Panax ginseng is widely used as functional food and traditional Chinese medicine. To satisfy the market supply and medication safety, biofertilizers are used as agents to stimulate the growth and production of P. ginseng. In this study, we used high-throughput sequencing and quantitative polymerase chain reaction to analyze microbial community in soils treated with biofertilizers during the development stages of P. ginseng. Ginsenoside content was detected using high-performance liquid chromatography analysis to evaluate the effects of biofertilizer application. In this study, the incidence rate of P. ginseng root rot significantly declined by 40.3–47.3% after application of disease-biocontrol biofertilizers. Bacterial diversity showed increasing trends in soils treated with 3.0–4.5 ml kg−1 of disease-biocontrol biofertilizers compared with those in untreated soils. Principal coordinate analysis ordination revealed that bacterial communities were changed by biofertilizers depending on their application concentration. Relative abundance of potentially beneficial bacterial agents, such as Bacillus, Burkholderia, Rhizobium, Streptomyces, and Mycobacterium, significantly increased compared with that in control. Fusarium of low abundance observed in soils treated with biofertilizers compared with that in untreated soils. P. ginseng yield was enhanced by 17.0–19.1%, and ginsenoside (Rg1 and Rb1) contents were improved after biofertilizer application. Our results reveal that biofertilizers reduced the incidence rate of root rot, increased bacterial diversity, promoted the relative abundance of potentially beneficial bacterial taxa, decreased the abundance of potentially harmful bacterial agents, and then enhanced the yield and quality of P. ginseng.

As a valuable medicinal plant, the yield of Panax ginseng is seriously affected by autotoxicity, which is a common phenomenon due to continuous cropping. However, the mechanism of autotoxicity in P. ginseng is still unknown. In total, high throughput sequencing of 18 RNA-Seq libraries produced 996,000 000 100-nt reads that were assembled into 72,732 contigs. Compared with control, 3697 and 2828 genes were significantly up- and down-regulated across different tissues and time points, respectively. Gene Ontology enrichment analysis showed that ‘enzyme inhibitor activity’, ‘carboxylesterase activity’, ‘pectinesterase activity’, ‘centrosome cycle and duplication’ and ‘mitotic spindle elongation’ were enriched for the up-regulated genes. Transcription factors including AP2s/ERFs, MYBs, and WRKYs were up-regulated in roots after benzoic acid treatment. Moreover, reactive oxygen species, peroxidases and superoxide dismutase contigs were up-regulated in roots after benzoic acid treatment. Physiological and biochemical indexes showed that the proline and malondialdehyde content were restored to lower levels at a later stage after benzoic acid treatment. Benzoic acid inhibited the root hair development in a dose-dependent manner, and several differential expressed genes potentially involved in hair development were identified. Several key contigs in the flavonoid and ginsenoside biosynthesis pathways were repressed. Finally, 58,518 alternative splicing (AS) events from 12,950 genes were found after benzoic acid treatment. Interestingly, contigs in the ginsenoside biosynthetic pathway underwent AS, providing useful information about post-transcriptional regulation in P. ginseng. This study revealed the stress-response molecular mechanisms in P. ginseng induced by benzoic acid.

Panax ginseng C. A. Meyer is a highly valued medicinal plant. Cylindrocarpon destructans is a destructive pathogen that causes root rot and significantly reduces the quality and yield of P. ginseng. However, an efficient method to control root rot remains unavailable because of insufficient understanding of the molecular mechanism underlying C. destructans-P. ginseng interaction. In this study, C. destructans-induced transcriptomes at different time points were investigated using RNA sequencing (RNA-Seq). De novo assembly produced 73,335 unigenes for the P. ginseng transcriptome after C. destructans infection, in which 3,839 unigenes were up-regulated. Notably, the abundance of the up-regulated unigenes sharply increased at 0.5 d postinoculation to provide effector-triggered immunity. In total, 24 of 26 randomly selected unigenes can be validated using quantitative reverse transcription (qRT)-PCR. Gene ontology enrichment analysis of these unigenes showed that “defense response to fungus”, “defense response” and “response to stress” were enriched. In addition, differentially expressed transcription factors involved in the hormone signaling pathways after C. destructans infection were identified. Finally, differentially expressed unigenes involved in reactive oxygen species and ginsenoside biosynthetic pathway during C. destructans infection were indentified. To our knowledge, this study is the first to report on the dynamic transcriptome triggered by C. destructans. These results improve our understanding of disease resistance in P. ginseng and provide a useful resource for quick detection of induced markers in P. ginseng before the comprehensive outbreak of this disease caused by C. destructans.

The bacterial communities of 1‐ to 6‐year ginseng rhizosphere soils were characterized by culture‐independent approaches, random amplified polymorphic DNA (RAPD), and amplified ribosomal DNA restriction analysis (ARDRA). Culture‐dependent method (Biolog) was used to investigate the metabolic function variance of microbe living in rhizosphere soil. Results showed that significant genetic and metabolic function variance were detected among soils, and, with the increasing of cultivating years, genetic diversity of bacterial communities in ginseng rhizosphere soil tended to be decreased. Also we found that Verrucomicrobia, Acidobacteria, and Proteobacteria were the dominants in rhizosphere soils, but, with the increasing of cultivating years, plant disease prevention or plant growth promoting bacteria, such as Pseudomonas, Burkholderia, and Bacillus, tended to be rare.