The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as “What’s in my soil?”, to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.

Clavibacter michiganensis subsp. michiganensis (Smith) Davis et al. (Cmm) and Ralstonia solanacearum Yabuuchi et al. (Smith) (Rs) are important seed-borne bacterial pathogens of tomato (Solanum lycopersicum) listed as A2 pests in the EPPO (European and Mediterranean Plant Protection Organization) region. At present, there are few strategies to control these pathogens, and seed control with eco-compatible approaches is widely encouraged. In this work, the essential oils (EOs) of oregano (Origanum vulgare), garlic (Allium sativum), basil (Ocimum basilicum), cinnamon (Cinnamomum zeylanicum), clove buds (Syzygium aromaticum), thyme (Thymus vulgaris), and Trametes versicolor extract (Tve) were tested in vitro for their antimicrobial activity against Cmm and Rs (broth microdilution method). The tested EOs and the Tve extract caused a significant inhibition of bacterial growth, with very promising MBC (minimum bactericidal concentration) and MIC90 (minimum inhibitory concentration causing a 90% growth inhibition) values. Moreover, an in vivo germination test showed no major reduction in seed germination when the substances were applied as seed treatment. A rapid molecular screening method has been developed, through real-time PCR, for the specific quantification of Cmm in the presence of a vegetable matrix to test in vivo the antimicrobial efficacy of oregano and cinnamon oil on seed treatment without resorting to whole plant essays, which are time- and space-consuming.

Using morphological and cultural characteristics for identification, 36 Fusarium isolates were recovered from diseased roots, stems, and seeds of soybean from several localities throughout Vojvodina Province, Serbia. Based on molecular characterization, 12 Fusarium species were identified: F. acuminatum, F. avenaceum, F. commune, F. equiseti, F. graminearum, F. incarnatum, F. oxysporum, F. proliferatum, F. solani, F. sporotrichioides, F. subglutinans, and F. tricinctum. The elongation factor 1-α–based phylogeny grouped the isolates into 12 well-supported clades, but polymorphisms among sequences in some clades suggested the use of the species complex concept: (i) F. incarnatum-equiseti species complex (FIESC)—F. incarnatum and F. equiseti; (ii) F. oxysporum species complex (FOSC)—F. oxysporum; (iii) F. solani species complex (FSSC)—F. solani; and (iv) F. acuminatum/F. avenaceum/F. tricinctum species complex (FAATSC)—F. acuminatum, F. avenaceum, and F. tricinctum. Pathogenicity tests showed that the most aggressive species causing soybean seed rot were F. sporotrichioides, F. graminearum, FIESC, and F. avenaceum. Furthermore, F. subglutinans, FSSC, and F. proliferatum showed a high percentage of pathogenicity on soybean seeds (80 to 100%), whereas variability in pathogenicity occurred within isolates of F. tricinctum. FOSC, F. commune, and F. acuminatum had the lowest pathogenicity. To our knowledge, this is the first study of the characterization of Fusarium species on soybean in Serbia. This study provides valuable information about the composition of Fusarium species and pathogenicity that will be used in further research on soybean resistance to Fusarium-based diseases.

Seedborne pathogens represent a critical issue for successful agricultural production worldwide. Seed treatment with plant protection products constitutes one of the first options useful for reducing seed infection or contamination and preventing disease spread. Basic substances are active, non-toxic substances already approved and sold in the EU for other purposes, e.g., as foodstuff or cosmetics, but they can also have a significant role in plant protection as ecofriendly, safe, and ecological alternatives to synthetic pesticides. Basic substances are regulated in the EU according to criteria presented in Article 23 of Regulation (EC) No 1107/2009. Twenty-four basic substances are currently approved in the EU and some of them such as chitosan, chitosan hydrochloride, vinegar, mustard seed powder, and hydrogen peroxide have been investigated as seed treatment products due to their proven activity against fungal, bacterial, and viral seedborne pathogens. Another basic substance, sodium hypochlorite, is under evaluation and may be approved soon for seed decontamination. Potential basic substances such as essential oils, plant extracts, and ozone were currently found effective as a seed treatment for disease management, although they are not yet approved as basic substances. The aim of this review, run within the Euphresco BasicS project, is to collect the recent information on the applications of basic substances and potential basic substances for seed treatment and describe the latest advanced research to find the best application methods for seed coating and make this large amount of published research results more manageable for consultation and use.

The fruit crop pest Drosophila suzukii(Matsumura, 1931)(Diptera: Drosophilidae) is a highly polypha-gous invasive pestlisted in the EPPO A2 list. This specieshas been reported as host of a variety of cultivatedplantsandwild fruits.Herein,we report the record of someD.suzukiiviable specimensthatwere found in olives directly collected from the tree branches in four differentsites of Latium and Umbria (Italy). Adults emerging from these pupae were collected and morphological and molecular analysiswere carried out to confirm the speciesidentity. Olive tissues alterations wereobserved in associationwiththe presence of the species.The analysis of the available literature showed us that this is the first record of D. suzukiias a phytophagous species on the olive tree in Italy and probably worldwide