A synthetic microbiome to promote sulfur utilization: Based on dominant microbes in wild rice rhizosphere

Abstract

Abstract Sulfur (S) is one of the main components of important biomolecules, which has been paid more attention in the anaerobic environment of rice cultivation. In this study, 12 accessions of rice materials, belonging to two Asian rice domestication systems and one African rice domestication system, were used by shotgun metagenomics sequencing to compare the structure and function of rhizosphere microbiome between wild and cultivated rice. Compared with cultivated rice, S-cycling microbial community in wild rice rhizosphere showed higher diversity, closer correlation and lower evenness. Furthermore, the sulfur cycle functional genes were significantly different between wild and cultivated rice rhizosphere in the processes of sulfate reduction and other sulfur compounds conversion, implicating that wild rice had a stronger mutually-beneficial relationship with rhizosphere microbiome. To assess the effects of synthetic microbiomes, the dissimilatory sulfate reduction dominated in wild rice was selected as the direction to improve sulfur utilization in cultivated rice. Comamonadaceae and Rhodospirillaceae, two families containing the genes of two key steps in the dissimilatory sulfate reduction, aprA and dsrA respectively, were isolated to construct the synthetic microbiome. Compared with the control group and the inoculated with different proportions groups, the dissimilatory sulfate reduction in cultivated rice rhizosphere was significantly improved in the inoculated with equal proportions group. It confirmed that the synthetic microbiome can promote the S-cycling in rice, and suggested that may be feasible to construct the synthetic microbiome step by step based on functional genes to achieve the target functional pathway. In summary, this study reveals the response of rice rhizosphere microbial community structure and function to domestication, and provides a new idea for the construction of synthetic microbiome.