Genomics-Informed Multiplex PCR Scheme for Rapid Identification of Rice-Associated Bacteria of the Genus Pantoea

Establishment and application of the Recombinase-Aided Amplification-Lateral Flow Dipstick detection method for Pantoea ananatis on rice

Pantoea ananatis is a major pathogen that causes the new bacterial blight in rice, and its symptoms very similar to rice bacterial blight. Therefore, there is a dire need for an accurate and rapid method for detecting P. ananatis. In this study, an early and rapid visual detection method for P. ananatis was established. Using GyrB gene as the target sequence, an innovative recombinase-aided amplification detection system integrated with a lateral flow dipstick (RAA-LFD) was constructed. The optimized RAA-LFD detection method can be initiated at body temperature and does not rely on precise instruments. It does not require DNA extraction and can be used directly with plant tissue fluids. The results can be visualized after 10 minutes of amplification. The specificity and sensitivity tests showed that the RAA-LFD method could detect P. ananatis, whereas other common plant pathogens were not detected, and its detection sensitivity for P. ananatis DNA reached 100 copies/µL. The detection of diseased tissues indicated that this method could accurately detect P. ananatis in artificially inoculated rice tissues in the early stages of infection before symptoms. The RAA-LFD detection system established in this study is simple and fast, with visual results, excellent specificity, and high sensitivity. It is semi-quantitative and should be used for the early detection and rapid field diagnosis of new leaf blight, which provides technical support for the early warning and real-time detection of field samples.

Analysis of Italian isolates of Pantoea stewartii subsp. stewartii and development of a real-time PCR-based diagnostic method

Pantoea stewartii subsp. stewartii (Pss) causes Stewart's vascular wilt of maize, and it is responsible for serious crop losses. Pss is indigenous to North America and spreads with maize seeds. The presence of Pss has been notified in Italy since 2015. The risk assessment of the entry of Pss in the EU from the United States through seed trade is in the order of magnitude of hundred introductions per year. Several molecular or serological tests were developed for the detection of Pss and used as official analysis for the certification of commercial seeds. However, some of these tests lack adequate specificity, not allowing to correctly discriminate Pss from P. stewartii subsp. indologenes (Psi). Psi is occasionally present in maize seeds and is avirulent for maize. In this study, several Italian isolates of Pss recovered in 2015 and 2018 have been characterized by molecular, biochemical, and pathogenicity tests; moreover, their genomes have been assembled through MinION and Illumina-sequencing procedures. Genomic analysis reveals multiple introgression events. Exploiting these results, a new primer combination has been defined and verified by real-time PCR, allowing the development of a specific molecular test able to detect the presence of Pss down to the concentration of 103  CFU/ml in spiked samples of maize seed extracts. Due to the high analytical sensitivity and specificity achieved with this test, the detection of Pss has been improved disentangling the inconclusive results in Pss maize seed diagnosis, overcoming its misidentification in place of Psi. Altogether, this test addresses the critical issue associated with maize seeds imported from regions where Stewart's disease is endemic.

A one-step multiplex PCR assay for the detection and differentiation of four species of Clarireedia causing dollar spot on turfgrass

BACKGROUND

Dollar spot (DS) is one of the most destructive and economically important diseases of cool- and warm-season turfgrasses worldwide. A total of six species causing DS disease in the genus Clarireedia have been described, and four of them have been reported to be distributed countrywide in China. Identification of different species of Clarireedia is a prerequisite for the effective management of DS disease.

RESULTS

Here we report a novel polymerase chain reaction (PCR)-based method for the detection and differentiation of the four species of Clarireedia associated with DS on turfgrass in China: C. jacksonii, C. paspali, C. monteithiana and C. hainanense. Species-specific genes were identified for each species by comparative genomics analysis. Four primer pairs were designed and mixed to amplify species-specific PCR fragments with differential sizes for the four species of Clarireedia in a single multiplex PCR assay. No PCR products were generated from the DNA templates of other common fungal pathogens associated with multiple turfgrass diseases. The multiplex PCR method developed can be used for the rapid and accurate detection and differentiation of the four species of Clarireedia from pure cultures as well as from infected turfgrass blades with DS symptoms.

CONCLUSION

The study developed a one-step multiplex PCR assay for the detection and differentiation of four species of Clarireedia causing DS on turfgrass in China, which will have important implications for DS management in China and worldwide. © 2022 Society of Chemical Industry.

Pest categorisation of Pantoea ananatis

The EFSA Plant Health Panel performed a pest categorisation of Pantoea ananatis, a Gram-negative bacterium belonging to the Erwiniaceae family. P. ananatis is a well-defined taxonomic unit; nonetheless, its pathogenic nature is not well defined and non-pathogenic populations are known to occupy several, very different environmental niches as saprophytes, or as plant growth promoting bacteria or biocontrol agents. It is also described as a clinical pathogen causing bacteraemia and sepsis or as a member of the gut microbiota of several insects. P. ananatis is the causal agent of different diseases affecting numerous crops: in particular, centre rot of onion, bacterial leaf blight and grain discoloration of rice, leaf spot disease of maize and eucalyptus blight/dieback. A few insect species have been described as vectors of P. ananatis, among them, Frankliniella fusca and Diabrotica virgifera virgifera. This bacterium is present in several countries in Europe, Africa, Asia, North and South America, and Oceania from tropical and subtropical regions to temperate areas worldwide. P. ananatis has been reported from the EU territory, both as pathogen on rice and maize and as an environmental, non-pathogenic bacterium in rice marshes and poplar rhizosoil. It is not included in EU Commission Implementing Regulation 2019/2072. The pathogen can be detected on its host plants using direct isolation, or PCR-based methods. The main pathway for the entry of the pathogen into the EU territory is host plants for planting, including seeds. In the EU, there is a large availability of host plants, with onion, maize, rice and strawberry being the most important ones. Therefore, disease outbreaks are possible almost at any latitude, except in the most northern regions. P. ananatis is not expected to have frequent or consistent impact on crop production and is not expected to have any environmental impact. Phytosanitary measures are available to mitigate the further introduction and spread of the pathogen into the EU on some hosts. The pest does not satisfy the criteria, which are within the remit for EFSA to evaluate whether the pest meets the definition of a Union quarantine pest. P. ananatis is probably widely distributed in different ecosystems in the EU. It may impact some specific hosts such as onions while on other hosts such as rice it has been reported as a seed microbiota without causing any impact and can even be beneficial to plant growth. Hence, the pathogenic nature of P. ananatis is not fully established.

First report of rice bacterial leaf blight disease caused by Pantoea ananatis in the United States

In August 2021, bacterial leaf blight-like symptoms were observed on 14 out of 570 rice genotypes (Oryza sativa) in research field plots of global rice germplasm grown in Arkansas (eXtra Figure S1. A & B). The disease was characterized by spreading lesions on leaves, panicle sterility and reduced yield in highly susceptible, mature rice germplasm. No spread of disease to nearby plants was observed. Isolations were performed at Colorado State University, where soakates from symptomatic leaves were spread onto nutrient agar. After 72 h at 28°C, uniform, distinct, yellow-colored bacterial colonies were observed. To screen for the presence of common rice bacterial pathogens, PCR amplification directly from colonies or from DNA isolated from symptomatic field-collected leaves was performed. Primers specific for Xanthomonas oryzae pvs. oryzae and oryzicola (Lang et al., 2010), Burkholderia glumae (Echeverri-Rico et al., 2021), and Pseudomonas fuscovaginae (Ash et al., 2014) did not amplify indicating these organisms were not present. Sequencing of 16S rRNA gene (Weisburg et al., 1991) amplicons suggested the bacteria belonged to the genera Pantoea and Sphingomonas (NCBI accession no. OP683332 and OP683333, respectively). Amplicons resulting from primers specific to the gyrB gene region of P. ananatis (Kini et al., 2021) were sequenced and the fragment was compared to the P. ananatis PA13 reference genome using a BLAST analysis. One candidate (AR358) showed 100% identity with the P. ananatis gyrB region. Primers specific for Sphingomonas sp. (Bangratz et al., 2020) confirmed the second candidate (AR359) as a Sphingomonas sp. The identity of P. ananatis was confirmed by the Plant Pathogen Confirmatory Diagnostics Laboratory (Beltsville, MD, USA). To determine pathogenicity, leaves from 7-day-old seedlings of rice (Oryza sativa) cultivar Kitaake were scissor-clip inoculated (Kauffman et al., 1973) with four different treatments and compared to control leaves inoculated with sterile water. Treatments for the experiment consisted of bacterial suspensions (108 CFU/ml) of the two candidate organisms, P. ananatis (strain AR358) or Sphingomonas sp. (strain AR359), individually or in a 1:1 ratio of P. ananatis:Sphingomonas sp., or soakate from infected field tissue. Lesions similar to those observed in the field were only detected on leaves inoculated with P. ananatis or infected field tissue soakate at 7-days post-inoculation (eXtra Figure S1. C). Bacteria were recovered from the leaves of the artificially inoculated seedlings from three treatments (P. ananatis, P. ananatis:Sphingomonas sp. and soakate from the infected field tissue) and were determined to be P. ananatis based on colony morphology, amplification of 16s rRNA, and gyrB sequence data. Our results confirm the pathogenicity of P. ananatis to rice and fulfill Koch's postulates. P. ananatis was also recovered from several similarly diseased rice breeding lines at the University of Arkansas System Division of Agriculture Rice Research and Extension Center. We conclude that P. ananatis is the causal pathogen for leaf blight-like symptoms observed in the global rice cultivars grown in Arkansas. P. ananatis was previously reported as a pathogen on rice in several rice growing regions, including China (Yu et al., 2021), India (Reshma et al., 2022), and Africa (Kini et al., 2017), however, this is the first report of P. ananatis as a pathogen of rice in the United States.

Beneficial Effect and Potential Risk of Pantoea on Rice Production

Bacteria from the genus Pantoea have been reported to be widely distributed in rice paddy environments with contradictory roles. Some strains promoted rice growth and protected rice from pathogen infection or abiotic stress, but other strain exhibited virulence to rice, even causing severe rice disease. In order to effectively utilize Pantoea in rice production, this paper analyzed the mechanisms underlying beneficial and harmful effects of Pantoea on rice growth. The beneficial effect of Pantoea on rice plants includes growth promotion, abiotic alleviation and disease inhibition. The growth promotion may be mainly attributed to nitrogen-fixation, phosphate solubilization, plant physiological change, the biosynthesis of siderophores, exopolysaccharides, 1-aminocyclopropane-1-carboxylic acid deaminase and phytohormones, including cytokinin, indole-3-acetic acid (IAA), auxins, abscisic acid and gibberellic acid, while the disease inhibition may be mainly due to the induced resistance, nutrient and spatial competition, as well as the production of a variety of antibiotics. The pathogenic mechanism of Pantoea can be mainly attributed to bacterial motility, production of phytohormones such as IAA, quorum sensing-related signal molecules and a series of cell wall-degrading enzymes, while the pathogenicity-related genes of Pantoea include genes encoding plasmids, such as the pPATH plasmid, the hypersensitive response and pathogenicity system, as well as various types of secretion systems, such as T3SS and T6SS. In addition, the existing scientific problems in this field were discussed and future research prospects were proposed.

Validation of Species-Specific PCR Assays for the Detection of Pantoea ananatis, P. agglomerans, P. allii, and P. stewartii

Species of Pantoea represent a group of plant pathogenic bacteria that infect a variety of agro-economically important plant species. Among these, a complex of P. ananatis, P. allii, P. agglomerans, and P. stewartii subsp. indologenes cause center rot in onion, resulting in significant economic losses. As species of Pantoea are phenotypically closely related, identification of Pantoea species relies on the sequencing and phylogenetic analysis of housekeeping genes. To aid in rapid identification of Pantoea species, efforts have been made in developing species-specific primers to be used in PCR assays. In the current study, two P. ananatis, one P. allii, one P. agglomerans, and three P. stewartii published primers as well as newly developed P. agglomerans PagR primers were evaluated for their specificity against 79 Pantoea strains, belonging to 15 different species. To ensure that selected primers were evaluated against accurately identified species, sequencing and phylogenetic analysis of housekeeping gene infB were conducted. Thereafter, PCR assays using selected species-specific primers were performed. The results showed that previously described P. ananatis-specific PANA_1008; P. allii-specific allii-leuS; P. stewartii-specific PANST_rpoB, 3614galE, and DC283galE primers; and one newly designed P. agglomerans-specific PagR primer pair were highly specific for their target Pantoea species. They accurately identified these strains into their species and, in some cases, their subspecies level. The findings of the current study will facilitate rapid and reliable identification of P. ananatis, P. agglomerans, P. allii, and P. stewartii.

Detection and Control of Pantoea agglomerans Causing Plum Bacterial Shot-Hole Disease by Loop-Mediated Isothermal Amplification Technique

Plum bacterial shot-hole caused by Pantoea agglomerans (P. agglomerans) is one of the primary bacterial diseases in plum tree planting areas, resulting in abnormal growth of plum trees and severe economic losses. Early diagnosis of P. agglomerans is crucial to effectively control plant diseases. In this study, loop-mediated isothermal amplification (LAMP) analysis for genome-specific gene sequences was developed for the specific detection of P. agglomerans. We designed the LAMP primers based on the gyrB gene of P. agglomerans. The best reaction system was 0.2 μmol·L-1 for outer primer F3/B3 and 1.6 μmol·L-1 for inner primer FIP/BIP. The LAMP reaction was optimal at 65°C for 60 min based on the color change and gel electrophoresis. This technology distinguished P. agglomerans from other control bacteria. The detection limit of the LAMP technology was 5 fg·μl-1 genomic DNA of P. agglomerans, which is 1,000 times that of the traditional PCR detection method. The LAMP technology could effectively detect the DNA of P. agglomerans from the infected leaves without symptoms after indoor inoculation. Furthermore, the LAMP technology was applied successfully to detect field samples, and the field control effect of 0.3% tetramycin after LAMP detection reached 82.51%, which was 7.90% higher than that of conventional control. The proposed LAMP detection technology in this study offers the advantages of ease of operation, visibility of results, rapidity, accuracy, and high sensitivity, making it suitable for the early diagnosis of plum bacteria shot-hole disease.