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Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.

The use of biocontrol agents based on endophytic bacteria against phloem-feeding insects is limited by a lack of knowledge and understanding of the mechanism of action of the endophyte community that makes up the plant microbiome. In this work, the mechanisms of the additive action of endophytic strains B. subtilis 26D and B. subtilis 11VM on the resistance of bread spring wheat against greenbug aphid Schizaphis graminum, was studied. It was shown that B. subtilis 26D secreted lipopeptide surfactin and phytohormones cytokinins, and B. subtilis 11VM produced iturin and auxins into the cultivation medium. Both strains and their lipopeptide-rich fractions showed direct aphicidal activity against greenbug aphid. For the first time, it was shown that B. subtilis 26D and B. subtilis 11VM in the same manner, as well as their lipopeptide-rich fractions, activated the expression of salicylate- and ethylene-dependent PR genes, and influenced plant redox metabolism, which led to an increase in plant endurance against aphids. The composition of endophytic strains B. subtilis 26D + B. subtilis 11VM had an additive effect on plant resistance to aphids due to an increase in the number of endophytic bacterial cells, and, as well as due to the synergistic effect of their mixture of lipopeptides − surfactin + iturin, both on the aphid mortality and on the expression of PR1 and PR3 genes. All these factors can be the reason for the observed increase in the growth of plants affected by aphids under the influence of B. subtilis 26D and B. subtilis 11VM, individually and in composition. The study demonstrates the possibility of creating in the future an artificial composition to enhance plant microbiome with endophytic bacteria, which combines growth-promoting and plant immunity stimulating properties against phloem-feeding insects. This direction is one of the most promising approaches to green pesticide discovery in the future.

Endophytic plant-growth-promoting microorganisms can protect plants against pathogens, but they have rarely been investigated as potential biocontrol agents and triggers of induced systemic resistance (ISR), regulated by phytohormones, against viruses. We studied the role of endophytic strains Bacillus subtilis 26D and B. subtilis Ttl2, which secrete ribonucleases and phytohormones, in the induction of tomato plant resistance against potato virus X and potato virus Y in a greenhouse condition. The endophytes reduced the accumulation of viruses in plants, increased the activity of plant ribonucleases and recovered the fruit yield of infected tomato plants. Both the 26D and Ttl2 strains induced ISR by activating the transcription of genes related to salicylate- and jasmonate-dependent responses. The 26D and Ttl2 strains increased the content of cytokinins and decreased the level of indolacetic acid in plants infected with PVX or PVY. PVY led to an increase of the abscisic acid (ABA) content in tomato plants, and PVX had the opposite effect. Both strains reduced the ABA content in plants infected with PVY and induced ABA accumulation in plants infected with PVX, which led to an increase in the resistance of plants. This is the first report of the protection of tomato plants against viral diseases by foliar application of endophytes.

Plant damage caused by defoliating insects has a long-term negative effect on plant growth and productivity. Consequently, the restoration of plant growth after exposure to pathogens or pests is the main indicator of the effectiveness of the implemented defense reactions. A short-term Leptinotarsa decemlineata Say attack on potato tube-grown plantlets (Solanum tuberosum L.) led to a reduction of both the length and mass of the shoots in 9 days. The decrease of the content of phytohormones—indole-3-acetic acid (IAA), abscisic acid (ABA), zeatin and zeatin–riboside—in shoots of damaged potato plants was found. Endophytic strain Bacillus subtilis 26D (Cohn) is capable of secreting up to 83.6 ng/mL IAA and up to 150 ng/mL cytokinins into the culture medium. Inoculation of potato plants with cells of the B. subtilis 26D increases zeatin–riboside content in shoots and the mass of roots of undamaged plants, but does not influence content of IAA and ABA and growth of shoots. The presence of B. subtilis 26D in plant tissues promoted a rapid recovery of the growth rates of shoots, as well as the wet and dry mass of roots of plants after the pest attack, which we associate with the maintenance of a high level of IAA, ABA and cytokinins in their tissues.

Plant viruses are globally responsible for the significant crop losses of economically important plants. All common approaches are not able to eradicate viral infection. Many non-conventional strategies are currently used to control viral infection, but unfortunately, they are not always effective. Therefore, it is necessary to search for efficient and eco-friendly measures to prevent viral diseases. Since the genomic material of 90% higher plant viruses consists of single-stranded RNA, the best way to target the viral genome is to use ribonucleases (RNase), which can be effective against any viral disease of plants. Here, we show the importance of the search for endophytes with protease and RNase activity combined with the capacity to prime antiviral plant defense responses for their protection against viruses. This review discusses the possible mechanisms used to suppress a viral attack as well as the use of local endophytic bacteria for antiviral control in crops.

Bacillus thuringiensis Berliner (Bt) and B. cereus sensu stricto Frankland and Frankland are closely related species of aerobic, spore-forming bacteria included in the B. cereus sensu lato group. This group is one of the most studied, but it remains also the most mysterious species of bacteria. Despite more than a century of research on the features of these ubiquitous bacteria, there are a lot of questionable issues related to their taxonomy, resistance to external influences, endophytic existence, their place in multidimensional relationships in the ecosystem, and many others. The review summarizes current data on the mutualistic relationships of Bt and B. cereus bacteria with plants, the structure of the phytomicrobiomes including Bt and B. cereus, and the abilities of plant-associated and endophytic strains to improve plant resistance to various environmental factors and its productivity. Key findings on the possibility of the use of Cry gene promoter for transcription of the target dsRNA and simultaneous release of pore-forming proteins and provocation of RNA-interference in pest organisms allow us to consider this group of microorganisms as unique tools of genetic engineering and biological control. This will open the prospects for the development and direct change of plant microbiomes, and possibly serve as the basis for the regulation of the entire agroecosystem.

Cytokinins (CKs) and abscisic acid (ABA) play an important role in the life of both plants and pathogenic fungi. However, the role of CKs and ABA in the regulation of fungal growth, development and virulence has not been sufficiently studied. We compared the ability of two virulent isolates (SnB and Sn9MN-3A) and one avirulent isolate (Sn4VD) of the pathogenic fungus Stagonospora nodorum Berk. to synthesize three groups of hormones (CKs, ABA and auxins) and studied the effect of exogenous ABA and zeatin on the growth, sporulation and gene expression of necrotrophic effectors (NEs) and transcription factors (TFs) in them. Various isolates of S. nodorum synthesized different amounts of CKs, ABA and indoleacetic acid. Using exogenous ABA and zeatin, we proved that the effect of these hormones on the growth and sporulation of S. nodorum isolates can be opposite, depends on both the genotype of the isolate and on the concentration of the hormone and is carried out through the regulation of carbohydrate metabolism. ABA and zeatin regulated the expression of fungal TF and NE genes, but correlation analysis of these parameters showed that this effect depended on the genotype of the isolate. This study will contribute to our understanding of the role of the hormones ABA and CKs in the biology of the fungal pathogen S. nodorum.

Novel properties of a previously obtained Bacillus subtilis 26DCryChS strain are described. The B. subtilis 26DCryChS strain is able to produce Cry1Ia δ-endotoxin from B. thuringiensis B-5351 and to exist in internal plant tissues of potato plants in the same manner as the endophytic B. subtilis 26D source strain (487 ± 53 and 420 ± 63 CFU*103/g, respectively). B. subtilis 26DCryChS, as much as the original B. subtilis 26D strain, inhibited mycelium growth of oomycete Phytophthora infestans (Mont.) de Bary and reduced late blight symptoms development on plants by 35% compared with non-treated ones, as well as showed insecticidal activity against Leptinotarsa decemlineata. Production of the fluorescent GFP protein in the B. subtilis 26D genome allowed visualizing the endophytes around damaged sites on beetle intestines. Bacillus strains under investigation induced systemic resistance to P. infestans and L. decemlineata through the activation of the transcription of PR genes in potato plants. Thus, the B. subtilis 26DCryChS strain was able to induce transcription of jasmonate-dependent genes and acquired the ability to promote transcription of a salicylate-dependent gene (PR1) in plants infected with the late blight agent and damaged by Colorado potato beetle larvae. The B. subtilis 26DCryChS strain could be put forward as a modern approach for biocontrol agents design.

Phytophthora infestans is, worldwide, one of the main causal agents of epiphytotics in potato plantings. Prevention strategies demand integrated pest management, including modeling of beneficial microbiomes of agroecosystems combining microorganisms and natural products. Chitooligosaccharides and their derivatives have great potential to be used by agrotechnology due to their ability to elicit plant immune reactions. The effect of combining Bacillus subtilis 26D and 11VM and conjugates of chitin with hydroxycinnamates on late blight pathogenesis was evaluated. Mechanisms for increasing the resistance of potato plants to Phytophthora infestans were associated with the activation of the antioxidant system of plants and an increase in the level of gene transcripts that encode PR proteins: basic protective protein (PR-1), thaumatin-like protein (PR-5), protease inhibitor (PR-6), and peroxidase (PR-9). The revealed activation of the expression of marker genes of systemic acquired resistance and induced systemic resistance under the influence of the combined treatment of plants with B. subtilis and conjugates of chitin with hydroxycinnamates indicates that, in this case, the development of protective reactions in potato plants to late blight proceeds synergistically, where B. subtilis primes protective genes, and chitosan composites act as a trigger for their expression.

One of the main insect potato pests is the Colorado potato beetle ( Leptinotarsa decemlineata Say). It contains some microbial associates which can affect diverse interactions between host plant and the herbivorous insect. Previously, the most common L. decemlineata microsymbiont isolated from anterior and posterior parts of beetle gut was defined as Enterobacter BC-8. The role of Enterobacter BC-8 in manipulating plant defenses was investigated using antibiotics-treated beetles and model system simulating beetles attacks (wounding plants treated with Enterobacter BC-8 suspension). We demonstrated that the symbiotic bacteria suppressed plant defenses such as hydrogen peroxide and phenolic compounds accumulation and activity of peroxidases and trypsin inhibitors. It is worth noting that the influence of the insect symbionts on potato plants stimulated salicylate-sensitive genes and the marker of salicylate signaling pathway. Transcription activities of jasmonate-sensitive genes which encode some defense proteins against herbivores, were suppressed. So, Enterobacter BC-8 plays the role in salicylate/jasmonate crosstalks manipulating to suppress plant defense mechanisms.