Specialized microbiomes counteract salinity stress in plants

The root microbiota is crucial for plant productivity and stress tolerance. Still, our understanding of the factors that structure these microbial communities is limited, and we lack a theoretical framework to predict their assemblage and interactions. Here, we used rice as a model system to explore the hypothesis that microbiomes from specific environments enhance plant tolerance to salinity. We used 16S rRNA sequencing to track salinity-induced changes in microbiomes of plants inoculated with either a rice field microbiome, or a halotolerant microbiome, compared to only the seed microbiome. We found, that the root-associated compartments harboured distinct microbiomes, but salinity explained most of the observed variation. At high salinity, plants inoculated with rice field or halotolerant microbiomes displayed enhanced growth compared to plants surviving with the seed microbiome. Generally, the rice field microbiome had the highest plant growth-promoting effect. However, assemblages of the halotolerant microbiome promoted more similar network structures between different salinities. Salinity responsive bacteria and keystone taxa were taxonomically diverse and responded in guilds of taxa to the salinity levels, across the microbiome inoculations. Rice plants interacted with the rice field and halotolerant microbiomes to shape rhizosphere microbial community composition and co-occurrence patterns, supporting plant growth at high salinity.