Co-cultivating rice plants with Azolla filiculoides modifies root architecture and timing of developmental stages

Innovative strategies for increasing the yield of rice, the staple food for more than half of the global population, are needed to keep pace with the expected worldwide population increase, and sustainably forefront the challenges posed by climate change. Traditionally, in Southern-East Asian countries, rice farming benefits from the use of Azolla spp., either as green manure or as co-cultivated plants, for the supply of nitrogen. Azolla spp. are ferns that, in virtue of their symbiosis with the nitrogen-fixing cyanobacterium Trichormus azollae, fix atmospheric nitrogen and release it to the environment upon decomposition of their biomass. However, if and to what extent actively growing Azolla plants impact on the development of co-cultivated rice plantlets remains to be understood. To address this point here we employed an experimental model to follow the growth and development of roots and aerial organs of rice seedlings when co-cultivated with Azolla filiculoides. We show that actively growing A. filiculoides plants alter the architecture of the roots, the transcriptome of the roots, and the hormonal profiles of both roots and leaves. Overall design: We cultivated rice plants in the presence of actively growing Azolla filiculoides (co-cultivation, R+Af) and in control conditions (rice plants alone, R). At least three boxes per treatment with four rice plants each were employed as replicates for each experiment. RNA from the roots of three biological replicates per treatment at 15 DAT was extracted and sequenced for RNAseq and differential gene expression analysis.