Plant Beneficial Microbes Controlling Late Blight Pathogen, Phytophthora infestans

Potato (Solanum tuberosum) as a food source and culinary ingredient varies is the fourth most produced noncereal crop in the world. Among multiple biotic stresses, late blight caused by Phytophthora infestans is the most destructive disease. Control of this pathogen is usually by the synthetic fungicides which have been fueled by the public concern about toxicity and environmental impact and development of pathogens resistance. Biological control agents (BCAs) seems the potentially alternative to these pesticides, biological disease control is now recognized and constitute an important tool in integrated pest management. BCAs strains should be able to protect the host plant from pathogens and fulfill the requirement for strong colonization. Bacteria such as Bacillus, Pseudomonas and Streptomyces and fungi such as Trichoderma and Penicillium were the most reported as a BCA against P. infestans using different direct antagonistic mode on the pathogen (via e.g. parasitism, antibiosis, or competition) or via exerting their biocontrol activity indirectly by induction in the plant of an induced systemic resistance to the pathogen. In this study, we present an overview and discussion of the use of beneficial microbes (bacteria and fungi) as novel BCAs for biocontrol of P. infestans.

An improved PCR method for rapid and accurate identification of mating types in the late blight pathogen Phytophthora infestans

Mating type is a critical trait in heterothallic organisms. In plant pathogenic oomycetes, like the late blight pathogen Phytophthora infestans, it is usually identified through pairing between tester and candidate isolates, a method which is both laborious and applicable to live isolates only. Therefore, developing simple and fast PCR tests to reliably identify P. infestans mating types is of great interest for population genetic studies. A multiplex PCR assay combining the amplification of a locus diagnostic for P. infestans and of one diagnostic for the A1 mating type was developed and validated on a collection of 1441 samples, covering the current and past diversity of European P. infestans populations. These samples obtained from either freeze-dried mycelium or from FTA cards on which diseased leaflets had been pressed. The multiplex assay correctly identified mating types in 97.4 % of these samples. The main source of incorrect assignment was the lack of amplification of the A1 diagnostic allele, due to insufficient DNA quality and/or quantity in the reaction mix. This multiplex PCR, applicable to both live and stored material, thus constitutes a useful addition to the set of molecular tools available for population typing in P. infestans.

Natural genetic diversity in the potato resistance gene RB confers suppression avoidance from Phytophthora effector IPI-O4

RB is a potato gene that provides resistance to a broad spectrum of genotypes of the late blight pathogen Phytophthora infestans. RB belongs to the CC-NB-LRR (coiled-coil, nucleotide-binding, leucine-rich repeat) class of resistance (R) genes, a major component of the plant immune system. The RB protein detects the presence of Class I and II IPI-O effectors from P. infestans to initiate a hypersensitive resistance response, but this activity is suppressed in the presence of the Class III effector IPI-O4. Using natural genetic variation of RB within potato wild relatives, we identified two amino acids in the CC domain that alter interactions needed for suppression of resistance by IPI-O4. We have found that separate modification of these amino acids in RB can diminish or expand the resistance capability of this protein against P. infestans in both Nicotiana benthamiana and potato. Our results demonstrate that increased knowledge of the molecular mechanisms that determine resistance activation and R protein suppression by effectors can be utilized to tailor-engineer genes with the potential to provide increased durability.

Genetic aspects of potato resistance to phytophthorosis

Phytophthora infestans Mont. de Bary is the main oomycete pathogen of cultivated crops in the family Solanaceae, especially potato (Solanum tuberosum). Because potato is the fourth most cultivated crop worldwide, its annual losses from late blight are tremendous. Studies of the basic mechanisms of interaction between potato and the late blight pathogen not only expand the fundamental knowledge in this area, but also open up new possibilities for regulating these interactions in order to increase resistance to the pathogen. The interaction of potato and the late blight pathogen can be considered from a genetic point of view, and it is interesting to consider both the response of the potato to the colonization process by P. infestans and the change in gene activity in late blight during plant infection. We can also investigate this process by changing the profile of secondary metabolites of the host and the pathogen. In addition to fundamental work in this area, applied work in the form of the development of new preparations for protecting potatoes is of no less importance. This review briefly describes the main stages of studies of potato resistance to late blight, starting almost from the first works. Much attention is paid to key works on changing the profile of secondary metabolites phytoalexins. A separate section is devoted to the description of both qualitative and quantitative characteristics of potato resistance to the late blight pathogen: their contribution to overall resistance, gene mapping, and regulation capabilities. Both types of traits are important for potato breeding: quantitative resistance due to R-genes is quickly overcome by the pathogen, while quantitative trait loci make it possible to create varieties with almost absolute resistance due to the pyramid of effective genes. The latest approaches in molecular biology make it possible to study translatomic profiles, which makes it possible to look at the interaction of potatoes and the late blight pathogen at a different angle. It has been shown that the process of potato colonization affects not only the activity of various genes and the profile of secondary metabolites: proteins­markers of the response to infection from potatoes have also been identified: they are pathogen-bound proteins and plastid carbonic anhydrase. On the part of P. infestans, fungal cellulose synthase proteins and haustorium-specific membrane protein were markers of infection. Thus, the review contains information on the most relevant complex studies of the genetic mechanisms of potato resistance to late blight.

smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites

Degradome sequencing is commonly used to generate high-throughput information on mRNA cleavage sites mediated by small RNAs (sRNA). In our datasets of potato (Solanum tuberosum, St) and Phytophthora infestans (Pi), initial predictions generated high numbers of cleavage site predictions, which highlighted the need of improved analytic tools. Here, we present an R package based on a deep learning convolutional neural network (CNN) in a machine learning environment to optimize discrimination of false from true cleavage sites. When applying smartPARE to our datasets on potato during the infection process by the late blight pathogen, 7.3% of all cleavage windows represented true cleavages distributed on 214 sites in P. infestans and 444 sites in potato. The sRNA landscape of the two organisms is complex with uneven sRNA production and cleavage regions widespread in the two genomes. Multiple targets and several cases of complex regulatory cascades, particularly in potato, was revealed. We conclude that our new analytic approach is useful for anyone working on complex biological systems and with the interest of identifying cleavage sites particularly inferred by sRNA classes beyond miRNAs.

Altitudinal Heterogeneity of UV Adaptation in Phytophthorainfestans Is Associated with the Spatial Distribution of a DNA Repair Gene

Climate change is considered a major threat to society and nature. UV irradiation is the most important environmental genotoxic agent. Thus, how elevated UV irradiation may influence human health and ecosystems has generated wide concern in the scientific community, as well as with policy makers and the public in general. In this study, we investigated patterns and mechanisms of UV adaptation in natural ecosystems by studying a gene-specific variation in the potato late blight pathogen, Phytophthora infestans. We compared the sequence characteristics of radiation sensitive 23 (RAD23), a gene involved in the nucleotide excision repair (NER) pathway and UV tolerance, in P. infestans isolates sampled from various altitudes. We found that lower genetic variation in the RAD23 gene was caused by natural selection. The hypothesis that UV irradiation drives this selection was supported by strong correlations between the genomic characteristics and altitudinal origin (historic UV irradiation) of the RAD23 sequences with UV tolerance of the P. infestans isolates. These results indicate that the RAD23 gene plays an important role in the adaptation of P. infestans to UV stress. We also found that different climatic factors could work synergistically to determine the evolutionary adaptation of species, making the influence of climate change on ecological functions and resilience more difficult to predict. Future attention should aim at understanding the collective impact generated by simultaneous change in several climate factors on species adaptation and ecological sustainability, using state of the art technologies such as experimental evolution, genome-wide scanning, and proteomics.

Pathogens which threaten food security: Phytophthora infestans, the potato late blight pathogen

Potato late blight, caused by Phytophthora infestans, is a critical disease of potato and other solanaceous crops, such as tomato. The history of late blight is, in some ways, the history of modern plant pathology. It received much attention in the mid 1800’s by causing the Irish potato famine, and the pathogen played a prominent role in the development of the concept of plant disease and plant pathogens. The pathosystem has also been important in the development of pesticides that are active against plant pathogens, and has also been a model system in understanding concepts ranging from cellular processes, such as how resistance to plant pathogens functions, to large scale processes, such as implementation of regional plant disease warning systems. P.infestans has a secured a place in modern potato production, both in developed and less-developed countries.

Small talk and large impact: the importance of small RNA molecules in the fight against plant diseases.

This short and general chapter summarizes how plants and pathogens communicate using not only proteins for recognition and signal transduction or other metabolites but also RNA molecules where small RNAs with sizes between 21 to 40 nt are most important. These small RNAs can move between plants and a range of interacting pathogenic organisms in both directions, that is, a 'cross-kingdom' communication process. The first reports on RNA-based communications between plants and plant pathogenic fungi appeared about 10 years ago. Since that time, we have learnt much about sRNA biology in plants and their function in different parasitic organisms. However, many questions on the processes involved remain unanswered. Such information is crucial in order to sustain high crop production. Besides giving a brief background, we highlight the interactions between the potato late blight pathogen and its plant host potato.

EFFECT OF THE COMPLEX OF ENDOPHYTIC BACTERIA BACILLUS WITH SALICYLIC AND JASMONIC ACIDS ON THE STATE OF THE PRO- / ANTIOXIDANT SYSTEM OF PLANTS AND THE RESISTANCE OF POTATOES WHEN INFECTED WITH LATE BLIGHT UNDER STRESS

There was researched the effect of Bacillus subtilis bacteria in combination with salicylic (SA) and jasmonic (JA) acids on the state of the pro / antioxidant system (hydrogen peroxide content, catalase, peroxidase, superoxide dismutase activity) in connection with the development of potato resistance to late blight pathogen - oomycete Phytophthora infestans (Mont.) de Bary under moisture deficit conditions. Plants grown from microtubers of the Rannyaya Rosa cultivar were sprayed with a suspension of B. subtilis (108 cells / ml) and a mixture of bacteria with SA (10-6 M), JA (10-7 M), SA + JA (1:1). 3 days after treatment, the plants were infected with P. infestans (105 spores / ml) and cultivated under artificial soil drought conditions by reducing irrigation. When soil moisture reached 40±5% (7 days after infection), biochemical parameters were assessed in plants. A decrease in the degree of leaves damage by P. infestans was revealed when treated with B. subtilis in combination with SA and JA. The mechanism of increasing the resistance of potato plants to late blight when treated with Bacillus subtilis bacteria in combination with signaling molecules under conditions of drought was associated with the accumulation of H2O2 and modulation of antioxidant enzymes activity.

Small talk and large impact: the importance of small RNA molecules in the fight against plant diseases.

This short and general chapter summarizes how plants and pathogens communicate using not only proteins for recognition and signal transduction or other metabolites but also RNA molecules where small RNAs with sizes between 21 to 40 nt are most important. These small RNAs can move between plants and a range of interacting pathogenic organisms in both directions, that is, a 'cross-kingdom' communication process. The first reports on RNA-based communications between plants and plant pathogenic fungi appeared about 10 years ago. Since that time, we have learnt much about sRNA biology in plants and their function in different parasitic organisms. However, many questions on the processes involved remain unanswered. Such information is crucial in order to sustain high crop production. Besides giving a brief background, we highlight the interactions between the potato late blight pathogen and its plant host potato.