Soil contamination alters the willow rhizosphere metatranscriptome and the root-rhizosphere interactome

Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport and landfilling. However, the complexity of the interaction between the willows and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species (Salix caprea hybrid cv. 'S365', S. eriocephala cv. 'S25', S. miyabeana cv. 'SX67' and S. purpurea 'Fish Creek') and the plant root metatranscriptome for one of these willow species (S. purpurea) growing in petroleum-hydrocarbon contaminated and non-contaminated soils on a former petroleum refinery site. Within an overriding effect of soil contamination, microbial transcript abundance patterns in the rhizosphere varied significantly between willow species, mostly in contaminated soils. Significant differences in the abundance of transcripts related to different bacterial and fungal taxa or to hydrocarbon-degradation pathways were observed between willow species. When comparing transcript abundance in contaminated vs. non-contaminated soil for each willow species individually, transcripts for many microbial taxa and functions were significantly more abundant in contaminated rhizosphere soil for S. eriocephala, S. myabeana and S. purpurea, in contrast to what was observed in the rhizosphere of S. caprea. This agrees with the previously reported sensitivity of S. myabeana to contamination, and the superior tolerance of S. myabeana and S. purpurea to soil contamination at that site. A comparison of the rhizosphere metatranscriptome with the plant root metatranscriptome in the S. purpurea species revealed a complete reorganization of the linkages between root and rhizosphere pathways when comparing willows growing in contaminated and non-contaminated soils, suggesting that plant and microbes react differently to contaminants. Overall, our results shed new light onto the response of the willow-microbiota holobiont to soil contamination at the transcriptomic level.