Organic farming significantly improves microbial community structure, network complexity, and functional diversity in the Gannan navel orange orchard

In recent years, improper agricultural management practices have led to the loss of biodiversity and poor fruit quality in orchards. Converting conventional farming to organic farming is an environmentally responsible approach to improving sustainable fruit production. However, questions remain regarding how the microbial community responds to different farming practices in citrus trees. Here, we explored and compared the microbial community structure and functional diversity of the Gannan navel orange orchard under organic and conventional farming using 16S rRNA gene sequencing and Biolog Eco-Plate analysis. The results showed that the microbial diversity (α-diversity index) under organic farming was higher than that under conventional farming, especially in the soil and fruit. The predominant bacteria found in the soil, root, leaf, and fruit were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes. However, distinct abundance patterns were observed under different farming practices. Actinobacteria, Bacteroidetes, and Firmicutes were more abundant in root and fruit compartments under organic farming, indicating that organic farming promotes the enrichment of copiotrophic bacteria (r-strategists). Furthermore, organic farming resulted in a considerable increase in the relative abundance of Burkholderia and Streptomyces in root tissues (the genus level), indicating that organic farming probably favors the proliferation of beneficial microorganisms and antagonists of pathogenic species. Interestingly, organic farming exhibited a more complex microbial network. Biolog analysis further revealed higher functional diversity of the soil microbial community under organic farming when compared with that under conventional farming. These findings provide evidence that organic farming improves the microbial community structure and promotes its functional diversity in the citrus orchards, contributing to the overall health and production of the citrus crop.