Production of medicinal tubers of Rehmannia glutinosa is severely hindered by replanting issues. However, a mechanistic understanding of the plant-soil factors associated with replant problems is currently limited. Thus, we aimed to identify the R. glutinosa root exudates, evaluate their potential phytotoxicity and profile the interactions between the plant and its associated rhizobiome. Stereomicroscopy and liquid chromatography coupled to a quadrupole/time of flight mass spectrometer were used to monitor and identify secreted metabolites, respectively. Seedling bioassays were used to evaluate the phytotoxicity of R. glutinosa root exudates. Two complimentary experiments were performed to investigate allelochemical fate in rhizosphere soil and profile the associated microbiota. Root specific microbes were further isolated from R. glutinosa rhizosphere. Impacts of isolated strains were evaluated by co-cultivation on plate and on seedlings in tissue culture, with a focus on their pathogenicity. Interactions between key R. glutinosa root exudates and isolated rhizobiomes were investigated to understand the potential for plant-soil feedbacks. Quantification and phytotoxic analysis of metabolites released from R. glutinosa indicated catalpol was the most abundant and bioactive metabolite in root exudates. Subsequent microbial profiling in soil containing accumulated and ecologically significant levels of catalpol identified several taxa (e.g., Agromyces, Lysobacter, Pseudomonas, Fusarium) that were specifically shifted. Isolation of R. glutinosa rhizobiomes obtained several root specific strains. A significant antagonistic effect between strain Rh7 (Pseudomonas aeruginosa) and two pathogenic strains Rf1 (Fusarium oxysporum) and Rf2 (Fusarium solani) was observed. Notably, the growth of strain Rh7 and catalpol concentration showed a hormesis-like effect. Field investigation further indicated catalpol was increasingly accumulated in the rhizosphere of replanted R. glutinosa, suggesting that interactions of biocontrol agents and pathogens are likely regulated by the presence of bioactive root exudates and in turn impact the rhizo-ecological process. In summary, this research successfully monitored the release of R. glutinosa root exudates, identified several abundant bioactive R. glutinosa secreted metabolites, profiled associated root specific microbes, and investigated the plant-soil feedbacks potentially regulated by catalpol and associated rhizobiomes. Our findings provide new perspectives toward an enhanced understanding R. glutinosa replant problems.

Rhizosphere bacteria play important role in soil nutrient cycling and plant growth, and their richness and diversity are influenced by soil management systems. However, the specific changes in tobacco rhizosphere bacterial community structure in continuous and tobacco-rice rotation cropping systems remain uninvestigated. In this study, soil properties and the composition of the rhizosphere bacterial community in tobacco monocropping and tobacco-rice rotation cropping systems were analyzed. Moreover, the comparison of rhizosphere bacterial community structure between tobacco continuous and tobacco-rice rotation cropping systems was performed via high-throughput sequencing. The changes in the composition of the rhizosphere bacterial community were investigated at different tobacco growth stages. The results showed that continuous tobacco cropping increased the soil soluble organic carbon (SOC), total nitrogen (TN), and the content of other nutrients (e.g., available phosphorus and available potassium) compared to tobacco-rice rotation cropping. However, monocropping decreased bacterial alpha-diversity and altered the community composition when compared to the rotation cropping system. At the phylum level, the relative abundance of Proteobacteria, Gemmatimonadetes, and Bacteroidetes increased in the continuous cropping soil, while that of Acidobacteria, Firmicutes, and Actinobacteria decreased. At the genera level, the average abundance of the dominant genus Bacillus varied from 12.96% in continuous cropping libraries to 6.33% in the rotation cropping libraries (p < 0.05). Additionally, several other taxa, such as o_Acidobacteriales and Candidatus_Solibacter decreased from 7.63 to 6.62% (p < 0.05) and 4.52 to 2.91% (p < 0.05), respectively. However, the relative abundance of f_Gemmatimonadaceae and c_Subgroup_6 showed an increase of 1.46% (p < 0.05) and 1.63% (p < 0.05) in the tobacco-rice rotation cropping system, respectively. The results of NMDS indicated that the rhizobacteria community structure differed in the two cropping systems. In tobacco, the rhizosphere bacterial community structure showed no significant changes in the prosperous long-term stage and topping stage, but the composition changed significantly in the mature stage.

Consecutive monoculture practice facilitates enrichment of rhizosphere pathogenic microorganisms and eventually leads to the emergence of replant disease. However, little is known about the interaction relationship among pathogens enriched in rhizosphere soils, Nucleotide binding-leucine-rich repeats (NB-LRR) receptors that specifically recognize pathogens in effector-triggered immunity (ETI) and physiological indicators under replant disease stress in Rehmannia glutinosa. In this study, a controlled experiment was performed using different kinds of soils from sites never planted R. glutinosa (NP), replanted R. glutinosa (TP) and mixed by different ration of TP soils (1/3TP and 2/3TP), respectively. As a result, different levels of TP significantly promoted the proliferation of Fusarium oxysporum f.sp. R. glutinosa (FO). Simultaneously, a comparison between FO numbers and NB-LRR expressions indicated that NB-LRRs were not consecutively responsive to the FO proliferation at transcriptional levels. Further analysis found that NB-LRRs responded to FO invasion with a typical phenomenon of “promotion in low concentration and suppression in high concentration”, and 6 NB-LRRs were identified as candidates for responding R. glutinosa replant disease. Furthermore, four critical hormones of salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and abscisic acid (ABA) had higher levels in 1/3TP, 2/3TP and TP than those in NP. Additionally, increasing extents of SA contents have significantly negative trends with FO changes, which implied that SA might be inhibited by FO in replanted R. glutinosa. Concomitantly, the physiological indexes reacted alters of cellular process regulated by NB-LRR were affected by complex replant disease stresses and exhibited strong fluctuations, leading to the death of R. glutinosa. These findings provide important insights and clues into further revealing the mechanism of R. glutinosa replant disease.

Rehmannia chingii (2n = 2x = 28) is an important folk medicinal plant with high therapeutic value, particularly due to its richness in iridoid glycosides. However, research on its evolution and gene functional identification has been hindered by the lack of a high-quality genome. Here, we present the 1.169 Gb telomere-to-telomere (T2T) genome sequence of R. chingii. Phylogenetic analysis confirms that Rehmannia belongs to the Orobanchaceae family. We find that structural genes of the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway and the iridoid pathway are predominantly expressed in R. chingii leaves. Further analyses reveal a cytochrome P450 gene cluster localized on chromosome 8, and identify RcCYP72H7 within this cluster as an aucubin epoxidase, capable of catalyzing aucubin epoxidation to form catalpol. The genome offers valuable resources for studying iridoid glycoside biosynthesis and the evolutionary history of Rehmannia, and will help to faciliate genetic improvement of R. chingii for pharmaceutical and health-related applications.

The composition of Pseudostellaria heterophylla (Tai-Zi-Shen, TZS) is greatly influenced by the growing area of the plants, making it significant to distinguish the origins of TZS. However, traditional methods for TZS origin identification are time-consuming, laborious, and destructive. To address this, two or three TZS accessions were selected from four different regions of China, with each of these resources including distinct quality grades of TZS samples. The visible near-infrared (Vis/NIR) and short-wave infrared (SWIR) hyperspectral information from these samples were then collected. Fast and high-precision methods to identify the origins of TZS were developed by combining various preprocessing algorithms, feature band extraction algorithms (CARS and SPA), traditional two-stage machine learning classifiers (PLS-DA, SVM, and RF), and an end-to-end deep learning classifier (DCNN). Specifically, SWIR hyperspectral information outperformed Vis/NIR hyperspectral information in detecting geographic origins of TZS. The SPA algorithm proved particularly effective in extracting SWIR information that was highly correlated with the origins of TZS. The corresponding FD-SPA-SVM model reduced the number of bands by 77.2% and improved the model accuracy from 97.6% to 98.1% compared to the full-band FD-SVM model. Overall, two sets of fast and high-precision models, SWIR-FD-SPA-SVM and SWIR-FD-DCNN, were established, achieving accuracies of 98.1% and 98.7% respectively. This work provides a potentially efficient alternative for rapidly detecting the origins of TZS during actual production.