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Soil fungi communities play a vital role in the plant-soil ecosystem and affect plant growth and health, but the underlying mechanism controlling soil fungi communities in understory wild ginseng soil is still unknown. To study that mechanism, a pot culture experiment adding different leaf litters based on a completely randomized design was carried out. The results indicated that 1990 operational taxonomic units were obtained from eighteen samples. Ascomycota and Basidiomycota, the two dominant phyla, accounted for 84.57% of the total valid reads at the phylum level. The observed species and Chao 1 index in treatment E were significantly lower than those in the other treatments, although no significant differences were found among the Shannon index of all treatments (p > 0.05). Different types of leaf litter significantly changed the fungal community composition; specifically, Ascomycota was higher in broad leaf litter treatments (A, C, D and E) than in the coniferous leaf litter treatment (B), but Basidiomycota showed the opposite trend, indicating that Ascomycota and Basidiomycota could be used to identify the species of coniferous and broad leaves. The active biomarker fungal (Bmf), 36 different phylotypes, were identified by a linear discriminant analysis effect size algorithm in all treatments, and some Bmf may participate in the decomposition of different tree litters. Additionally, the changes in fungal community diversity and composition were closely related to the changes in soil microbial biomass carbon, total nitrogen and available phosphorus in all treatment soils. Overall, our study indicated that leaf litter changed the soil fungal community structure, and some Bmf were directly involved in leaf litter decomposition. Bmf is more indicative and helpful for distinguishing leaf species.

Rusty root is a widespread problem in ginseng production, which can reduce ginseng quality and root price. The formation of rusty root is a complex process caused by multiple factors, primarily soil physicochemical factors and microorganisms. However, the precise roles played by these factors in the development of this disease remain unclear, especially the role of microorganisms. Deciphering the structure of the rhizosphere microbial communities will provide a more comprehensive and deeper understanding of rusty root disease. Rhizosphere microbial communities from five ginseng fields with different rusty root grades and indices were characterized by MiSeq sequencing. The pattern of beta diversity indicated that rusty root disease might be positively correlated with bacterial community structure, but not with fungal community structure. Rusty root may be caused by excessive Fe (II) oxidation and Fe (III) deposition accompanied by aluminum (Al) and manganese (Mn), in which nitrate-dependent Fe (II)-oxidizing bacteria, including Acidobacteria, Chloroflexi, and Nitrospirae, play a driving role. Moreover, the accumulation of iron (Fe), Al, and Mn could enhance growth and weak invasion of some fungi, thus exacerbating the rust symptoms. However, no correlation was found between the relative abundance of the genus Ilyonectria and rusty root grade or index (P > 0.05); suggesting that Ilyonectria species may not be essential for rusty root disease. Thus, the oxidation and deposition of rhizosphere Fe, Al, and Mn facilitated by nitrate-dependent Fe (II)-oxidizing bacteria might be key factors contributing to rusty root disease. Further studies on the inhibition of Fe, Al, and Mn transformation and accumulation, and application of iron/nitrogen-cycling related bacteria in ginseng soil might elucidate effective methods for preventing rusty root.

Continuous cropping of American ginseng (Panax quinquefolius L.) is often associated with the scarcity or unavailability of soil nutrients and an imbalance of rhizosphere microbiota, resulting in low yield and poor plant quality. Inoculation with arbuscular mycorrhizal fungi (AMF) improves plant growth and production by facilitating nutrient acquisition and by modifying the abundance and diversity of rhizosphere microorganisms. In the present study, we investigated the mechanisms by which continuous cropping of American ginseng caused growth inhibition and how AMF biofertilizer application relieved these cropping obstacles. The results showed that: 1) continuous cropping of American ginseng significantly decreased the emergence rate, shoot and root dry weight, rhizosphere soil pH, the contents of ammonium, available phosphorus (P), and available potassium (K) in the rhizosphere, while increasing the root rot disease index and the soil content of nitrate; 2) continuous cropping of American ginseng decreased the diversity of bacteria, while increasing the diversity of fungi, and increased the relative abundances of Acidobacteria and Ascomycota, while decreasing the relative abundances of Actinobacteria, Firmicutes and Zygomycota; 3) in contrast, the application of AMF biofertilizer relieved the negative effects of continuous cropping American ginseng; 4) significant positive correlations were found between Pseudarthrobacter, Streptomyces and the content of ammonium, between Bacillus and the content of available K, and between Mortierella elongata and the content of available P, suggesting that the increase of rhizosphere plant-beneficial bacteria and fungi promoted the contents of available nutrients in the rhizosphere; 5) application of AMF biofertilizer significantly decreased the abundances of soil-borne pathogenic fungi Fusarium oxysporum, F. solani and the deleterious bacteria Candidatus Solibacter. In summary, our results suggest that AMF biofertilizer application improved the continuous cropping of American ginseng growth by increasing the AMF inoculation rate, by recruiting rhizosphere beneficial bacteria and fungi that promote plant-uptake of nitrogen (N) and P, and by suppressing soil-borne pathogens. Therefore, AMF biofertilizer is a probiotic agent that prevents microbial imbalances and nutrient deficiencies during continuous cropping of American ginseng.