There is a concerted understanding of the accumulation of soil pathogens as the major driving factor of negative plant-soil feedback (NPSF). However, our knowledge of the connection between plant growth, pathogen build-up and soil microbiome assemblage is limited. In this study, significant negative feedback between the soil and sanqi ( Panax notoginseng ) was found, which were caused by the build-up of the soil-borne pathogens Fusarium oxysporum , F. solani , and Monographella cucumerina . Soil microbiome analysis revealed that the rhizospheric fungal and bacterial communities were changed with the growth of sanqi. Deep analysis of the phylum and genus levels corroborated that rhizospheric fungal Ascomycota, including the soil-borne pathogens F. oxysporum , F. solani , and especially M. cucumerina , were significantly enriched with the growth of sanqi. However, the bacteria Firmicutes and Acidobacteria, including the genera Pseudomonas , Bacillus, Acinetobacter and Burkholderia , were significantly suppressed with the growth of sanqi. Using microbial isolation and in vitro dual culture tests, we found that most isolates derived from the suppressed bacterial genera showed strong antagonistic ability against the growth of sanqi soil-borne pathogens. Interestingly, inoculation of these suppressed isolates in consecutively cultivated soil could significantly alleviate NPSF. In summary, sanqi growth can suppress antagonistic bacteria through re-assemblage of the rhizosphere microbiome and cause the accumulation of soil-borne pathogens, eventually building negative feedback loops between the soil and plants.

Black shank, caused by Phytophthora parasitica var. nicotianae, is a widespread and destructive disease of tobacco. Crop rotation is essential in controlling black shank. Here, we confirmed that rotating black shank-infested fields with rapeseed (Brassica napus) suppressed the incidence this disease. Further study demonstrated that rapeseed roots have a strong ability to attract zoospores and subsequently stop the swimming of zoospores into cystospores. Then, rapeseed roots secrete a series of antimicrobial compounds, including 2-butenoic acid, benzothiazole, 2-(methylthio)benzothiazole, 1-(4-ethylphenyl)-ethanone, and 4-methoxyindole, to inhibit the cystospore germination and mycelial growth of P. parasitica var. nicotianae. Thus, rapeseed rotated with tobacco suppresses tobacco black shank disease through the chemical weapons secreted by rapeseed roots.

Background and aims Ginsenosides are the main bioactive components of Panax plants which could be secreted by root and show autotoxicity to root cells or promote the growth of soil-borne pathogens. However, comprehensive understanding of the effect of ginsenosides on soil microbiota is still lacking. Methods The ginsenosides in root exudates of P. notoginseng were quantified and exogenous ginsenosides on soil microbiota were tested using 16S rRNA and ITS gene tag sequencing. Then its underlying mechanism was deciphered through studying effects of ginsenosides on growth of the ginsenoside-modified culturable fungi and bacteria as well as the relationships between these fungi and bacteria. Results Exogenous root exudates and mixtures of Rg 1 + Rb 1 + Rd had similar ability to drive the change of soil microbiota. Further studies demonstrated that Rg 1 + Rb 1 + Rd mixture could enrich or suppress special fungi and bacteria to modify soil community through differential utilization of carbon source during the early stage (30 days), followed by antagonism between ginsenoside-modified fungi and bacteria to determine soil microbial community modification at later stage (60 and 90 days). Conclusions Ginsenosides were the main substances in exogenous root exudates of P. notoginseng that drove the change in soil microbiota, mediating the special interaction between the plant and the microbiota.

Autotoxic ginsenosides, secreted by sanqi into soil, could enrich Burkholderia sp. to alleviate negative plant-soil feedback (NPSF) by degrading autotoxins and antagonizing the root rot pathogen. In detail, ginsenosides could stimulate the growth and biofilm formation of Burkholderia sp.

Dendrobium huoshanense is used to treat various diseases in traditional Chinese medicine. Recent studies have identified active components. However, the lack of genomic data limits research on the biosynthesis and application of these therapeutic ingredients. To address this issue, we generated the first chromosome-level genome assembly and annotation of D. huoshanense. We integrated PacBio sequencing data, Illumina paired-end sequencing data, and Hi-C sequencing data to assemble a 1.285 Gb genome, with contig and scaffold N50 lengths of 598 kb and 71.79Mb, respectively. We annotated 21,070 protein-coding genes and 0.96 Gb transposable elements, constituting 74.92% of the whole assembly. In addition, we identified 252 genes responsible for polysaccharide biosynthesis by Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation. Our data provide a basis for further functional studies, particularly those focused on genes related to glycan biosynthesis and metabolism, and have implications for both conservation and medicine.