Impact of rice straw management strategies on rice rhizosphere microbiomes

Abstract Rice is the third most important crop worldwide. Unfortunately, in most rice-producing countries, crop residues are burned, increasing emissions of greenhouse gases and toxic compounds. Incorporation of rice straw (RS) into the soil, either or not accompanied by a microbial inoculum, may offer a viable alternative. However, the effects of such treatments on soil, including the microbial community structure and function in the next crop cycle, still remain largely unknown. Here, we studied the effect of four different RS management strategies (leaving RS as mulch with or without a microbial inoculum, incorporation of RS into the soil with microbial inoculum, and RS burning) on rice growth and flowering-stage rhizosphere microbiomes. The relevant microbiomes were examined by amplicon sequencing based on the 16S rRNA and ITS1 gene regions. In comparison to the zero situation, all four treatments tended to increase the soil organic carbon content, albeit without significant differences. Furthermore, none of the treatments had major effects on either (rice) crop yield or phytopathogen incidence in the next cycle. However, leaving RS as a mulch incited a decrease in soil pH, and showed a trend of reducing yield by up to 1 ton·ha−1. Moreover, the different RS treatments affected the structures and predicted functions of the bacteriomes and fungomes in the rice rhizosphere. The mulching treatment was associated with an enhanced abundance of Acidobacteria, particularly Bryobacter spp. In contrast, the non-mulch treatments incited raised abundances of GammaProteobacteria, Bacteroidia and Campylobacteria. The rice rhizosphere fungomes, consisting mostly of Ascomycota, were less affected by the treatments, although the microbial inoculum was shown to drive the respective fungome structures.