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

RESEARCH ARTICLE Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae Lionel Lebreton*, Anne-Yvonne Guillerm-Erckelboudt, Kévin Gazengel, Juliette Linglin, Morgane Ourry, Pascal Glory, Alain Sarniguet, Stéphanie Daval, Maria J. ManzanaresDauleux, Christophe Mougel ID IGEPP, INRA, AGROCAMPUS OUEST, Université Rennes, Le Rheu, France a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Lebreton L, Guillerm-Erckelboudt A-Y, Gazengel K, Linglin J, Ourry M, Glory P, et al. (2019) Temporal dynamics of bacterial and fungal communities during the infection of Brassica rapa roots by the protist Plasmodiophora brassicae. PLoS ONE 14(2): e0204195. https://doi.org/ 10.1371/journal.pone.0204195 Editor: Richard A. Wilson, University of NebraskaLincoln, UNITED STATES Received: August 24, 2018 Accepted: January 29, 2019 Published: February 25, 2019 Copyright: © 2019 Lebreton et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. The raw sequence data sets are available on the European Nucleotide Archive database (https:// www.ebi.ac.uk/ena) system under the project accession number PRJEB26948. Root and soil samples accession numbers range from ERS2513216 to ERS2513353 for 16S and 18S rDNA. * Abstract 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. Introduction All plant tissues including roots [1,2], leaves [3,4] and seeds [5,6] are surrounded by a large diversity of microorganisms assembled in microbial communities or microbiota. These microbial assemblies represent a continuum of symbiosis with the plant ranging from parasitic to PLOS ONE | https://doi.org/10.1371/journal.pone.0204195 February 25, 2019 1 / 26 The impact of a pathogen on the plant root and rhizosphere microbiota Funding: This work was supported by a Scientific Installation Aid grant (n˚ 300 01003) to CM from Rennes Métropole (https://metropole.rennes.fr/lesaides-la-recherche?idParent=13&typeParent= taxonomy_term). This work, through the involvement of Bioinformatics service of the GenoSol platform of the infrastructure ANAEEServices, received a grant from the French state through the National Agency for Research under the program “Investments for the Future” (reference ANR-11-INBS-0001), as well as grants from the Regional Council of Bourgogne Franche Comté. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. mutualistic interactions with complex microbe-microbe and microbe-plant interactions. Plant growth and health (including development, nutrition, physiology and defense) is influenced by these hosted complex microbial networks. Indeed, microbiota can stimulate seed germination and plant growth, help plants fight off disease, promote stress resistance, and influence plant fitness [7]. Thus, the plant microbiota extends the capacity of plants to adapt to their environment and contribute in shaping the plant phenotype. Among these plant compartments, root and rhizosphere are the most studied habitats for microbial communities owing to their great potential for plant nutrition and health [1,8,9]. These microbial communities are mainly recruited by the plant from the soil [2,10,11] which is considered as the main microbial seed bank [12]. Many of these microorganisms including Archaea- and Eubacteria, fungi, and oomycetes live in the rhizosphere, defined as the narrow zone of soil that is influenced by root secretions [13,14]. Microbial community assemblies in the rhizosphere are governed by both abiotic and biotic factors. Soil properties, geographical location and land cover in interaction with agronomical practices are the main factors that structure these communities [2,15,16]. Plant species and plant genotypes also determine to a lesser extent which members from the soil pool of microorganisms can grow and thrive in the rhizosphere [10,15,17,18]. Plants may modulate the rhizosphere microbiota to their benefit by selectively stimulating microorganisms showing traits that are beneficial to plant growth and health [9,19]. Rhizodeposits released by plant are known to account for variations of the diversity of microbial communities in the rhizosphere [20]. The modifications of the diversity of microbial communities are then expected to mirror variations of the composition of rhizodeposits. These rhizodeposits include both water-soluble exudates and more complex organic compounds from sloughed-off root cells and tissues [21]. The proportion of photosynthates released in the rhizosphere and composition of the corresponding rhizodeposits have been shown to vary during the plant’s life cycle according to changes in plant physiology during the course of development and the level of symbiotic associations [22]. In addition, the genetic structure of bacterial and fungal commu (...truncated)