In recent years, environmental-friendly measures have been developed for managing crop diseases as alternative to chemical pesticides, including the use of natural compounds such as chitosan. In this chapter, the common uses of this natural product in agriculture and its potential uses in plant disease control are reviewed. The last advanced researches as seed coating, plant resistance elicitation and soil amendment applications are also described. Chitosan is a deacetylated derivative of chitin that is naturally present in the fungal cell wall and in crustacean shells from which it can be easily extracted. Chitosan has been reported to possess antifungal and antibacterial activity and it showed to be effective against seedborne pathogens when applied as seed treatment. It can form physical barriers (film) around the seed surface, and it can vehicular other antimicrobial compounds that could be added to the seed treatments. Chitosan behaves as a resistance elicitor inducing both local and systemic plant defence responses even when applied to the seeds. The chitosan used as soil amendment was shown to give many benefits to different plant species by reducing the pathogen attack and infection. Concluding, the chitosan is an active molecule that finds many possibilities for application in agriculture, including plant disease control.

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.

Seed decay is one of the most important diseases of soybean (Glycine max (L.) Merr.) which can greatly affect seed quality. Some of the most damaging causal agents of soybean seed decay are Diaporthe longicolla, D. sojae, D. caulivora, and D. aspalathi (Li, 2011). A total of 94 single-conidial isolates were obtained from soybean seeds collected throughout the soybean-producing area in Serbia from 1996 to 2015. Isolates were separated into two groups (A and B) according to their morphological features. In group A, 70 isolates were assigned with the following morphological characteristics: white mycelium, black stromatic structures, pycnidial conidiomata with alpha conidia and rarely beta conidia, and absence of perithecia (Hobbs et al. 1985). Twenty-four isolates were assigned to group B with culture characteristics that included white mycelium, pycnidial conidiomata with alpha and beta conidia, and perithecia (Udayanga et al. 2015). Using sequence comparison of the internal transcribed spacer (ITS1-5.8S-I...

Although Phomopsis longicolla is primarily known as a seedborne pathogen, it can be isolated from all parts of the plant. The disease lesions observed on the basal parts of soybean stems were slightly sunken with irregular shapes and sizes, bordered by a thin black margin. Within the lesions themselves, large and diffusely distributed pycnidia with α and β conidia, typical of the genus Phomopsis, were observed. The percentages of the two types of conidia varied considerably, but β conidia were predominant in most of the pycnidia. The presence of these reproductive organs indicated that the symptoms could have been caused by Phomopsis sojae. However, after isolation on a nutritive medium, all cultural and morphological characteristics clearly indicated that the isolated fungus was P. longicolla, whose identification was subsequently confirmed by sequencing three genomic regions. Monosporic isolates, with different ratios of α and β conidia, exhibited a high level of pathogenicity on soybean, after artificial inoculation. Both types of conidia were observed on the stems of the inoculated soybean plants. Beta conidia also formed quickly on medium made of soybean seeds and mature stems after exposure to low temperatures (−10°C). This study suggests that P. longicolla is capable of a massive production of β conidia, not only in old fungal cultures as it had until now been believed, but also in infected soybean plants in the field.

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.