Root filtering, rather than host identity or age, determines the composition of root-associated fungi and oomycetes in three naturally co-occurring Brassicaceae

The plant family Brassicaceae includes some of the most studied hosts of plant microbiomes, improving our knowledge of microbial diversity, community assembly rules, and effects on host performance. Compared to bacteria, eukaryotes in the microbiome of Brassicaceae remain understudied, especially under field conditions. Here, we assessed the impact of host identity and age on the assembly of fungal and oomycete root communities, using DNA metabarcoding of roots and associated soil of three annual co-habiting Brassicaceae collected at two growth stages from a site untouched for a long time. Our results showed that communities of root-associated fungi are more diverse and structured across factors than those of oomycetes. In both cases, plant identity and growth stage had little influence on the community structure of fungi and oomycetes, whereas soil/root compartment had a strong effect by filtering, resulting in a reduction of the number of microorganisms in roots as compared to the surrounding soil. The enrichment in roots with respect to soil of specific fungi and oomycetes, such as members of the Helotiales or the Peronosporales, suggests a specialization towards the asymptomatic colonization of plant tissues that could be relevant to host fitness and health.