The species variability and potential environmental functions ofTaxusrhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries fromTaxusrhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria and Chloroflexi was higher inT. cuspidata var. nanaandT. × mediarhizospheres than inT. maireirhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperateTaxusrhizospheres had more unclassified fungi, Basidiomycota and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres and exemplify the method shift in research and development of resource plant rhizosphere.

Plants release a set of chemical compounds, called exudates, into the rhizosphere, under normal conditions and in response to environmental stimuli and surrounding soil organisms. Plant root exudates play indispensable roles in inhibiting the growth of harmful microorganisms, while also promoting the growth of beneficial microbes and attracting symbiotic partners. Root exudates contain a complex array of primary and specialized metabolites. Some of these chemicals are only found in certain plant species for shaping the microbial community in the rhizosphere. Comprehensive understanding of plant root exudates has numerous applications from basic sciences to enhancing crop yield, production of stress-tolerant crops, and phytoremediation. This review summarizes the metabolomics workflow for determining the composition of root exudates, from sample preparation to data acquisition and analysis. We also discuss recent advances in the existing analytical methods and future perspectives of metabolite analysis.

Continuous cropping of ginseng (Panax ginseng Meyer) cultivated in farmland for an extended period gives rise to soil-borne disease. The change in soil microbial composition is a major cause of soil-borne diseases and an obstacle to continuous cropping. The impact of cultivation modes and ages on the diversity and composition of the P. ginseng rhizosphere microbial community and technology suitable for cropping P. ginseng in farmland are still being explored.

It is a new consensus that any living organism depends on its partners to strive under environmental conditions along their living period. Plants are also highly dependent on their associated microbes, which can support its development and proper protection under stressors. Along their evolution, plants learned to interact to soil microbiota, extracting their utmost capacity to provide resources for plant development and successful colonization of terrestrial systems, where the great soil biodiversity is keen on properly exert this role. Functional systems, such as the rhizosphere, provide evidences of the powerful selection exerted by plants upon the living soil microbes. In counterpart, the anthropogenic activity, mainly in forms of agricultural managements, has neglected this symbiosis, interfering in soil biodiversity, and consequently, reducing plant development through the interference in their association with beneficial microbes. This mini review has collected information to build a suitable hypothesis that if we better learn about the connection between plants and its associated microbiota in nature, we can lead agriculture to a better exploration of this omnipresent source of nutrients and protection, increasing yield and sustainability.Copyright © 2017 Elsevier Ltd. All rights reserved.

Panax ginseng cultivated under the forest is popular because its shape and effective ingredients are similar to wild ginseng. The growth of P. ginseng in the larch forest is generally better than in the broad-leaved forest, and the incidence rate of diseases is low. Therefore, the selection of forest species is one of the basic factors in the successful cropping of P. ginseng.Illumina HiSeq high-throughput sequencing was used to analyze the 16S rRNA/ITS gene sequence of P. ginseng rhizosphere soil under larch forest to study the rhizosphere microbiome's diversity and community composition structure.The species classification and richness of rhizosphere bacterial and fungal communities in the same-aged P. ginseng were similar. Consistent with the soil system of commonly cultivated crops, Proteobacteria, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, Chloroflexi, and Basidiomycota, Ascomycota were the dominant phylum of bacteria and fungi, respectively. Compared with the soil without planting P. ginseng, the diversity of microorganisms and community structure of continuous planting for 2 years, 5 years, and 18 years of P. ginseng rhizosphere soil had little change. The accumulation levels of Ilyonectria, Fusarium, Gibberella, and Cylindrocarpon were not significantly increased with planting P. ginseng and the increased age of cropping P. ginseng.The results of this study showed that the soil function of the larch forest was good, which provided a theoretical basis for the land selection and soil improvement of cultivating P. ginseng under the larch forest.© 2023. BioMed Central Ltd., part of Springer Nature.

Ginseng red skin root syndrome (GRS) is one of the most common ginseng (Panax ginseng Meyer) diseases. It leads to a severe decline in P. ginseng quality and seriously affects the P. ginseng industry in China. However, as a root disease, the characteristics of the GRS rhizosphere microbiome are still unclear.The amplicon bacterial 16 S rRNA genes and fungal ITS (Internal Transcribed Spacer) regions Illumina sequencing technology, combined with microbial diversity and composition analysis based on R software, was used to explore the relationship between soil ecological environment and GRS.There were significant differences in the diversity and richness of soil microorganisms between the rhizosphere with different degrees of disease, especially between healthy P. ginseng (HG) and heavily diseased groups. The variation characteristics of microbial abundance in different taxa levels were analyzed. The interaction network of rhizosphere microorganisms of P. ginseng under GRS background was established. We also found that different P. ginseng rhizosphere microbial communities have multiple changes in stability and complexity through the established interaction network. Microbes closely related to potential pathogenic fungi were also identified according to the interaction network, which provided clues for looking for biological control agents. Finally, the Distance-based redundancy analysis (dbRDA) results indicated that total phosphorus (TP), available potassium (AK), available phosphorus (AP), catalase (CAT), invertase (INV) are the key factors that influence the microbial communities. Moreover, the content of these key factors in the rhizosphere was negatively correlated with disease degrees.In this study, we comprehensively analyzed the rhizosphere characteristics of P. ginseng with different levels of disease, and explored the interaction relationship among microorganisms. These results provide a basis for soil improvement and biological control of field-grown in the future.© 2022. The Author(s).

Fungal endophytes isolated from mountain-cultivated ginseng (MCG, Panax ginseng Meyer) were explored for their diversity and biocontrol activity against ginseng pathogens (Alternaria panax, Botrytis cinerea, Cylindrocarpon destructans, Pythium sp. and Rhizoctonia solani). A total of 1,300 isolates were isolated from three tissues (root, stem and leaf) from MCGs grown in 24 different geographic locations in Korea. In total, 129 different fungal isolates were authenticated by molecular identification based on internal transcribed spacer (ITS) sequences. The fungal endophytes belonged to Ascomycota (81.7%), Basidiomycota (7.08%), Zygomycota (10%) and Unknown (1.15%), with 59 genera. Analysis of diversity indices across sampling sites suggested species abundance as a function of geographical and environmental factors of the locations. Shannon diversity index and richness in the different tissues revealed that root tissues are colonized more than stem and leaf tissues, and also certain fungal endophytes are tissue specific. Assessment of the ethyl acetate extracts from 129 fungal isolates for their biocontrol activity against 5 ginseng pathogens revealed that Trichoderma polysporum produces the antimcriobial metabolite against all the pathogens. This result indicates the promise of its potential usage as a biocontrol agent.

Panax notoginseng, an important Chinese medicinal herb, can be mainly cultivated in two planting patterns, cropland planting (DT) and understory planting (LX). We speculate that the rhizosphere microbiome may vary in DT and LX and may play an important role in promoting the growth and health of P. notoginseng. In the present study, culture-independent Illumina HiSeq was employed to investigate the rhizosphere bacteria and fungi under DT and LX planting patterns. Predominant phyla include Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Ascomycota in the two planting patterns. DT has higher alpha diversity index than LX. The predominant LX-core genera include Bradyrhizobium, Streptomyces, and Actinomadura, and the predominant DT-core genera include Sphingomonas, Variovorax, and Novosphingobium. Total relative abundance of the disease-suppression phylum (Proteobacteria, Firmicutes, and Actinobacteria) and the potential plant growth-promoting rhizobacteria (PGPR) were both significantly higher in LX than in DT. We also identified over-presented microbial functional traits mediating plant–microbe and microbe–microbe interactions, nutrition acquisition, and plant growth promotion in P. notoginseng rhizosphere. Our findings provide a valuable reference for studying beneficial microbes and pathogens of P. notoginseng planted in DT and LX.

Panax notoginseng has long been used as a Chinese herb with high medicinal value. The endophytic bacteria in this medicinal plant have multiple biological functions. High-throughput sequencing is a rapidly evolving technique that helps profile the endophytic bacterial community structure of medicinal plants. However, few studies on the endophytic bacteria in P. notoginseng, particularly in dry P. notoginseng roots as a raw medicinal material, have been conducted. In this study, fresh P. notoginseng and dry P. notoginseng were analysed using high-throughput sequencing on an Illumina MiSeq platform to explore the diversity and functions of the endophytic bacteria in different parts of P. notoginseng. The results showed that a total of 201 operational taxonomic units were obtained from fresh P. notoginseng and dry P. notoginseng. The dominant phyla in the fresh and dry P. notoginseng were Proteobacteria (85.9%) and Firmicutes (99.9%), respectively, whereas the dominant genera in these samples were Enterobacter (84.4%) and Bacillus (99.6%), respectively. Fresh P. notoginseng exhibited a higher degree of endophytic bacterial diversity than dry P. notoginseng, but functional prediction of metabolism indicated that the relative abundance of the metabolic function of terpenoids and polyketides synthesis in the dry sample was higher than that in the fresh sample. Our study indicates significant differences in the diversity and metabolic function of the endophytic bacteria between fresh and dry P. notoginseng, providing useful information for the exploitation and utilization of endophytic bacteria resources from P. notoginseng.

Panax quinquefolius L. (American ginseng) is widely used in medicine due to its wealth of diverse pharmacological effects. Endophytes colonize within P. quinquefolius in multiple tissue types. However, the relationship between endophytes and the production of their active ingredients in different parts of the plant is not clear.

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

Panax ginseng cannot be cultivated on the same land consecutively for an extended period, and the underlying mechanism regarding microorganisms is still being explored.Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) and BIOLOG methods were used to evaluate the microbial genetic and functional diversity associated with the P. ginseng rhizosphere soil in various cultivation ages and modes.The analysis of microbial diversity using PCR-DGGE showed that microbial communities were significantly variable in composition, of which six bacterial phyla and seven fungal classes were detected in P. ginseng soil. Among them, Proteobacteria and Hypocreales dominated. Fusarium oxysporum, a soilborne pathogen, was found in all P. ginseng soil samples except R0. The results from functional diversity suggested that the microbial metabolic diversity of fallow soil abandoned in 2003 was the maximum and transplanted soil was higher than direct-seeding soil and the forest soil uncultivated P. ginseng, whereas the increase in cultivation ages in the same mode led to decreases in microbial diversity in P. ginseng soil. Carbohydrates, amino acids, and polymers were the main carbon sources utilized. Furthermore, the microbial diversity index and multivariate comparisons indicated that the augmentation of P. ginseng cultivation ages resulted in decreased bacterial diversity and increased fungal diversity, whereas microbial diversity was improved strikingly in transplanted soil and fallow soil abandoned for at least one decade.The key factors for discontinuous P. ginseng cultivation were the lack of balance in rhizosphere microbial communities and the outbreak of soilborne diseases caused by the accumulation of its root exudates.

American ginseng (Panax quinquefoliumL.) is a perennial plant that is cultivated for medicinal purposes. Unfortunately, outbreaks of root rot disease in American ginseng (AG) reduce yields and result in serious economic losses. Information on the dynamics of soil microbial communities associated with healthy and diseased AG of different ages is limited. The present study explored the differences in field soil microbial community structure, composition, interaction, and their predictive functions associated with healthy and diseased AG at different growth ages. Changes in soil physicochemical properties were also examined to determine the possible reasons for disease outbreaks. Results revealed that in different growth years, the genera of soil-borne pathogens, such asAlternaria,Botrytis,Cladosporium,Sarocladium, andFusarium, were increased in diseased AG soil samples in comparison with those in the healthy AG soil samples. In contrast, the abundance of some key and potentially beneficial microbes, such asBacillus,Chaetomium,Dyella,Kaistobacter,Paenibacillus,Penicillium, andTrichoderma, was decreased. Additionally, as AG plants age, the relative abundance of symbiotic fungi tended to decrease, while the relative abundance of potential plant pathogenic fungi gradually increased. Various soil properties, such as available phosphorus, the ratio of total nitrogen to total phosphorus (N/P), and pH, were significantly (P< 0.05) associated with microbial community composition. Our findings provide a scientific basis for understanding the relationship among the root rot disease outbreaks in American ginseng as well as their corresponding soil microbial communities and soil physicochemical properties.

Root rot is a main disease in Panax notoginseng, which is severe and difficult to control. Arbuscular mycorrhizal fungi (AMF) are known to effectively prevent plant diseases caused by soil-borne pathogens. However, the potential role of AMF as a biocontrol agent against root\n rot in P. notoginseng is still unclear. This study aims to investigate the efficacy of AMF, including Funneliformis mosseae, Rhizophagus intraradices and Claroideoglomus etunicatum, individually and in combination, for controlling root rot in P. notoginseng seedlings.\n The effect of different AMF on the indicators of P. notoginseng growth, superoxide dismutase, peroxidase activity, proline, malondialdehyde, soluble sugars and proteins were measured. The effects of different AMF on root rot resistance were comprehensively evaluated using the subordinate\n function method. The results showed that the incidence of root rot decreased from 75% to 12.5%–50.0% after inoculation with different AMF agents, and the disease index decreased from 22.92% to 6.25%–16.67%. Moreover, AMF significantly increased the growth parameters of P. notoginseng,\n such as plant height (6.35%–41.73%), stem diameter (12.98%–45.96%), fresh weight (6.28%–95.35%), and leaf area (8.89%–97.71%). Moreover, AMF also improved the content of chlorophyll (2.40%–50.67%) and rate of net photosynthetic (52.08%– 279.17%), enhancing\n superoxide dismutase (4.02%–114.89%) and peroxidase activity (85.60%–139.98%), as well as promoting the accumulation of soluble sugars (30.21%–90.00%), proteins (3.31%–65.81%), and proline (4.02%–114.89%) in the root and leaf, while reducing the malondialdehyde\n content (19.99%–139.98%). Particularly, C. etunicatum was found to be the most effective in promoting growth and disease resistance in P. notoginseng. These findings provide insights into the potential use of AMF as an effective biocontrol agent to manage root rot.

Root exudates contain a complex array of primary and specialized metabolites that play important roles in plant growth due to their stimulatory and inhibitory activities that can select for specific microbes. In this study, we investigated the effects of different root exudate concentrations on the growth of ginseng (Panax ginseng C. A. Mey), ginsenoside levels, and soil fungal community composition and diversity. The results showed that low root exudate concentrations in the soil promoted ginseng rhizome biomass and ginsenoside levels (Rg1, Re, Rf, Rg2, Rb1, Ro, Rc, Rb2, Rb3, and Rd) in rhizomes. However, the rhizome biomass and ginsenoside levels gradually decreased with further increases in the root exudate concentration. ITS sequencing showed that low root exudate concentrations in the soil hardly altered the rhizosphere fungal community structure. High root exudate concentrations altered the structure, involving microecological imbalance, with reduced abundances of potentially beneficial fungi (such as Mortierella) and increased abundances of potentially pathogenic fungi (such as Fusarium). Correlation analysis showed that rhizome biomass and ginsenoside levels were significantly positively correlated with the abundances of potentially beneficial fungi, while the opposite was true for potentially pathogenic fungi. Overall, low root exudate concentrations promote the growth and development of ginseng; high root exudate concentrations lead to an imbalance in the rhizosphere fungal community of ginseng and reduce the plant’s adaptability. This may be an important factor in the reduced ginseng yield and quality and soil sickness when ginseng is grown continuously.