MIcrobiome and RNA-seq of rice roots and leaves. Effects of applying Trichoderma asperellum to rice (Oryza sativa) roots and leaves on plant-associated microbiome and plant responses

Previous studies showed that dipping rice roots in one specific Trichoderma asperellum strain at the transplanting stage or applying the strain as a foliar spray post transplanting led to significant reduction in rice blast (caused by Magnaporthe oryzae) and increased rice grain yield in Tanzania. We investigated the effect of dipping at transplanting or post-transplanting spraying on root-associated microbiome or leaf epiphytes via am-plicon sequencing, and on plant responses via RNA-seq. Both root dipping and foliar ap-plication with T. asperellum spore suspension only had limited impact on root/rhizosphere microbiome and leaf epiphytes after 1 and 4 weeks of treatment, re-spectively. However, both treatments led to significant and persistent changes in plant responses in leaves. Moreover, root dipping led to greater and more persistent changes in plant responses than foliar spraying. However, although both treatments led to in-creased grain yield in previous field studies, many of induced plant response changes in terms of differentially expressed genes differed in their directional changes between root dipping and foliar spraying, particularly those related to chloroplast activities. The large non-overlapping induced plant changes between root dipping and foliar spraying explain the additive effects of the two treatments in increasing grain yield in previous field stud-ies. The present results also suggest that reduction of blast due to foliar application of T. asperellum is unlikely due to direct antagonism against M. oryzae, but more likely via in-duced plant defence responses. The present results support the use of both microbial application approaches, particularly root dipping, to improve rice productivity in subsist-ence farming.