Detection of Viable Xanthomonas fragariae Cells in Strawberry Using Propidium Monoazide and Long-Amplicon Quantitative PCR

A Rapid and Reliable Propidium Monoazide Polymerase Chain Reaction for Detecting Viable Pseudomonas syringae pv. actinidiae

Pseudomonas syringae pv. actinidiae (Psa) is responsible for causing kiwifruit canker disease. The detection of Psa is commonly carried out using normal PCR and culture-based isolation. However, normal PCR does not differentiate between live and dead cells, potentially resulting in the incorrect estimation of the amount of infectious substance in a sample. Such an incorrect estimation could result in unnecessary phytosanitary strategies and control measures. This study attempts to establish a specific assay for detecting only live Psa bacterial cells. To achieve this, a pair of strain-specific primers designed from HopZ3 effector were used, and the traditional PCR method was assessed using a nucleic acid-binding dye (propidium monoazide-PMA), establishing a PMA-PCR system and conditions for detecting live Psa in this study. Sensitivity tests showed a detection limit of 10 cfu/mL and 1 pg/μL. This method was also tested in diseased kiwifruit tissues and can be seen as a rapid and dependable replacement to PCR methods for detecting only those infective kiwifruit materials with viable Psa.

A Quantitative PCR Assay for Specific Detection of Pseudomonas cannabina pv. alisalensis

Pseudomonas cannabina pv. alisalensis is a gram-negative bacterium that causes bacterial leaf blight in Brassica crops, an important disease that could bring severe damage to the host plants. The aim of this study was to develop a tool that can reliably and accurately quantify P. cannabina pv. alisalensis and distinguish it from other closely related bacterial pathogens. Two species and six pathovars of Pseudomonas were tested: three pathovars, P. syringae pv. coriandricola, P. syringae pv. philadelphi, and P. syringae strains from Vicia faba, were found or confirmed to be members of P. cannabina based on the multilocus sequence analysis and repetitive element sequence-based PCR results. The quantitative PCR (qPCR) assay was evaluated for specificity and examined for detection limit in pure bacterial cells and bacteria-spiked plant samples. The assay was applied in monitoring the quantities of the P. cannabina pv. alisalensis DNA over time in inoculated turnip green leaves. The newly developed qPCR assay detected the target DNA in P. cannabina pv. alisalensis suspension as low as 100 CFU/ml and did not detect any of the nontarget bacteria. The qPCR assay detected P. cannabina pv. alisalensis in all the inoculated samples at least 5 days before the symptoms became visible; bacterial quantity increased significantly in the first 3 days after inoculation but slowed down afterward. The new qPCR assay for P. cannabina pv. alisalensis detection will facilitate early detection and disease diagnosis, assist research to provide epidemiological insights for the pathogen, and guide implementation of strategies to manage disease and prevent its spread.

A reliable qPCR technique for detecting viable Xanthomonas arboricola pv. pruni cells

Xanthomonas arboricola pv. pruni (Xap) is the causal agent of bacterial spot of stone fruits and almond (Prunus spp). Detection of Xap is typically carried out using quantitative real-time PCR (qPCR) combined with culture-based isolation. However, qPCR does not differentiate between viable and dead cells, potentially leading to an overestimation of the infective population in a sample. Such overestimation could result in unnecessary phytosanitary measures. The present study aims to develop a specific protocol ideally targeting to detection of only live Xap bacterial cells. To address this challenge, the viable quantitative PCR (v-qPCR) method was evaluated using three nucleic acid-binding dyes: propidium monoazide (PMA), a combination of PMA and ethidium monoazide (EMA), and PMAxx™, an improved version of PMA. PMAxx™ proved to be the most suitable dye for the detection and quantification of living bacterial cells. This methodology was also evaluated in infected plant material over time and can be considered a rapid and reliable alternative to PCR methods for detecting only those putative infective Xap that may pose a risk for Prunus crops. KEY POINTS: • Protocol to detect biofilm and planktonic viable X. arboricola pv. pruni cells. • Host validated protocol. • Benefits, reduction of chemicals in disease control.

New Approaches to Plant Pathogen Detection and Disease Diagnosis

Detecting plant pathogens and diagnosing diseases are critical components of successful pest management. These key areas have undergone significant advancements driven by breakthroughs in molecular biology and remote sensing technologies within the realm of precision agriculture. Notably, nucleic acid amplification techniques, with recent emphasis on sequencing procedures, particularly next-generation sequencing, have enabled improved DNA or RNA amplification detection protocols that now enable previously unthinkable strategies aimed at dissecting plant microbiota, including the disease-causing components. Simultaneously, the domain of remote sensing has seen the emergence of cutting-edge imaging sensor technologies and the integration of powerful computational tools, such as machine learning. These innovations enable spectral analysis of foliar symptoms and specific pathogen-induced alterations, making imaging spectroscopy and thermal imaging fundamental tools for large-scale disease surveillance and monitoring. These technologies contribute significantly to understanding the temporal and spatial dynamics of plant diseases.

Development of a Long-Amplicon Propidium Monoazide-Quantitative PCR Assay for Detection of Viable Xanthomonas arboricola pv. pruni Cells in Peach Trees

Bacterial spot is one of the most serious diseases of peach caused by the pathogen Xanthomonas arboricola pv. pruni (XAP), leading to early defoliation and unmarketable fruit. The pathogen can overwinter in peach twigs and form spring cankers, which are considered the primary inoculum source for early season leaf and fruitlet infection. The amount of overwintering bacterial inoculum plays a critical role for the bacterial spot development, but no reliable quantification method is available. Thus, we developed a long-amplicon propidium monoazide (PMA)-quantitative PCR (qPCR) assay for specific detection of viable XAP cells. The optimized PMA-qPCR assay used 20 μM of PMAxx for pure bacterial suspensions and 100 μM for peach twig tissues. The Qiagen Plant Pro Kit with an additional lysozyme digestion step was the DNA extraction protocol that yielded the best detection sensitivity with the bacteria-spiked peach twig extracts. The PMA-qPCR assay was tested with different mixtures of viable and heat-killed XAP cells in pure bacterial suspensions and bacteria-spiked peach twig tissues. The results showed that this assay enabled sensitive, specific, and accurate quantification of viable XAP cells as low as 103 CFU/ml with the presence of up to 107 CFU/ml of dead XAP cells, while suppressing the amplification of DNA from dead cells. For mixtures of viable and dead cells, the PMA-qPCR results were linearly correlated with the predicted concentrations of viable XAP (R2 > 0.98). Thus, the PMA-qPCR assay will be a suitable tool for quantifying overwintering XAP population on peach trees.

Bacterial Leaf Spot Susceptibility Screening of Chili Pepper Cultivars Using qPCR Determination of Xanthomonas euvesicatoria pv. euvesicatoria Titers

Bacterial leaf spot is a serious disease of chili pepper (Capsicum spp.) caused by Xanthomonas euvesicatoria pv. euvesicatoria. Conventional resistance screening is time and resource intensive. It was considered that a quick and simple determination of cultivar susceptibility could be achieved through estimating bacterial titers of inoculated plants. A SYBR quantitative polymerase chain reaction (qPCR)-based assay was compared with conventional PCR, then used to detect and enumerate pathogen titers in serial dilutions and DNA extracted from infected plant leaves. The qPCR detection limit was approximately 1 CFU µl-1, 10 times more sensitive than conventional PCR. A linear correlation (R2 = 0.994) was obtained from the standard curve comparing plate-truthed serial dilutions of the pathogen with the qPCR cycle threshold. Six strains were used to inoculate cultivars Hugo and Warlock. One strain, X. euvesicatoria pv. euvesicatoria BRIP62403, was consistently the most virulent based on visual symptoms and pathogen titers in planta inferred by qPCR performed on DNA extracted from infected leaves 2 and 6 weeks postinoculation. Visual observations 6 weeks after inoculation were highly correlated (R2 = 0.8254) to pathogen titers. The qPCR method was used to categorize 20 chili pepper cultivars 2 weeks after inoculation. A high positive correlation (R2 = 0.6826) was observed between visual scoring and pathogen titers from 20 chili pepper cultivars, facilitating categorization of susceptible, intermediate, and resistant cultivars. The qPCR approach developed here facilitates susceptibility screening of chili pepper cultivars at an early stage of selection and could be readily adapted to a range of other pathosystems.

Whole-genome sequencing and comparative genome analysis of Xanthomonas fragariae YM2 causing angular leaf spot disease in strawberry

Background

Angular leaf spot disease caused by plant pathogenic bacterium Xanthomonas fragariae seriously threatens strawberry crop production globally.

Methods

In this study, we sequenced the whole genome of X. fragariae YM2, isolated from Yunnan Province, China. In addition, we performed a comparative genome analysis of X. fragariae YM2 with two existing strains of X. fragariae YL19 and SHQP01 isolated from Liaoning and Shanghai, respectively.

Results

The results of Nanopore sequencing showed that X. fragariae YM2 comprises one single chromosome with a contig size of 4,263,697 bp, one plasmid contig size of 0.39 Mb, a GC content ratio of 62.27%, and 3,958 predicted coding genes. The genome of YM2 comprises gum, hrp, rpf, and xps gene clusters and lipopolysaccharide (LPS), which are typical virulence factors in Xanthomonas species. By performing a comparative genomic analysis between X. fragariae strains YM2, YL19, and SHQP01, we found that strain YM2 is similar to YL19 and SHQP01 regarding genome size and GC contents. However, there are minor differences in the composition of major virulence factors and homologous gene clusters. Furthermore, the results of collinearity analysis demonstrated that YM2 has lower similarity and longer evolutionary distance with YL19 and SHQP01, but YL19 is more closely related to SHQP01.

Conclusions

The availability of this high-quality genetic resource will serve as a basic tool for investigating the biology, molecular pathogenesis, and virulence of X. fragariae YM2. In addition, unraveling the potential vulnerabilities in its genetic makeup will aid in developing more effective disease suppression control measures.

Survival of Xanthomonas fragariae on Common Materials

Xanthomonas fragariae causes strawberry angular leaf spot (ALS), an important disease for the strawberry nursery industry in North America. To identify potential inoculum sources, the survival of X. fragariae was examined on the surfaces of 11 common materials found in nurseries: corrugated cardboard, cotton balls, cotton cloth (t-shirt), strawberry leaf, sheet metal, plastic, rubber, Tyvek, wood (balsa), glass (microscope slide), and latex (latex glove). Prefabricated rectangular samples (7.62 by 2.54 cm) of each material were immersed in a bacterial suspension for 15 min, after which the samples were stored at approximately 20°C (room temperature) or -4°C (the cold storage temperature for dormant plants in strawberry nurseries) for 1, 3, 7, 14, 30, 60, 90, 180, 270, and 365 days after inoculation (DAI). After the storage period elapsed, bacteria were recovered from the surfaces of each of the samples with phosphate-buffered saline (PBS)-soaked cotton balls. Survival rate was determined with a viability real-time quantitative PCR procedure and in a plant bioassay that involved rub inoculation of strawberry leaflets with the PBS-soaked cotton balls used to recover bacteria from the samples. Results showed that X. fragariae could survive on all surfaces but that survival rate differed among materials and storage temperature. All materials were capable of harboring viable bacteria up to 7 DAI when stored at -4°C based on the formation of lesions on inoculated leaves in the plant bioassay. The longest survival observed was 270 DAI on cardboard stored at -4°C. At room temperature, cardboard, cotton balls, cotton t-shirt, and strawberry leaf tissue supported small bacterial populations up to 14 DAI. The information from this study can be used to improve sanitation practices for ALS management in strawberry nurseries.

A Long-Amplicon Viability-qPCR Test for Quantifying Living Pathogens that Cause Bacterial Spot in Tomato Seed

Bacterial spot is one of the most serious diseases of tomato. It is caused by four species of Xanthomonas: X. euvesicatoria, X. gardneri, X. perforans, and X. vesicatoria. Contaminated or infected seed can be a major source of inoculum for this disease. The use of certified pathogen-free seed is one of the primary management practices to reduce the inoculum load in commercial production. Current seed testing protocols rely mainly on plating the seed extract and conventional PCR; however, the plating method cannot detect viable but nonculturable cells, and the conventional PCR assay has limited capability to differentiate DNA extracted from viable or dead bacterial cells. To improve the sensitivity and specificity of the tomato seed testing method for bacterial spot pathogens, a long-amplicon quantitative PCR (qPCR) assay coupled with propidium monoazide (PMA-qPCR) was developed to quantify selectively the four pathogenic Xanthomonas species in tomato seed. The optimized PMA-qPCR procedure was evaluated on pure bacterial suspensions, bacteria-spiked seed extracts, and seed extracts of inoculated and naturally infected seed. A crude DNA extraction protocol also was developed, and PMA-qPCR with crude bacterial DNA extracts resulted in accurate quantification of 10⁴ to 10⁸ CFU/ml of viable bacteria when mixed with dead cells at concentrations as high as 10⁷ CFU/ml in the seed extracts. With DNA purified from concentrated seed extracts, the PMA-qPCR assay was able to detect DNA of the target pathogens in seed samples spiked with ≥75 CFU/ml (about 0.5 CFU/seed) of the viable pathogens. Latent class analysis of the inoculated and naturally infected seed samples showed that the PMA-qPCR assay had greater sensitivity than plating the seed extracts on the semiselective modified Tween Medium B and CKTM media for all four target species. Being much faster and more sensitive than dilution plating, the PMA-qPCR assay has potential to be used as a standalone tool or in combination with the plating method to improve tomato seed testing and advance the production of clean seed.

Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.