Response of soil bacterial community composition and function to Gastrodia elata Bl. consecutive monoculture: Insights from metagenomic analysis

Abstract

Gastrodia elata Bl. monoculture practice commonly contributes to yield decline over consecutive planting cycles. Given the critical role of soil microbiota in soil biogeochemical cycling, understanding microbiome shifts under consecutive cultivation could provide insights for yield sustainability. However, knowledge gap remains regarding which microbial taxa response to consecutive monoculture and how they respond. Thus, the composition and function of soil bacterial communities in a field where G. elata had been cultured for one year (CC1), consecutively cultured for 2 years (CC2), and no-tillage control (CK) were compared. Both CC1 and CC2 increased the soil bacterial richness and evenness, as evidenced by ACE (p = 0.0025) and Simpson (p = 0.006) indices. Principal coordinates analysis revealed distinct clustering of bacterial community structures, with CC1 and CC2 samples significantly separated from control (CK) samples (R=0.636, p = 0.001). Comparative analysis showed that CC1 and CC2 treatments significantly reduced the relative abundances of Arthrobacter and Candidatus_Acidoferrum compared to CK, while increasing the abundances of Afipia, Alloacidobacterium, Bradyrhizobium and Burkholderia. Soil pH (R=0.4721, p = 0.009), alkali-hydrolytic nitrogen (AN; R=0.4855, p = 0.012), available phosphorus (AP; R=0.4474, p = 0.014), and total potassium (total K; R=0.5149, p = 0.005) emerged as the key edaphic factors shaping bacterial community structure and composition. G. elata cultivation, either single-cycle or consecutive, significantly reduced the abundance of GT41, GT83, GH109, GH33, and GT5 (p < 0.05). Conversely, AA3_2, GH13_11, GH13_16, GH39, GH51, and GH103 showed the opposite trend. Our findings highlight the complexity of microbial feedback mechanisms and soil-microbiome interactions under G. elata monoculture conditions.