Objectives The nutrient and water absorption of navel orange are highly dependent on arbuscular mycorrhizal fungi (AM fungi). The community structure and diversity of AM fungi determine the function of ecosystem and navel orange yield. Ganzhou City of Jiangxi Province is the largest navel orange production area in China, known as the “hometown of navel oranges in China”. We studied the AM fungal community characteristics in the main navel orange production areas, so as to provide scientific guidance for the development of AM fungal fertilizer and navel orange industry.

Methods Rhizosphere soil samples were collected in Zhanggong District, Huichang County, and Xinfeng County, the three tyoical navel orange (Citrus sinensis Osbeck cv. Cara) production areas. Illumina MiSeq high-throughput sequencing technology combined with DADA2 algorithm were used to analyze the AM fungal community. Conventional chemical methods were used to analyze the soil chemical properties. Redundancy analysis (RDA) and correlation analysis were used to determine the relationships between AM fungal community and soil properties.

Results The rhizosphere soil chemical properties in the 3 regions were not significantly different, except for alkali-hydrolyzed nitrogen content. A total of 90437 genetic sequences and 186 ASVs were obtained from the rhizosphere soils of navel orange, belonging to 1 phylum, 3 class, 3 orders, 4 family, 4 genera, and 16 species. Among them, Glomus was the absolutely dominant genus, with a relative abundance of 97.70%, while Glomus_sp was the dominant genus, with a relative abundance of 18.52%. The α diversities (ASV number, Shannon index, and Pielous index) of AM fungal communities were significantly different among the three regions. In Xinfeng County, the Shannon index was higher than that in Zhanggong District and Huichang County (P<0.05), the ASV number was higher than that in Huichang County (P<0.05), while the Pielous index was higher than that in Zhanggong District (P<0.05). The AM fungal community structure did not show significant regional differences. The relative abundance of Glomus in the three regions showed a descent order of Zhanggong District>Huichang County>Xinfeng County, while that of Glomus_sp showed an order of Huichang County>Zhanggong District>Xinfeng County. The relative abundance of genera did not show significant regional differences (P>0.05), while the relative abundance of Glomus_Toljander08-Unk1_VTX00222, one of AM fungal species, in Xinfeng County was higher than that in the other two regions (P<0.05). RDA showed that soil organic matter was the most important factor affecting AM fungal diversity in rhizosphere soil of navel orange, with a contribution of 66%, and AM fungal diversity decreased with the increasing of soil organic matter content. However, AM fungal community structure was mainly influenced by soil available phosphorus, alkali-hydrolyzed nitrogen, and organic matter.

Conclusions The α diversity of AMF community in the rhizosphere soil of navel orange exhibits regions differences, while AM fungal community structure shows less regional difference, and increased soil organic matter is adverse to maintain AM fungal community diversity.