Metatranscriptomics of the rhizosphere of crop plants

Plant-microbe interactions in the rhizosphere play key roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea, and an oat mutant (sad1) deficient in production of antifungal avenacins. Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than five-fold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, while the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2-oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without PCR bias. This revealed profound differences in the rhizosphere microbiome particularly at the kingdom level between plants.