The impact of climate change on vegetable crop diseases and their management: the value of phytotron studies for the agricultural industry and associated stakeholders

Climate change is having a significant impact on global agriculture, and in particular on vegetable crops, which play a critical role in global nutrition. Recently, increasing research has concentrated on the impact of climate change on vegetable crop diseases, with several studies being conducted in phytotrons, which have been used to explore effects of increased temperatures and CO2 concentrations, to simulate future scenarios. This review focuses on the combined effects of temperature and carbon dioxide increases on foliar and soil-borne vegetable diseases, as evaluated under phytotron conditions. The influence of climate change on mycotoxin production and disease management strategies is also explored through case studies. The results offer valuable information that can be used to guide both seed and agrochemical industries, and to develop disease-resistant varieties and innovative control measures, including biocontrol agents, considering the diseases that are likely to become prevalent under future climatic scenarios. Recommendations on how to manage vegetable diseases under ongoing climate change are proposed to facilitate the adaptation and enhanced resilience of plants to the changing conditions. A proactive and comprehensive response to climate-induced challenges in vegetable farming is imperative to ensure food security and sustainability.

Characterization and Pathogenicity of Fungal Species Associated with Dieback of Apple Trees in Northern Italy

Severe dieback symptoms were recently observed on apple (Malus × domestica) trees in Northern Italy, representing a growing concern for producers. Surveys were conducted over a 3-year period (2019 to 2021), and five apple orchards, from 5 to 12 years old, were monitored. A total of 33 fungal isolates isolated from symptomatic plants was selected for characterization. The species identification was achieved through multilocus phylogenetic analyses performed on sequences of three genomic loci (ITS, tub2, and tef1). Morphological features were assessed, and the average growth rate at different temperatures was determined. Seven species were identified in association with dieback of apple trees: Botryosphaeria dothidea, Cadophora luteo-olivacea, Diaporthe rudis, Diplodia seriata, Eutypa lata, Kalmusia longispora, and Paraconiothyrium brasiliense. All the species were pathogenic when inoculated on healthy apple plants. B. dothidea resulted in the most aggressive infections. This study provides an insight into the fungal species diversity associated with apple dieback and provides basis for further investigations to assess the phytosanitary status of plant materials to recommend and implement effective management strategies.

Effects of fungicide application on physiological and molecular responses of grapevine (Vitis vinifera L.): a comparison between copper and sulfur fungicides applied alone and in combination with novel fungicides

BACKGROUND

Chemical products against fungi and oomycetes pose serious environmental issues. In the last decade, the use of less impacting active ingredients was encouraged to reduce chemical inputs in viticulture. In this study, the effect of different antifungal compounds on grapevine agronomic, physiological, and molecular responses in the vineyard was evaluated in addition to protection against powdery and downy mildews.

RESULTS

In 2 years and in two Vitis vinifera cultivars (Nebbiolo and Arneis), a conventional crop protection approach, based on traditional fungicides (sulfur and copper), was compared to combined strategies. A well-known resistance inducer (potassium phosphonate), Bacillus pumilus strain QST 2808 and calcium oxide, both active ingredients whose biological interaction with grapevine is poorly characterized, were applied in the combined strategies in association with chemical fungicides. Despite a genotype effect occurred, all treatments optimally controlled powdery and downy mildews, with minimal variations in physiological and molecular responses. Gas exchange, chlorophyll content and photosystem II efficiency increased in treated plants at the end of season, along with a slight improvement in the agronomic performances, and an activation of molecular defense processes linked to stilbene and jasmonate pathways.

CONCLUSION

The disease control strategies based on potassium phosphonate, Bacillus pumilus strain QST 2808 or calcium oxide combined with traditional chemical compounds did not cause severe limitations in plant ecophysiology, grape quality, and productive yields. The combination of potassium phosphonate and calcium oxide with traditional fungicides can represent a valuable strategy for reducing copper and sulfur inputs in the vineyards, including those organically managed. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

First Report of Gnomoniopsis fragrariae causing leaf spots on strawberry in Italy

Strawberry (Fragaria × ananassa Duch.) is widely cultivated in Italy. During May-June 2022, mild symptoms of an unknown leaf spot disease appeared on 5-10% of June-bearing strawberry (cv. Elodì) plants transplanted in July 2021 in a commercial farm located in the province of Cuneo, North Italy. During September-November 2022, the symptoms appeared also on 10-15% of the plants transplanted in July 2022. The disease was scattered throughout the field, large 600 m2, both on new and senescent leaves. Fungicides (sulphur, Tiovit Jet; penconazole, Topas 10 EC) were applied to the plants according to integrated pest management during the growing period. The disease symptoms were purplish to brown necrotic leaf spots up to 1-3 mm in diameter and chlorotic leaf margins. Black lesions were occasionally observed on the petioles, appearing as small necrotic or larger elongated lesions causing leaf death. Peritechia were observed in planta after about 4 months from sampling and measured (144 to 239 μm and 200 to 291 μm, n = 10). Diseased leaves and petioles from about 10 plants were surface disinfested for 1 min in 1% NaClO, rinsed with sterile water and plated on potato dextrose agar (PDA) amended with 25 mg streptomycin sulphate/liter. A fungus with white cottony colonies was repeatedly recovered and maintained in pure culture on PDA. Biguttulate conidia with rounded ends were measured (4.3 to 8.0 μm and 1.2 to 2.9 μm, average 6.1× 2.3 μm, n = 50) from 21-day old colonies grown in PDA at 22°C and 12 h photoperiod. According to colony and conidia morphology, the isolate was identified as Gnomoniopsis sp. (Walker et al., 2010). The fungal DNA was extracted from a pure culture of one isolate selected as a representative (code FR2-22), by using the E.Z.N.A. Fungal DNA Mini Kit (Omega Bio-Tek, Darmstadt, Germany). The identification was carried out by amplifying and sequencing the internal transcribed spacer (ITS) region and the partial translation elongation factor 1-α (TEF) gene using the primers ITS1/ITS4 and EF-728F/EF2 (Udayanga et al., 2021), respectively. The purified PCR products were sequenced at the BMR Genomics Centre (Padova, Italy) obtaining 551bp (ITS) and 652bp (TEF) sequences deposited in GenBank (Accession nos. OQ179950 and OQ190173, respectively). A BLASTn search of both sequences revealed to be 100% identical to the ITS and TEF loci of Gnomoniopsis fructicola sequences of the isolates VPRI_15547 and CBS 275.51 deposited in GenBank with accession Nos. MT378345 and MT383092. The pathogenicity of the isolate FR2-22 was assessed in two trials by biological tests (3 replicates with 1 plant per replicate/pot) in two greenhouse compartments, kept at temperature 20-24°C and at humidity 80-90%. Healthy leaves of forty-day-old strawberry plants (cv. Elodì) were sprayed with 1-5 x106 conidia/ml obtained from the FR2-22 isolate grown on PDA at 25°C for 20 days. The control (water-sprayed plants) was kept in the same conditions. Small leaf spots similar to the symptoms previously observed in the farm were observed 15 days post inoculation. Furthermore, 30 to 40% of leaves developed symptoms similar to those observed in the field after 25-40 days, while the control remained health. The same fungal isolate was repeatedly reisolated from the affected leaves and petioles and identified based on TEF sequencing. Gnomoniopsis fragariae comb. nov., designed as new name for Gnomoniopsis fructicola (Udayanga et al., 2021), has previously been reported on Fragaria × ananassa plants in Australia and in the USA (Farr and Rossman, 2023). To the best of our knowledge, this is the first report of G. fragariae on strawberry in Italy. The impact of the disease caused by this pathogen could be of high importance in the future of strawberry production in Italy. Healthy propagation material and strict disease management practices in nurseries is a requirement to avoid disease epidemics.

First report of Diaporthe eres causing stem blight and dieback on highbush blueberry (Vaccinium corymbosum) in Italy

Vaccinium corymbosum L. is a woody deciduous shrub belonging to the Ericaceae family. During the last decade, Northern Italy has become a major area for blueberry cultivation and production in Europe, supplying other countries with high quality fruit (FAOSTAT 2020). In June 2020, plant stem and branch wilting with brownish necrotic internal lesions were observed on 20% of around 250 plants of the cultivar (cv.) Draper cultivated in a soilless culture system located in Peveragno (Piedmont, Cuneo Province, 44°21'05.6''N, 07°37'23.2''). Dieback and death of the plants also occurred. Fifteen symptomatic plants were collected. Wood pieces (5-10 mm) excised from diseased stems and branches were sterilized in 1% sodium hypochlorite for 1 min, rinsed in sterile distilled water and dried on sterile absorbent paper. Small fragments (2-3 mm), obtained from the edge of the necrotic tissues, were plated on potato dextrose agar (PDA) amended with 25 mg/L of streptomycin sulfate. Plates were incubated at 25 ± 1°C under a 12 h photoperiod and, five days after, colonies with the same characteristics of Diaporthe spp. were established from single hyphal tip transfers. Two representative strains (CVG1130 and CVG1131) were grown on PDA from single hyphal-tip transfers. After 7 days, white colonies with fluffy, aerial, mycelium reaching 8.3 cm were observed. colonies turned gray after three weeks producing dark brown pycnidia. Aseptate, hyaline, fusiform to ellipsoidal, measuring 6.3 to 8.4 × 2.2 to 3.0 μm alpha conidia were produced. No beta conidia were observed. The DNA of the same strains was extracted and a polymerase chain reaction (PCR) was performed for the ITS (primer set: ITS1-ITS4) (GenBank Accession no. ON834528; ON834529), tef (EF1-728/EF1-986) (GenBank Accession no. ON843715; ON843716) and tub2 (T1/Bt2b) (GenBank Accession no. ON843713; ON843714) regions, in accordance with previous studies (Gomes et al. 2013, Bezerra et al. 2021). Sequences analysed with BLASTn algorithm (Altschul et al. 1997) exhibited 98% identity with the ex-type strain CBS 138594 of Diaporthe eres for ITS (GenBank Accession no. KJ210529), 100% identity for tub2 (GenBank Accession no. KJ420799) and 99% identity for tef (GenBank Accession no. KJ210550). The maximum likelihood method based on combined sequences of ITS, tef and tub2 loci was performed, and the isolates CVG1130 and CVG1131 clustered with several reference strains of D. eres (Supplementary figure). To fulfil Koch's postulates, pathogenicity tests were performed on 1-year-old blueberry potted plants cv. Draper and Duke. A small piece of the bark tissue was removed with a sterile-bladed scalpel to expose the cambium. Mycelium plugs (5 mm diameter), obtained from 10-day-old cultures of the strains CVG1130 and CVG1131, were placed with the mycelium in contact with the internal plant tissues. Three plants were used for each isolate and the inoculation points were sealed with Parafilm®. The same number of plants treated with sterile PDA plugs were used as control. Plants were placed in a growth chamber at 25°C for 3 weeks. After this period, symptoms similar to those observed in the field appeared on the inoculated plants, while control plants remained healthy. A fungus with the same morphological characteristics of D. eres was reisolated from inoculated plants and identified by sequencing the tub2 gene to confirm Koch's postulates. Diaporthe eres was previously reported on different Vaccinium spp. in Chile, Lithuania, the Netherlands and the U.S.A. (Farr and Rossman, 2022). To our knowledge, this is the first report of D. eres associated with stem blight and dieback of highbush blueberry in Italy. Duke and Draper are among the most cultivated blueberry cultivars in Piedmont, where the spread of D. eres could represent a serious threat.

First Report of Gray Leaf Spot Caused by Pyricularia oryzae on Common Millet in Italy

Common millet (Panicum miliaceum L.) is a niche crop cultivated in Italy for its high nutritional and gluten-free characteristics. These aspects combined with its sustainability and adaptability to paddy soils make it relevant in crop rotation with rice in some organic farms in Northwestern Italy. In September 2021, in a farm producing organic rice located in Rovasenda (VC), Italy (GPS: 45°54'82"N, 8°.31'96"E), plants of millet (var. San Marino), sown on July 1st and almost at physiological maturity, were observed with gray leaf spot symptoms with an incidence of 50% in a 12.5 ha field cultivated in a yearly rotation with rice. Oval shape lesions (between 1 and 5 cm long and 0.5 to1 cm wide) with a light gray colored centers and dark reddish-brown edges were observed on the length of the leaf blade. Gray colonies producing conidia morphologically like Pyricularia developed from 140 symptomatic leaf fragments with a 2% frequency. Monosporic cultures were obtained from five colonies and were grown on Potato Dextrose Agar for morphological and molecular identification. The colonies showed gray, fluffy mycelium, with a smooth margin, with a radius of 28 to 30 mm after 10 days at 28°C. The isolates produced hyaline, pyriform, and 2-septate conidia 17.9 to 33.5 µm (average 25.7 µm) long and 8.3 to 11.7 µm (average 10. µm) wide (n=50) on PDA. Conidiophores were solitary, erect, straight, or curved, septate, and measured 80.2 to 221.3 µm (average 150.7 µm) long and 3.6 to 5.8 µm (average 4.7 µm) wide (n=50). The molecular identification of one single-conidia isolate was confirmed by PCR and sequence comparison of the region of the transposon Pot2 (Harmon et al., 2003). BLASTn searches of GenBank using transposon Pot2 (ON843711) representative isolate 21-03-C, revealed 99.79% identity to P. oryzae (Syn. Magnaporthe oryzae) isolate MD1 (MK608664). Pathogenicity tests were carried out by suspending conidia from a 14-days old culture on PDA in sterile water at a concentration of 1×105 CFU/ml. Twenty seeds of P. miliaceum were sown in pots filled with a steamed mix of white peat and perlite, 80:20 v/v, and maintained at 28°C under a 12 hours day/night light cycle. Diseased leaves of 10 plants were inoculated by aspersion of 10 ml of the conidial suspension of isolate 21-03-C 2 weeks after the sowing (Harmon et al.; 2003). Plants were incubated in a near moisture-saturated environment in plastic bags at 28°C for 72h, after which symptoms were visually assessed. Ten control plants, inoculated with 10 ml of sterile distilled water remained healthy. P. oryzae was reisolated from leaves showing oblong, whitish lesions, surrounded by light brown margins and identified by resequencing of transposon Pot2. P. oryzae has been already reported on millet in South Korea as causal agent of blast (Klaubauf et al.; 2014). To our knowledge, this is the first report of P. oryzae as a pathogen of millet in Italy and in Europe. Further studies should be conducted to characterize these millet isolates by assessing their virulence on Oryza sativa and the implications in the adoption of P. miliaceum in rotation with rice, to prevent possible carry over of the pathogen on the main crop.

Do the ends justify the means? Impact of drought progression rate on stress response and recovery in Vitis vinifera

Plants are frequently exposed to prolonged and intense drought events. To survive, species must implement strategies to overcome progressive drought while maintaining sufficient resources to sustain the recovery of functions. Our objective was to understand how stress rate development modulates energy reserves and affects the recovery process. Grenache Vitis vinifera cultivar was exposed to either fast-developing drought (within few days; FDD), typical of pot experiments, or slow-developing drought (few weeks, SDD), more typical for natural conditions. FDD was characterized by fast (2-3 days) stomatal closure in response to increased stress level, high abscisic acid (ABA) accumulation in xylem sap (>400 μg L^-1 ) without the substantial changes associated with stem priming for recovery (no accumulation of sugar or drop in xylem sap pH). In contrast, SDD was characterized by gradual stomatal closure, low ABA accumulation (<100 μg L^-1 ) and changes that primed the stem for recovery (xylem sap acidification from 6 to 5.5 pH and sugar accumulation from 1 to 3 g L^-1 ). Despite FDD and SDD demonstrating similar trends over time in the recovery of stomatal conductance, they differed in their sensitivity to xylem ABA. Grenache showed near-isohydric and near-anisohydric behavior depending on the rate of drought progression, gauging the risk between hydraulic integrity and photosynthetic gain. The isohydry observed during FDD could potentially provide protection from large sudden swings in tension, while transitioning to anisohydry during SDD could prioritize the maintenance of photosynthetic activity over hydraulic security.

Improving sustainable hydrogen production from green waste: [FeFe]-hydrogenases quantitative gene expression RT-qPCR analysis in presence of autochthonous consortia

BACKGROUND

Bio-hydrogen production via dark fermentation of low-value waste is a potent and simple mean of recovering energy, maximising the harvesting of reducing equivalents to produce the cleanest fuel amongst renewables. Following several position papers from companies and public bodies, the hydrogen economy is regaining interest, especially in combination with circular economy and the environmental benefits of short local supply chains, aiming at zero net emission of greenhouse gases (GHG). The biomasses attracting the largest interest are agricultural and urban green wastes (pruning of trees, collected leaves, grass clippings from public parks and boulevards), which are usually employed in compost production, with some concerns over the GHG emission during the process. Here, an alternative application of green wastes, low-value compost and intermediate products (partially composted but unsuitable for completing the process) is studied, pointing at the autochthonous microbial consortium as an already selected source of implementation for biomass degradation and hydrogen production. The biocatalysts investigated as mainly relevant for hydrogen production were the [FeFe]-hydrogenases expressed in Clostridia, given their very high turnover rates.

RESULTS

Bio-hydrogen accumulation was related to the modulation of gene expression of multiple [FeFe]-hydrogenases from two strains (Clostridium beijerinckii AM2 and Clostridium tyrobutyricum AM6) isolated from the same waste. Reverse Transcriptase quantitative PCR (RT-qPCR) was applied over a period of 288 h and the RT-qPCR results showed that C. beijerinckii AM2 prevailed over C. tyrobutyricum AM6 and a high expression modulation of the 6 different [FeFe]-hydrogenase genes of C. beijerinckii in the first 23 h was observed, sustaining cumulative hydrogen production of 0.6 to 1.2 ml H₂/g VS (volatile solids). These results are promising in terms of hydrogen yields, given that no pre-treatment was applied, and suggested a complex cellular regulation, linking the performance of dark fermentation with key functional genes involved in bio-H₂ production in presence of the autochthonous consortium, with different roles, time, and mode of expression of the involved hydrogenases.

CONCLUSIONS

An applicative outcome of the hydrogenases genes quantitative expression analysis can be foreseen in optimising (on the basis of the acquired functional data) hydrogen production from a nutrient-poor green waste and/or low added value compost, in a perspective of circular bioeconomy.

First report of Fusarium commune causing root and crown rot on maize in Italy

Maize (Zea mays L.) is a cereal crop of great economic importance in Italy; production is currently of 62,587,469 t, with an area that covers 628,801 ha, concentrated in northern Italy (ISTAT 2020). Fusarium species are associated with root and crown rot causing failures in crop establishment under high soil moisture. In 2019 maize seedlings collected in a farm located in San Zenone degli Ezzelini (VI, Italy) showed root and crown rot symptoms with browning of the stem tissues, wilting of the seedling, and collapsing due to the rotting tissues at the base of the stem. The incidence of diseased plants was approximately 15%. Seedlings were cleaned thoroughly from soil residues under tap water. Portions (about 3-5 mm) of tissue from roots and crowns of the diseased plants were cut and surface disinfected with a water solution of NaClO at 0.5% for 2 minutes and rinsed in sterile H20. The tissue fragments were plated on Potato Dextrose Agar (PDA) amended with 50 mg/l of streptomycin sulfate and incubated for 48-72 hours at 25oC. Over the 80 tissue fragments plated, 5% were identified as Fusarium verticillioides, 60% as Fusarium spp., 35% developed saprophytes. Fusarium spp. isolates that showed morphological characteristics not belonging to known pathogenic species on maize were selected and used for further investigation while species belonging to F. oxysporum were discarded. Single conidia of the Fusarium spp. colonies were cultured on PDA and Carnation Leaf Agar (CLA) for pathogenicity tests, morphological and molecular identification. The colonies showed white to pink, abundant, densely floccose to fluffy aerial mycelium. Colony reverse showed light violet pigmentation, in rings on PDA. On CLA the isolates produced slightly curved macronidia with 3 septa 28.1 - 65.5 µm long and 2.8-6.3 µm wide (n=50). Microconidia were cylindrical, aseptate, 4.5 -14.0 µm long and 1.5-3.9 µm wide (n=50). Spherical clamydospores were 8.8 ± 2.5 µm size (n=30), produced singly or in pairs on the mycelium, according to the description by Skovgaard et al. (2003) for F. commune. The identity of two single-conidia strains was confirmed by sequence comparison of the translation elongation factor-1α (tef-1α), and RNA polymerase II subunit (rpb2) gene fragments (O'Donnell et al. 2010). BLASTn searches of GenBank, and Fusarium-ID database, using the partial tef-1α (MW419921, MW419922) and rpb2 (MW419923, MW419924) sequences of representative isolate DB19lug07 and DB19lug20, revealed 99% identity for tef-1α and 100% identity to F. commune NRRL 28387(AF246832, AF250560). Pathogenicity tests were carried out by suspending conidia from a 10-days old culture on PDA in sterile H2O to 5×104 CFU/ml. Fifty seeds were immersed in 50 ml of the conidial suspension of each isolate for 24 hours and in sterile water (Koch et al. 2020). The seeds were drained, dried at room temperature, and sown in trays filled with a steamed mix of white peat and perlite, 80:20 v/v, and maintained at 25°C and RH of 80-85% for 14 days with 12 hours photoperiod. Seedlings were extracted from the substrate, washed under tap water, and observed for the presence of root and crown rots like the symptoms observed on the seedlings collected in the field. Control seedlings were healthy and F. commune was reisolated from the symptomatic ones and identified by resequencing of tef-1α gene. F. commune has been already reported on maize (Xi et al. 2019) and other plant species, like soybean (Ellis et al. 2013), sugarcane (Wang et al. 2018), potato (Osawa et al. 2020), indicating that some attention must be paid in crop rotation and residue management strategies. To our knowledge this is the first report of F. commune as a pathogen of maize in Italy. References Ellis M L et al. 2013. Plant Disease, 97, doi: 10.1094/PDIS-07-12-0644-PDN. ISTAT. 2020. http://dati.istat.it/Index.aspx?QueryId=33702. Accessed December 28, 2020. Koch, E. et al. 2020. Journal of Plant Diseases and Protection. 127, 883-893 doi: 10.1007/s41348-020-00350-w O'Donnell K et al. 2010. J. Clin. Microbiol. 48:3708. https://doi.org/10.1128/JCM.00989-10 Osawa H et al. 2020. Journal of General Plant Pathology, doi.org/10.1007/s10327-020-00969-5. Skovgaard K 2003. Mycologia, 95:4, 630-636, DOI: 10.1080/15572536.2004.11833067. Wang J et al. 2018. Plant Disease, 102, doi/10.1094/PDIS-07-17-1011-PDN Xi K et al. 2019. Plant Disease, 103, doi/10.1094/PDIS-09-18-1674-PDN.

First Report of Brown Rot Caused by Monilinia polystroma on Apple in Italy

Brown rot is a common apple disease in Italy, caused by Monilinia fructicola, M. laxa and M. fructigena (Martini et al. 2013). In September 2020, in a 'Jeromine' apple orchard under integrated pest management located in Scarnafigi (44°39'N, 7°33'E, north-western of Italy), fruits (8.6%) showing brown to blackish firm lesions (6.0 to 8.0 cm diameter) were observed. In some fruits, rots were covered by yellowish stromata. Two isolates (MPI1; MPI2) were obtained from two symptomatic apples and cultured on potato dextrose agar (PDA) for 7 days at 25°C in 12-h light/12-h dark regime. A white-to-greyish mycelium with slightly undulate margins and irregular, black stromata developed on PDA after 12 days incubation. Conidia, observed in branched monilioid chains, (Suppl. Fig. 1) were one-celled, globose, limoniform, hyaline, 38 to 58 μm (mean: 48) × 20 to 44 μm (mean: 33). Based on morphology, the isolates were tentatively identified as Monilinia polystroma (G.C.M. Leeuwen) Kohn. A polymerase chain reaction with primers ITS1 and ITS4 was performed on internal transcribed spacer (ITS) region 1 and 2 and 5.8S gene. The sequenced amplicons (435 bp - 445 bp; GenBank Accession No. MW600854; MW600855) showed 100% identity to the reference isolate of M. polystroma (HQ846944) and to other isolates from apples (AM937114; JX315717) and plum (GU067539). The ITS region of M. polystroma had five nucleotides to distinguish it from the closest species M. fructigena (Zhu et al. 2016; MH862738) (Suppl. Fig. 2). The pathogenicity of both isolates was tested on mature 'Jeromine' apples (10.1% total soluble solids). Three replicates of six apples per isolate were surface disinfected with 1% NaClO. A mycelial plug (5 mm) from colony grown on PDA was inserted using a cork borer into a hole (6 mm) in each fruit (Vasić et al. 2016). Apples inoculated with sterile PDA plugs were used as control. Fruits were placed at 22 ± 1 °C, 85% relative humidity and 12 h light/12 h dark regime. Lesion size was measured after 3, 6 and 9 days of incubation. All inoculated fruits developed typical brown rot symptoms 6 days after inoculation and yellowish stromata appeared on the surface; control fruit remained healthy (Suppl. Fig. 3). The virulence of both isolates was statistically similar (Suppl. Table 1). M. polystroma was reisolated from all inoculated fruits and confirmed by molecular methods. This is the first report of M. polystroma on apple in Italy. M. polystroma was previously reported on apple in Hungary (Petróczy et al. 2009), on apricot in Switzerland (Hilber-Bodmer et al. 2012), on peach and pear in Italy (Martini et al. 2014; 2015), on plum in China (Zhu et al. 2016), and on apple in Serbia (Vasić et al. 2018). The emergence of this pathogen for pome and stone fruit production in Europe stimulates to study its biology and epidemiology, and its fitness and management, as compared to the other endemic Monilinia species.

Genetic Diversity and Pathogenicity of Botryosphaeriaceae Species Associated with Symptomatic Citrus Plants in Europe

This study represents the first survey studying the occurrence, genetic diversity, and pathogenicity of Botryosphaeriaceae species associated with symptomatic citrus species in citrus-production areas in five European countries. Based on morphological features and phylogenetic analyses of internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA), translation elongation factor 1-alpha (TEF1) and β-tubulin (TUB2) genes, nine species were identified as belonging to the genera Diplodia, Dothiorella, Lasiodiplodia, and Neofusicoccum. Isolates of Neofusicoccum parvum and Diplodia pseudoseriata were the most frequently detected, while Dothiorella viticola had the widest distribution, occurring in four of the five countries sampled. Representative isolates of the nine Botryosphaeriaceae species used in the pathogenicity tests caused similar symptoms to those observed in nature. Isolates assayed were all re-isolated, thereby fulfilling Koch's postulates. Isolates of Diplodia pseudoseriata and Diplodia olivarum are recorded for the first time on citrus and all species found in our study, except N. parvum, are reported for the first time on citrus in Europe.

Characterization of Alternaria Species Associated with Heart Rot of Pomegranate Fruit

This study was aimed at identifying Alternaria species associated with heart rot disease of pomegranate fruit in southern Italy and characterizing their mycotoxigenic profile. A total of 42 Alternaria isolates were characterized. They were obtained from pomegranate fruits with symptoms of heart rot sampled in Apulia and Sicily and grouped into six distinct morphotypes based on macro- and microscopic features. According to multigene phylogenetic analysis, including internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a SCAR marker (OPA10-2), 38 isolates of morphotypes 1 to 5 were identified as Alternaria alternata, while isolates of morphotype 6, all from Sicily, clustered within the Alternaria arborescens species complex. In particular, isolates of morphotype 1, the most numerous, clustered with the ex-type isolate of A. alternata, proving to belong to A. alternata. No difference in pathogenicity on pomegranate fruits was found between isolates of A. alternata and A. arborescens and among A. alternata isolates of different morphotypes. The toxigenic profile of isolates varied greatly: in vitro, all 42 isolates produced tenuazonic acid and most of them other mycotoxins, including alternariol, alternariol monomethyl ether, altenuene and tentoxin.

Monitoring and Surveillance of Aerial Mycobiota of Rice Paddy through DNA Metabarcoding and qPCR

The airborne mycobiota has been understudied in comparison with the mycobiota present in other agricultural environments. Traditional, culture-based methods allow the study of a small fraction of the organisms present in the atmosphere, thus missing important information. In this study, the aerial mycobiota in a rice paddy has been examined during the cropping season (from June to September 2016) using qPCRs for two important rice pathogens (Pyricularia oryzae and Bipolaris oryzae) and by using DNA metabarcoding of the fungal ITS region. The metabarcoding results demonstrated a higher alpha diversity (Shannon–Wiener diversity index H′ and total number of observed species) at the beginning of the trial (June), suggesting a higher level of community complexity, compared with the end of the season. The main taxa identified by HTS analysis showed a shift in their relative abundance that drove the cluster separation as a function of time and temperature. The most abundant OTUs corresponded to genera such as Cladosporium, Alternaria, Myrothecium, or Pyricularia. Changes in the mycobiota composition were clearly dependent on the average air temperature with a potential impact on disease development in rice. In parallel, oligotyping analysis was performed to obtain a sub-OTU identification which revealed the presence of several oligotypes of Pyricularia and Bipolaris with relative abundance changing during monitoring.

Development of a Sensitive TaqMan qPCR Assay for Detection and Quantification of Venturia inaequalis in Apple Leaves and Fruit and in Air Samples

A TaqMan quantitative PCR (qPCR) assay based on the translation elongation factor 1-α gene was developed for the quantification of Venturia inaequalis in leaves and fruits of Malus × domestica and in spore trap samples. The designed primers and hydrolysis probe amplified a specific 86-bp fragment for V. inaequalis. The specificity of the assay was tested using 35 strains of V. inaequalis and 20 different fungal species, including common pathogens of apple and other species of Venturia. The limit of detection was 20 fg, which is lower than a single genome of V. inaequalis. The selectivity of the assay was tested using DNA from three cultivars of Malus × domestica, and no influence on pathogen amplification was found. The assay was also validated for repeatability and reproducibility. With this assay, it was possible to detect and quantify V. inaequalis in four cultivars (Ambrosia, Florina, Golden Delicious, and Mondial Gala) in both symptomatic and asymptomatic leaves and in symptomatic Golden Delicious apple fruit stored for 2 months. Furthermore, the assay was successfully tested on spore trap samples originating from apple orchards. The quantification of the molecular assay when compared with the estimated number of V. inaequalis cells, using an optical microscope, showed a correlation coefficient of 0.8186. The developed technique could be used to detect V. inaequalis in asymptomatic samples without any cross-reaction with other fungal species. Furthermore, to improve the efficacy of disease management with a timely application of fungicides, this assay could be used for the analysis of spore trap samples by using an implemented extraction method.

Biological and molecular interplay between two viruses and powdery and downy mildews in two grapevine cultivars

Grapevine may be affected simultaneously by several pathogens whose complex interplay is largely unknown. We studied the effects of infection by two grapevine viruses on powdery mildew and downy mildew development and the molecular modifications induced in grapevines by their multiple interactions. Grapevine fanleaf virus (GFLV) and grapevine rupestris stem pitting-associated virus (GRSPaV) were transmitted by in vitro-grafting to Vitis vinifera cv Nebbiolo and Chardonnay virus-free plantlets regenerated by somatic embryogenesis. Grapevines were then artificially inoculated in the greenhouse with either Plasmopara viticola or Erysiphe necator spores. GFLV-infected plants showed a reduction in severity of the diseases caused by powdery and downy mildews in comparison to virus-free plants. GFLV induced the overexpression of stilbene synthase genes, pathogenesis-related proteins, and influenced the genes involved in carbohydrate metabolism in grapevine. These transcriptional changes suggest improved innate plant immunity, which makes the GFLV-infected grapevines less susceptible to other biotic attacks. This, however, cannot be extrapolated to GRSPaV as it was unable to promote protection against the fungal/oomycete pathogens. In these multiple interactions, the grapevine genotype seemed to have a crucial role: in 'Nebbiolo', the virus-induced molecular changes were different from those observed in 'Chardonnay', suggesting that different metabolic pathways may be involved in protection against fungal/oomycete pathogens. These results indicate that complex interactions do exist between grapevine and its different pathogens and represent the first study on a topic that still is largely unexplored.

Alternaria Leaf Spot Caused by Alternaria Species: An Emerging Problem on Ornamental Plants in Italy

Serious outbreaks of Alternaria leaf spot and plant decay have recently been recorded on several ornamental plants in the Biella Province (Northern Italy). Twenty-two fungal isolates were obtained from Alternaria infected plant tissues from 13 ornamental hosts. All the isolates were identified morphologically as small-spored Alternaria species. Multilocus sequence typing, carried out by means of ITS, rpb2, tef1, endoPG, Alt a 1, and OPA10-2, assigned 19 isolates as Alternaria alternata, two isolates as belonging to the Alternaria arborescens species complex, and one isolate as an unknown Alternaria sp. Haplotype analyses of ornamental and reference A. alternata isolates from 12 countries identified 14 OPA10-2 and 11 endoPG haplotypes showing a relatively high haplotype diversity. A lack of host specialization or geographic distribution was observed. The host range of the studied A. alternata isolates expanded in cross-pathogenicity assays, and more aggressiveness was frequently observed on the experimental plants than on the host plants from which the fungal isolates were originally isolated. High disease severity, population expansion, intraspecies diversity, and increased range of experimental hosts were seen in the emergence of Alternaria disease on ornamentals. More epidemiological and molecular studies should be performed to better understand these diseases, taking into consideration factors such as seed transmission and ongoing climate changes.

Effect of Drying Temperatures and Exposure Times on Aspergillus flavus Growth and Aflatoxin Production on Artificially Inoculated Hazelnuts

ABSTRACT

Aspergillus flavus may colonize hazelnuts and produce aflatoxins in the field and during storage. The main purpose of this study was to investigate the influence of drying temperature and exposure times on the viability of A. flavus and its ability to produce aflatoxins during the drying process and storage. Hazelnuts were inoculated with A. flavus and dried at different temperatures to reach 6% moisture content and a water activity (aw) of 0.71, a commercial requirement to avoid fungal development and aflatoxin contamination. Hazelnuts were dried at 30, 35, 40, 45, and 50°C and subsequently stored at 25°C for 14 days. After drying at 30, 35, and 40°C, increased amounts of A. flavus were evident, with the highest concentration occurring after drying at 35°C ([6.1 ± 2.4] × 106A. flavus CFU/g). At these temperatures, aflatoxins were detected only at 30 and 35°C. Aflatoxins, however, were present at higher levels after drying at 30°C, with concentrations of 1.93 ± 0.77 μg/g for aflatoxin B1 (AFB1) and 0.11 ± 0.04 μg/g for aflatoxin B2 (AFB2). After 14 days of storage, the highest A. flavus concentration and the highest levels of mycotoxins were detected in samples treated at 35°C ([8.2 ± 2.1] × 107A. flavus CFU/g and 9.30 ± 1.58 μg/g and 0.89 ± 0.08 μg/g for AFB1 and AFB2, respectively). In hazelnuts dried at 45 or 50°C, no aflatoxins were found either after drying or storage, and a reduction of A. flavus viable conidia was observed, suggesting that a shorter and warmer drying is essential to guarantee nut safety. The lowest temperature that guarantees the lack of aflatoxins should be selected to maintain the organoleptic quality of hazelnuts. Therefore, 45°C should be the recommended drying temperature to limit A. flavus growth and aflatoxin contamination on hazelnuts.

HIGHLIGHTS

A Compost Treatment Acts as a Suppressive Agent in Phytophthora capsici - Cucurbita pepo Pathosystem by Modifying the Rhizosphere Microbiota

Phytophthora capsici Leonian (PHC) is a filamentous pathogen oomycete that causes root, fruit, foliar and crown rot over a wide host range, including the economically and nutritionally important summer squash (Cucurbita pepo var. cylindrica L.) crop. PHC chemical control strategies are difficult to adopt, due to the limited number of registered chemicals that are permitted and the scalar harvest system. For these reasons, other strategies, such as the use of waste-based composts that can act as suppressive agents against several soilborne pathogens, have been studied intensively. It is well known that compost's microbiota plays an important role to confer its suppressive ability. In this study, four different composts were analyzed with both 16S rRNA gene and 18S rRNA gene real-time PCR amplification and with 26S gene amplicon-based sequencing; the total abundance of the bacterial and fungal communities was found to be higher compared to literature, thus confirming that the four composts were a good inoculum source for agricultural applications. The core mycobiota was mainly composed of 31 genera; nevertheless, it was possible to observe a clear predominance of the same few taxa in all the composts. The four composts were then tested, at different concentrations (1-10-20% v/v), to establish their ability to confer suppressiveness to the Phytophthora capsici (PHC) - Cucurbita pepo pathosystem in controlled greenhouse pot trials. A total of 12 compost mixtures were considered, and of these, one (Trichoderma-enriched compost at 10% v/v) was able to statistically reduce the disease incidence caused by PHC (by 50% compared to the untreated control). Hence, the microbiota composition of the most effective compost treatment was investigated and compared with untreated and chemical (metalaxyl) controls. Mycobiota sequencing showed genera differences between the three treatments, with relative abundances of several fungal genera that were significantly different among the samples. Moreover, PCA analyses clustered the compost treatment differently from the chemical and the untreated controls. These findings suggest that suppressive activity of a compost is strictly influenced by its microbiota and the applied dosage, but the ability to induce a shaping in the rhizosphere microbial composition is also required.

Characterization of Colletotrichum ocimi Population Associated with Black Spot of Sweet Basil (Ocimum basilicum) in Northern Italy

Black spot is a major foliar disease of sweet basil (Ocimum basilicum) present in a typical cultivation area of northern Italy, including the Liguria and southern Piedmont regions, where this aromatic herb is an economically important crop. In this study, 15 Colletotrichum isolates obtained from sweet basil plants with symptoms of black spot sampled in this area were characterized morphologically and by nuclear DNA analysis using internal transcribed spacers (ITS) and intervening 5.8S nrDNA as well as part of the β-tubulin gene (TUB2) regions as barcode markers. Analysis revealed all but one isolate belonged to the recently described species C. ocimi of the C. destructivum species complex. Only one isolate was identified as C. destructivum sensu stricto (s.s.). In pathogenicity tests on sweet basil, both C. ocimi and C. destructivum s.s. isolates incited typical symptoms of black spot, showing that although C. ocimi prevails in this basil production area, it is not the sole causal agent of black spot in northern Italy. While no other hosts of C. ocimi are known worldwide, the close related species C. destructivum has a broad host range, suggesting a speciation process of C. ocimi within this species complex driven by adaptation to the host.

HPLC-MS/MS Method for the Detection of Selected Toxic Metabolites Produced by Penicillium spp. in Nuts

Penicillium spp. are emerging as producers of mycotoxins and other toxic metabolites in nuts. A HPLC-MS/MS method was developed to detect 19 metabolites produced by Penicillium spp. on chestnuts, hazelnuts, walnuts and almonds. Two extraction methods were developed, one for chestnuts and one for the other three nuts. The recovery, LOD, LOQ and matrix effect were determined for each analyte and matrix. Correlation coefficients were always >99.99%. In walnuts, a strong signal suppression was observed for most analytes and patulin could not be detected. Six strains: Penicillium bialowiezense, P. brevicompactum, P. crustosum, P. expansum, P. glabrum and P. solitum, isolated from chestnuts, were inoculated on four nuts. Chestnuts favored the production of the largest number of Penicillium toxic metabolites. The method was used for the analysis of 41 commercial samples: 71% showed to be contaminated by Penicillium-toxins. Cyclopenin and cyclopenol were the most frequently detected metabolites, with an incidence of 32% and 68%, respectively. Due to the risk of contamination of nuts with Penicillium-toxins, future studies and legislation should consider a larger number of mycotoxins.

Aspergillus fumigatus population dynamics and sensitivity to demethylation inhibitor fungicides in whole-crop corn, high moisture corn and wet grain corn silages

BACKGROUND

Aspergillus fumigatus, the causal agent of aspergillosis in humans, is commonly present as a saprophyte in various organic substrates, such as spoiled silages. Aspergillosis is generally combated with demethylation inhibitor (DMI) fungicides, but the recent appearance of resistant medical and environmental strains made current treatment strategies less reliable. The goal of this study was to determine the evolution of A. fumigatus populations during the ensiling process of whole-crop corn, high moisture corn and wet grain corn, and to monitor the sensitivity of isolates from treated and untreated fields to one medical and one agricultural DMI fungicide.

RESULTS

A. fumigatus was isolated from fresh forage at harvest at rather low concentrations (10²  cfu g^-1 ). The low frequency lingered during the silage process (at 60 and 160 days), whereas it significantly increased during air exposure (at 7 and 14 days of air exposure). Field treatment of corn with a mixture of prothioconazole and tebuconazole did not affect the sensitivity of A. fumigatus isolates. One of 29 isolates from the untreated plot was resistant to voriconazole. A unique amino acid substitution (E427K) was detected in the cyp51A gene of 10 of 12 sequenced isolates, but was not associated with DMI resistance.

CONCLUSION

A. fumigatus significantly increased during aerobic deterioration of ensilaged corn after silo opening, compared with the low presence in fresh corn and during ensiling. Field treatment of corn with DMI fungicides did not affect the sensitivity of A. fumigatus isolates collected from fresh and ensiled corn. © 2019 Society of Chemical Industry.

Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Microbial Ecology and Chemical-Physical Grape Characteristics at Harvest

Viticulture is a cropping system in which treatment against fungal diseases (in particular powdery and downy mildews) can be extremely frequent. Accordingly, a reduction in antimicrobial treatments and the application of environmentally-friendly compounds are becoming increasingly important for a more sustainable viticulture. In addition to their effect against pathogens, the impact of these products on the quality of the grapes is very important for the oenological industries, but unfortunately at present few data are available. We evaluated the effect of the application of biocontrol products and resistance inducers in the vineyard on the mechanical properties, microbial ecology, technological and phenolic maturity of Vitis vinifera "Nebbiolo" grapes at harvest. The yield and vigor of vines were not influenced by the treatments, nor were the production of primary and secondary metabolites. However, the active ingredients influenced the mechanical properties of the skin (hardness and thickness). A significant hardening of the skin was detected when laminarin and chito-oligosaccharides were used, and sulfur induced a thickening of the skin with potential consequences for wine quality. Furthermore, the yeast community present on grape berries was influenced by the treatments. The abundance of Aureobasidium pullulans, the dominant species on the grape berry, changed in response to the compounds used. In addition, Alternaria sp. was reduced in some treatments with a potentially positive effect on the quality and the safety of the grapes. This study provides an overview of the effect of biocontrol products and resistance inducers on microbial ecology and "Nebbiolo" grape quality, contributing to the establishment of more sustainable and effective defense strategies in viticulture.

Expression and role of CYP505A1 in pathogenicity of Fusarium oxysporum f. sp. lactucae

BACKGROUND

Cytochrome P450 enzymes (CYPs) are monooxygenases present in every domain of life. In fungi CYPs are involved in virulence. Fusarium wilt of lettuce, caused by F. oxysporum f. sp. lactucae, is the most serious disease of lettuce. F. oxysporum f.sp. lactucae MSA35 is an antagonistic fungus. Pathogenic formae specialis of F. oxysporum possess a CYP belonging to the new family CYP505. This enzyme hydroxylates saturated fatty acids that play a role in plant defence.

METHODS

Molecular tools were adopted to search for cyp505 gene in MSA35 genome. cyp505 gene expression analysis in pathogenic and antagonistic Fusarium was performed. The enzyme was expressed in its recombinant form and used for catalytic reactions with fatty acids, the products of which were characterized by mass spectrometry analysis.

RESULTS

A novel MSA35 self-sufficient CYP505 is differentially expressed in antagonistic and pathogenic F. oxysporum. Its expression is induced by the host plant lettuce in both pathogenesis and antagonism during the early phase of the interaction, while it is silenced during the late phase only in antagonistic Fusarium. Mass-spectrometry investigations proved that CYP505A1 mono-hydroxylates lauric, palmitic and stearic acids.

CONCLUSIONS

The ability of CYP505A1 to oxidize fatty acids present in the cortical cell membranes together with its differential expression in its Fusarium antagonistic form point out to the possibility that this enzyme is associated with Fusarium pathogenicity in lettuce.

GENERAL SIGNIFICANCE

The CYP505 clan is present in pathogenic fungal phyla, making CYP505A1 enzyme a putative candidate as a new target for the development of novel antifungal molecules.

Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew

The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera "Nebbiolo" and "Moscato" cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using Biolog^TM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, "Moscato" plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the "Nebbiolo" plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application.

Rapid Detection of Monilinia fructicola and Monilinia laxa on Peach and Nectarine using Loop-Mediated Isothermal Amplification

Monilinia laxa and M. fructicola are two causal agents of brown rot, one of the most important diseases in stone fruit. Two species cause blight on blossoms and twigs and brown rot on fruit in pre- and postharvest. Both species are distributed worldwide in North and South America, Australia, and Japan. In Europe, M. laxa is endemic, while M. fructicola was introduced in 2001 and it is now widespread in several countries. Currently, both species coexist in European stone fruit orchards. Monilinia spp. overwinter in cankers and mummified fruit. Mummy monitoring during winter permits growers to understand which species of Monilinia will be prevalent in an orchard during the following season, permitting planning of an appropriate crop protection. Traditionally, the identification has been carried out using morphological features and even with polymerase chain reaction (PCR)-based assays that requires time and well-equipped laboratories. In this study, two isothermal-based methods were designed to identify these pathogens in a faster way than using traditional methods. The loop-mediated amplification (LAMP) assays were validated on some isolates of Monilinia spp. coming from the mummy monitoring according to the international European and Mediterranean Plant Protection Organization standard (PM7/98), taking into account specificity, sensitivity, repeatability, and reproducibility. The sensitivity of both assays was checked by monitoring (at different time points) two nectarine varieties artificially inoculated and stored at two different temperatures. The reliability of both LAMP assays against the quantification of the inoculum was compared with previously published quantitative PCR assays. Both LAMP methods were able to detect a low number of cells. These LAMP methods could be a useful tool for monitoring brown rot causal agents in the field and during postharvest.

Ready-to-Eat Salad Crops: A Plant Pathogen's Heaven

The ready-to-eat salad sector, also called fresh-cut or bagged salads, is a fast-growing segment of the fresh-food industry. The dynamism and specialization of this sector, together with the lack of adequate crop rotation, the globalization of the seed market, and climate change, are the main causes of the development of many new diseases that cause severe production losses. Newly detected diseases of the most important crops grown (lettuce, wild and cultivated rocket, lamb's lettuce, chicory, endive, basil, spinach, and Swiss chard) are critically discussed. The management of these diseases represents a formidable challenge, since few fungicides are registered on these minor-use crops. An interesting feature of the ready-to-eat salad sector is that most crops are grown under protection, often in soilless systems, which provide an environment helpful to the implementation of innovative control methods. Current trends in disease management are discussed, with special focus on the most sustainable practices.

Priming xylem for stress recovery depends on coordinated activity of sugar metabolic pathways and changes in xylem sap pH

Some plant species are capable of significant reduction of xylem embolism during recovery from drought despite stem water potential remains negative. However, the functional biology underlying this process is elusive. We subjected poplar trees to drought stress followed by a period of recovery. Water potential, hydraulic conductivity, gas exchange, xylem sap pH, and carbohydrate content in sap and woody stems were monitored in combination with an analysis of carbohydrate metabolism, enzyme activity, and expression of genes involved in sugar metabolic and transport pathways. Drought resulted in an alteration of differential partitioning between starch and soluble sugars. Upon stress, an increase in the starch degradation rate and the overexpression of sugar symporter genes promoted the efflux of disaccharides (mostly maltose and sucrose) to the apoplast. In turn, the efflux activity of the sugar-proton cotransporters caused a drop in xylem pH. The newly acidic environment induced the activity of apoplastic invertases leading to the accumulation of monosaccharides in the apoplast, thus providing the main osmoticum necessary for recovery. During drought and recovery, a complex network of coordinated molecular and biochemical signals was activated at the interface between xylem and parenchyma cells that appeared to prime the xylem for hydraulic recovery.

Emergence of Leaf Spot Disease on Leafy Vegetable and Ornamental Crops Caused by Paramyrothecium and Albifimbria Species

The genera Paramyrothecium and Albifimbria have been established from the former genus Myrothecium and they generally comprise common soil-inhabiting and saprophytic fungi. Within these genera, only two fungi have been recognized as phytopathogenic thus far: P. roridum and A. verrucaria, both of which cause necrotic leaf spots and plant collapse. Severe leaf necrosis and plant decay have been observed in Northern and Southern Italy on leafy vegetable crops. Thirty-six strains of Paramyrothecium- and Albifimbria-like fungi were isolated from affected plants belonging to eight different species. Based on morphological characteristics, 19 strains were assigned to A. verrucaria, whereas the remaining strains, which mostly resembled Paramyrothecium-like fungi, could not be identified precisely. Molecular characterization of six loci (internal transcribed spacer [ITS], β-tubulin [tub2], calmodulin [cmdA], translation elongation factor 1-alpha [tef1], large subunit ribosomal RNA [LSU], and mitochondrial ATP 6synthase 6 [ATP6]) of the 36 new isolates and three previously ITS-characterized isolates assigned all strains to four species: A. verrucaria, P. roridum, P. foliicola, and P. nigrum. Single and concatenated phylogenetic analyses were conducted, and they clearly distinguished the isolated fungi into four different groups. A. verrucaria, P. roridum, P. foliicola, and P. nigrum were able to induce leaf necrosis singly, and they were confirmed to be the causal agents of the leaf spot disease through pathogenicity assays. The involvement of fungi previously considered saprophytic (i.e., P. foliicola and P. nigrum) in the development of plant disease for the first time deserves particular attention because of the possibility of their transmission by seeds and the limited knowledge of their management with chemicals.

Influence of different biological control agents and compost on total and nitrification-driven microbial communities at rhizosphere and soil level in a lettuce - Fusarium oxysporum f. sp. lactucae pathosystem

AIMS

The response of rhizosphere and bulk soil indigenous microbial communities focusing on nitrifiers was evaluated after the application of different biological control agents (BCAs; Bacillus, Trichoderma, Pseudomonas) and compost in controlling lettuce Fusarium wilt.

METHODS AND RESULTS

Experiments were conducted 'in situ' over two lettuce cropping seasons. Total fungal, bacterial and archaeal populations and the nitrifiers were analysed using quantitative polymerase chain reaction method. The pathogen, Fusarium oxysporum forma specialis lactucae (FOL), Bacillus, Trichoderma and Pseudomonas and three antifungal genes (chiA, 2,4-diacetylphloroglucinol - phlD and HCN synthase - hcnAB genes) were also assessed. Quantitative data were corroborated with disease severity (DS), potential nitrification activity and soil chemical parameters. The application of BCAs and compost resulted in the disease reduction by as much as 69%, confirmed by significant negative correlations between Bacillus subtilis, Trichoderma and Pseudomonas sp. abundances and DS. The FOL presence in the untreated control resulted in the nitrifiers niche differentiation.

CONCLUSIONS

The used treatments were efficient against Fusarium wilt and did not influence negatively the nontarget microbial communities.

SIGNIFICANCE AND IMPACT OF THE STUDY

The use of BCAs and compost appears as an effective and safe strategy to implement sustainable agricultural practices.

Differentiation of Pythium spp. from vegetable crops with molecular markers and sensitivity to azoxystrobin and mefenoxam

BACKGROUND

Pythium species attack various vegetable crops causing seed, stem and root rot, and 'damping-off' after germination. Pythium diseases are prevalently controlled by two classes of fungicides, QoIs with azoxystrobin and phenlyamides with mefenoxam as representatives. The present study aimed to test the sensitivity of six Pythium species from different vegetable crops to azoxystrobin and mefenoxam and differentiating species based on ITS, cytochrome b and RNA polymerase I gene sequences.

RESULTS

The inter- and intra-species sensitivity to azoxystrobin was found to be stable, with the exception of one Pythium paroecandrum isolate, which showed reduced sensitivity and two cytochrome b amino acid changes. For mefenoxam, the inter-species sensitivity was quite variable and many resistant isolates were found in all six Pythium species, but no RNA polymerase I amino acid changes were observed in them. ITS and cytochrome b phylogenetic analyses permitted a clear separation of Pythium species corresponding to globose- and filamentous-sporangia clusters.

CONCLUSION

The results document the necessity of well-defined chemical control strategies adapted to different Pythium species. Since the intrinsic activity of azoxystrobin among species was stable and no resistant isolates were found, it may be applied without species differentiation, provided it is used preventatively to also control highly aggressive isolates. For a reliable use of mefenoxam, precise identification and sensitivity tests of Pythium species are crucial because its intrinsic activity is variable and resistant isolates may exist. Appropriate mixtures and/or alternation of products may help to further delay resistance development. © 2018 Society of Chemical Industry.

Combined Effect of CO2 and Temperature on Wheat Powdery Mildew Development

The effect of simulated climate changes by applying different temperatures and CO2 levels was investigated in the Blumeria graminis f. sp. tritici/wheat pathosystem. Healthy and inoculated plants were exposed in single phytotrons to six CO2+temperature combinations: (1) 450 ppm CO2/18-22°C (ambient CO2 and low temperature), (2) 850 ppm CO2/18-22°C (elevated CO2 and low temperature), (3) 450 ppm CO2/22-26°C (ambient CO2 and medium temperature), (4) 850 ppm CO2/22-26°C (elevated CO2 and medium temperature), (5) 450 ppm CO2/26-30°C (ambient CO2 and high temperature), and (6) 850 ppm CO2/26-30°C (elevated CO2 and high temperature). Powdery mildew disease index, fungal DNA quantity, plant death incidence, plant expression of pathogenesis-related (PR) genes, plant growth parameters, carbohydrate and chlorophyll content were evaluated. Both CO2 and temperature, and their interaction significantly influenced powdery mildew development. The most advantageous conditions for the progress of powdery mildew on wheat were low temperature and ambient CO2. High temperatures inhibited pathogen growth independent of CO2 conditions, and no typical powdery mildew symptoms were observed. Elevated CO2 did not stimulate powdery mildew development, but was detrimental for plant vitality. Similar abundance of three PR transcripts was found, and the level of their expression was different between six phytotron conditions. Real time PCR quantification of Bgt was in line with the disease index results, but this technique succeeded to detect the pathogen also in asymptomatic plants. Overall, future global warming scenarios may limit the development of powdery mildew on wheat in Mediterranean area, unless the pathogen will adapt to higher temperatures.

Development of Loop-Mediated Isothermal Amplification Assays for the Detection of Seedborne Fungal Pathogens Fusarium fujikuroi and Magnaporthe oryzae in Rice Seed

Bakanae disease (caused by Fusarium fujikuroi) and rice blast (caused by Magnaporthe oryzae) are two of the most important seedborne pathogens of rice. The detection of both pathogens in rice seed is necessary to maintain high quality standards and avoid production losses. Currently, blotter tests are used followed by morphological identification of the developing pathogens to provide an incidence of infection in seed lots. Two loop-mediated isothermal amplification assays were developed with primers designed to target the elongation factor 1-α sequence of F. fujikuroi and the calmodulin sequence of M. oryzae. The specificity, sensitivity, selectivity, repeatability, and reproducibility for each assay was assessed in line with the international validation standard published by the European and Mediterranean Plant Protection Organization (PM7/98). The results showed a limit of detection of 100 to 999 fg of DNA of F. fujikuroi and 10 to 99 pg of M. oryzae DNA. When combined with a commercial DNA extraction kit, the assays were demonstrated to be effective for use in detection of the pathogens in commercial batches of infected rice seed of different cultivars, giving results equivalent to the blotter method, thus demonstrating the reliability of the method for the surveillance of F. fujikuroi and M. oryzae in seed-testing laboratories.

Molecular characterization and sensitivity to demethylation inhibitor fungicides of Aspergillus fumigatus from orange-based compost

Aspergillus fumigatus, the causal agent of human aspergilloses, is known to be non-pathogenic in plants. It is present as saprophyte in different types of organic matter and develops rapidly during the high-temperature phase of the composting process. Aspergilloses are treated with demethylation inhibitor (DMI) fungicides and resistant isolates have been recently reported. The present study aims to estimate the abundance, genetic diversity and DMI sensitivity of A. fumigatus during the composting process of orange fruits. Composting of orange fruits resulted in a 100-fold increase in A. fumigatus frequency already after 1 week, demonstrating that the degradation of orange fruits favoured the growth of A. fumigatus in compost. Most of A. fumigatus isolates belonged to mating type 2, including those initially isolated from the orange peel, whereas mating type 1 evolved towards the end of the composting process. None of the A. fumigatus isolates expressed simultaneously both mating types. The 52 investigated isolates exhibited moderate SSR polymorphisms by formation of one major (47 isolates) and one minor cluster (5 isolates). The latter included mating type 1 isolates from the last sampling and the DMI-resistant reference strains. Only few isolates showed cyp51A polymorphisms but were sensitive to DMIs as all the other isolates. None of the A. fumigatus isolates owned any of the mutations associated with DMI resistance. This study documents a high reproduction rate of A. fumigatus during the composting process of orange fruits, requesting specific safety precautions in compost handling. Furthermore, azole residue concentrations in orange-based compost were not sufficient to select A. fumigatus resistant genotypes.

Microbiological Parameters in the Primary Production of Berries: A Pilot Study

The primary production of fresh soft fruits was considered to be a suspected critical point for the contamination of frozen berries that were responsible for the large 2013⁻2014 Hepatitis A virus (HAV) outbreak in Europe. In this study, an Italian berries’ production area was studied for its agro-technical characteristics, and the fresh fruits were analyzed for the presence of enteric viruses (HAV and Norovirus (NoV) genogroup I and genogroup II (GGI and GGII)), the enumeration of hygienic quality parameters, and the prevalence of bacterial pathogens. A total of 50 producers were sampled, who specialized in the exclusive or shared cultivation of berries. Escherichia coli was detected in two blackberry samples, whereas HAV and Norovirus were not detected. The samples were negative for Salmonella spp., Listeria monocytogenes, and Shiga toxin-producing Escherichia coli (STEC). The farms’ attributes were not associated with positive samples, apart from the presence of E. coli and the aerobic mesophilic bacteria for blackberry that were statistically correlated. In blueberries, the high aerobic mesophilic count could likely be associated with the resistance of the outer layer to handling. However, the two pathogens (Salmonella spp. and STEC) and the targeted viruses (HAV, NoV GGI and GGII) were not detected, highlighting the low risk of foodborne pathogens and viral contamination at the primary production stage of the berry food chain in the area considered in this pilot study.

Thyme and Savory Essential Oil Vapor Treatments Control Brown Rot and Improve the Storage Quality of Peaches and Nectarines, but Could Favor Gray Mold

The effect of biofumigation, through slow-release diffusors, of thyme and savory essential oils (EO), was evaluated on the control of postharvest diseases and quality of peaches and nectarines. EO fumigation was effective in controlling postharvest rots. Naturally contaminated peaches and nectarines were exposed to EO vapors for 28 days at 0 °C in sealed storage cabinets and then exposed at 20 °C for five days during shelf-life in normal atmosphere, simulating retail conditions. Under low disease pressure, most treatments significantly reduced fruit rot incidence during shelf-life, while, under high disease pressure, only vapors of thyme essential oil at the highest concentration tested (10% v/v in the diffusor) significantly reduced the rots. The application of thyme or savory EO favored a reduction of brown rot incidence, caused by Monilinia fructicola, but increased gray mold, caused by Botrytis cinerea. In vitro tests confirmed that M. fructicola was more sensitive to EO vapors than B. cinerea. Essential oil volatile components were characterized in storage cabinets during postharvest. The antifungal components of the essential oils increased during storage, but they were a low fraction of the volatile organic compounds in storage chambers. EO vapors did not influence the overall quality of the fruit, but showed a positive effect in reducing weight loss and in maintaining ascorbic acid and carotenoid content. The application of thyme and savory essential oil vapors represents a promising tool for reducing postharvest losses and preserving the quality of peaches and nectarines.

Identification of bakanae disease resistance loci in japonica rice through genome wide association study

BACKGROUND

Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses.

RESULTS

A germplasm collection of japonica rice was screened for F. fujikuroi resistance, allowing the identification of accessions with high-to-moderate levels of resistance to bakanae. A GWAS approach uncovered two genomic regions highly associated with the observed phenotypic variation for response to bakanae infection on the short arm of chromosome 1 (named as qBK1_628091) and on the long arm of chromosome 4 (named as qBK4_31750955). High levels of phenotypic resistance to bakanae were associated to the cumulated presence of the resistant alleles at the two resistance loci, suggesting that they can provide useful levels of disease protection in resistance breeding. A fine comparison with the genomic positions of qBK1_628091 and qBK4_31750955 with respect to the QTLs for bakanae resistance reported in the literature suggests that the resistant loci here described represent new genomic regions associated to F. fujikuroi resistance. A search for candidate genes with a putative role in bakanae resistance was conducted considering all the annotated genes and F. fujikuroi-related DEGs included in the two genomic regions highlighting several gene functions that could be involved in resistance, thus paving the way to the functional characterization of the resistance loci.

CONCLUSIONS

New effective sources for bakanae resistance were identified on rice chromosomes 1 and 4 and tools for resistance breeding are provided.

Characterization of Aspergillus section Flavi isolated from fresh chestnuts and along the chestnut flour process

An extensive sampling of Aspergillus section Flavi considered to be the main agent responsible for aflatoxin contamination, was carried out in the field and along the processing phases of chestnut flour production in 2015. Fifty-eight isolates were characterized by means of biological, molecular and chemical assays. The highest incidence of Aspergillus section Flavi was found in the field. The identification of the isolates was based on β-tubulin and calmodulin gene sequences. A. flavus was found to be the dominant species, and this was followed by A. oryzae var effusus, A. tamarii, A. parasiticus and A. toxicarius. Nineteen percent of the strains produced aflatoxins in vitro and forty percent in vivo. The pathogenicity assay on chestnut showed 56 virulent strains out of 58. The molecular, morphological, chemical and biological analyses of A. flavus strains showed an intraspecific variability. These results confirm that a polyphasic approach is necessary to discriminate the species inside the Aspergillus section Flavi. The present research is the first monitoring and characterization of aflatoxigenic fungi from fresh chestnut and the chestnut flour process, and it highlights the risk of a potential contamination along the whole chestnut production chain.

Development and Validation of a TaqMan Real-Time PCR Assay for the Specific Detection and Quantification of Fusarium fujikuroi in Rice Plants and Seeds

Bakanae disease, which is caused by the seedborne pathogen Fusarium fujikuroi, is found throughout the world on rice. A TaqMan real-time PCR has been developed on the TEF 1-α gene to detect F. fujikuroi in different rice tissues. Three primer/probe sets were tested. The selected set produced an amplicon of 84 bp and was specific for F. fujikuroi with respect to eight Fusarium species of rice and six other rice common pathogens. The assay was validated for specificity, selectivity, sensitivity, repeatability, and reproducibility. The detection limit was set at 27.5 fg of DNA, which is approximately equivalent to one haploid genome of F. fujikuroi. The developed TaqMan real-time assay was able to efficiently detect and quantify F. fujikuroi from rice culms, leaves, roots, and seeds. At 1 week post-germination (wpg), the pathogen was more diffused in the green tissues, while at 3 wpg it was uniformly spread also in the roots. The highest concentration of F. fujikuroi was measured in the M6 cultivar, which showed around 1,450 fungal cells/g. The assay was sufficiently sensitive to detect a few genomic equivalents in the rice seeds, corresponding to 9.89 F. fujikuroi cells/g. The assay permitted bakanae disease to be detected in asymptomatic tissues at the early rice development stages.

Verrucarin A and roridin E produced on spinach by Myrothecium verrucaria under different temperatures and CO2 levels

The behavior of Myrothecium verrucaria, artificially inoculated on spinach, was studied under seven different temperature conditions (from 5 to 35 °C) and under eight different combinations of temperature and CO₂ concentration (14-30 °C and 775-870 or 1550-1650 mg/m³). The isolate used for this study was growing well on spinach, and the mycotoxins verrucarin A and roridin E were produced under all tested temperature and CO₂ conditions. The maximum levels of verrucarin A (18.59 ng/g) and roridin E (49.62 ng/g) were found at a temperature of 26-30 °C and a CO₂ level of 1550-1650 mg/m³. Rises in temperature as well as in temperature and CO₂ concentrations had a significant effect by increasing Myrothecium leaf spots on spinach. The biosynthesis of verrucarin A was significantly increased at the highest temperature (35 °C), while roridin E was influenced by the CO₂ concentration. These results show that a positive correlation between climate condition and macrocyclic trichothecene production is possible. However, because of the ability of M. verrucaria to produce mycotoxins, an increase in temperature could induce the spread of M. verrucaria in temperate regions; this pathogen may gain importance in the future.

Static Hot Air and Infrared Rays Roasting are Efficient Methods for Aflatoxin Decontamination on Hazelnuts

Aflatoxins are a group of secondary metabolites produced by members of Aspergillus Section Flavi that are dangerous to humans and animals. Nuts can be potentially contaminated with aflatoxins, often over the legal threshold. Food processes, including roasting, may have different effects on mycotoxins, and high temperatures have proven to be very effective in the reduction of mycotoxins. In this work, two different roasting methods-traditional static hot air roasting and infra-red rays roasting-were applied and compared for the detoxification of hazelnuts from Italy and Turkey. At the temperature of 140 °C for 40 min of exposure, detoxification was effective for both roasting techniques. Residual aflatoxins after infra-red rays treatments were lower compared to static hot air roasting. On Italian hazelnuts, residual aflatoxins were lower than 5%, while for Turkish hazelnuts they were lower than 15% after 40 min of exposure to an infra-red rays roaster. After roasting, the perisperm was detached from the nuts and analyzed for aflatoxin contents. Residual aflatoxins in the perisperm ranged from 80% up to 100%. After roasting, the lipid profile and the nutritional quality of hazelnuts were not affected. Fatty acid methyl esters analyses showed a similar composition for Italian and Turkish hazelnuts.