Microbial community shifts in Pythium ultimum-inoculated suppressive substrates

In this study, the role of compost amendments for the biocontrol of Pythium ultimum was evaluated in bioassays with cucumber (Cucumis sativa L. variety “Chinesische Schlangen”). The addition of compost to the peat-based growing substrates resulted in a significant reduction of disease symptoms of cucumber plants in the presence of P. ultimum compared to pure substrate. Microbial community composition of compost-amended substrates and with different levels of P. ultimum inoculum (0, 5‰) was analyzed by polymerase-chain-reaction-based techniques. To detect and compare dominant bacterial and fungal representatives of suppressive substrate mixes with different pathogen inoculum, 16S and 18S rRNA clone libraries were established. Phylogenetic analysis of the 16S rRNA clones revealed Actinobacteria and α-Proteobacteria to be the prominent classes in the presence of P. ultimum, which are not part of the dominant microflora in the mixes without the pathogen. 18S rRNA sequences for the Pythium-inoculated compost supplemented samples were dominated by Chytridiomycota and Sordariomycetes, whereas in uncontaminated soil–compost mixes, a large part of the sequences were related to Homobasidiomycetes. Thus, it is assumed that the presence of P. ultimum induces distinct shifts in microbial communities favoring to groups known to comprise potential biocontrol agents.