Short Communication. Virulence of barley leaf rust in the South of Russia in 2017-2019

Aim of study: To analyze the structure of Puccinia hordei populations by virulence in southern Russia during 2017-2019. Area of study: South of Russia, the leading Russian region for barley production where barley leaf rust is an important foliar disease. Material and methods: Uredinial samples of P. hordei were collected at the production sites of winter barley in the south of Russia. Single uredinial isolates (total 95) were tested for virulence with 17 differentials with Rph resistance genes. Main results: No isolates found virulent to the host line with the Rph13 gene. There was a decrease in the number of fungal isolates virulent to the host lines with Rph5 and Rph7 genes. In 2017 and 2019, isolates containing a large number of virulence alleles (from 11 to 15) prevailed. In 2018, isolates with low (1-5) and medium (6-10) frequency of virulent alleles prevailed, as well as avirulent isolates. The values of the Nei index via diversity showed high similarity of the pathogen populations in 2017-2018 (N = 0.05) and minor differences in 2017-2019 and 2018-2019 (N = 0.13 and 0.16, respectively). The greatest frequency of virulence alleles in accordance with the Nei (Hs) index was noted for the 2018 population (Hs = 0.36). For the 2017 and 2019 populations, this indicator was average (Hs = 0.29 and 0.20, respectively). Research highlights: Analysis of genetics of the P. hopdei population is important for the strategy of varietal distribution in the region and development of rust-resistant cultivars.

Evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through short sequence duplications

Neisseria commensals are an indisputable source of resistance for their pathogenic relatives. However, the evolutionary paths commensal species take to reduced susceptibility in this genus have been relatively underexplored. Here, we leverage in vitro selection as a powerful screen to identify the genetic adaptations that produce azithromycin resistance (≥ 2 μg/mL) in the Neisseria commensal, N. elongata. Across multiple lineages (n = 7/16), we find mutations that reduce susceptibility to azithromycin converge on the locus encoding the 50S ribosomal L34 protein (rpmH) and the intergenic region proximal to the 30S ribosomal S3 protein (rpsC) through short tandem duplication events. Interestingly, one of the laboratory evolved mutations in rpmH is identical (7LKRTYQ12), and two nearly identical, to those recently reported to contribute to high-level azithromycin resistance in N. gonorrhoeae. Transformations into the ancestral N. elongata lineage confirmed the causality of both rpmH and rpsC mutations. Though most lineages inheriting duplications suffered in vitro fitness costs, one variant showed no growth defect, suggesting the possibility that it may be sustained in natural populations. Ultimately, studies like this will be critical for predicting commensal alleles that could rapidly disseminate into pathogen populations via allelic exchange across recombinogenic microbial genera.

Resistance of the Wheat Cultivar ‘Renan’ to Septoria Leaf Blotch Explained by a Combination of Strain Specific and Strain Non-Specific QTL Mapped on an Ultra-Dense Genetic Map

Quantitative resistance is considered more durable than qualitative resistance as it does not involve major resistance genes that can be easily overcome by pathogen populations, but rather a combination of genes with a lower individual effect. This durability means that quantitative resistance could be an interesting tool for breeding crops that would not systematically require phytosanitary products. Quantitative resistance has yet to reveal all of its intricacies. Here, we delve into the case of the wheat/Septoria tritici blotch (STB) pathosystem. Using a population resulting from a cross between French cultivar Renan, generally resistant to STB, and Chinese Spring, a cultivar susceptible to the disease, we built an ultra-dense genetic map that carries 148,820 single nucleotide polymorphism (SNP) markers. Phenotyping the interaction was done with two different Zymoseptoria tritici strains with contrasted pathogenicities on Renan. A linkage analysis led to the detection of three quantitative trait loci (QTL) related to resistance in Renan. These QTL, on chromosomes 7B, 1D, and 5D, present with an interesting diversity as that on 7B was detected with both fungal strains, while those on 1D and 5D were strain-specific. The resistance on 7B was located in the region of Stb8 and the resistance on 1D colocalized with Stb19. However, the resistance on 5D was new, so further designated Stb20q. Several wall-associated kinases (WAK), nucleotide-binding and leucine-rich repeats (NB-LRR) type, and kinase domain carrying genes were present in the QTL regions, and some of them were expressed during the infection. These results advocate for a role of Stb genes in quantitative resistance and for resistance in the wheat/STB pathosystem being as a whole quantitative and polygenic.

Application of a Bacteriophage–Sanitizer Combination in Post-Harvest Control of E. coli O157:H7 Contamination on Spinach Leaves in the Presence or Absence of a High Organic Load Produce Wash

Foodborne illness due to the consumption of contaminated products continues to be a serious public health issue. Bacteriophages might provide a natural and effective way to control and reduce the pathogenic bacterial population on food products. Researchers have conducted various experiments to prove their effectiveness against different pathogens and their ability to act as a natural intervention to control pathogen populations, especially in the food industry. In this study, a cocktail of bacteriophages (phages) was added to wash water in the presence of a high organic load along with commercially used sanitizers (chlorine or Sanidate 5.0) to study the efficacy of the phage–sanitizer combination in the challenge water. It was determined that in the absence of organic loads, the sanitizer by itself or the combination with phages significantly (p < 0.001) reduced the contamination by 3.00–5.00 log CFU/mL. In the presence of organic loads, the sanitizer by itself did not contribute to a significant reduction (p > 0.05) compared to the control. However, the sanitizer–phage combination led to a 3.00-log and 6.00-log reduction (p < 0.001) of the pathogen at the end of 3 and 6 h, respectively, in the presence of high organic loads. Therefore, utilizing a combination treatment (phage–sanitizer) might be one solution to reduce pathogen contamination in the food industry, especially the fresh produce industry, thus providing safe food for consumption.

Polyclonal pathogen populations accelerate the evolution of antibiotic resistance in patients

Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection for de novo variants. Here we show that pulmonary populations of the opportunistic pathogen P. aeruginosa are often polyclonal. Crucially, resistance evolves rapidly in patients colonized by polyclonal populations through selection for pre-existing resistant strains. In contrast, resistance evolves sporadically in patients colonized by monoclonal populations due to selection for novel resistance mutations. However, strong trade-offs between resistance and fitness occur in polyclonal populations that can drive the loss of resistant strains. In summary, we show that the within-host diversity of pathogen populations plays a key role in shaping the emergence of resistance in response to treatment.One sentence summaryAntibiotic resistance evolves quickly in patients colonized by polyclonal pathogen populations.

Genetic Diversity and Population Structure of Didymella rabiei Affecting Chickpea in Ethiopia

Ascochyta blight, also known as chickpea blight, which is caused by the fungal pathogen, Didymella rabiei, is an important disease affecting chickpea (Cicer arietinum L.) in many countries. We studied the genetic diversity and population structure of 96 D. rabiei isolates collected from three geographic populations in Ethiopia using simple sequence repeat (SSR) markers. We confirmed the genetic identity of 89 of the D. rabiei isolates by sequencing their rRNA internal transcribed spacer region genes. The chickpea blight pathogen isolates were genetically diverse, with a total of 51 alleles identified across 6 polymorphic SSR loci, which varied from 3 to 18 (average 8.5) alleles per SSR marker. The observed heterozygosity and expected heterozygosity ranged from 0.01 to 0.92 and 0.19 to 0.86, respectively. The mean polymorphic information content value of the D. rabiei populations was 0.58, with a mean gene diversity of 0.61 among loci. Gene flow (Nm = number of migrants) for the three populations of D. rabiei isolates ranged from 1.51 to 24.10 (average 6.2) migrants/cluster. However, the genetic variation between the D. rabiei populations was small (8%), with most of the variation occurring within populations (92%). Principal component analysis to visualize genetic variation showed that the D. rabiei isolates obtained from most of the chickpea samples formed roughly three groups on a two-dimensional coordinate plane. Similarly, the clustering of individuals into populations based on multi-locus genotypes (using Clumpak) grouped isolates into three clusters but with individual isolate admixtures. Hence, no clear geographic origin-based structuring of populations could be identified. To our knowledge, this is the first report of D. rabiei diversity in Ethiopia. Virulence studies should be conducted to develop chickpea varieties that are resistant to more aggressive pathogen populations.

Taxonomic and pathogenic diversity of the blast pathogen populations infecting wheat and grasses in Minas Gerais

The blast disease of Poaceae is caused by a large species complex, among which P. oryzae is composed of several host-specialized lineages. The Pyricularia oryzae Triticum pathotype (PoT) causes the blast disease in wheat, but is also capable of infecting other grasses, which may serve as an inoculum reservoir for epidemics in wheat. In Brazil, severe wheat blast epidemics are most common in the Cerrado region. The dominant hypothesis is that signal grass (Urochloa sp.) and other gramineous plants harbor the wheat blast pathogen, thus serving as a major reservoir of inoculum for epidemics in wheat. A two-year survey of the Pyricularia blast pathogens was conducted in both wheat and non-wheat areas as well as prior (February) and during (May) the wheat growing season in Minas Gerais. A total of 1,368 plant samples representative of 31 Poaceae species, including wheat, were collected and inspected for the presence of blast symptoms. During the isolations, 932 isolates were obtained, being one fourth obtained from gramineous plants. A subset of 572 isolates was selected for identification at the species level based on portions of the CH7-BAC9 gene sequences. Most of the isolates (n = 494) were P. oryzae, within which 68% were PoT and 32% non-PoT based on two PCR assays targeting (MoT3 and C17 PCR assays). The PoT lineage was found predominantly (97%) in wheat and rarely in the other hosts, even nearby wheat fields (2.1%), as well as at longer distances from wheat regions (0.1%). The blast pathogen population isolated from signal grass grouped in different clades from PoT, and therefore referred to Urochloa lineage (PoU). A series of cross-inoculation greenhouse experiments was conducted using wheat (cv. BRS Guamirim and BR 18-Terena) and signal grass (cv. Marandu) as host and 14 PoT and six PoU isolates as pathogen factor. In the first leaf-inoculation experiment, results showed a significant interaction between host and pathogen; PoT was strongly/weakly aggressive towards wheat/signal grass and PoU was strongly/weakly aggressive towards signal grass/wheat. In inoculated wheat heads, PoT was more aggressive (&gt;91% infected spikelets) than PoU (52% infected spikelets). In a third experiment, four signal grass cultivars (Marandu, Basilisk, Piatã, and Xaraés) were inoculated with the same set of 20 isolates. Similarly, signal grass cultivars were generally more susceptible to PoU than PoT. Severity induced by PoU was twice (7.7% severity) as high as PoT (3.8%) and so was the number of conidia/leaf produced by PoU (47,500) and PoT (23,200). Two groups of signal grass cultivars were formed, the most susceptible composed of Marandu and Basilisk and the least susceptible composed of Piatã and Xaraés. Results of our study confirm the host-specialization and the shaping of the blast populations according to the host. We further suggest that grasses in general, especially signal grass, may not play a major role as an inoculum reservoir for PoT, as it harbors mainly the PoU population. However, due to the large extent of pasture-growing regions and cross-infection ability in wheat, signal grass may harbor amounts of PoT inoculum that are sufficient for initiating leaf and head blast epidemics in wheat blast in Minas Gerais state.

Virulence of Phytophthora infestans isolates from potato in Spain

The oomycete Phytophthora infestans is responsible for the disease known as late blight in potato and tomato. It is the plant pathogen that has caused the greatest impact on humankind so far and, despite all the studies that have been made, it remains the most important in this crop. In Spain during the last years a greater severity of the disease has been observed in both, potato and tomato, probably due to genetic changes in pathogen populations described recently. The aim of this study was the characterization of the physiological strains of 52 isolates of P. infestans obtained in different potato-growing areas in Spain. For this purpose, inoculations on detached leaves were performed in order to determine compatibility or incompatibility reactions. A total of 17 physiological races were found. The less frequent virulence factors were Avr5 and Avr8. By studying the epidemiology of the pathogen, a specific breeding program for late blight resistance can be implemented.

Complex adaptive architecture of quantitative resistance erosion in a plant fungal pathogen

Plant pathogens often adapt to plant genetic resistance so characterization of the architecture under-lying such an adaptation is required to understand the adaptive potential of pathogen populations. Erosion of banana quantitative resistance to a major leaf disease caused by polygenic adaptation of the causal agent, the fungus Pseudocercospora fijiensis, was recently identified in the northern Caribbean region. Genome scan and quantitative genetics approaches were combined to investigate the adaptive architecture underlying this adaptation. Thirty-two genomic regions showing host se-lection footprints were identified by pool sequencing of isolates collected from seven plantation pairs of two cultivars with different levels of quantitative resistance. Individual sequencing and phenotyping of isolates from one pair revealed significant and variable levels of correlation be-tween haplotypes in 17 of these regions with a quantitative trait of pathogenicity (the diseased leaf area). The multilocus pattern of haplotypes detected in the 17 regions was found to be highly varia-ble across all the population pairs studied. These results suggest complex adaptive architecture un-derlying plant pathogen adaptation to quantitative resistance with a polygenic basis, redundancy, and a low level of parallel evolution between pathogen populations. Candidate genes involved in quantitative pathogenicity and host adaptation of P. fijiensis were highlighted in genomic regions combining annotation analysis with available biological data.

The relative susceptibility of grapevine rootstocks to black foot disease is dependent on inoculum pressure

Black foot disease of grapevines is a major economic issue for the viticulture industry worldwide. The disease is mainly associated with a complex of pathogen species within the genera Dactylonectria and Ilyonectria. The susceptibility of six grapevine rootstock cultivars to black foot disease under field conditions was assessed. Callused rootstocks of 101-14, 5C, 420A, Riparia Gloire, Schwarzmann and 3309C were planted into soil containing low natural pathogen populations or inoculated with isolates representing the species diversity in New Zealand. Disease incidence, disease severity and dry weight accumulation were assessed after 8 months of growth. Root and shoot dry weights were not significantly affected by inoculation treatment, but differed among rootstock cultivars, with cultivar 420A having the lowest root and shoot dry weight, cultivar 3309C having the largest shoot dry weight and cultivar 5C the largest root dry weight. The relative susceptibility of rootstocks differed significantly depending on whether they were grown under low natural inoculum pressure or a higher pressure in artificially inoculated soil. Schwarzmann and Riparia Gloire rootstock cultivars were the least susceptible under natural low inoculum pressure, but were the most susceptible in inoculated soil. In contrast, 5C was one of the most susceptible under low inoculum levels but was the least susceptible under high pathogen pressure. The result of the study indicate that black foot pathogen inoculum levels in soil affect the relative susceptibility of grapevine rootstocks to infection, and may have implications for the selection of rootstocks for planting.