Real-time on-site detection of the three 'Candidatus Liberibacter' species associated with HLB disease: a rapid and validated method

Digital PCR assays for quantifying trichothecene-producing Fusarium species, including Fusarium langsethiae, F. poae, and F. sporotrichioides, in oats

Fusarium fungi cause Fusarium head blight (FHB) in oats, reducing yield and contaminating grains with harmful trichothecene mycotoxins. FHB symptoms in oats are often not visually distinct, necessitating alternative detection methods. We developed digital PCR (dPCR) assays as the most accurate DNA-based method to detect trichothecene-producing Fusarium species commonly found in oats. Building on existing quantitative PCR (qPCR) assays, we developed dPCR assays targeting all trichothecene producers (the Tri5 gene), or specific to F. langsethiae (Fl), F. poae (Fp), and F. sporotrichioides (Fs). All targeted single copy genes, except F. poae which targeted rDNA which is a variable and multi-copy target (and hence not as reliable as the other assays for quantification). Optimized dPCR assays showed excellent linearity (R2 = 0.99) and greater resilience than qPCR to varying oat DNA concentrations. Overall, when comparing assay sensitivity using both fungal and field oat DNA extracts, dPCR assays were superior to qPCR for Tri5, Fl, and Fs, but the converse was true for Fp. Performance comparisons using field samples showed moderate to perfect agreement between qPCR and dPCR for Tri5 and Fl (κ = 0.5 and 0.86) and poor agreement for Fp (κ = 0.00). Strong correlations were observed between the methods for Tri5, Fl, and Fp (r = 0.88-0.97), but unlike dPCR, qPCR did not detect Fs in any of the field samples. We conclude that the dPCR assays for Tri5, Fl, and Fs offer a reliable method for quantification while that for Fp is reliable for fungal detection but less reliable for quantification of the pathogen in field samples.

Huanglongbing as a Persistent Threat to Citriculture in Latin America

Citrus commercial species are the most important fruit crops in the world; however, their cultivation is seriously threatened by the fast dispersion of emerging diseases, including Huanglongbing (HLB) citrus greening. HLB disease is vectored by psyllid vectors and associated with phloem-limited α-proteobacteria belonging to the Candidatus Liberibacter genus. Climatic change and trade globalization have led to the rapid spread of HLB from its origin center in Southeast Asia, causing a great economic impact in the main production areas, including East Asia (China), the Mediterranean basin, North America (the United States), and Latin America (Brazil and Mexico). Despite important advances to understand the HLB epidemiology, Candidatus Liberibacter genetics, psyllid vector control, the molecular citrus-Candidatus Liberibacter interaction, and the development of integral disease management strategies, the study areas have been mostly restricted to high-tech-producing countries. Thus, in this review, we provide an overview of the epidemiology, distribution, genetic diversity, management aspects, and omics analysis of HLB in Latin America, where this information to date is limited.

Assessing delimiting strategies to identify the infested zones of quarantine plant pests and diseases

Following the discovery of a quarantine plant pest or disease, delimitation is urgently conducted to define the boundaries of the infested area, typically through surveys that detect the presence or absence of the pest. Swift and accurate delimitation is crucial after a pest or pathogen enters a new region for containment or eradication. Delimiting an area that is too small allows the pest to spread uncontrollably, while delimited areas that are too large can lead to excessive economic costs, making eradication cost-prohibitive. Despite its significance, there is a lack of comprehensive reviews on delimiting strategies and their effectiveness in managing plant pests; many current practices are ad-hoc and not scientifically based. In this study, we used an individual-based model to simulate the spread of Huanglongbing (citrus greening), a priority EU pest, and evaluated three delimiting strategies across various host distribution landscapes. We found that an adaptive strategy was most effective, especially when tailored to the polycyclic nature of the pest. This underscored the need for specific delimiting approaches based on the epidemiological characteristics of the target pest.

Genetic Signatures of Contrasted Outbreak Histories of "Candidatus Liberibacter asiaticus", the Bacterium That Causes Citrus Huanglongbing, in Three Outermost Regions of the European Union

In an era of trade globalization and climate change, crop pathogens and pests are a genuine threat to food security. The detailed characterization of emerging pathogen populations is a prerequisite for managing invasive species pathways and designing sustainable disease control strategies. Huanglongbing is the disease that causes the most damage to citrus, a crop that ranks #1 worldwide in terms of fruit production. Huanglongbing can be caused by three species of the phloem-limited alpha-proteobacterium, "Candidatus Liberibacter," which are transmitted by psyllids. Two of these bacteria are of highest concern, "Ca. Liberibacter asiaticus" and "Ca. Liberibacter africanus," and have distinct thermal optima. These pathogens are unculturable, which complicates their high-throughput genetic characterization. In the present study, we used several genotyping techniques and an extensive sample collection to characterize Ca. Liberibacter populations associated with the emergence of huanglongbing in three French outermost regions of the European Union (Guadeloupe, Martinique and Réunion). The outbreaks were primarily caused by "Ca. Liberibacter asiaticus," as "Ca. Liberibacter africanus" was only found at a single location in Réunion. We emphasize the low diversity and high genetic relatedness between samples from Guadeloupe and Martinique, which suggests the putative movement of the pathogen between the two islands and/or the independent introduction of closely related strains. These samples were markedly different from the samples from Réunion, where the higher genetic diversity revealed by tandem-repeat markers suggests that the disease was probably overlooked for years before being officially identified in 2015. We show that "Ca. Liberibacter asiaticus" occurs from sea level to an altitude of 950 m above sea level and lacks spatial structure. This suggests the pathogen's medium- to long-distance movement. We also suggest that backyard trees acted as relays for disease spread. We discuss the implications of population biology data for surveillance and management of this threatful disease.

Uncovering the presence of CVPD disease in citrus varieties of South Sulawesi, Indonesia: A molecular approach

BACKGROUND

The citrus vein phloem degeneration (CVPD) disease is one of important diseases that infects citrus plants and threatens global citrus production and quality due to its severe symptoms and rapid spread. In the 2000s, South Sulawesi Province as one of the citrus producers in Indonesia reported CVPD infection. To date, it is still uncertain as to whether the citrus production center has already been rid of the CVPD infection, keeping in mind the low prevalence of certified citrus saplings use and sub-optimal management of plantations by farmers.

RESULTS

Field observation results revealed varied chlorosis symptoms from young to productive cultivation, which certainly makes it appealing to find out the presence of the causative bacterium, as it has yet to be known whether all the leaves with positive chlorosis symptoms carry the bacterium Candidatus Liberibacter asiaticus. Citrus saplings that appear healthy may carry CVPD pathogens as the incubation period of CVPD pathogens in the host plant spans three to five months. Thus, it is necessary to find the right, rapid way to detect the presence of CVPD pathogens in the citrus plant. The most effective method to use is PCR as the bacterium Candidatus L. asiaticus is non-culturable in vitro, but it is detectable using 16S rDNA. Sampling of leaves with CVPD symptoms was conducted purposively from eight varieties in five citrus cultivation locations, i.e., Pangkep, Sidrap, Bantaeng, Luwu Utara, and Kepulauan Selayar Regencies. DNA isolation was carried out following the Genomic DNA Kit (Geneaid) procedure, followed by detection using the specific pathogenic primer pair OI1 (5' GCG CGT ATG CAA TAC GAG CGG C 3') and OI2c (5' GCC TCG CGA CTT CGC AAC CCA T 3').

CONCLUSION

The PCR visualization result shows seven positive samples with DNA fragments measuring 1160 bp. The seven samples were samples of the Key lime, tangerine, Mandarin (cv. batu 55), and Mandarin (cv. selayar), each being derived from Sidrap, Luwu Utara, and Bantaeng. The average disease incidence rate was 66.56 %. Based on the field observation results, the insect vector Diaphorina citri was nowhere to be found in the five citrus cultivation locations in South Sulawesi.