Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain

Abstract

Root (rhizome) rot of Polygonatum plants has received substantial attention because it threatens yield and sustainable utilization in the polygonati rhizome industry. However, the potential pathogens that cause rhizome rot as well as the direct and indirect (via root-associated microbes) strategies by which Polygonatum defends against pathogens remain largely unknown. Herein, we used integrated multiomics of plant-targeted metabolomics and transcriptomics, microbiome, and culture-based methods to systematically investigate the interactions between the Polygonatum cyrtonema Hua root-associated microbiota and pathogens. We found that root rot inhibited P. cyrtonema rhizome growth and that the fresh weight significantly decreased (P < 0.001). The transcriptomic and metabonomic results showed that the expression of differentially expressed genes (DEGs) related to specialized metabolic and systemic resistance pathways, such as glycolysis/gluconeogenesis and flavonoid biosynthesis, cycloartenol synthase activity (related to saponin synthesis), mitogen-activated protein kinase (MAPK) signaling, and plant hormone signal transduction, was particularly increased in diseased rhizomes. Consistently, the contents of lactose, d-fructose, sarsasapogenin, asperulosidic acid, botulin, myricadoil, and other saponins, which are functional medicinal compounds present in P. cyrtonema rhizomes, were also increased in diseased plants infected with rhizome rot. The microbiome sequencing and culture results showed that root rot disrupted the P. cyrtonema bacterial and fungal communities and reduced the microbial diversity in the rhizomes and rhizosphere soil. We further found that a clear enrichment of Streptomyces violascens XTBG45 (HJB-XTBG45) in the healthy rhizosphere could control the root rot caused by Fusarium oxysporum and Colletotrichum spaethianum. Taken together, our results indicate that P. cyrtonema can modulate the plant immune system and metabolic processes and enrich beneficial root microbiota to defend against pathogens. IMPORTANCE Root (rhizome or tuber) reproduction is the main method for the agricultural cultivation of many important cash crops, and infected crop plants rot, exhibit retarded growth, and experience yield losses. While many studies have investigated medicinal plants and their functional medicinal compounds, the occurrence of root (rhizome) rot of plant and soil microbiota has received little attention. Therefore, we used integrated multiomics and culture-based methods to systematically study rhizome rot on the famous Chinese medicine Polygonatum cyrtonema and identify pathogens and beneficial microbiota of rhizome rot. Rhizome rot disrupted the Polygonatum-associated microbiota and reduced microbial diversity, and rhizome transcription and metabolic processes significantly changed. Our work provides evidence that rhizome rot not only changes rhizome transcription and functional metabolite contents but also impacts the microbial community diversity, assembly, and function of the rhizome and rhizosphere. This study provides a new friendly strategy for medicinal plant breeding and agricultural utilization.

Keywords: PSM; Streptomyces; medicinal plant; polysaccharide and saponins; rhizome rot; root microbiota.

FIG 1

Rhizome metabolite analysis of healthy and diseased plants. (A) Diagram of a healthy and diseased P. cyrtonema plant and the belowground compartments, including the rhizome soil, rhizosphere soil, zone soil, and furrow soil; H-rhizome, healthy rhizome; D-rhizome, diseased rhizome. (B) Principal-component analysis (PCA) of rhizome saponins and other metabolites of the healthy and diseased rhizomes. (C) Fresh weight of two samples; t test, P < 0.001. (D) Polysaccharide content of two samples; t test, P < 0.05. (E) Heatmap clustering of the relative content in rhizome saponins and other metabolites; n = 12.

FIG 2

Transcriptome analysis of healthy and diseased rhizomes. (A) Expression patterns of defense genes in healthy and diseased rhizomes; n = 12; genes with an FPKM of <10 expression were removed during heatmap generation. (B and C) Annotation and KEGG (top 20) (B) and GO (top 15) (C) pathway analysis of the identified DEGs.

FIG 3

Microbial community analysis of healthy and diseased rhizome soil. (A and B) Alpha-Shannon diversity indices of bacterial (A) and fungal (B) communities in the healthy and diseased P. cyrtonema rhizome soil. The healthy sample bacterial and fungal alpha indices were 4.9272 and 3.9818, respectively, and diseased sample bacterial and fungal alpha indices were 2.9047 and 1.8935, respectively, on average; n = 12, Student’s t test, P < 0.001. (C and D) PCA of bacterial (C) and fungal (D) community beta diversity of the healthy and diseased rhizome soil; bacteria: R = 0.9685, P = 0.003; fungi: R = 0.9241, P = 0.003. (E and F) Bacterial and fungal genera community structure of the healthy and diseased rhizome soil. (E) Bacterial community (top 10 genera in relative abundance). (F) Fungal genera community.

FIG 4

Bacterial and fungal community and differential analysis of all healthy and diseased plant samples. (A and B) Alpha-Shannon diversity indices of bacterial (A) and fungal (B) communities of all soil samples; n = 27, Student’s t test. (C and D) PCA of bacterial and fungal community beta diversity of all samples (healthy rhizome versus diseased rhizome, ANOSIM; bacterial: R = 0.96, P = 0.003; fungal: R = 0.93, P = 0.003) to a larger extent than that in the rhizosphere (healthy versus diseased rhizosphere, ANOSIM; bacterial: R = 0.36, P = 0.003; fungal: R = 0.62, P = 0.003; on average, respectively); healthy versus diseased plant, ANOSIM; zone and furrow bacterial: R = 0.01, P = 0.385/R = −0.04, P = 0.674; fungal: R = 0.13, (P = 0.054/R = 0.1, P = 0.1564; on average, respectively). (E and F) Significance test between healthy and diseased rhizosphere soil bacterial and fungal community groups; Wilcoxon rank sum test.

FIG 5

Differentiation analysis of all healthy and diseased rhizome soil. (A) Isolated fungal communities in the diseased P. cyrtonema rhizome (top 25 strains). (B) Inoculation of different potential pathogens and the effect of HJB-XTBG45 on the P. cyrtonema rhizome. There were 5 biological replicates per treatment. (b and c) The plants of the inoculated strain showed disease characteristics similar to those of the field. (a and d to f) No disease characteristics were found in these plants. (a) CK; (b) inoculation of C. spaethianum; (c) inoculation of F. oxysporum; (d) inoculation of F. oxysporum and Streptomyces violascens XTBG45; (e) inoculation of Candida sp.; (f) inoculation of F. solani. (C) Relative abundance of Streptomyces between healthy and diseased rhizomes; Wilcoxon rank sum test and t test, P < 0.01. (D) Inhibitory effects of Streptomyces violascens XTBG45 (HJB-XTBG45) on F. oxysporum, C. spaethianum, and F. solani.