Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng

Abstract

Rhizosphere and root-associated microbial communities are known to be related to soil-borne disease and plant health. In the present study, the microbial communities in rhizosphere soils and roots of both healthy and diseased Panax notoginseng were analyzed by high-throughput sequencing of 16S rRNA for bacteria and 18S rRNA internal transcribed spacer for fungi, to reveal the relationship of microbial community structure with plant health status. In total, 5593 bacterial operational taxonomic units (OTUs) and 963 fungal OTUs were identified in rhizosphere soils, while 1794 bacterial and 314 fungal OTUs were identified from root samples respectively. Principal coordinate analysis separated the microbial communities both in the rhizosphere soils and roots of diseased P. notoginseng from healthy plants. Compared to those of healthy P. notoginseng, microbial communities in rhizosphere soils and roots of diseased plants showed a decrease in alpha diversity. By contrast, bacterial community dissimilarity increased and fungal community dissimilarity decreased in rhizosphere soils of diseased plants, while both bacterial and fungal community dissimilarity in roots showed no significant difference between healthy and diseased plants. Redundancy analysis at the phylum level showed that mycorrhizal colonization and soil texture significantly affected microbial community composition in rhizosphere soils, whereas shoot nutrition status had a significant effect on microbial community composition in root samples. Our study provided strong evidence for the hypothesis that microbial diversity could potentially serve as an indicator for disease outbreak of medicinal plants, and supported the ecological significance of microbial communities in maintaining plant healthy and soil fertility.

Unveiling of Dominant Fungal Pathogens Associated With Rusty Root Rot of Panax notoginseng Based on Multiple Methods

“…These observations indicate that Fusarium might not be an important pathogen for P. notoginseng, or at least not a dominant pathogen, which differs from the findings of a previous report (Ma et al 2013). However, the present observations of the dominant Ilyonectria and the minor presence of Fusarium in the symptomatic roots are consistent with the recent survey of fungal communities on symptomatic P. notoginseng (Wu et al 2015). Therefore, fungal community analysis is an effective method for "overviewing" the possible dominant pathogen in the symptomatic samples, providing effective guidance for elucidating the specific important pathogen.…”

“…It prefers a warm, wet, shady, and cool environment, with soil humidity ranging from 25 to 30% and relative air humidity from 70 to 85% (Guan et al 2011), conditions which also facilitate the infection of numerous phytopathogens (Chen et al 2001). Root rot is the most destructive disease of P. notoginseng, which significantly reduces root quality and decreases yield by 5 to 20%, sometimes even exceeding 70% (Sun et al 2004;Wu et al 2015). Root rot has been the major threat to cultivation and sustainable development of this plant.…”

Diversity and composition of rhizospheric soil and root endogenous bacteria in Panax notoginseng during continuous cropping practices

“…Illumina sequencing approaches using 16S rDNA gene markers should expand the current understanding of plant‐microbe relationships and comprehensive descriptions of the full bacterium diversity associated with the rhizospheric and endophytic roots of P. notoginseng . To our knowledge, few studies have utilized MiSeq as a platform to study the soil bacterial diversity of P. notoginseng and only at a single timepoint . Here, this new sequencing technique was employed for the first time to analyse progressive changes in soil bacterial community structure and diversity during the continuous cropping of P. notoginseng .…”

“…However, studies examining soil and root microbial communities and diversity in response to continuous cropping utilizing non‐culture‐based methods have not been reported. Further, there is no available information regarding the vast microbial diversity comprising the combination of root and rhizospheric soil microorganisms during continuous cropping .…”

Bacterial diversity associated with poplar trees grown on a Hg-contaminated site: Community characterization and isolation of Hg-resistant plant growth-promoting bacteria

“…Illumina MiSeq platform Schmidt et al, 2013;Wu et al, 2015) and a culture-dependent approaches to investigate the composition and assembly of characterize bacterial communities investigate bacterial diversity and isolate Hgresistant PGPB in the rhizosphere, endosphere and phyllosphere of a polarpoplars plantation at a Hg-contaminated site. We hypothesized that the presence of a poplar tree plantation on an industrial dump would significantly and differentially shape the bacterial communities from the different soils and poplar habitats.…”