Microbiome analysis of rice rhizospheric soil in different growth stages using high-throughput amplicon sequencing of 16S rRNA genes

Abstract The rhizosphere of soil is inhabited by a variety of microbes. The rhizospheric microbiome contributes greatly to various aspects like growth, metabolism, and yield. There is only limited information about the composition of the microbiome during different growth stages of the rice crop. Therefore, the goal of the current study was to compare, and analyze the microbial diversity in rice rhizospheric soil among various growth phases like the vegetative phase(before initiation of Panicle), reproductive phase (minimum tillers with grains), and ripening phase (maximum filling of tillers with grains ready for harvest) by adopting next-generation high throughput amplicon sequencing of 16SrRNA gene. This study addressed 5148 OTU that includes microbes belonging to major Phylum Proteobacteria, Acidobacteria, Gemmatimonadetes, Bacteriodetes, Nitrospirae, Actinobacteria, and Chloroflexi during all growth stages of rice. Genera such as Anaeromyxobacter, Candidatus, and Kaistobacter are prevalently present in all growth stages of rice in varying degrees. Interestingly, Genera such as GOUTA19, 4-29, Sulfuricurvum, Thiobacillus, Geobacter, and Nitrospira were present maximum at the vegetative and reproductive stages of rice. Alpha & Beta diversity showed that there were variations between all the growth stages of rice. UPGMA tree revealed the evolutionary lineage of microbial communities present in the ripening stage significantly different from the other two stages of rice. The current results demonstrate that a unique group of bacteria inhabit the rice rhizosphere during three growth phases which play important roles in improving crop health and sustainable productivity.