Mangrove endophytes enhance yield and convey salt tolerance to Nipponbare rice

Global climate change increasingly challenges agriculture with flooding and salinity. Among strategies to enhance crop resilience to these stresses, we showed two mangrove strains that can enhance flooding and salinity tolerance in rice plants. Two strains massively enhanced the growth and yield of Oryza sativa cv. Nipponbare under hydroponic growth conditions with and without salt treatment. The bacteria-induced transcriptome changes in O. sativa roots related to ABA-signaling with suberin deposition in root tissues explain the altered responses of colonized rice plants to hypoxic and saline stress conditions. While enhancing yield and grain quality, bacterially colonized rice plants also show much earlier flowering, thereby massively shortening the life cycle of rice plants and opening the possibility for an additional harvest per year. These results show that microbes can be a powerful tool for enhancing the yield and resilience of rice to hypoxic and saline stress conditions. Oryza sativa plants were grown in growth chambers at 27/25°C (day/night) with a 12:12 h light/dark cycle, the light intensity of 200 µmol photons m−2 s−1, and 70% humidity. For RNASeq analysis, the 5-days-old seedlings were transferred to buckets containing Hoagland solution supplemented with 0 or 100 mM NaCl. After 24h, the shoots and roots were collected separately and flash-frozen in liquid N2 before RNA extraction. Total RNA was extracted from roots and shoots of 6-day-old mock and AK164, AK171 colonized plants using Direct-zol RNA Miniprep Plus Kit following the manufacturer’s instructions (ZYMO RESEARCH; USA). RNA libraries were prepared for sequencing using ....protocol. RNA-seq was carried out on three independent biological replicates.