were detected in all samples at concentrations of < limit of quantification (LOQ)-105.0 μg kg-1 , < LOQ-32.1 μg kg-1 , < LOQ-74.2 μg kg-1 and < LOQ-15.1 μg kg-1 , respectively. Altenuene was never found in pear paste samples. Tenuazonic acid, alternariol, tentoxin and alternariol menomethyl ether should be focused on due to their toxicity and detection rates.

CONCLUSION

To the best of our knowledge, this is the first report on the detection method and residue levels of Alternaria toxins in pear paste. The proposed method and research data can provide technical support for the Chinese government to continuously monitor and control Alternaria toxins in pear paste, especially tenuazonic acid. It can also provide a useful reference for related researchers. © 2023 Society of Chemical Industry.

Mechanisms of Alternaria pathogenesis in animals and plants

Alternaria species are cosmopolitan fungi darkly pigmented by melanin that infect numerous plant species causing economically important agricultural spoilage of various food crops. Alternaria spp. also infect animals, being described as entomopathogenic fungi but also infecting warm-blooded animals, including humans. Their clinical importance in human health, as infection agents, lay in the growing number of immunocompromised patients. Moreover, Alternaria spp. are considered some of the most abundant and potent sources of airborne sensitizer allergens causing allergic respiratory diseases, as severe asthma. Among the numerous strategies deployed by Alternaria spp. to attack their hosts, the production of toxins, carrying critical concerns to public health as food contaminant, and the production of hydrolytic enzymes such as proteases, can be highlighted. Alternaria proteases also trigger allergic symptoms in individuals with fungal sensitization, acting as allergens and facilitating antigen access to the host subepithelium. Here, we review the current knowledge about the mechanisms of Alternaria pathogenesis in plants and animals, the strategies used by Alternaria to cope with the host defenses, and the involvement Alternaria allergens and mechanisms of sensitization.

Molecular Characterization and Pathogenicity of Alternaria spp. Associated with Black Rot of Sweet Cherries in Italy

Black rot is limiting the production of sweet cherries in Italy. Dark brown to black patches and sunken lesions on fruits are the most common symptoms of Alternaria black rot on sweet cherry fruits. We isolated 180 Alternaria spp. from symptomatic cherry fruits 'Kordia', 'Ferrovia', and 'Regina' harvested in Northern Italy, over three years, from 2020 to 2022. The aim was to identify and characterize a selection of forty isolates of Alternaria spp. based on morphology, pathogenicity, and combined analysis of rpb2, Alt-a1, endoPG and OPA10-2. The colonies were dark greyish in the center with white margins. Ellipsoidal or ovoid shaped conidia ranging from 19.8 to 21.7 μm in length were observed under a microscope. Based on the concatenated session of four gene regions, thirty-three out of forty isolates were identified as A. arborescens species complex (AASC), and seven as A. alternata. Pathogenicity was evaluated on healthy 'Regina' sweet cherry fruits. All the tested strains were pathogenic on their host. This study represents the first characterization of Alternaria spp. associated with black rot of cherries in Italy and, to the best of our knowledge, it is also the first report of AASC as an agent of black rot of sweet cherries in Italy.

Small-spored Alternaria spp. (section Alternaria) are common pathogens on wild tomato species

The wild relatives of modern tomato crops are native to South America. These plants occur in habitats as different as the Andes and the Atacama Desert and are, to some degree, all susceptible to fungal pathogens of the genus Alternaria. Alternaria is a large genus. On tomatoes, several species cause early blight, leaf spots and other diseases. We collected Alternaria-like infection lesions from the leaves of eight wild tomato species from Chile and Peru. Using molecular barcoding markers, we characterized the pathogens. The infection lesions were caused predominantly by small-spored species of Alternaria of the section Alternaria, like A. alternata, but also by Stemphylium spp., Alternaria spp. from the section Ulocladioides and other related species. Morphological observations and an infection assay confirmed this. Comparative genetic diversity analyses show a larger diversity in this wild system than in studies of cultivated Solanum species. As A. alternata has been reported to be an increasing problem in cultivated tomatoes, investigating the evolutionary potential of this pathogen is not only interesting to scientists studying wild plant pathosystems. It could also inform crop protection and breeding programs to be aware of potential epidemics caused by species still confined to South America.

Screening, Identification, and Growth Promotion of Antagonistic Endophytes Associated with Chenopodium quinoa Against Quinoa Pathogens

Fungal disease is one of the important reasons for crop yield reduction. Isolation of important endophytes with biocontrol and growth-promoting effects is of great significance for the exploitation of beneficial microbial resources and the biological control of crop fungal diseases. In this study, endophytes from roots, stems, and leaves of quinoa at different growth and development stages were isolated and purified; then the antagonistic activity and growth-promoting characteristics of antagonistic endophytes were determined. Finally, the antagonistic endophytes were identified by morphological characteristics and ITS/16S rRNA sequence analysis. Our results showed that 122 endophytic fungi and 371 endophytic bacteria were isolated from quinoa, of which three endophytic fungi and seven endophytic bacteria were screened that had inhibitory activity against quinoa pathogenic fungi. Most of the antagonistic strains could produce indole-3 acetic acid and had the ability to dissolve organic phosphorus. In addition, the bacterial suspension of endophytic bacteria had the ability to promote the seed germination and plant growth of quinoa. The endophytic fungi with antagonistic activity were identified as Penicillium raperi and P. pulvillorum; the endophytic bacteria were identified as Bacillus paralicheniformis, B. tequilensis, and B. velezensis, respectively. The strains of quinoa endophytes in this study can provide rich microbial resources and a theoretical basis for biological control of plant fungal diseases and agricultural production.

Random amplified microsatellites (RAMS) analysis ascertains genetic variation of Alternaria alternata causing black spot disease on Carya illinoinensis in South Africa

Limited information regarding the occurrence of black spot disease of pecan (Carya illinoinensis), caused by A. alternata, in South Africa is known. The pecan industry is growing rapidly, so it is essential to understand the impact of the fungal pathogen to pecan health. In this study, the genetic variation of 364 A. alternata isolates was investigated by two RAMS primers (CCA5 and CGA5). In total, 6,525 alleles were produced, with a minimum of 3,182 alleles on the CGA5 primer and maximum of 3,343 alleles for CCA5 primer. Further analysis of the primers showed relatively low genetic diversity of A. alternata isolate populations, with mean values; (H = 0.12) and Shannon's information index (I = 0.20). The analysis of molecular variance (AMOVA) revealed significant differences between populations, with 88% of the genetic variation was found within populations (Nm = 3.59, PhiPT = 0.12), and were not significantly different (p > 0.001). While 12% variation was observed among populations (Nm = 2.89, PhiPT = 0.08) and the estimates were statistically significant (p < 0.001). STRUCTURE HARVESTER output showed that K value is K = 8, where ΔK cannot find the true number of populations because of less variation. The dendrogram cluster tree generated by Ward's analysis unveiled two main distinct clades and 10 sub-clades, revealing similar findings as those of PCoA analysis clusters. Therefore, it was evident that these analyses depicted no distinct relationship between the A. alternata isolates and their geographic locations or the prevalence of distribution among the populations.

Characterization of Alternaria alternata and Alternaria scrophulariae Brown Spot in Colombian quinoa (Chenopodium quinoa)

Alternaria is a saprophytic and opportunistic fungus with a worldwide distribution that can affect the quality of various agricultural products, such as fruits, cereals, and pseudocereals. This research was carried out to investigate the population of this genus associated with quinoa cultivation in plots located in the Boyacá department (Colombia), the country's third-largest quinoa-producing department. The present study found 17 Alternaria isolates, of which 13 were identified as A. alternata and 4 as A. scrophulariae (formerly A. conjuncta) employed molecular markers of internal transcribed spacer (ITS) region and translation elongation factor 1α (TEF-1α). In the pathogenicity test under greenhouse conditions, all the Alternaria isolates showed some degree of pathogenicity on Piartal quinoa cultivar plants although no significant differences were found in isolates. The severity indices ranged from 2 to 5, and the percentage of affected leaves per plant ranged between 15% and 40%. This fungus affected the foliar tissue of quinoa, resulting in chlorotic and necrotic spots, symptoms that can generate a reduction in the quality and productivity of crops. This is the first time that the pathogenicity of Alternaria spp. in the Piartal variety has been described and the first report of this genera in quinoa crops of Colombia.

Screening of Anti-Inflammatory Activity and Metabolomics Analysis of Endophytic Fungal Extracts; Identification and Characterization of Perylenequinones and Terpenoids from the Interesting Active Alternaria Endophyte

Patients suffering from inflammatory chronic diseases are classically treated with anti-inflammatory drugs but unfortunately are highly susceptible to becoming resistant to their treatment. Finding new drugs is therefore crucial and urgent and research on endophytic fungi is a promising way forward. Endophytic fungi are microorganisms that colonize healthy plants and live within their intercellular tissues. They are able to produce a large variety of secondary metabolites while allowing their host to stay healthy. A number of these molecules are endowed with antioxidant or antimicrobial as well as cytotoxic properties, making them very interesting/promising in the field of human therapy. The aim of our study was to investigate whether extracts from five endophytic fungi isolated from plants are endowed with anti-inflammatory activity. Extracts of the endophytic fungi Alternaria alternata from Calotropis procera leaves and Aspergillus terreus from Trigonella foenum-graecum seeds were able to counteract the lipopolysaccharide (LPS) pro-inflammatory effect on THP-1 cells differentiated into macrophages. Moreover, they were able to induce an anti-inflammatory state, rendering them less sensitive to the LPS pro-inflammatory stimulus. Taken together, these results show that these both endophytic fungi could be interesting alternatives to conventional anti-inflammatory drugs. To gain more detailed knowledge of their chemical richness, phytochemical analysis of the ethyl acetate extracts of the five endophytic fungi studied was performed using HPTLC, GC-MS and LC-MS with the Global Natural Products Social (GNPS) platform and the MolNetEnhancer tool. A large family of metabolites (carboxylic acids and derivatives, steroid derivatives, alkaloids, hydroxyanthraquinones, valerolactones and perylenequinones) were detected. The purification of endophytic fungus extract of Alternaria alternate, which diminished TNF-α production of 66% at 20 µg/mL, incubated one hour before LPS addition, led to the characterization of eight pure compounds. These molecules are altertoxins I, II, III, tricycloalternarenes 3a, 1b, 2b, anthranilic acid, and o-acetamidobenzoic acid. In the future, all these pure compounds will be evaluated for their anti-inflammatory activity, while altertoxin II has been shown in the literature as the most active mycotoxin in terms of anti-inflammatory activity.

Chenopodium quinoa, a New Host for Alternaria Section Alternata and Alternaria Section Infectoriae Causing Yellow Leaf Blotch Disease

Quinoa (Chenopodium quinoa Willd.) is a native American crop mainly grown in the Andes of Bolivia and Peru. During the last decades, the cultivation of quinoa has expanded to more than 125 countries. Since then, several diseases of quinoa have been characterized. A leaf disease was observed on quinoa plants growing in an experimental plot in Eastern Denmark in 2018. The symptoms produced by the associated fungi consisted of small yellow blotches on the upper surface of leaves with a pale chlorotic halo surrounding the lesion. These studies used a combination of morphology, molecular diagnostics, and pathogenicity tests to identify two different Alternaria species belonging to Alternaria sections Infectoriae and Alternata as the causal agent of observed disease symptoms. To the best of our knowledge, this is the first report of Alternaria spp. as foliar pathogens of quinoa. Our findings indicate the need for additional studies to determine potential risks to quinoa production.

Alternaria arborescens and A. italica Causing Leaf Blotch on Celtis julianae in China

Celtis julianae Schneid. is widely planted as a versatile tree species with ecological and economic significance. In September 2022, a leaf blotch disease of C. julianae was observed in Nanjing, Jiangsu, China, with an infection incidence of 63%. The disease led to severe early defoliation, significantly affecting the ornamental and ecological value of the host tree. The accurate identification of pathogens is imperative to conducting further research and advancing disease control. Koch's postulates confirmed that the fungal isolates (B1-B9) were pathogenic to C. julianae. The morphology of the characteristics of the pathogen matched those of Alternaria spp. The internal transcribed spacer region (ITS), large subunit (LSU) and small subunit (SSU) regions of rRNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Alternaria major allergen gene (Alt a 1), RNA polymerase second largest subunit (RPB2), and portions of translation elongation factor 1-alpha (TEF1-α) genes were sequenced. Based on multi-locus phylogenetic analyses and morphology, the pathogenic fungi were identified as Alternaria arborescens and A. italica. The findings provided useful information for disease management and enhanced the understanding of Alternaria species diversity in China. This is the first report of A. arborescens and A. italica causing leaf blotch of C. julianae in China and worldwide.

Variation in the Outcome of Plant-Mediated Pathogen Interactions in Potato: Effects of Initial Infections on Conspecific vs. Heterospecific Subsequent Infections

Plants are often attacked sequentially by multiple enemies. Pathogen sequential co-infections can lead to indirect interactions mediated by plant induced responses whose outcome is contingent on differences in the magnitude and type of plant induced defences elicited by different species or guilds. To date, however, most studies have tested unidirectional effects of one pathogen on another, not discerning between conspecific vs. heterospecific infections, and often not measuring plant induced responses underlying such outcomes. To address this, we conducted a greenhouse experiment testing for the impact of initial infection by two leaf pathogens (Alternaria solani and Phytophthora infestans) on subsequent infection by each of these pathogens on potato (Solanum tuberosum) plants, and also measured induced plant defences (phenolic compounds) to inform on interaction outcomes. We found contrasting results depending on the identity of the initially infecting pathogen. Specifically, initial infection by A. solani drove induced resistance (lower necrosis) by subsequently infecting A. solani (conspecific induced resistance) but had no effect on subsequent infection by P. infestans. In contrast, initial infection by P. infestans drove induced resistance to subsequent infection by both conspecifics and A. solani. Patterns of plant induced defences correlated with (and potentially explained) induced resistance to conspecific but not heterospecific (e.g., in the case of P. infestans) subsequent infection. Overall, these results further our understanding of plant-mediated pathogen interactions by showing that plant-mediated interactions between pathogen species can be asymmetrical and in some cases not reciprocal, that pathogen species can vary in the importance of conspecific vs. heterospecific effects, and shed mechanistic insight into the role of plant induced responses driving such interactions.

Different diagnostic approaches for the characterization of the fungal community and Fusarium species complex composition of Italian durum wheat grain and correlation with secondary metabolite accumulation

BACKGROUND

The evolution of the fungal communities associated with durum wheat was assessed using different diagnostic approaches. Durum wheat grain samples were collected in three different Italian cultivation macro-areas (north, center and south). Fungal isolation was realized by potato dextrose agar (PDA) and by deep-freezing blotter (DFB). Identification of Fusarium isolates obtained from PDA was achieved by partial tef1α sequencing (PDA + tef1α), while those obtained from DFB were identified from their morphological characteristics (DFB + mc). The fungal biomass of eight Fusarium species was quantified in grains by quantitative polymerase chain reaction (qPCR). Fungal secondary metabolites were analyzed in grains by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Correlations between Fusarium detection techniques (PDA + tef1α; DFB + mc and qPCR) and mycotoxins in grains were assessed.

RESULTS

Alternaria and Fusarium showed the highest incidence among the fungal genera developed from grains. Within the Fusarium community, PDA + tef1α highlighted that F. avenaceum and F. graminearum were the most represented members, while, DFB + mc detected a high presence of F. proliferatum. Alternaria and Fusarium mycotoxins, principally enniatins, were particularly present in the grain harvested in central Italy. Deoxynivalenol was mainly detected in northern-central Italy.

CONCLUSIONS

The adoption of the different diagnostic techniques of Fusarium detection highlighted that, for some species, qPCR was the best method of predicting their mycotoxin contamination in grains. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Disclosing the native blueberry rhizosphere community in Portugal-an integrated metagenomic and isolation approach

Backgorund

The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop's resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices.

Methods

In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms.

Results

Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants.

Discussion

This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.

Temporal and Habitat Dynamics of Soil Fungal Diversity in Gravel-Sand Mulching Watermelon Fields in the Semi-Arid Loess Plateau of China

Mulching is an important agricultural management tool for increasing watermelon productivity and land-use efficiency because it helps improve water use efficiency and reduce soil erosion. However, there is relatively little available information regarding the effects of long-term continuous monoculture farming on soil fungal communities and related fungal pathogens in arid and semiarid regions. In this study, we characterized the fungal communities of four treatment groups, including gravel-sand-mulched farmland, gravel-sand-mulched grassland, fallow gravel-sand-mulched grassland, and native grassland, using amplicon sequencing. Our results revealed that the soil fungal communities differed significantly between mulched farmland and mulched grassland as well as the fallow mulched grassland. Gravel-sand mulch significantly impaired the diversity and composition of soil fungal communities. Soil fungal communities were more sensitive to gravel-sand mulch in grassland than in other habitats. Long-term continuous monoculture (more than 10 years) led to decreased abundance of Fusarium species, which contains include agronomically important plant pathogens. In the gravel-mulched cropland, some Penicillium and Mortierella fungi were significantly enriched with increasing mulch duration, suggesting potential beneficial properties of those fungi that could be applied to disease control. We also found that long-term gravel mulching in continuous monoculture farming could potentially form disease-suppressive soils and alter soil microbial biodiversity and fertility. Our study provides insights into the exploration of novel agricultural management strategies along with continuous monoculture practice to control watermelon wilt disease by maintaining a more sustainable and healthier soil environment. IMPORTANCE Gravel-sand mulching is a traditional agricultural practice in arid and semiarid regions, providing a surface barrier for soil and water conservation. However, application of such practice in monocropping systems may lead to outbreaks of several devastating plant diseases, such as watermelon Fusarium wilt. Our results with amplicon sequencing suggest that soil fungal communities differ significantly between mulched farmland and mulched grassland and are more sensitive to gravel-sand mulch in grassland. Under continuous monoculture regimens, long-term gravel mulch is not necessarily detrimental and may result in decreased Fusarium abundance. However, some known beneficial soil fungi may be enriched in the gravel-mulch cropland as mulch duration increases. A possible explanation for the reduction in Fusarium abundance may be the formation of disease-suppressive soils. This study provides insight into the need to explore alternative strategies using beneficial microbes for sustainable watermelon wilt control in continuous monocropping system.

Plant-Fungi Interactions: Where It Goes?

Fungi live different lifestyles-including pathogenic and symbiotic-by interacting with living plants. Recently, there has been a substantial increase in the study of phytopathogenic fungi and their interactions with plants. Symbiotic relationships with plants appear to be lagging behind, although progressive. Phytopathogenic fungi cause diseases in plants and put pressure on survival. Plants fight back against such pathogens through complicated self-defense mechanisms. However, phytopathogenic fungi develop virulent responses to overcome plant defense reactions, thus continuing their deteriorative impacts. Symbiotic relationships positively influence both plants and fungi. More interestingly, they also help plants protect themselves from pathogens. In light of the nonstop discovery of novel fungi and their strains, it is imperative to pay more attention to plant-fungi interactions. Both plants and fungi are responsive to environmental changes, therefore construction of their interaction effects has emerged as a new field of study. In this review, we first attempt to highlight the evolutionary aspect of plant-fungi interactions, then the mechanism of plants to avoid the negative impact of pathogenic fungi, and fungal strategies to overcome the plant defensive responses once they have been invaded, and finally the changes of such interactions under the different environmental conditions.

Species diversity and molecular characterization of Alternaria section Alternaria isolates collected mainly from cereal crops in Canada

Alternaria is often one on the most abundant fungal genera recovered from a wide array of plant hosts and environmental substrates. Many species within the sub-generic Alternaria section Alternaria are common plant pathogens that cause pre-harvest losses due to reduced productivity and post-harvest losses due to spoilage and contamination with mycotoxins. As certain species of Alternaria may have distinct mycotoxin profiles, and very broad host ranges, understanding the distribution of species by geography and host is critical for disease prediction, toxicological risk assessment, and guiding regulatory decisions. In two previous reports, we performed phylogenomic analyses to identify highly informative molecular markers for Alternaria section Alternaria, and validated their diagnostic ability. Here, we perform molecular characterization of 558 section Alternaria strains, collected from 64 host genera in 12 countries, using two of these section-specific loci (ASA-10 and ASA-19) along with the RNA polymerase II second largest subunit (rpb2) gene. The majority of strains (57.4%) originated from various cereal crops in Canada, which formed the main focus of our study. Phylogenetic analyses were used to classify strains into section Alternaria species/lineages, demonstrating that the most common species on Canadian cereal crops are Alternaria alternata and A. arborescens. Further population genetic analyses were consistent with A. alternata being a widely distributed species with relatively low levels of geographic isolation (i.e., Canadian isolates did not form distinct clades when compared to other regions). Our expanded sampling of A. arborescens has greatly increased the known diversity of this group, with A. arborescens isolates forming at least three distinct phylogenetic lineages. Proportionally, A. arborescens is more prevalent in Eastern Canada than in Western Canada. Sequence analyses, putative hybrids, and mating-type distributions provided some evidence for recombination events, both within and between species. There was little evidence for associations between hosts and genetic haplotypes of A. alternata or A. arborescens.

Fungicide-free management of Alternaria leaf blotch and fruit spot on apple indicates Alternaria spp. as secondary colonizer

The fungal genus Alternaria is a pan-global pathogen of > 100 crops, and is associated with the globally expanding Alternaria leaf blotch in apple (Malus x domestica Borkh.) which leads to severe leaf necrosis, premature defoliation, and large economic losses. Up to date, the epidemiology of many Alternaria species is still not resolved as they can be saprophytic, parasitic or shift between both lifestyles and are also classified as primary pathogen able to infect healthy tissue. We argue that Alternaria spp. does not act as primary pathogen, but only as a necrosis-dependent opportunist. We studied the infection biology of Alternaria spp. under controlled conditions and monitored disease prevalence in real orchards and validated our ideas by applying fungicide-free treatments in 3-years field experiments. Alternaria spp. isolates were not able to induce necroses in healthy tissue, but only when prior induced damages existed. Next, leaf-applied fertilizers, without fungicidal effect, reduced Alternaria-associated symptoms (- 72.7%, SE: ± 2.5%) with the same efficacy as fungicides. Finally, low leaf magnesium, sulphur, and manganese concentrations were consistently linked with Alternaria-associated leaf blotch. Fruit spot incidence correlated positively with leaf blotch, was also reduced by fertilizer treatments, and did not expand during storage unlike other fungus-mediated diseases. Our findings suggest that Alternaria spp. may be a consequence of leaf blotch rather than its primary cause, as it appears to colonize the physiologically induced leaf blotch. Taking into account existing observations that Alternaria infection is connected to weakened hosts, the distinction may appear slight, but is of great significance, as we can now (a) explain the mechanism of how different stresses result in colonization with Alternaria spp. and (b) substitute fungicides for a basic leaf fertilizer. Therefore, our findings can result in significant decreases in environmental costs due to reduced fungicide use, especially if the same mechanism applies to other crops.

Effect of prevailing winds and land use on Alternaria airborne spore load

Alternaria spores are a common component of the bioaerosol. Many Alternaria species are plant pathogens, and their conidia are catalogued as important aeroallergens. Several aerobiological studies showing a strong relationship between concentrations of airborne spore and meteorological parameters have consequently been developed. However, the Alternaria airborne load variation has not been thoroughly investigated because it is difficult to assess their sources, as they are a very common and widely established phytopathogen. The objective of this study is to estimate the impact of vegetation and land uses as potential sources on airborne spore load and to know their influence, particularly, in cases of long-medium distance transport. The daily airborne spore concentration was studied over a 5-year period in León and Valladolid, two localities of Castilla y León (Spain), with differences in their bioclimatic and land use aspects. Moreover, the land use analysis carried out within a 30 km radius of each monitoring station was combined with air mass data in order to search for potential emission sources. The results showed a great spatial variation between the two areas, which are relatively close to each other. The fact that the spore concentrations recorded in Valladolid were higher than those in León was owing to prevailing winds originating from large areas covered by cereal crops, especially during the harvest period. However, the prevailing winds in León came from areas dominated by forest and shrubland, which explains the low airborne spore load, since the main Alternaria sources were the grasslands located next to the trap. Furthermore, the risk days in this location presented an unusual wind direction. This study reveals the importance of land cover and wind speed and direction data for establishing potential airborne routes of spore transport in order to improve the Alternaria forecasting models. The importance of conducting Alternaria aerobiological studies at a local level is also highlighted.

Metabolite Analysis of Alternaria Mycotoxins by LC-MS/MS and Multiple Tools

Alternaria fungi are widely distributed plant pathogens that invade crop products, causing significant economic damage. In addition, toxic secondary metabolites produced by the fungi can also endanger consumers. Many of these secondary metabolites are chemically characterized as mycotoxins. In this study, Q Exactive Orbitrap mass spectrometry was used for the non-targeted analysis of the metabolome of seven Alternaria isolates cultured on Potato Carrot Agar (PCA), Potato Dextrose Agar (PDA) and Potato Sucrose Agar (PSA) medium. Due to the difficulty of detecting modified toxins, an analytical strategy with multiple visual analysis tools was also used to determine the presence of sulfate conjugated toxins, as well as to visualize the molecular network of Alternaria toxins. The results show that PSA medium exhibits more advantageous properties for the culture of Alternaria, with more toxigenic species and quantities and more obvious metabolic pathways. Based on high-resolution tandem mass spectrometry (MS/MS) data, the mycotoxins and their metabolites were mainly clustered into four groups: alternariol (AOH)/alternariol monomethyl ether (AME)/altenusin (ALU)/altenuene (ALT)/dehydroaltenusin (DHA)/Desmethyldehydroaltenusin (DMDA) families, Altertoxin-I (ATX-I) family, tentoxin (TEN) family and tenuazonic acid (TeA) family. Moreover, the PSA medium is more suitable for the accumulation of AOH, AME, ALU, ALT, DHA and DMDA, while the PDA medium is more suitable for the accumulation of ATX-I, TEN and TeA. This research may provide theoretical support for the metabolomics study of Alternaria.

Sclerotinia sclerotiorum (Lib.) de Bary: Insights into the Pathogenomic Features of a Global Pathogen

Sclerotinia sclerotiorum (Lib.) de Bary is a broad host-range fungus that infects an inclusive array of plant species and afflicts significant yield losses globally. Despite being a notorious pathogen, it has an uncomplicated life cycle consisting of either basal infection from myceliogenically germinated sclerotia or aerial infection from ascospores of carpogenically germinated sclerotia. This fungus is unique among necrotrophic pathogens in that it inevitably colonizes aging tissues to initiate an infection, where a saprophytic stage follows the pathogenic phase. The release of cell wall-degrading enzymes, oxalic acid, and effector proteins are considered critical virulence factors necessary for the effective pathogenesis of S. sclerotiorum. Nevertheless, the molecular basis of S. sclerotiorum pathogenesis is still imprecise and remains a topic of continuing research. Previous comprehensive sequencing of the S. sclerotiorum genome has revealed new insights into its genome organization and provided a deeper comprehension of the sophisticated processes involved in its growth, development, and virulence. This review focuses on the genetic and genomic aspects of fungal biology and molecular pathogenicity to summarize current knowledge of the processes utilized by S. sclerotiorum to parasitize its hosts. Understanding the molecular mechanisms regulating the infection process of S. sclerotiorum will contribute to devising strategies for preventing infections caused by this destructive pathogen.

Molecular docking and dynamics simulation study of quinones and pyrones from Alternaria solani and Alternaria alternata with HSP90: an important therapeutic target of cancer

Although cancer continues to be one of the world's major causes of death, current cancer drugs have many serious side effects. There remains a need for new anticancer agents to overcome these shortcomings. Alternaria is one of the most widespread fungal genera, many species of which produce several classes of metabolites with potential polypharmacological activities. A few quinones and pyrones from Alternaria spp. have proven to exert cytotoxic effects against certain cancer cell lines, but their molecular mode of action is not known. The current study aimed to investigate the potential mechanisms that underlie the anticancer activity of a few selected quinones and pyrones from Alternaria solani and Alternaria alternata by molecular docking and dynamic simulation approaches. The selected metabolites were screened for their binding affinity to Heat shock protein 90 (HSP90), which is a known anticancer drug target. Molecular docking studies have revealed that Macrosporin, Altersolanol B, Fonsecin, and Neoaltenuene have good binding affinities with the target protein and the stabilities of the formed complexes were evaluated through molecular dynamics simulations. By analyzing the Root Mean Square Distance (RMSD), Root Mean Square Fluctuation (RMSF), and Principal Component Analysis (PCA) plots obtained from molecular dynamics simulations, this study shows that the complexes of all 4 lead molecules with target protein are stable over a 100 ns period. Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations were used to compute the binding free energies. The lead molecules were studied using in-silico analysis to determine their drug-likeness based on their Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) and physicochemical properties. The results demonstrate that Macrosporin, Fonsecin, and Neoaltenuene could become promising anticancer molecules that target HSP90.Communicated by Ramaswamy H. Sarma.

Root uptake and metabolization of Alternaria toxins by winter wheat plants using a hydroponic system

Fungi of the genus Alternaria are ubiquitous in the environment. Their mycotoxins can leach out of contaminated plants or crop debris into the soil entering the plant via the roots. We aim to evaluate the importance of this entry pathway and its contribution to the overall content of Alternaria toxins (ATs) in wheat plants to better understand the soil-plant-phytopathogen system. A hydroponic cultivation system was established and wheat plants were cultivated for up to two weeks under optimal climate conditions. One half of the plants was treated with a nutrient solution spiked with alternariol (AOH), alternariol monomethyl ether (AME), and tenuazonic acid (TeA), whereas the other half of the plants was cultivated without mycotoxins. Plants were harvested after 1 and 2 weeks and analyzed using a QuEChERS-based extraction and an in-house validated LC-MS/MS method for quantification of the ATs in roots, crowns, and leaves separately. ATs were taken up by the roots and transported throughout the plant up to the leaves after 1 as well as 2 weeks of cultivation with the roots showing the highest ATs levels followed by the crowns and the leaves. In addition, numerous AOH and AME conjugates like glucosides, malonyl glucosides, sulfates, and di/trihexosides were detected in different plant compartments and identified by high-resolution mass spectrometry. This is the first study demonstrating the uptake of ATs in vivo using a hydroponic system and whole wheat plants examining both the distribution of ATs within the plant compartments and the modification of ATs by the wheat plants.

Stress Response to Climate Change and Postharvest Handling in Two Differently Pigmented Lettuce Genotypes: Impact on Alternaria alternata Invasion and Mycotoxin Production

Many species of Alternaria are important pathogens that cause plant diseases and postharvest rots. They lead to significant economic losses in agriculture and affect human and animal health due to their capacity to produce mycotoxins. Therefore, it is necessary to study the factors that can result in an increase in A. alternata. In this study, we discuss the mechanism by which phenol content protects from A. alternata, since the red oak leaf cultivar (containing higher phenols) showed lower invasion than the green one, Batavia, and no mycotoxin production. A climate change scenario enhanced fungal growth in the most susceptible cultivar, green lettuce, likely because elevated temperature and CO₂ levels decrease plant N content, modifying the C/N ratio. Finally, while the abundance of the fungi was maintained at similar levels after keeping the lettuces for four days at 4 °C, this postharvest handling triggered TeA and TEN mycotoxin synthesis, but only in the green cultivar. Therefore, the results demonstrated that invasion and mycotoxin production are cultivar- and temperature-dependent. Further research should be directed to search for resistant cultivars and effective postharvest strategies to reduce the toxicological risk and economic losses related to this fungus, which are expected to increase in a climate change scenario.

Alternaria alternata Isolated from Infected Pears (Pyrus communis) in Italy Produces Non-Host Toxins and Hydrolytic Enzymes as Infection Mechanisms and Exhibits Competitive Exclusion against Botrytis cinerea in Co-Infected Host Fruits

Alternaria alternata is one of the most devastating phytopathogenic fungi. This microorganism causes black spots in many fruits and vegetables worldwide, generating significant post-harvest losses. In this study, an A. alternata strain, isolated from infected pears (Pyrus communis) harvested in Italy, was characterized by focusing on its pathogenicity mechanisms and competitive exclusion in the presence of another pathogen, Botrytis cinerea. In in vitro assays, the fungus produces strong enzymatic activities such as amylase, xylanase, and cellulase, potentially involved during the infection. Moreover, it secretes four different toxins purified and identified as altertoxin I, alteichin, alternariol, and alternariol 4-methyl ether. Only alteichin generated necrotic lesions on host-variety pears, while all the compounds showed moderate to slight necrotic activity on non-host pears and other non-host fruit (lemon, Citrus limon), indicating they are non-host toxins. Interestingly, A. alternata has shown competitive exclusion to the competitor fungus Botrytis cinerea when co-inoculated in host and non-host pear fruits, inhibiting its growth by 70 and 65%, respectively, a result not observed in a preliminary characterization in a dual culture assay. Alteichin and alternariol 4-methyl ether tested against B. cinerea had the best inhibition activity, suggesting that the synergism of these toxins and enzymatic activities of A. alternata are probably involved in the competitive exclusion dynamics in host and non-host pear fruits.

Environmental Filtering Drives Fungal Phyllosphere Community in Regional Agricultural Landscapes

To adapt to climate change, several agricultural strategies are currently being explored, including a shift in land use areas. Regional differences in microbiome composition and associated phytopathogens need to be considered. However, most empirical studies on differences in the crop microbiome focused on soil communities, with insufficient attention to the phyllosphere. In this study, we focused on wheat ears in three regions in northeastern Germany (Magdeburger Börde (MBB), Müncheberger Sander (MSA), Uckermärkisches Hügelland (UKH)) with different yield potentials, soil, and climatic conditions. To gain insight into the fungal community at different sites, we used a metabarcoding approach (ITS-NGS). Further, we examined the diversity and abundance of Fusarium and Alternaria using culture-dependent and culture-independent techniques. For each region, the prevalence of different orders rich in phytopathogenic fungi was determined: Sporidiobolales in MBB, Capnodiales and Pleosporales in MSA, and Hypocreales in UKH were identified as taxonomic biomarkers. Additionally, F. graminearum was found predominantly in UKH, whereas F. poae was more abundant in the other two regions. Environmental filters seem to be strong drivers of these differences, but we also discuss the possible effects of dispersal and interaction filters. Our results can guide shifting cultivation regions to be selected in the future concerning their phytopathogenic infection potential.

Alternaria alternata, the Causal Agent of a New Needle Blight Disease on Pinus bungeana

Pinus bungeana, an endangered and native coniferous tree species in China, has considerable timber and horticulture value. However, little is known about needle diseases in P. bungeana. A needle blight of P. bungeana has been observed in Hebei Province, China. P. bungeana inoculated with mycelial plugs of fungal isolates presented symptoms similar to those observed under field conditions. Ten virulent fungal isolates were identified as a small-spored Alternaria species based on morphological observations. Maximum likelihood and Bayesian phylogenetic analyses carried out with multilocus sequence typing of eight regions (SSU, LSU, ITS, gapdh, tef1, Alt a 1, endoPG, OPA10-2) assigned the pathogen to Alternaria alternata. This is the first report of A. alternata causing needle blight on P. bungeana in China.

Comprehensive review on patulin and Alternaria toxins in fruit and derived products

Mycotoxins are toxic secondary metabolites produced by certain fungi, which can contaminate various food commodities, including fruits and their derived products. Patulin and Alternaria toxins are among the most commonly encountered mycotoxins in fruit and their derived products. In this review, the sources, toxicity, and regulations related to these mycotoxins, as well as their detection and mitigation strategies are widely discussed. Patulin is a mycotoxin produced mainly by the fungal genera Penicillium, Aspergillus, and Byssochlamys. Alternaria toxins, produced by fungi in the Alternaria genus, are another common group of mycotoxins found in fruits and fruit products. The most prevalent Alternaria toxins are alternariol (AOH) and alternariol monomethyl ether (AME). These mycotoxins are of concern due to their potential negative effects on human health. Ingesting fruits contaminated with these mycotoxins can cause acute and chronic health problems. Detection of patulin and Alternaria toxins in fruit and their derived products can be challenging due to their low concentrations and the complexity of the food matrices. Common analytical methods, good agricultural practices, and contamination monitoring of these mycotoxins are important for safe consumption of fruits and derived products. And Future research will continue to explore new methods for detecting and managing these mycotoxins, with the ultimate goal of ensuring the safety and quality of fruits and derived product supply.

Fabrication of CuO nanoparticles composite ε-polylysine-alginate nanogel for high-efficiency management of Alternaria alternate

Although ε-poly-l-lysine (ε-PL) has a good potential as a green fungicide, high concentration is usually required during its controlling of plant disease. On the other hand, same problems also appeared in the study of CuONP based nano pesticides. In this manuscript, a new composite alginate nanogel (ALGNP) that containing CuONP and ε-PL was fabricated via in situ reduction of CuONP in nanogel and ε-PL surface coating. Based on the chelation of amide bond of ε-PL and Cu²⁺ released by CuONP, the synergy effect between Cu²⁺ and ε-PL layer of the nanogel make the nanogel (CuONP@ALGNP@PL) performed high anti-fungal activity under low Cu²⁺ and ε-PL concentration (Cu concentration was 40.09 μg/mL, ε-PL concentration was 11.90 μg/mL). Study showed that the nanogel could more significantly destroy the fungal cell membrane than CuONP@ALGNP and ALGNP@PL, also better than commercial fungicide CuCaSO₄ (Cu concentration was 120 μg/mL). Furthermore, CuONP@ALGNP@PL could seriously affect the spore production, spore germination rate and bud tube elongation length of Alternaria alternate. Moreover, CuONP@ALGNP@PL also inhibit Botrytis cinerea, Phytophthora, Thanatephorus cucumeris and Fusarium graminearum. These results showed that composite of CuONP and ε-PL based on nanogel can decrease the raw materials application amount, and achieve a high disease controlling ability, which provides a new perspective for preventing fungal diseases.

A Melanin-Deficient Isolate of Venturia inaequalis Reveals Various Roles of Melanin in Pathogen Life Cycle and Fitness

Venturia inaequalis is the ascomycetous pathogen causing apple scabs and forms dark-pigmented spores and partially melanised infection structures. Although melanin is considered to be essential for the infection of host tissue, a spontaneously occurring melanin-deficient mutant was isolated from an abaxial side of an apple leaf and can be cultivated in vitro as well as in vivo. The morphology and development of the melanin-deficient-isolate SW01 on leaves of susceptible apple plants were compared to that of the corresponding wild-type isolate HS1. White conidia of SW01 were often wrinkled when dry and significantly increased their volume in suspension. Germination and formation of germtubes and appressoria were not impaired; however, the lack of melanisation of the appressorial ring structure at the interface with the plant cuticle significantly reduced the infection success of SW01. The colonisation of leaf tissue by non-melanised subcuticular hyphae was not affected until the initiation of conidiogenesis. Non-melanised conidiophores penetrated the plant cuticle from inside less successfully than the wild type, and the release of white conidia from less solid conidiophores above the cuticle was less frequent. Melanin in the outer cell wall of V. inaequalis was not required for the survival of conidia under ambient temperature or at -20 °C storage conditions, however, promoted the tolerance of the pathogen to copper and synthetic fungicides affecting the stability and function of the fungal cell wall, plasma membrane, respiration (QoIs) and enzyme secretion, but had no effect on the sensitivity to sulphur and SDHIs. The roles of melanin in different steps of the V. inaequalis life cycle and the epidemiology of apple scabs are discussed.

Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions

Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant's defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant-fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as "non-proteinaceous effectors". Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts. However, there are no clear functional approaches to study the role of these SM and sRNA effectors. Undoubtedly, fungal SM and sRNA effectors are now a treasured land to seek. Therefore, understanding the role of fungal SM and sRNA effectors may provide insights into the infection process and identification of the interacting host genes that are targeted by these effectors. This review discusses the role of fungal SMs and sRNAs during plant-fungal interactions. It will also focus on the translocation of sRNA effectors across kingdoms, the application of cross-kingdom RNA interference in managing plant diseases and the tools that can be used to predict and study these non-proteinaceous effectors.