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.

本研究以病原菌根肿菌（Plasmodiophora brassicae）侵染与健康的大白菜为研究对象，对比其根际与根系微生物群组成的时间动态变化。接种根肿菌后，研究在5个采样节点开展病害监测，采样覆盖从早期根毛侵染到后期根瘤发育的全病程阶段。根肿病的首发症状于接种后14天（DAI，days after inoculation）出现，并在14至35 DAI期间急剧加重。研究通过对细菌16S与真菌18S分子标记进行高通量DNA测序，表征了健康与接种植株根际土壤及根系的微生物群落结构，并在各采样节点开展对比分析。在健康植株中，变形菌门（Proteobacteria）与拟杆菌门（Bacteroidetes）为大白菜根际与根系微生物群的优势类群。相较于根系，根际细菌群落中放线菌门（Actinobacteria）与厚壁菌门（Firmicutes）的相对丰度更高。此外，健康植株的真菌群落在最后两个采样节点间发生显著转变，尤以植物根系为甚：子囊菌门（Ascomycota）真菌在多数采样阶段占据主导地位，随后被壶菌门（Chytridiomycota）的一类真菌取代。根肿菌的寄生侵染会在根肿病病程的根系次生皮层侵染阶段后期，扰乱根际及根系相关微生物群落的组装过程。在此阶段，根际中的黄杆菌属（Flavisolibacter）与链霉菌属（Streptomyces）、根系中的芽孢杆菌属（Bacillus）的相对丰度在病原菌侵染后显著降低。被根肿菌定殖的植株根际，壶菌门真菌的侵染程度显著更高，这或反映出二者在该微生境中存在互利共生关系。