Development of Primers and Probes for Genus and Species Specific Detection of 'Candidatus Liberibacter Species' by Real-Time PCR

Multiplex Quantitative PCR for the Detection of Bacteria Associated with Huanglongbing 'Candidatus Liberibacter asiaticus,' 'Ca. L. americanus,' and 16Sr IX Group Phytoplasma

The occurrence of 'Candidatus Liberibacter' spp. and 'Ca. Phytoplasma' spp. associated with blotchy mottle symptoms poses challenges to huanglongbing (HLB) diagnosis using molecular techniques. The ability to detect multiple targets simultaneously and specifically is a key aspect met by quantitative PCR (qPCR). A set of primers and hydrolysis probes useful in either single or multiplex reactions for the detection and quantification of HLB-associated bacteria were developed. Sequences from conserved genes of the ribosomal proteins for Liberibacter and phytoplasma circumvent the lack of specificity and cross-reactivity problems related to 16Sr DNA gene amplification, allowing precise and specific detection of HLB-associated bacteria in citrus and in the Liberibacter vector, Diaphorina citri. The triplex reaction exhibited high quality and precision as a robust tool for quantifying 'Ca. L. asiaticus' (CLas), 'Ca. L. americanus' (CLam), and 16Sr IX phytoplasma. Triplex qPCR showed consistent results and comparable sensitivity to the ribonuclease reductase test, although quantification cycle (Cq) values were higher when compared with 16SrDNA qPCR. Detection tests using field samples indicate that the qPCR triplex can identify HLB-associated bacteria in samples with varying levels of symptoms, ranging from typical to asymptomatic. Assessment of field samples from growers indicated more than 78.6% had Cq lower than 35.0, below the cutoff established for qPCR reactions used in this work. qPCR triplex is a safe, specific, and sufficiently sensitive technique for detecting CLas, CLam, and 16Sr IX phytoplasma simultaneously, in both citrus and D. citri samples. Its application is of importance in assisting growers in making decisions for HLB management.

A Transmission Assay of 'Candidatus Liberibacter asiaticus' Using Citrus Phloem Sap and Topical Feeding to Its Insect Vector, Diaphorina citri

'Candidatus Liberibacter asiaticus', the putative causal agent of citrus greening disease, is transmitted by the Asian citrus psyllid, Diaphorina citri, in a propagative, circulative, and persistent manner. Unfortunately, 'Ca. L. asiaticus' is not yet available in pure culture to carry out Koch's postulates and to confirm its etiology. When a pure culture is available, an assay to test its infectivity in both the insect vector and the plant host will be crucial. Herein, we described a transmission assay based on the use of phloem sap extracted from infected citrus plants and topical feeding to D. citri nymphs. Phloem sap was collected by centrifugation, diluted with 0.1 M phosphate buffer pH 7.4 containing 20% (wt/vol) sucrose and 0.1% ascorbic acid (wt/vol) as an antioxidant, and delivered to third through fifth instar nymphs by placing droplets on the mouthparts. Nymphs unfolded the stylets and acquired the phloem sap containing the bacterial pathogen. Nymphs were then placed onto Citrus macrophylla seedlings (10 nymphs per seedling) for an inoculation period of 2 weeks. A transmission rate of up to 80% was recorded at 6 months postinoculation. The method could be a powerful tool to test the transmissibility of the bacterial pathogen after various treatments to reduce the viability of the bacteria or to block its transmission. In addition, it might be a potent assay to achieve Koch's postulates if a pure culture of 'Ca. L. asiaticus' becomes available.

Potential of resistance inducers for citrus huanglongbing management via soil application and assessment of induction of pathogenesis-related protein genes

Huanglongbing (HLB) or citrus greening currently is the most devastating citrus disease worldwide. Unfortunately, no practical cure has been available up to now. This makes the control of HLB as early as possible very important to be conducted. The objective of this study was to investigate the efficacy of the application of salicylic acid (SA) and Phenylacetic acid (PAA) on one-year-old seedlings of different citrus species (Citrus reticulata, C. sinensis, C. aurantifolii) growing on C. volkameriana and C. aurantium by soil drench methods. Factorial analysis of variance showed the percent change in "Candidatus Liberibacter asiaticus" titer and disease severity on a different combination of citrus species growing on the two rootstocks treated with inducers and Oxytetracycline (OTC) were significantly different compared to the untreated plants. SA alone or in combination with OTC provided excellent (P-value < 0.05) control of HLB based on all parameters. The interaction between both factors (Rootstocks x Citrus species) significantly influenced the Ct value (P-value = 0.0001). "Candidatus Liberibacter asiaticus" titer in plants treated with OTC was reduced significantly with a range of -18.75 up to -78.42. Overall, the highest reduction was observed in the application of OTC on sweet orange growing on C. volkameriana (-78.42), while the lowest reduction was observed in the same cultivar which was treated with a combination of SA and OTC (-3.36). Induction of pathogenesis-related (PR) genes, i.e., PR1, PR2, and PR15, biosynthesis of Jasmonic acid and ethylene which are also important pathways to defense activity were also significantly increased in treated plants compared to untreated plants. This study suggests that the application of inducer alone is acceptable for HLB management. We proposed the application of SA and PAA as a soil drench on the citrus seedlings as promising, easy, and environmentally safe for HLB disease control on citrus seedlings.

A new and accurate qPCR protocol to detect plant pathogenic bacteria of the genus 'Candidatus Liberibacter' in plants and insects

Four pathogenic bacterial species of the genus 'Candidatus Liberibacter', transmitted by psyllid vectors, have been associated with serious diseases affecting economically important crops of Rutaceae, Apiaceae and Solanaceae families. The most severe disease of citrus plants, huanglongbing (HLB), is associated with 'Ca. Liberibacter asiaticus' (CaLas), 'Ca. Liberibacter americanus' (CaLam) and 'Ca. Liberibacter africanus' (CaLaf), while 'Ca. Liberibacter solanacearum' (CaLsol) is associated with zebra chip disease in potatoes and vegetative disorders in apiaceous plants. Since these bacteria remain non-culturable and their symptoms are non-specific, their detection and identification are done by molecular methods, mainly based on PCR protocols. In this study, a new quantitative real-time PCR protocol based on TaqMan probe, which can also be performed in a conventional PCR version, has been developed to detect the four known phytopathogenic species of the genus Liberibacter. The new protocol has been validated according to European Plant Protection Organization (EPPO) guidelines and is able to detect CaLas, CaLam, CaLaf and CaLsol in both plants and vectors, not only using purified DNA but also using crude extracts of potato and citrus or psyllids. A comparative analysis with other previously described qPCR protocols revealed that this new one developed in this study is more specific and equally or more sensitive. Thus, other genus-specific qPCR protocols have important drawbacks regarding the lack of specificity, while with the new protocol there was no cross-reactions in 250 samples from 24 different plant and insect species from eight different geographical origins. Therefore, it can be used as a rapid and time-saving screening test, as it allows simultaneous detection of all plant pathogenic species of 'Ca. Liberibacter' in a one-step assay.

Nontargeted metabolomics-based multiple machine learning modeling boosts early accurate detection for citrus Huanglongbing

Early accurate detection of crop disease is extremely important for timely disease management. Huanglongbing (HLB), one of the most destructive citrus diseases, has brought about severe economic losses for the global citrus industry. The direct strategies for HLB identification, such as quantitative real-time polymerase chain reaction (qPCR) and chemical staining, are robust for the symptomatic plants but powerless for the asymptomatic ones at the early stage of affection. Thus, it is very necessary to develop a practical method used for the early detection of HLB. In this study, a novel method combining ultra-high performance liquid chromatography/mass spectrometry (UHPLC/MS)-based nontargeted metabolomics and machine learning (ML) was developed for conducting the early detection of HLB for the first time. Six ML algorithms were selected to build the classifiers. Regularized logistic regression (LR-L2) and gradient-boosted decision tree (GBDT) outperformed with the highest average accuracy of 95.83% to not only classify healthy and infected plants but identify significant features. The proposed method proved to be practical for early detection of HLB, which tackled the shortcomings of low sensitivity in the conventional methods and avoid the problems such as lighting condition interference in spectrum/image recognition-based ML methods. Additionally, the discovered biomarkers were verified by the metabolic pathway analysis and content change analysis, which was remarkably consistent with the previous reports.

Generous Hosts: 'Candidatus Liberibacter asiaticus' Growth in Madagascar Periwinkle (Catharanthus roseus) Highlights Its Nutritional Needs

'Candidatus Liberibacter asiaticus', the putative causal agent of citrus greening, is not available in pure culture yet. In addition to trees of citrus and citrus relatives, 'Ca. L. asiaticus' can grow in Madagascar periwinkle (Catharanthus roseus). Using gas chromatography-mass spectrometry, we compared the phloem sap composition in sweet orange 'Valencia' (Citrus sinensis) and periwinkle plants after the infection with 'Ca. L. asiaticus'. Interestingly, in contrast to our previous studies of total leaf metabolites, we found that, compared with uninfected phloem sap, the organic acids implicated in the tricarboxylic acid cycle (TCA) cycle including citrate, isocitrate, succinate, fumarate, and malate were reduced significantly in the infected phloem saps of both species. As a result of the reduction of organic acids content, the pH of infected phloem saps was increased. We hypothesize that the bacterial growth induces the mitochondrial TCA cycle in parenchyma cells to produce more of these compounds to be used as a bacterial carbon source. Once these compounds reach a low level in the phloem sap, the bacterium may send a signal, yet to be identified, to initiate a feedback loop to further induce the TCA cycle. Phloem blockage might be another reason behind the reduced translocation of TCA cycle intermediates within the phloem. The net result, localized availability of organic acids, likely benefits bacterial growth and may explain the unequal distribution of 'Ca. L. asiaticus' within infected trees. These findings may help in designing media for the pure culturing of 'Ca. L. asiaticus'.

A Review of the 'Candidatus Liberibacter africanus' Citrus Pathosystem in Africa

It has been nearly 100 years since citrus growers in two distinct regions in the northern provinces of South Africa noticed unusual symptoms in their citrus trees, causing significant crop losses. They had no idea that these symptoms would later become part of an almost global pandemic of a disease called greening or huanglongbing (HLB). The rapid spread of the disease indicated that it might be caused by a transmissible pathogen, but it took >50 years to identify the causative agent as 'Candidatus Liberibacter africanus'. Recently, the disease appeared in more African countries, spreading by both infected planting material and Trioza erytreae. To date, five 'Ca. L. africanus' subspecies have been identified in various rutaceous species, with 'Ca. L. africanus subsp. clausenae' the only subspecies for which a biovar was detected in citrus. Efforts to detect and differentiate HLB-causing Liberibacter species are ongoing, and recent developments are discussed here. This review focuses on aspects of the African form of HLB, including its specific bacterial species and subspecies, its main insect vector, its geographic distribution, and current management strategies.

Metabolomic analysis elucidates how shade conditions ameliorate the deleterious effects of greening (Huanglongbing) disease in citrus

Under tropical and subtropical environments, citrus leaves are exposed to excess sunlight, inducing photoinhibition. Huanglongbing (HLB, citrus greening), a devastating phloem-limited disease putatively caused by Candidatus Liberibacter asiaticus, exacerbates this challenge with additional photosynthetic loss and excessive starch accumulation. A combined metabolomics and physiological approach was used to elucidate whether shade alleviates the deleterious effects of HLB in field-grown citrus trees, and to understand the underlying metabolic mechanisms related to shade-induced morpho-physiological changes in citrus. Using metabolite profiling and multinomial logistic regression, we identified pivotal metabolites altered in response to shade. A core metabolic network associated with shade conditions was identified through pathway enrichment analysis and metabolite mapping. We measured physio-biochemical responses and growth and yield characteristics. With these, the relationships between metabolic network and the variables measured above were investigated. We found that moderate-shade alleviates sink limitation by preventing excessive starch accumulation and increasing foliar sucrose levels. Increased growth and fruit yield in shaded compared with non-shaded trees were associated with increased photosystem II efficiency and leaf carbon fixation pathway metabolites. Our study also shows that, in HLB-affected trees under shade, the signaling of plant hormones (auxins and cytokinins) and nitrogen supply were downregulated with reducing new shoot production likely due to diminished needs of cell damage repair and tissue regeneration under shade. Overall, our findings provide the first glimpse of the complex dynamics between cellular metabolites and leaf physiological functions in citrus HLB pathosystem under shade, and reveal the mechanistic basis of how shade ameliorates HLB disease.

Influence of Rootstock on the Leaf Volatile Organic Compounds of Citrus Scion Is More Pronounced after the Infestation with Diaphorina citri

Nowadays, citrus greening or Huanglongbing is considered the most destructive disease in the citrus industry worldwide. In the Americas and Asia, the disease is caused by the putative pathogen, ‘Candidatus Liberibacter asiaticus’ and transmitted by the psyllid vector, Diaphorina citri. It has been shown that volatile organic compounds (VOC) that are released from citrus leaves attract the psyllid vector. Herein, we tested whether the rootstock influenced the stored VOC profile in the scion leaves and if these influences were altered after infestation with D. citri. The VOC profiles of the hexane-extracted leaves of the mandarin hybrid ‘Sugar Belle’ that were grafted on three different rootstocks (C-35, sour orange (SO), and US-897) with and without infestation with D. citri were studied. The GC-MS analysis showed that the scion VOC profiles of the non-infested control trees were similar to each other, and rootstock was not a strong influence. However, after one month of infestation with D. citri, clear differences in the scion VOC profiles appeared that were rootstock dependent. Although the total scion leaf VOC content did not differ between the three rootstocks, the infestation increased scion monoterpenes significantly on US-897 and C-35 rootstock, increased terpene alcohols on US-897 and SO rootstock, and increased sesquiterpenes on SO. Infestation with D. citri significantly reduced fatty acids and fatty acid esters across all of the rootstocks. Therefore, our results suggest that rootstock choice could influence scions with an inducible volatile defense by enhancing the amounts of VOCs that are available for repelling vectors or for signaling to their natural enemies or parasitoids. According to this study, US-897 may be the best choice among the three that were studied herein, due to its diverse and robust VOC defense response to infestation with D. citri.

Potato Zebra Chip: An Overview of the Disease, Control Strategies, and Prospects

Potato (Solanum tuberosum L.) is an important food crop worldwide. As the demand for fresh and processed potato products is increasing globally, there is a need to manage and control devastating diseases such as zebra chip (ZC). ZC disease causes major yield losses in many potato-growing regions and is associated with the fastidious, phloem-limited bacterium Candidatus Liberibacter solanacearum (CLso) that is vectored by the potato-tomato psyllid (Bactericera cockerelli Šulc). Current management measures for ZC disease mainly focus on chemical control and integrated pest management strategies of the psyllid vector to limit the spread of CLso, however, they add to the costs of potato production. Identification and deployment of CLso and/or the psyllid resistant cultivars, in combination with integrated pest management, may provide a sustainable long-term strategy to control ZC. In this review, we provide a brief overview of the ZC disease, epidemiology, current management strategies, and potential new approaches to manage ZC disease in the future.

Effect of Adjuvants on Oxytetracycline Uptake upon Foliar Application in Citrus

Recently in Florida, foliar treatments using products with the antibiotics oxytetracycline and streptomycin have been approved for the treatment of citrus Huanglongbing (HLB), which is caused by the putative bacterial pathogen ‘Candidatus Liberibacter asiaticus’. Herein, we assessed the levels of oxytetracycline and ‘Ca. L. asiaticus’ titers in citrus trees upon foliar applications with and without a variety of commercial penetrant adjuvants and upon trunk injection. The level of oxytetracycline in citrus leaves was measured using an oxytetracycline ELISA kit and ‘Ca. L. asiaticus’ titer was measured using quantitative PCR. Low levels of oxytetracycline were taken up by citrus leaves after foliar sprays of oxytetracycline in water. Addition of various adjuvants to the oxytetracycline solution showed minimal effects on its uptake by citrus leaves. The level of oxytetracycline in leaves from trunk-injected trees was higher than those treated with all foliar applications. The titer of ‘Ca. L. asiaticus’ in the midrib of leaves from trees receiving oxytetracycline by foliar application was not affected after four days and thirty days of application, whereas the titer was significantly reduced in oxytetracycline-injected trees thirty days after treatment. Investigation of citrus leaves using microscopy showed that they are covered by a thick lipidized cuticle. Perforation of citrus leaf cuticle with a laser significantly increased the uptake of oxytetracycline, decreasing the titer of ‘Ca. L. asiaticus’ in citrus leaves upon foliar application. Taken together, our findings indicate that trunk injection is more efficient than foliar spray even after the use of adjuvants. Our conclusion could help in setting useful recommendations for the application of oxytetracycline in citrus to improve tree health, minimize the amount of applied antibiotic, reduce environmental exposure, and limit off-target effects.

Species-specific genomic sequences for classification of bacteria

Modern bacterial classification relies on genomic relatedness. Genetic variation in bacterial populations present a big challenge for taxonomic classification and recently several bacterial species have been reclassified based on the intra-species genome comparison. These were facilitated by next generation sequencing technologies and advances in genome comparison approaches which led to the rearrangement of diverse bacterial species and revolution in the microbial classification system. One of the outcome of these studies is the development of suitable DNA barcodes as reliable and cost-effective method for identifying various bacterial genera. Towards refining this further, we have applied a genome comparison approach in 1104 bacterial genome assemblies (excluding plasmids) to identify unique genomic segments among intra-species genome assemblies. Using extensive bioinformatics analysis, we have identified species-specific genomic regions and designed unique primers for 100 different species (belonging to 62 genera) which includes 62 pathogenic and 13 opportunistic pathogenic bacterial species and built a database (http://slsdb.manipal.edu/bact/). These species-specific genomic regions will have a major impact on in silico and molecular methods aimed at bacterial classification and identification. These may also serve as better DNA barcodes than the markers currently used for delineation of bacteria and may also find application in various translational research programs.

Field Detection of Citrus Huanglongbing Associated with ' Candidatus Liberibacter Asiaticus' by Recombinese Polymerase Amplification within 15 min

' Candidatus Liberibacter asiaticus' (Las) is the most prevalent bacterium associated with huanglongbing, which is one of the most destructive diseases of citrus. In this paper, an extremely rapid and simple method for field detection of Las from leaf samples, based on recombinase polymerase amplification (RPA), is described. Three RPA primer pairs were designed and evaluated. RPA amplification was optimized so that it could be accomplished within 10 min. In combination with DNA crude extraction by a 50-fold dilution after 1 min of grinding in 0.5 M sodium hydroxide and visual detection via fluorescent DNA dye (positive samples display obvious green fluorescence while negative samples remain colorless), the whole detection process can be accomplished within 15 min. The sensitivity and specificity of this RPA-based method were evaluated and were proven to be equal to those of real-time PCR. The reliability of this method was also verified by analyzing field samples.

Rapid, Sensitive, and Carryover Contamination-Free Loop-Mediated Isothermal Amplification-Coupled Visual Detection Method for 'Candidatus Liberibacter asiaticus'

Huanglongbing is a devastating citrus disease, and 'Candidatus Liberibacter asiaticus' (Las) is the most prevalent huanglongbing-associated bacterium. Its field detection remains challenging. In this work, a visual, rapid, sensitive, and carryover contamination-free method was developed for field detection of Las. Leaf samples were treated with 500 μL of 0.5 M sodium hydroxide solution for 3 min, and 50-fold dilutions were directly amplified by loop-mediated isothermal amplification. Then, a novel SYTO-9-based visual detection method was used to evaluate amplification results without uncapping operation. Negative samples remained colorless, while positive samples generated obvious green fluorescence, which could be easily distinguished by the naked eye with a mini-fluorescent-emission cartridge developed originally. The proposed detection method could be accomplished within 40 min and is about 100 times more sensitive than conventional TaqMan polymerase chain reaction. The reliability of this method was also verified by analyzing practical samples.

Relative Abundance of Potato Psyllid Haplotypes in Southern Idaho Potato Fields During 2012 to 2015, and Incidence of 'Candidatus Liberibacter solanacearum' Causing Zebra Chip Disease

Zebra chip (ZC) disease, a serious threat to the potato industry, is caused by the bacterium 'Candidatus Liberibacter solanacearum' (Lso). Five haplotypes (hapA to hapE) of this pathogen have been described so far in different crops, with only hapA and hapB being associated with ZC in potato. Both haplotypes are vectored and transmitted to a variety of solanaceaeous plants by the tomato/potato psyllid, Bactericera cockerelli (Šulc). Psyllids are native to North America, and four haplotypes have been identified and named based on their predominant geographic association: Northwestern, Central, Western, and Southwestern. Although all psyllid haplotypes have been found in southern Idaho potato fields, data on relative haplotype abundances and dynamic changes in the fields over time have not previously been reported. Here, psyllid samples collected in Idaho potato fields from 2012 to 2015 were used to clarify spatial and temporal patterns in distribution and abundance of psyllid and Lso haplotypes. A shift from hapA toward hapB population of Lso was revealed during these four seasons, indicating possible evolution of Lso in Idaho fields. Although we confirmed that Western psyllids were the most abundant by far during the four seasons of observation, we also observed changes in abundance of other haplotypes, including increased diversity of psyllid haplotypes during 2015. Seasonal changes observed for the Northwestern and Central haplotypes could potentially be linked to psyllid migration and/or habitat changes. South-central Idaho exhibited more diversity in psyllid haplotypes than southwestern Idaho.

Live Population Dynamics of 'Candidatus Liberibacter asiaticus', the Bacterial Agent Associated with Citrus Huanglongbing, in Citrus and Non-Citrus Hosts

Citrus huanglongbing (HLB) is a century-old destructive disease which presents an unprecedented challenge to citrus industries worldwide. In Florida, HLB is associated with the phloem-limited bacterium 'Candidatus Liberibacter asiaticus' and is mainly transmitted by Asian citrus psyllid (Diaphorina citri). Quantification of the pathogen population in a host aids in investigation of virulence mechanisms and disease management. Recently a procedure was developed to detect live bacterial populations using a novel DNA-binding dye, propidium monoazide, in conjunction with real-time polymerase chain reaction (PMA-qPCR). Chinese box orange (Severinia buxifolia) is a common ornamental present in Florida which could host D. citri and 'Ca. L. asiaticus'. For 20 months, the change of the live 'Ca. L. asiaticus' populations in graft- and psyllid-transmitted Valencia sweet orange (Citrus sinensis 'Valencia') and S. buxifolia plants was monitored by PMA-qPCR. Our results showed that the live 'Ca. L. asiaticus' population was significantly lower in the months of December, January, and February than the rest of the year in both hosts. No statistically significant pattern in the total bacterial population was observed in either host. This pattern may indicate a seasonal growth of 'Ca. L. asiaticus' along with the growth of both plants. These new findings should provide useful information on HLB management.

Nested-quantitative PCR approach with improved sensitivity for the detection of low titer levels of Candidatus Liberibacter asiaticus in the Asian citrus psyllid, Diaphorina citri Kuwayama

Candidatus Liberibacter asiaticus (CLas) is a phloem-limited bacterium transmitted by the Asian citrus psyllid, Diaphorina citri, and the presumptive causal agent of citrus greening disease. The current method of detection for CLas within plant and insect samples is by a presence/absence qPCR assay using the CLas 16S rDNA gene target. Although qPCR is highly sensitive, low bacterial titers or suboptimal qPCR conditions can result in false-negatives. Using a nested qPCR assay, we determined the false-negative rate of the 16S presence/absence qPCR assay was greater than 50%. Studies to determine the performance parameters of the qPCR assays for CLas 16S and Wingless (Wg), the D. citri endogenous gene, using plasmid and psyllid DNA, revealed suboptimal and variable performance of the 16S assay in psyllid samples. Average efficiencies and sensitivity limits of the plasmid assays were 99.0% and 2.7 copies of template for Wg, respectively, and 98.5% and 2.2-22.1 copies for 16S, respectively. Variability in efficiency was significantly greater in psyllid samples for both gene targets compared to the corresponding plasmid assays, and efficiencies as low as 76% were obtained for 16S. A secondary structure analysis revealed the formation of two stem-loop structures that block the forward and probe binding sites in the 16S template, which could hinder amplification. In summary, our results suggest that suboptimal qPCR efficiency is not uncommon for the 16S presence/absence qPCR assay, which combined with lowCLas titers in some samples, could contribute significantly to the under-reporting of CLas infection in psyllid and plant samples.