Iron-nitrogen coupling mediates soil microbial community composition and gene expression during the formation of rusty root in Panax ginseng from three northeast provinces in China

Ginseng, a crucial medicinal plant in China, faces challenges due to rusty roots (GRR). Our early work linked GRR to nitrate-reducing Fe (II) oxidation (NRFO). However, the interaction between the NRFO and soil microorganisms how impact the GRR occurrence remain elusive. To elucidate how iron and nitrogen influence microbial community structure, diversity and functional characteristics during the soil of GRR occurrence. Here, we showed that the GRR occurred might be related to the soil microbial abundance associated with NRFO increased, such as Shewanella, Geobacter and Acidovorax (P < 0.05). Interestingly, LeFSe analysis suggested that soil microorganism (Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium) involved in nitrogen cycling were enriched in GRR soils (P < 0.05, LDA > 2.5). Moreover, structural equation model analysis showed that increasing pH-mediated Fe (II) content and upregulation of expression genes (i.e., K15637) controlling microbial cell death may be significantly correlated with the decrease in bacterial diversity (P < 0.05), thus increasing the occurrence index of GRR (P < 0.01). Additionally, metagenomics function annotations indicated that the genes enriched in cell wall/membrane/envelope biogenesis and the carbohydrate uptakes were decreased, which may also be one of the factors contributing to the aggravation of GRR. Furthermore, we found that the genus of Bryobacter, Sphingobium and Luteibacter enriched in healthy samples soil may inhibit GRR. In conclusion, ironnitrogen coupling alters microbial communities, diversity and gene expression, impacting GRR occurrence. These findings provide a new perspective for understanding the formation mechanism of GRR based on the influence of iron and nitrogen cycle on microbial gene expression.