Systematic exploration into plant-microbe antagonism using the unicellular algae Chlamydomonas reinhardtii

Microorganisms’ interactions with the host dramatically influence plant growth, development and resilience. Research of negative microbial effects on plants is largely focused on acute plant diseases, but many pathogenic microbes in the soil can cause more subtle, chronic effects on plants. In order to comprehensively delve into the complexity of the plant-microbiota interaction network, we established unique genome-wide approaches utilizing the unicellular green algae Chlamydomonas reinhardtii. We developed both agar-based and soil-based assays and screened ~150 bacterial strains isolated from Arabidopsis thaliana roots for effects on Chlamydomonas growth. Interestingly, we found eight strains that exhibited antagonism towards Chlamydomonas, six of which were pathogenic to Arabidopsis as well. The growth-inhibiting strains are divided into three genera - Burkholderia, Paenibacillus and Pseudomonas. To test whether the pathogenicity was specific to photosynthetic organisms, we tested their effects on several non-photosynthetic microorganisms: E.coli, B. subtilis and S. cereviciae, and found that the two Burkholderia strains inhibited Arabidopsis and Chlamydomonas, but not any of the non-photosynthetic organisms, and did so in a contact-dependent manner. Next, we utilized large null mutant collections as well as UV-mutagenized Chlamydomonas strains to hunt for colonies resistant to bacterial growth inhibition, and detected several candidates. Genetic characterization to follow in both algae and bacteria should be a promising path to elucidate pathogenic mechanisms. Target genes identified can be potential subjects for genetic engineering to improve crop yield and fitness.