Zinc is an essential minor element for rice growth and human health, which can also change the structure of the microorganisms. However, it remains unclear for the effects of zinc fertilizer on microbiome function in agricultural soils and crops. To solve this research gap, we investigated the relationship between improving rice (Oryza sativa L.) yield, Zn concentration, soil microbial community diversity, and function by the application of Zn fertilizer. The field trials included three rice varieties (Huanghuazhan, Nanjing9108, and Nuodao-9925) and two soil Zn levels (0 and 30 kg ha–1) in Jiangsu province, China. As a test, we studied the variety of soil bacterial composition, diversity, and function using 16S rRNA gene sequencing. The results showed that soil Zn application reduced the diversity of microbial community, but the bacterial network was more closely linked, and the metabolic function of bacterial community was improved, which increased the grain yield (17.34–19.52%) and enriched the Zn content of polished rice (1.40–20.05%). Specifically, redundancy analysis (RDA) and Mantel’s test results revealed soil total nitrogen (TN) was the primary driver that led to a community shift in the rice rhizosphere bacterial community, and soil organic carbon (SOC) was considered to have a strong influence on dominant phyla. Furthermore, network analysis indicated the most critical bacterial taxa were identified as Actinobacteria, Bacteroidetes, Proteobacteria, and Chloroflexi based on their topological roles of microorganisms. KEGG metabolic pathway prediction demonstrated that soil Zn application significantly (p < 0.05) improved lipid metabolism, amino acid metabolism, carbohydrate metabolism, and xenobiotic biodegradation. Overall, their positive effects were different among rice varieties, of which Nanjing-9108 (NJ9108) performed better. This study opens new avenues to deeply understand the plant and soil–microbe interactions by the application of fertilizer and further navigates the development of Zn-rich rice cultivation strategies.

Zinc is an essential minor element for the rice growth and the human health. Applying Zn fertilizer to rice ( Oryza sativa L.) is an effective way to boost yield and grain zinc content. As the most active component in soil, microorganisms can realize a virtuous cycle of soil nutrients and crop growth. However, current studies on the impacts of Zn fertilizer application on crop yield and grain Zn content are inconsistent. The mechanism during the process, especially concerning the soil bacterial community characteristics, is yet unclear. Therefore, it’s important to have a comprehensive understanding of the rice rhizosphere bacterial communities. We took advantage of 16S rRNA gene sequencing and co-occurrence network analysis to study the effects of Zn fertilizer application on the rice grain yield, Zn content and the soil bacterial community. Results showed that Zn application (ZS2, i.e., 10.35 kg ha Zn soil application + 3.10 kg ha foliar spraying) increased the grain yield (17.34%~19.52%) and enriched the Zn content of polished rice (1.40%~20.05%) compared with the control group (ZS0) treatments. This was closely correlated to the soil available Zn (AZ) contents (1.16%~85.69%). Furthermore, soil total nitrogen (TN) was considered as the primary driver which led to a community shift in the rice rhizosphere bacterial community. This was mainly due to the variation in the co-occurrence network which made more complex and stable caused by the Zn fertilizer application. Thus, the interaction between different species was strengthened. During the process, the most critical bacteria taxa were identified as Actinobacteria, Bacteroidetes, Proteobacteria, and Chloroflexi. KEGG metabolic pathway prediction demonstrated that Zn application may improve metabolism functions such as lipid metabolism, amino acid metabolism, carbohydrate metabolism, and xenobiotics biodegradation, which ultimately affected the yield and Zn content of rice grains. However, their positive effects were different among rice cultivars, of which Nanjing-9108 performed better. This study deepens the understanding of the interaction between Zn fertilizer, rice yield, Zn content of rice grain, and soil bacterial structure and further navigates the development of Zn-rich rice cultivation strategies.