Biology subjects

Mougel, C.

Publications and source records attributed to Mougel, C..

5 recordsLinked to original sources

bioRxiv2020

Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes

The contribution of surrounding plant microbiota to disease development has led to the postulation of the pathobiome concept, which represents the interaction between the pathogen, the host-plant, and the associated biotic microbial community, resulting or not in plant disease. The structure, composition and assembly of different plant-associated microbial communities (soil, rhizosphere, leaf, root) are more and more described, both in healthy and infected plants. A major goal is now to shift from descriptive to functional studies of the interaction, in order to gain a mechanistic understanding of how microbes act on plant growth and defense, and/or on pathogen development and pathogenicity. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, as well as the molecular response of the plant to the infection, with a dual-RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time-course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes, and three soils harboring High (H), Medium (M) or Low (L) microbiota diversities and displaying different levels of richness and diversity. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, and the modulations were dependent of the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant-host functions potentially involved in the change of plant disease level, such as pathogenicity-related genes (NUDIX effector) in P. brassicae and plant defense-related genes (glucosinolate metabolism) in B. napus. Author summaryThe untapped soil microbiota diversity can influence plant tolerance and resistance to several pests. A better understanding of the mechanisms underlying the plant / pests / microbiota interaction is required to contribute to the improvement of new plant protection methods taking into account sustainability, respect for the environment, and low input utilization. Our work showed that in the Plasmodiophora brassicae / Brassica napus pathosystem, the soil microbiota diversity modulated the disease symptom level and the pathogen development. We discovered that soil microbial composition modulated both the pathogen and the plant expression genes profiles. On one hand, the pathogen transcriptome was mainly modulated by the microbial communities at the end of infection, when the pathogen infects a susceptible plant genotype, and the expression of genes potentially involved in growth and pathogenicity was affected. On the other hand, the plant transcriptome was more modulated by the microbial communities at the early step of infection, in the most resistant genotype and the expression of genes potentially involved in defense was affected. This study provides new insights into the molecular basis of soil microbiota-mediated modulation of plant pest diseases.

pathology↗

bioRxiv2019

MinYS: Mine Your Symbiont by targeted genome assembly in symbiotic communities

Most metazoans are associated with symbionts. Characterizing the effect of a particular symbiont often requires to get access to its genome, which is usually done by sequencing the whole community. We present MinYS, a targeted assembly approach to assemble one particular genome of interest from such metagenomic data. First, taking advantage of a reference genome, a subset of the reads is assembled into a set of backbone contigs. Then, this draft assembly is completed using the whole metagenomic readset in a de novo manner. The resulting assembly is output as a genome graph, allowing to distinguish different strains with potential structural variants coexisting in the sample. MinYS was applied to 50 pea aphid re-sequencing samples, with low and high diversity, in order to recover the genome sequence of its obligatory bacterial symbiont, Buchnera aphidicola. It was able to return high quality assemblies (one contig assembly in 90% of the samples), even when using increasingly distant reference genomes, and to retrieve large structural variations in the samples. Due to its targeted essence, it outperformed standard metagenomic assemblers in terms of both time and assembly quality.

bioinformatics↗

bioRxiv2019

A core microbiota of the plant-earthworm interaction conserved across soils

Microorganisms participate in most crucial soil functions and services benefiting human activities, such as biogeochemical cycles, bioremediation and food production. Their activity happens essentially in hotspots created by major soil macroorganisms, like rhizosphere and cast shaped by plants and earthworms respectively1. While effects of individual macroorganism on soil microbes are documented, no studies attempted to decipher how the mosaic of microhabitats built by multiple macroorganisms and their interaction determine the structure of microbial communities. Here we show a joint shaping of soil bacterial communities by these two macroorganisms, with a prevalent role of plants over earthworms. In a controlled microcosm experiment with three contrasted soils and meticulous microhabitat sampling, we found that the simultaneous presence of barley and endogeic earthworms resulted in non-additive effects on cast and rhizosphere bacterial communities. Using a source-sink approach derived from the meta-community theory2,3, we found specific cast and rhizosphere core microbiota4,5 of the plant-eartworm interaction, detected in all soils only when both macroorganisms are present. We also evidenced a core network of the plant-earthworm interaction, with cosmopolitan OTUs correlated both in cast and rhizosphere of all soils. Our study provides a new framework to explore aboveground-belowground interactions through the prism of microbial communities. This multiple-macroorganisms shaping of bacterial communities also affects fungi and archaea, while being strongly influenced by soil type. Further functional investigations are needed to understand how these core microbiota and core network contribute to the modulation of plant adaptive response to local abiotic and biotic conditions.

ecology↗

bioRxiv2018

Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae

The temporal dynamics of rhizosphere and root microbiota composition was compared between healthy and infected Chinese cabbage plants by the pathogen Plasmodiophora brassicae. When inoculated with P. brassicae, disease was measured at five sampling dates from early root hair infection to late gall development. The first symptoms of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root from healthy and inoculated plants was characterized through high-throughput DNA sequencing of bacterial (16S) and fungal (18S) molecular markers and compared at each sampling date. In healthy plants, Proteobacteria and Bacteroidetes bacterial phyla dominated the rhizosphere and root microbiota of Chinese cabbage. Rhizosphere bacterial communities contained higher abundances of Actinobacteria and Firmicutes compared to the roots. Moreover, a drastic shift of fungal communities of healthy plants occurred between the two last sampling dates, especially in plant roots, where most of Ascomycota fungi dominated until they were replaced by a fungus assigned to the Chytridiomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly at a late step during the root secondary cortical infection stage of clubroot disease. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytridiomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.

ecology↗

bioRxiv2018

Computational analysis of the Plasmodiophora brassicae genome: mitochondrial sequence description and metabolic pathway database design

Plasmodiophora brassicae is an obligate biotrophic pathogenic protist responsible for clubroot, a root gall disease of Brassicaceae species. In addition to the reference genome of the P. brassicae European e3 isolate and the draft genomes of Canadian or Chinese isolates, we present the genome of eH, a second European isolate. Refinement of the annotation of the eH genome led to the identification of the mitochondrial genome sequence, which was found to be bigger than that of Spongospora subterranea, another plant parasitic Plasmodiophorid phylogenetically related to P. brassicae. New pathways were also predicted, such as those for the synthesis of spermidine, a polyamine up-regulated in clubbed regions of roots. A P. brassicae pathway genome database was created to facilitate the functional study of metabolic pathways in transcriptomics approaches. These available tools can help in our understanding of the regulation of P. brassicae metabolism during infection and in response to diverse constraints.

genomics↗