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Background Angelica sinensis (Oliv.) Diels ( A. sinensis ) is a Chinese herb grown in different geographical locations. It contains numerous active components with therapeutic value. Rhizosphere microbiomes affect various aspects of plant performance, such as nutrient acquisition, growth and development and plant diseases resistance. So far, few studies have investigated how the microbiome effects level of active components of A. sinensis. This study investigated whether changes in rhizosphere microbial communities and metabolites of A. sinensis vary with the soil microenvironment. Soils from the two main A. sinensis- producing areas, Gansu and Yunnan Province, were used to conduct pot experiments. The soil samples were divided into two parts, one part was sterilized and the other was unsterilized planting with the seedling variety of Gansu danggui 90–01. All seedlings were allowed to grow for 180 days. At the end of the experiment, radix A. sinensis were collected and used to characterize growth targets and chemical compositions. Rhizosphere soils were subjected to microbial analyses. Results Changes in metabolic profiles and rhizosphere microbial communities of A. sinensis grown under different soil microenvironments were similar. The GN (Gansu non-sterilized), YN (Yunnan non-sterilized), GS (Gansu sterilized), and YS (Yunnan sterilized) groups were significantly separated. Notably, antagonistic bacteria such as Sphingomonas , Pseudomonas , Lysobacter , Pseudoxanthomonas , etc. were significantly ( p  < 0.05) enriched in Gansu soil compared with Yunnan soil. Moreover, senkyunolide I and ligustilide dimers which were enriched in GS group were strongly positively correlated with Pseudomonas parafulva ; organic acids (including chlorogenic acid, dicaffeoylquinic acid and 5-feruloylquinic acid) and their ester coniferyl ferulate which were enriched in YS Group were positively associated with Gemmatimonadetes bacterium WY71 and Mucilaginibater sp., respectively. Conclusions The soil microenvironment influences growth and level/type of active components in A. sinensis . Further studies should explore the functional features of quality-related bacteria, identify the key response genes and clarify the interactions between genes and soil environments. This will reveal the mechanisms that determine the quality formation of genuine A. sinensis .

Purpose The interactions between rhizosphere microorganisms and pioneer plants play important roles in the restoration of ecological functions after a disturbance. Different pioneer species appear in the initial phase of ecological restoration. However, the patterns of the composition of different pioneer species shaping the microbial communities of the rhizosphere are still poorly understood. Methods Microcosm experiments were established to compare the taxonomic and functional features of rhizosphere bacterial with fungal communities in response to plant species composition. Results Both bacterial and fungal communities didn’t have significant variation related to the diversity, community composition, and predicted functions between rhizosphere soils collected from treatments containing different compositions of plant species. Rhizosphere bacteria were more sensitive to the external environment than fungi. The fungal diversity exhibited a more significant relationship with the traits of different plant species compared with bacteria. Similar plant traits, especially aboveground plant traits (i.e., total coverage, and aboveground biomass), were correlated with dominant taxa and functional profiles of the both bacterial and fungal community. Furthermore, network analyses showed that Gaiellales and Ganoderma were the key bacterial and fungal taxa, respectively, which played important roles in community assembly. Conclusions The composition of different pioneer species within a community had similar patterns of rhizosphere bacterial and fungal communities. The connection between plants and soil microorganisms was more likely related to plant traits instead of the species composition. Thus, the processes of plant growth and nutrient uptake, not the combinations of plant species, may be determinants of soil microbial community assemblage.

Excessive utilization of chemical fertilizers degrades the quality of medicinal plants and soil. Bio-organic fertilizers (BOFs) including microbial inoculants and microalgae have garnered considerable attention as potential substitutes for chemical fertilizer to enhance yield. In this study, a field experiment was conducted to investigate the effects of BOF partially substituting chemical fertilizer on the growth and quality of medicinal plant Polygala tenuifolia . The growth parameters, bioactive component contents, soil properties and composition of rhizosphere microorganisms were measured. The results indicated that substituting 40% of chemical fertilizer with microalgae showed the most pronounced growth-promoting effect, leading to a 29.30% increase in underground biomass and a 19.72% increase in 3,6’-disinapoylsucrose (DISS) content. Substituting 20% of chemical fertilizer with microalgae improved soil quality, significantly increasing soil organic matter content by 15.68% ( p <0.05). Microalgae addition significantly affected the rhizosphere bacterial community composition of P. tenuifolia , reducing the relative abundance of Cladosporium by 33.33% and 57.93%, while increasing the relative abundance of Chloroflexi by 31.06% and 38.27%, under 20% and 40% chemical fertilizer reduction, respectively. The relative abundance of Chloroflexi positively correlated with both the underground biomass and DISS content ( p <0.05), indicating that microalgae may stimulate Chloroflexi species associated with carbon cycling, thereby enhancing soil fertility, nutrient absorption, and ultimately leading to increased biomass accumulation and production of bioactive components in P. tenuifolia . In addition, there was no significant difference in underground growth and bioactive component contents between reduced chemical fertilizer dosage combined with solid microbial inoculant (SMI) and polyglutamic microbial inoculant (PMI), compared with 100% chemical fertilizer. Correlation analysis revealed that PMI could increase soil phosphorus availability through Streptomyces recruitment. In conclusion, our findings demonstrated that bio-organic fertilizers can partially substitute chemical fertilizer to improve soil properties and microorganisms, enhancing the growth and quality of P. tenuifolia . This provides a theoretical basis for increasing medicinal plant productivity under chemical fertilizer reduction.

Polygonatum kingianum Collett & Hemsl., is one of the most important traditional Chinese medicines in China. The purpose of this study is to investigate the relationship between herb quality and microbial-soil variables, while also examining the composition and structure of the rhizosphere microbial community in Polygonatum kingianum, the ultimate goal is to provide a scientific approach to enhancing the quality of P. kingianum. Illumina NovaSeq technology unlocks comprehensive genetic variation and biological functionality through high-throughput sequencing. And in this study it was used to analyze the rhizosphere microbial communities in the soils of five P. kingianum planting areas. Conventional techniques were used to measure the organic elements, pH, and organic matter content. The active ingredient content of P. kingianum was identified by High Performance Liquid Chromatography (HPLC) and Colorimetry. A total of 12,715 bacterial and 5487 fungal Operational Taxonomic Units (OTU) were obtained and taxonomically categorized into 81 and 7 different phyla. Proteobacteria, Bacteroidetes, and Acidobacteriae were the dominant bacterial phyla Ascomycota and Basidiomycota were the dominat fungal phyla. The key predictors for bacterial community structure included hydrolysable nitrogen and available potassium, while for altering fungal community structure, soil organic carbon content (OCC), total nitrogen content (TNC), and total potassium content (TPOC) were the main influencing factors. Bryobacter and Candidatus Solibacter may indirectly increase the polysaccharide content of P. kingianum , and can be developed as potential Plant Growth Promoting Rhizobacteria (PGPR). This study has confirmed the differences in the soil and microorganisms of different origins of P. kingianum , and their close association with its active ingredients. And it also broadens the idea of studying the link between plants and microorganisms.

The rhizosphere microbiota is associated with the plant response to phytophagous pest infestation through the plant-rhizosphere microbe axis. However, the responses of microbial community characteristics of flue-cured tobacco rhizosphere and non-rhizosphere soil to potato tuber moth (PTM) Phthorimaea operculella larval feeding is unclear. In this study, the microbial structural composition was analysed in the rhizosphere and non-rhizosphere soil of healthy and PTM infested flue-cured tobacco plants at the vigorous growth stage collected from the field (with four replicates per group) using Illumina MiSeq sequencing. The featured microbes, co-occurrence networks, and potential functions of tobacco rhizosphere and non-rhizosphere soil microbial communities were analysed. Amplicon data analyses showed that PTM infestation altered the microbial community composition in tobacco rhizosphere and non-rhizosphere and this alteration was similar between these two soil types. PTM infested plants showed enrichment of distinct microbial genera. For instance, the rhizosphere soil showed increased abundances of (bacteria) and (fungi), while the non-rhizosphere soil was enriched with (bacteria) and (fungi). In contrast, the rhizosphere of healthy plants were characterized by enrichment of (bacteria) and , (fungi), along with the non-rhizosphere soil dominated by (bacteria) and (fungi). Furthermore, PTM infestation altered the potential functions of flue-cured tobacco rhizosphere and non-rhizosphere soils, and reduced the complexity of rhizosphere bacterial and fungal communities, as well as the non-rhizosphere fungal community. Notable changes were observed in bacterial metabolic pathways and significantly up-regulated the function of symbiotroph of fungi (Lichenized) ( < 0.05). Together, these results enhance our understanding of how the underground microbiome of flue-cured tobacco responds to aboveground phytophagous insect (PTM) infestation, providing valuable insights that could facilitate translation into more effective PTM management practices.

The Hexi Corridor provides two-thirds of the nation’s total seed supply. However, long-term monocropping has restricted plant growth, increased annual disease incidence, and hindered the sustainable development of the local seed industry. A study examined the impact of two carbon-rich residues, both irradiated and non-irradiated, on the rhizosphere microbes associated with corn seed production using a pot experiment and high-throughput sequencing.The results indicated that irradiated residues increased bacterial diversity, reduced fungal diversity, altered microbial functionality, and decreased the relative abundance of pathogens. Additionally, plant growth and soil properties improved. Carbon-rich irradiated biogas and furfural residues promoted soil rhizosphere microbes in maize, responding to an increase in beneficial rhizosphere microorganisms. The impact of irradiation on rhizosphere microbes was more significant than that of incubation or non-irradiation. Irradiated biogas residue had a greater impact on bacterial diversity and functionality compared to irradiated furfural residue, whereas the effects on fungal diversity and functionality were reversed between the two residues.The application of two residues, with or without irradiation, improved soil physicochemical properties, enhanced plant growth, and reduced disease incidence. Carbon-rich resources, when combined with irradiation, promote soil rhizosphere microbial diversity and suppress pathogen invasion by encouraging beneficial microbes. Using irradiated carbon-rich resources can serve as an effective method for disease control and a sustainable solution to improve long-term corn seed production systems.

Abstract Blueberry is a shallow root plant in which the absorption of nutrients is inefficient, resulting in slow growth under artificial cultivation conditions. Endophytes play an important role in promoting plant growth; however, the effects of Trichoderma spp. and dark septate endophytes (DSEs) on host plant growth and soil microorganisms are still debatable. We isolated two endophytic fungal species, Trichoderma koningiopsis (TK) and a DSE (Amesia nigricolor; AN), from blueberry roots, which can solubilize insoluble phosphorus and produce amylase and cellulase to promote plant growth. We found that under dual inoculation, the colonization rate and colonization intensity of TK were higher than they were under single inoculation with TK, while the colonization rate and colonization intensity of AN were lower under dual inoculation than under single inoculation with AN. The plant nutrients, root activity, available potassium, and parts of soil phosphatase activities were highest under dual inoculation. TK inoculation resulted in the highest diversity and richness in the soil fungi and bacteria, followed by dual inoculation. The abundance of Ascomycota, Acidobacteriae, Firmicutes, and Actinobacteriota increased significantly, resulting in Trichoderma and Vicinamibacteria inoculated with TK, Chaetomium and Alicyclobacillales inoculated with AN, and Hypocreales and Burkholderiaceae with dual inoculation enriched in the soil. Single or dual inoculation of blueberry plants with Trichoderma koningiopsis and dark septate endophytes and investigated the changes of single or dual inoculation on blueberry growth, soil physicochemical properties, and the rhizosphere microbial community of soil, which the results clarify the effects of beneficial endophytic fungi on blueberry plants.

Panax quinquefolius L., with a history of over 300 years in traditional Chinese medicine, is notably rich in ginsenosides—its primary bioactive components. Although our previous study found that biochar application could enhance the content of ginsenoside Re, Rg and other contents in P. quinquefolius , its effect on the overall secondary metabolism of P. quinquefolius and its mechanism are still unclear. In this paper, the correlation between plant microbiome and secondary metabolites was studied from the perspective of plant rhizosphere microorganisms and endophytes, and the mechanism of biochar-induced metabolic reprogramming of P. quinquefolius was revealed. The results showed that biochar treatment significantly increased the accumulation of various substances in P. quinquefolius , including nucleosides, glycerophosphocholines, fatty acyls, steroidal glycosides, triterpenoids, and other bioactive compounds. Additionally, biochar treatment significantly enriched beneficial rhizosphere microorganisms such as Bacillus , Flavobacterium , and Devosia , while reducing the relative abundance of harmful fungi like Fusarium . Furthermore, it promoted endophytic Flavobacterium , Acaulospora , and Glomus , and suppressed pathogenic genera such as Plectosphaerella , Cladosporium , and Phaeosphaeria. These shifts in rhizosphere microbial community and endophytes structure and function were closely linked to the accumulation of secondary metabolites (e.g. ginsenosides Rg 3 , F2) in P. quinquefolius . Overall, our findings suggest that biochar may influence key endophytes and rhizosphere microorganisms to regulate the accumulation of secondary metabolites in P. quinquefolius. Therefore, this study provides valuable insights into the potential application of biochar in Chinese medicine agriculture.

The contribution of crops and soil microbial community structure and functional diversity in soil-borne diseases control mulberry plant production is still inadequately understood. In this work, a comparative study was undertaken on the microbial abundance, community structure, and functional diversity in the soil rhizosphere between the resistant (Kangqing 10) and the susceptible (Guisang 12) mulberry genotypes. The study deployed the use of dilution plate method, micro-ecology technology, and polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE) techniques. The study aimed at developing better crop management methods for mulberry cultivation as well as preventing and controlling the occurrence and impacts of bacterial wilt on mulberry productivity. The results indicated that the soil rhizosphere microorganisms were more abundant in the normal resistant mulberry genotype than in the normal susceptible mulberry genotype. Carbon source utilization was better in the normal susceptible mulberry genotype. These properties were lower in the sickly resistant mulberry genotype than in the susceptible sickly mulberry genotype. Through the PCR–DGGE, it was shown that the bacterial and fungal community structures of the resistant genotypes were more stable than those of the susceptible genotypes. Through correlation regression analysis, it was shown that the mulberry bacterial wilt significantly contributes to the loss of soil nutrients, particularly organic matter and nitrogen, a possible cause to disrupted balance between the soil microbial community and the loss of soil organic matter. Resistant genotype plants displayed more resistance to bacterial wilt. Therefore, this study recommends the need to promote the cultivation of resistant genotype mulberry for increased yield.

Rhizosphere microorganisms and soil physicochemical properties play a vital role in the natural restoration of plant communities. However, the mechanism of action between rhizosphere microorganisms and soil factors interact during natural restoration in plant communities is still unknown. Therefore, more attention is needed in this area based on typical vegetation, which supports the restoration of the structure and function of wetland ecosystems. Carex spp . and Artemisia selengensis communities are typical renewal wetland plant communities at cutting slash of Populus deltoides . In the current study, plots containing Carex spp. and Artemisia spp. in the slash were investigated, and an area of P. deltoides plantation on a lake shore was sampled as a control to navigate the rhizosphere microorganisms and soil physicochemical properties of the restored wetland plant community. The results revealed that the richness and diversity indices of the fungal community in the Carex spp. community were higher than those in the A. selengensis and P. deltoides undergrowth communities. Ascomycota was the dominant phylum in the soil of Carex spp. community whereas Basidiomycota was the dominant phylum in the A. selengensis community. The richness and diversity indices of the rhizosphere bacterial community in the control were higher than those in communities of Carex spp. and A. Selengensis. Proteobacteria and Actinobacteria were the dominant phyla of the rhizosphere bacterial community in the control plot. Soil water content (WC), proportion of clay (CY), and nutrient content, as well as catalase activity (CAT) in the soil of Carex spp. community were the highest, whereas those in the control were the lowest. Conversely, the bulk density (BK) and proportion of gravel in the control plot were the highest. RDA found that the CY, organic matter (OM), ammonium nitrogen (AN) and nitrate nitrogen (NN) content in the soil were the key factors affecting the structure and composition of the rhizosphere microbial community.