Biology subjects

Dumonceaux, T.

Publications and source records attributed to Dumonceaux, T..

6 recordsLinked to original sources

bioRxiv2025

'Candidatus Phytoplasma zeae': community-driven delineation of the maize bushy stunt phytoplasma, a Dalbulus-transmitted corn pathogen confined to the Americas

A novel phytoplasma species, Candidatus Phytoplasma zeae, is proposed based on ecological distinctiveness, vector specificity, whole-genome comparisons, and community consensus. This phytoplasma is associated with maize bushy stunt (MBS) disease in corn (Zea mays) and is transmitted exclusively by Dalbulus maidis and D. elimatus, two leafhopper species endemic to the Americas, and has been reported in Brazil, Colombia, Mexico, Peru, and several U.S. states. Here we sequenced and assembled the genome of MBS phytoplasma strains from Brazil, and U.S. to describe and propose this new species. Although the 16S rRNA gene sequence of the proposed reference strain, MBSP-BRRS, shares >99% identity with that of Ca. Phytoplasma asteris, key nucleotide polymorphisms distinguish Ca. P. zeae from other 16SrI-related phytoplasma species. Average nucleotide identity (ANI) and average amino acid identity (AAI) values between Ca. P. zeae and Ca. P. asteris are 97.70-98.00% and 96.65-96.88%, respectively, both near the established species delineation thresholds. Comparative genomic analyses revealed unique gene clusters in Ca. P. zeae associated with amino acid transport, defense mechanisms, and protein turnover, which may contribute to its specialization in corn. The ecological profile of Ca. P. zeae, including its narrow host range and restricted geographic distribution, supports its recognition as a novel species under Rule c of the IRPCM guidelines. The designation Candidatus Phytoplasma zeae is therefore proposed by members of the research community who have studied this pathogen for over a decade, with the MBSP-BrazilRS strain serving as the reference.

microbiology↗

bioRxiv2024

Loss of PMR4 callose synthase results in salicylic acid-independent and broad-spectrum resistance to clubroot in Arabidopsis and Brassica napus

The clubroot disease caused by protist Plasmodiophora brassicae is one of the most important diseases of Brassica crops. Growing clubroot-resistant cultivars remains the most effective and practical approach to managing clubroot disease. However, resistance gene-mediated immunity is rapidly overcome in the field when new pathotypes arise. In this study, we identified PMR4 as a potential gene target for creating a novel clubroot-resistant source. Recessive PMR4 mutations in Arabidopsis thaliana conferred broad-spectrum resistance to multiple P. brassicae pathotypes, independent of salicylic acid-mediated plant immunity. CRISPR/Cas9-mediated gene-editing was employed to create mutations in two PMR4 orthologs in the B. napus genome, and resulting homozygous mutants exhibited dual resistance to powdery mildew and clubroot. PMR4 is required for the callose deposition at wound and powdery mildew infection sites in leaves. This study reveals that callose deposition in roots is induced by P. brassicae infection and requires PMR4. It appears that the clubroot disease progression is arrested at the primary-to-secondary infection phase in pmr4-1 mutants. Together, this study demonstrates that PMR4-encoded callose synthase is a host susceptibility factor required for P. brassicae to complete its life cycle, and that PMR4 can be targeted against both powdery mildew and clubroot diseases in Brassica crops.

plant biology↗

bioRxiv2023

A new multiplex TaqMan qPCR targeting Clavibacter michiganensis virulence-related genes

Bacterial canker of tomato caused by Clavibacter michiganensis (Cm) is one of the most devastating bacterial diseases affecting the tomato industry worldwide. As the result of Cm colonization of the xylem, the susceptible host shows typical symptoms of wilt, marginal leaf necrosis, stem cankers, and ultimately plant death. However, is the ability of Cm to infect seeds and plants without causing symptoms what makes it an even more dangerous pathogen. Unfortunately, there are no resistant cultivars or effective chemical or biological control methods available to growers against Cm. Its control relies heavily on prevention. The implementation of a rapid and accurate detection tool is imperative to monitor the presence of Cm and prevent its spread. In this study, we developed a specific and sensitive multiplex TaqMan qPCR assay to detect Cm and distinguish it from related bacterial species that affect tomato plants. Two Cm chromosomal virulence-related genes, rhuM and tomA, were used as specific targets. The plant internal control tubulin alpha-3 was included in each of the multiplexes to improve the reliability of the assay. Specificity was evaluated with 37 bacterial strains and more than 120 samples, including other Clavibacter spp. and related and unrelated bacterial pathogens from different geographic locations affecting a wide variety of hosts. Results showed that the assay was able to screen all Cm strains against other related bacteria. The assay was validated on tissue and seed samples following artificial infection and all tested samples accurately detected the presence of Cm. The tool described here is highly specific, sensitive, and reliable for the detection of Cm and allows the quantification of Cm in seeds, roots, stems, and leaves, finding a lower abundance of Cm in the roots compared to the other parts of the plant. The diagnostic assay can also be adapted for multiple purposes such as seed certification programs, surveillance, biosafety, the effectiveness of control methods, border protection, and epidemiological studies.

microbiology↗

bioRxiv2023

Can leafhoppers help us trace the impact of climate change on agriculture?

SUMMARYClimate change is reshaping agriculture and insect biodiversity worldwide. With rising temperatures, insect species with narrow thermal margins are expected to be pushed beyond their thermal limits, and losses related to herbivory and diseases transmitted by them will be experienced in new regions. Several previous studies have investigated this phenomenon in tropical and temperate regions, locally and globally; however, here, it is proposed that climate changes impact on agriculture can be traced through the study of Nearctic migratory insects, specifically leafhoppers. To test this hypothesis, leafhoppers in strawberry fields located in the province of Quebec, eastern Canada, were evaluated. The strawberry-leafhopper pathosystem offers a unique opportunity because leafhoppers can transmit, among other diseases, strawberry green petal disease (SbGP), which is associated with pathogenic phytoplasmas. Here, we found that in the last ten years, the number of leafhoppers has been increasing in correspondence with the number of SbGP cases detected in eastern Canada, reporting for the first time ten species new to eastern Canada and two to the country, although the leafhopper diversity has been seriously affected. Our model using more than 34 000 leafhoppers showed that their abundance is influenced by temperature, a factor that we found also influences the microbiome associated with Macrosteles quadrilineatus, which was one of the most abundant leafhoppers we observed. One of our most striking findings is that none of the insecticides used by strawberry growers can control leafhopper incidence, which could be linked to microbiome changes induced by changing temperatures. We suggest that Nearctic leafhoppers can be used as sentinels to trace the multilayered effects of climate change in agriculture. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/544773v1_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@e984eorg.highwire.dtl.DTLVardef@3146a9org.highwire.dtl.DTLVardef@1160b9aorg.highwire.dtl.DTLVardef@53c39c_HPS_FORMAT_FIGEXP M_FIG C_FIG IN BRIEFThe current climate crisis is reshaping insect biodiversity and abundance, but little is known about the direct effect of this phenomenon on agriculture. In this study, we explored leafhoppers, a group of agriculturally important insect pests and disease vectors, as sentinels of the effect of climate change on agriculture. Our findings indicate that this group of insects can help us to understand the effect of the current climate crisis on insect invasions, diversity, abundance, disease dynamics and insecticide resistance and to take quick action to ensure food security while achieving more sustainable agriculture. HIGHLIGHTSO_LIMigratory leafhoppers benefit from temperature increases C_LIO_LILeafhopper-transmitted diseases have increased in the last decade C_LIO_LINew non-migratory leafhoppers can be found now in Nearctic regions C_LIO_LILeafhopper insecticide resistance could be linked to the insect microbiome C_LI

ecology↗

bioRxiv2020

First report of 'Candidatus Liberibacter asiaticus' affecting sour orange in urban areas of Mayabeque, Cuba

Candidatus Liberibacter asiaticus (CLas) is an unculturable, Gram-negative, phloem restricted plant pathogenic bacterium associated with a very serious disease of citrus worldwide known as Citrus Huanglongbing (HLB). CLas is widely spread in the Americas. In Cuba, CLas has been associated with HLB symptoms and has seriously affected the Cuban citrus industry. In this short communication we discuss the identification of CLas-infected sour orange in urban areas of Mayabeque Province in Cuba, an area previously unexplored for the presence of HLB, and a host widely cultivated in gardens and yards along Cuba. We used for the first time the bacteria molecular barcode chaperonin-60 universal target (cpn60 UT) to identify and to detect CLas in HLB-symptomatic host plants.

microbiology↗

bioRxiv2018

CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR

BackgroundMolecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with universal PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. MethodsWe present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. ResultsThe CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three Domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health.

microbiology↗