Changes in root-associated bacterial communities across growth stages of salt-tolerant and salt-sensitive rice grown in coastal saline-alkali soils.

Abstract

In this study, the root-associated bacterial communities of salt-tolerant and salt-sensitive rice grown in coastal saline-alkali soils were characterized at three major growth stages (jointing, heading and maturity) using Illumina MiSeq sequencing. The results showed that the growth stage had a stronger influence on endophytic bacterial diversity than the genotype, with diversity decreasing as growth progressed. However, the rhizospheric bacterial diversity was minimally affected by both growth stage and genotype. The variation in both rhizospheric and endophytic bacterial communities was primarily driven by the growth stages, but was also influenced by the genotype. Interestingly, there were distinct differences in changes in taxon abundance between the rhizospheric and endophytic bacterial communities, suggesting that the assembly mechanisms of these communities may differ, particularly in salt-sensitive rice. Additionally, certain genera were found to be enriched in the rhizosphere and endosphere compared to the bulk soil, and this enrichment varied depending on the growth stage and genotype. Notably, the dominant bacterium Clostridium was consistently enriched in the endosphere of salt-tolerant rice throughout all growth stages. This genus was also found to be more abundant overall in the rhizosphere and endosphere of salt-tolerant rice compared to salt-sensitive rice. These findings provide a deeper understanding of the co-evolution between rice and its associated microbes, and offer valuable insights for the isolation and application of beneficial root-associated bacteria in coastal saline-alkali soils.