Abundance and diversity of endophytic and rhizospheric diazotrophs associated with rice roots from different rice rotation systems under field conditions

Biological nitrogen fixation contributes greatly to the sustainability of agroecosystems. However, more information is needed about the impact that agricultural intensification, a frequent practice nowadays, would have on diazotrophic communities associated with plants. This work addresses the influence of intensifying rice cropping systems on the abundance, diversity, and structure of diazotrophic communities associated with rice roots (rhizospheric and endophytic bacteria) from a field experiment. Three different rice rotation systems (rice–pasture, rice–soybean, and continuous rice) at two crop growth stages (TBF: tillering before flooding and FF: flowering-flooded) were studied. The results showed that the rhizospheric soils had the greater nifH gene abundance, and the abundance and diversity of rhizospheric and endophytic diazotrophic communities significantly increased at the FF stage. Conversely, nifH abundance in bulk soils remained unaltered. Phylogenetically and metabolically diverse diazotrophic communities were found to be associated with rice roots from the different crop stages and rotations. According to multivariate, clustering and statistical analyses performed on results retrieved by nifH T-RFLP (primers F2/R6 and PolF/PolR and AluI), the interaction of root compartment and crop growth stage (PERMANOVA, p < 0.001) was the major driver of diazotrophic communities. Furthermore, a significant effect of the rice rotation systems on the structure of diazotrophic communities was found (PERMANOVA, p < 0.05), suggesting that crop intensification could impact diazotrophic communities associated with rice plants, which play a key role in plant growth promotion. The implications that this could have should be explored and considered when developing sustainable intensification strategies in rice production.