Bacterial abundance and community structure in rice seeds and their influencing factors

Abstract:

[Objective] Seeds are an important pathway for the intergenerational transmission of plant microbiota, while the systematic research on the microbiota carried by seeds remains to be carried out. In this study, we measured the bacterial abundance, determined the bacterial community structure, explored the effects of planting regions and rice cultivars on bacterial abundance and community structure, and identified the core bacterial taxa in rice seeds. [Methods] We collected 36 groups of samples of 18 rice cultivars, each from Hainan and Tianjin in China. Each group of samples contained 5 or 10 DNA samples, each of which was extracted from 3 seeds. The fluorescent quantitative PCR for bacterial 16S rDNA was employed to measure the bacterial abundance in seeds, and the factors influencing the abundance were explored. The 16S rDNA amplicon sequencing was performed to determine the bacterial community structure in seeds. Furthermore, bioinformatics tools were used to analyze the factors influencing bacterial community structure and the core bacterial taxa. [Results] We measured the bacterial abundance of 1 080 rice seeds and found that endophytic bacteria existed in the rice seeds after surface sterilization, with the average abundance of 1.53×10⁶ per gram of seeds. The bacterial abundance in seeds was affected by rice cultivars rather than planting regions. We measured the bacterial community structure of 180 amplicon libraries and found that the bacterial community in rice seeds was similar to that in rice plants, both dominated by Proteobacteria. Planting regions significantly affected the bacterial community structure in rice seeds. The rice seeds from different planting regions were clearly separated in principal co-ordinate analysis, while there was no significant difference between japonica and indica. In addition, rice seeds had core bacterial taxa, with the relative abundance up to 85.56%. [Conclusion] This study systematically revealed the bacterial abundance and community structure in rice seeds and their influencing factors, providing data and methods for using seed-borne microorganisms to improve rice health.