Biology subjects

Kyndt, T.

Publications and source records attributed to Kyndt, T..

4 recordsLinked to original sources

bioRxiv2025

Conserved transcriptional reprogramming in nematode infected root cells

Plant-parasitic nematodes are responsible for important annual losses in crop productivity worldwide1,2. Although the formation of feeding organs within the roots is essential for successful sedentary parasitism3, the molecular mechanisms underlying their development are poorly understood. This is partly because these organs originate from a limited number of root cells4-7, making difficult to capture the transcriptional reprogramming that occurs during the early stages of the infection. Here, we first developed a comparative host-pathogen framework to study the nematode infection process in Arabidopsis and rice. Using a cross-species single-cell transcriptomics approach, we identified a unique molecular signature in infected root cells and show that the cellular reprogramming during these early stages is highly conserved across both host-pathogen interactions. This transcriptional cell reprogramming is associated with stemness acquisition related to de novo organogenesis process. By cell-type specific gene regulatory network analysis, we identified AtATHB2/OsHOX28 as an evolutionary conserved and key regulator of the nematode infection process. Loss-of-function of this regulator in both species results in nematode resistance without affecting root growth. This discovery opens up new avenues for the development of sustainable nematode control strategies that could be translated across crop species.

plant biology↗

bioRxiv2024

Diterpenoid phytoalexins shape rice root microbiomes and their associations with root parasitic nematodes

Rice synthesizes diterpenoid phytoalexins (DPs) are known to operate in defense against foliar microbial pathogens and root-knot nematode Meloidogyne graminicola. Here, we examined the role of DPs in shaping riceassociated root microbiomes in nematode-infested rice paddy soils. Further, we assessed how DPs affect interactions between the root microbiomes and nematode communities, particularly rice root-knot nematodes from the Meloidogyne genus. We used 16S and ITS2 rRNA gene amplicon analysis to characterize the rice root-and rhizosphere-associated microbiomes of DP knock-out mutants and their wild-type parental line, at an early (17 days) and late (28 days) stage of plant development in field soil. Disruption of DP synthesis resulted in distinct composition and structure of microbial communities both relative to the parental/wild-type line but also between individual mutants, indicating specificity in DP-microbe interactions. Moreover, nematode-suppressive microbial taxa, including Streptomyces, Stenotrophomonas, Enterobacter, Massilia, and Acidibacter, negatively correlated with Meloidogyne. Comparative analysis revealed differential enrichment of microbial taxa in the roots of rice diterpenoid phytoalexin (DP) knock-out mutants versus wild-type, suggesting that DPs modulate specific taxa in the rice root microbiome. These findings indicate DPs role in plant-microbiome assembly and nematode interactions, further underscoring the potential of leveraging phytoalexins for sustainable management of crop diseases.

microbiology↗

bioRxiv2020

Genome-wide shifts in histone modifications at early stage of rice infection with Meloidogyne graminicola

Epigenetic processes play a crucial role in the regulation of plant stress responses, but their role in plant-pathogen interactions remains poorly understood. Although histone modifying enzymes have been observed to be deregulated in galls induced by root-knot nematodes (RKN, Meloidogyne graminicola) in rice, their influence on plant defence and their genome-wide impact have not been comprehensively investigated. In this study, we applied 3 chemical inhibitors of histone modifying enzymes on rice 24h before inoculation with RKN. Despite their distinct described effects on histone modifications, application of different concentrations led in all cases to reduced susceptibility to RKN. Infection assays on two overexpression lines of histone lysine methyltransferases and one histone deacetylase showed contrasting results in susceptibility, indicating that each histone mark has a specific role in plant defence against RKN in rice. At genome-wide level, three histone marks, H3K9ac, H3K9me2 and H3K27me3 were studied by chromatin-immunoprecipitation (ChIP)-sequencing on RKN-induced galls at 3 days post inoculation. While levels of H3K9ac and H3K27me3 were strongly enriched, H3K9me2 was generally depleted in galls versus control root tips. Differential histone peaks were generally associated with plant defence related genes. In conclusion, our results indicate that histone modifications respond dynamically to RKN infection, and specifically target plant-defence related genes. One-sentence summaryPost-translational histone modifications show a dynamic genome-wide response to root-knot nematode infection in rice and are specifically associated with plant defence genes.

plant biology↗

bioRxiv2020

A novel metabarcoding strategy for studying nematode communities

Nematodes are widely abundant soil metazoa and often referred to as indicators of soil health. While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the ecology of nematodes remains poorly elucidated, partly due to the lack of reliable and validated sequencing strategies. Objectives of the present study were (i) to compare commonly used primer sets and to identify the most suitable primer set for metabarcoding of nematodes; (ii) to establish and validate a high-throughput sequencing strategy for nematodes using Illumina paired-end sequencing. In this study, we tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition); SSU_04F/SSU_22R (18S rRNA, V1-V2 region); Nemf/18Sr2b (18S rRNA, V6-V8 region) from earlier studies; and MMSF/MMSR (18S rRNA, V4-V5 region), a newly developed primer set from this study. In order to test the primer sets, we used 22 samples of individual nematode species, 20 mock communities, 20 soil samples, 20 spiked soil samples (mock communities in soil), and 4 root/rhizosphere soil samples. We successfully amplified the target regions (I3-M11 partition of the COI gene; V1-V2, V4-V8 region of 18S rRNA gene) from these 86 DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the MMSF/MMSR and Nemf/18Sr2b were efficient in detecting nematode compared to JB and SSU primer sets based on annotation of sequence reads at genus and in some cases at species level. Therefore, these primer sets are suggested for studies of nematode communities in agricultural environments.

ecology↗