Beneficial Relationships Between Endophytic Bacteria and Medicinal Plants

Microbial allies: exploring fungal endophytes for biosynthesis of terpenoid indole alkaloids

Terpenoid indole alkaloids (TIAs) are natural compounds found in medicinal plants that exhibit various therapeutic activities, such as antimicrobial, anti-inflammatory, antioxidant, anti-diabetic, anti-helminthic, and anti-tumor properties. However, the production of these alkaloids in plants is limited, and there is a high demand for them due to the increasing incidence of cancer cases. To address this research gap, researchers have focused on optimizing culture media, eliciting metabolic pathways, overexpressing genes, and searching for potential sources of TIAs in organisms other than plants. The insufficient number of essential genes and enzymes in the biosynthesis pathway is the reason behind the limited production of TIAs. As the field of natural product discovery from biological species continues to grow, endophytes are being investigated more and more as potential sources of bioactive metabolites with a variety of chemical structures. Endophytes are microorganisms (fungi, bacteria, archaea, and actinomycetes), that exert a significant influence on the metabolic pathways of both the host plants and the endophytic cells. Bio-prospection of fungal endophytes has shown the discovery of novel, high-value bioactive compounds of commercial significance. The discovery of therapeutically significant secondary metabolites has been made easier by endophytic entities' abundant but understudied diversity. It has been observed that fungal endophytes have better intermediate processing ability due to cellular compartmentation. This paper focuses on fungal endophytes and their metabolic ability to produce complex TIAs, recent advancements in this area, and addressing the limitations and future perspectives related to TIA production.

Exploring Endophytic Bacteria from Artemisia spp. and Beneficial Traits on Pea Plants

Endophytic microorganisms represent promising solutions to environmental challenges inherent in conventional agricultural practices. This study concentrates on the identification of endophytic bacteria isolated from the root, stem, and leaf tissues of four Artemisia plant species. Sixty-one strains were isolated and sequenced by 16S rDNA. Sequencing revealed diverse genera among the isolated bacteria from different Artemisia species, including Bacillus, Pseudomonas, Enterobacter, and Lysinibacillus. AR11 and VR24 obtained from the roots of A. absinthium and A. vulgaris demonstrated significant inhibition on Fusarium c.f. oxysporum mycelial growth. In addition, AR11, AR32, and CR25 exhibited significant activity in phosphatase solubilization, nitrogen fixation, and indole production, highlighting their potential to facilitate plant growth. A comparative analysis of Artemisia species showed that root isolates from A. absinthium, A. campestris, and A. vulgaris have beneficial properties for inhibiting pathogen growth and enhancing plant growth. AR11 with 100% similarity to Bacillus thuringiensis, could be considered a promising candidate for further investigation as microbial biofertilizers. This finding highlights their potential as environmentally friendly alternatives to chemical pesticides, thereby contributing to sustainable crop protection practices.

Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum

Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products.

High-throughput sequencing-based analysis of the composition and diversity of the endophytic bacterial community in the roots of Dipsacus asperoides

This study employed Illumina high-throughput sequencing technology to investigate diversity and community structure of endophytic bacteria in wild D. asperoides growing in three distinct regions. The study analyzed the impact of region on endophytic bacteria, uncovered the core bacterial community, and furnished valuable insights for the screening of endophytic bacteria. This study identified 6,540 amplicon sequence variants (ASVs) coexisting with D. asperoides roots. These ASVs belong to 35 phyla, 84 classes, 204 orders, 365 families, and 708 genera. At the phylum level, the dominant phyla were Proteobacteria and Actinobacteria, while at the genus level, Acidothermus, Acidibacter, Bradyrhizobium, Frankia, and Pseudomonas emerged as the dominant genera. Furthermore, noticeable differences in endophytic bacterial communities were observed between the Yunnan and Guizhou regions. These findings can serve as a reference for the authentication of medicinal materials from various origins and the selection of active strains.

Temporal patterns of endophytic microbial heterogeneity across distinct ecological compartments within the Panax ginseng root system following deforestation for cultivation

Alterations in the microbial community significantly impact the yield and quality of ginseng. Yet, the dynamics of microbial community shifts within the root endophytes of ginseng across varying cultivation periods remain inadequately understood. This study zeroes in on the microbial community variations within the xylem (M), phloem (R), and fibrous roots (X) of ginseng during the fourth (F4) and fifth (F5) years of cultivation, aiming to bridge this research gap. We assessed soil physicochemical properties, enzyme activities, and nine individual saponins, complemented by high-throughput sequencing techniques (16S rDNA and ITS) to determine their profiles. The results showed that cultivation years mainly affected the microbial diversity of endophytic bacteria in ginseng fibrous roots compartment: the ASVs number and α-diversity Chao1 index of bacteria and fungi in F5X compartment with higher cultivation years were significantly higher than those in F4X compartment with lower cultivation years. It is speculated that the changes of fibrous roots bacterial groups may be related to the regulation of amino acid metabolic pathway. Such as D-glutamine and D-glutamate metabolism D-glutamine, cysteine and methionine metabolism regulation. The dominant bacteria in ginseng root are Proteobacteria (relative abundance 52.07-80.35%), Cyanobacteria (1.97-42.52%) and Bacteroidota (1.11-5.08%). Firmicutes (1.28-3.76%). There were two dominant phyla: Ascomycota (60.10-93.71%) and Basidiomycota (2.25-30.57%). Endophytic fungi were more closely related to soil physicochemical properties and enzyme activities. AN, TK, OP, SWC and EC were the main driving factors of endophytic flora of ginseng root. Tetracladium decreased with the increase of cultivation years, and the decrease was more significant in phloem (F4R: 33.36%, F5R: 16.48%). The relative abundance of Bradyrhizobium, Agrobacterium and Bacillus in each ecological niche increased with the increase of cultivation years. The relative abundance of Bradyrhizobium and Agrobacterium in F5X increased by 8.35 and 9.29 times, respectively, and Bacillus in F5M increased by 5.57 times. We found a variety of potential beneficial bacteria and pathogen antagonists related to ginseng biomass and saponins, such as Bradyrhizobium, Agrobacterium, Bacillus and Exophiala, which have good potential for practical application and development.

Bioremediation of Pb contaminated water using a novel Bacillus sp. strain MHSD_36 isolated from Solanum nigrum

The Pb bioremediation mechanism of a multi-metal resistant endophytic bacteria Bacillus sp. strain MHSD_36, isolated from Solanum nigrum, was characterised. The strain tested positive for the presence of plant growth promoters such as indoleacetic acid, 1-aminocyclopropane-1-carboxylate deaminase, siderophores, and phosphate solubilization. The experimental data illustrated that exopolysaccharides and cell hydrophobicity played a role in Pb uptake. The data further showed that the cell wall biosorbed a significant amount (71%) of the total Pb (equivalent to 4 mg/L) removed from contaminated water, compared to the cell membrane (11%). As much as 11% of the Pb was recovered from the cytoplasmic fraction, demonstrating the ability of the strain to control the influx of toxic heavy metals into the cell and minimize their negative impacts. Pb biosorption was significantly influenced by the pH and the initial concentration of the toxic ions. Furthermore, the presence of siderophores and biosurfactants, when the strain was growing under Pb stress, was detected through liquid chromatography mass spectrometry. The strain demonstrated a multi-component based Pb biosorption mechanism and thus, has a great potential for application in heavy metal bioremediation.

Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites

Background

Schisandra sphenanthera Rehd. et Wils. is a plant used in traditional Chinese medicine (TCM). However, great differences exist in the content of active secondary metabolites in various parts of S. sphenanthera. Do microorganisms critically influence the accumulation of active components in different parts of S. sphenanthera?

Methods

In this study, 16S/ITS amplicon sequencing analysis was applied to unravel microbial communities in rhizospheric soil and different parts of wild S. sphenanthera. At the same time, the active secondary metabolites in different parts were detected, and the correlation between the secondary metabolites and microorganisms was analyzed.

Results

The major components identified in the essential oils were sesquiterpene and oxygenated sesquiterpenes. The contents of essential oil components in fruit were much higher than that in stem and leaf, and the dominant essential oil components were different in these parts. The dominant components of the three parts were γ-muurolene, δ-cadinol, and trans farnesol (stem); α-cadinol and neoisolongifolene-8-ol (leaf); isosapathulenol, α-santalol, cedrenol, and longiverbenone (fruit). The microbial amplicon sequences were taxonomically grouped into eight (bacteria) and seven (fungi) different phyla. Community diversity and composition analyses showed that different parts of S. sphenanthera had similar and unique microbial communities, and functional prediction analysis showed that the main functions of microorganisms were related to metabolism. Moreover, the accumulation of secondary metabolites in S. sphenanthera was closely related to the microbial community composition, especially bacteria. In endophytic bacteria, Staphylococcus and Hypomicrobium had negative effects on five secondary metabolites, among which γ-muurolene and trans farnesol were the dominant components in the stem. That is, the dominant components in stems were greatly affected by microorganisms. Our results provided a new opportunity to further understand the effects of microorganisms on the active secondary metabolites and provided a basis for further research on the sustainable utilization of S. sphenanthera.

Description of Streptomyces naphthomycinicus sp. nov., an endophytic actinobacterium producing naphthomycin A and its genome insight for discovering bioactive compounds

Endophytic actinobacteria are a group of bacteria living inside plant tissue without harmful effects, and benefit the host plant. Many can inhibit plant pathogens and promote plant growth. This study aimed to identify a strain of Streptomyces as a novel species and study its antibiotics production. An endophytic actinobacterium, strain TML10T was isolated from a surface-sterilized leaf of a Thai medicinal plant (Terminalia mucronata Craib and Hutch). As a result of a polyphasic taxonomy study, strain TML10T was identified as a member of the genus Streptomyces. Strain TML10T was an aerobic actinobacterium with well-developed substrate mycelia with loop spore chains and spiny surface. Chemotaxonomic data, including cell wall components, major menaquinones, and major fatty acids, confirmed the affiliation of strain TML10T to the genus Streptomyces. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with a genome comparison study, allowed the genotypic and phenotypic differentiation of strain TML10T and the closest related type strains. The digital DNA-DNA hybridization (dDDH), Average nucleotide identity Blast (ANIb), and ANIMummer (ANIm) values between strain TML10T and the closest type strain, Streptomyces musisoli CH5-8T were 38.8%, 88.5%, and 90.8%, respectively. The name proposed for the new species is Streptomyces naphthomycinicus sp. nov. (TML10T = TBRC 15050T = NRRL B-65638T). Strain TML10T was further studied for liquid and solid-state fermentation of antibiotic production. Solid-state fermentation with cooked rice provided the best conditions for antibiotic production against methicillin-resistant Staphylococcus aureus. The elucidation of the chemical structures from this strain revealed a known antimicrobial agent, naphthomycin A. Mining the genome data of strain TML10T suggested its potential as a producer of antbiotics and other valuable compounds such as ε-Poly-L-lysine (ε-PL) and arginine deiminase. Strain TML10T contains the arcA gene encoding arginine deiminase and could degrade arginine in vitro.

Exploiting the role of plant growth promoting rhizobacteria in reducing heavy metal toxicity of pepper (Capsicum annuum L.)

Microorganisms are cost-effective and eco-friendly alternative methods for removing heavy metals (HM) from contaminated agricultural soils. Therefore, this study aims to identify and characterize HM-tolerant (HMT) plant growth-promoting rhizobacteria (PGPR) isolated from industry-contaminated soils to determine their impact as bioremediators on HM-stressed pepper plants. Four isolates [Pseudomonas azotoformans (Pa), Serratia rubidaea (Sr), Paenibacillus pabuli (Pp) and Bacillus velezensis (Bv)] were identified based on their remarkable levels of HM tolerance in vitro. Field studies were conducted to evaluate the growth promotion and tolerance to HM toxicity of pepper plants grown in HM-polluted soils. Plants exposed to HM stress showed improved growth, physio-biochemistry, and antioxidant defense system components when treated with any of the individual isolates, in contrast to the control group that did not receive PGPR. The combined treatment of the tested HMT PGPR was, however, relatively superior to other treatments. Compared to no or single PGPR treatment, the consortia (Pa+Sr+Pp+Bv) increased the photosynthetic pigment contents, relative water content, and membrane stability index but lowered the electrolyte leakage and contents of malondialdehyde and hydrogen peroxide by suppressing the (non) enzymatic antioxidants in plant tissues. In pepper, Cd, Cu, Pb, and Ni contents decreased by 88.0-88.5, 63.8-66.5, 66.2-67.0, and 90.2-90.9% in leaves, and 87.2-88.1, 69.4-70.0%, 80.0-81.3, and 92.3%% in fruits, respectively. Thus, these PGPR are highly effective at immobilizing HM and reducing translocation in planta. These findings indicate that the application of HMT PGPR could be a promising "bioremediation" strategy to enhance growth and productivity of crops cultivated in soils contaminated with HM for sustainable agricultural practices.

Longitudinal Distribution Map of the Active Components and Endophytic Fungi in Angelica sinensis (Oliv.) Diels Root and Their Potential Correlations

The three distinct medicinal parts of Angelica sinensis (Oliv.) Diels (Ang) roots are the head, body, and tail (ARH, ARB, and ART, respectively). How endophytic fungi shape the differences in metabolic components among these parts remains unclear. We quantified the distribution of active components and endophytic fungi along the ARH, ARB, and ART and their relationships. Based on the metabolic components and their abundances detected via non-target metabolism, the different medicinal parts were distinguishable. The largest number of dominant metabolic components was present in ART. The difference between ART and ARH was the greatest, and ARB was in a transitional state. The dominant active molecules in ART highlight their effects in haemodynamics improvement, antibacterial, anti-inflammatory, and hormone regulation, while ARH and ARB indicated more haemostasis, blood enrichment, neuromodulation, neuroprotection and tranquilisation, hepatoprotection, and antitumour activities than that of ART. The ARHs, ARBs, and ARTs can also be distinguished from each other based on the endophytic fungi at the microbiome level. The most dominant endophytic fungi were distributed in ART; the differences between ART and ARH were the largest, and ARB was in a transition state, which is consistent with the metabolite distributions. Structural equation modelling showed that the endophytic fungi were highly indicative of the metabolic components. Correlation analysis further identified the endophytic fungi significantly positively correlated with important active components, including Condenascus tortuosus, Sodiomyces alcalophilus, and Pleotrichocladium opacum. The bidirectional multivariate interactions between endophytic fungi and the metabolic components shape their spatial variations along the longitudinal direction in the Ang root.

Seasonal dynamics of phyllosphere epiphytic microbial communities of medicinal plants in farmland environment

Introduction

The phyllosphere of plants is inhabited by various microorganisms, which play a crucial role in plant physiological metabolism. Currently, there is limited research on the dynamic effects of species and seasons on plant phyllosphere microbial community diversity and microbial interactions.

Methods

In this study, high-throughput sequencing technology was used to sequence the leaf surface parasitic microorganisms of five medicinal plants (Bupleurum chinense, Atractylodes lancea, Salvia miltiorrhiza, Astragalus membranaceus, and Lonicera japonica).

Results

The results showed that bacteria and fungi clustered into 3,898 and 1,572 operational taxonomic units (OTUs), respectively. Compared to host species, seasons had a more significant impact on the a diversity of bacteria and fungi. The heterogeneity of phyllosphere microbial communities was greater in winter compared to summer. Key species analysis at the OTU level and Spearman correlation analysis demonstrated significant preferences in microbial interactions under plant and seasonal backgrounds. The network connections between bacterial and fungal communities significantly increased during seasonal transitions compared to connections with plants.

Discussion

This study enhances our understanding of the composition and ecological roles of plant-associated microbial communities in small-scale agricultural environments. Additionally, it provides valuable insights for assessing the biodiversity of medicinal plants.

Current status of research on endophytes of traditional Tibetan medicinal plant and their metabolites

The Qinghai-Tibet Plateau, known as the "Third Pole of the World," has a rich variety of medicinal plants that play an important role in the field of medicine due to its unique geographical environment. However, due to the limited resources of Tibetan medicinal plants and the fragility of the ecological environment of the Qinghai-Tibet Plateau, more and more Tibetan medicinal plants are on the verge of extinction. As a reservoir of biologically active metabolites, endophytes of medicinal plants produce a large number of compounds with potential applications in modern medicine (including antibacterial, immunosuppressive, antiviral, and anticancer) and are expected to be substitutes for Tibetan medicinal plants. This paper reviews 12 Tibetan medicinal plants from the Qinghai-Tibet Plateau, highlighting the diversity of their endophytes, the diversity of their metabolites and their applications. The results show that the endophytes of Tibetan medicinal plants are remarkably diverse, and the efficacy of their metabolites involves various aspects, such as antioxidant, anti-disease and anti-parasitic. In addition, conservation measures for the resources of Tibetan medicinal plants are summarised to provide a reference for an in-depth understanding of the endophytes of Tibetan medicinal plants and to stimulate the scientific community to bioprospect for the endophytes of Tibetan medicinal plants, as well as to provide ideas for their rational exploitation.

Contribution of endophytes towards improving plant bioactive metabolites: a rescue option against red-taping of medicinal plants

Medicinal plants remain a valuable source for natural drug bioprospecting owing to their multi-target spectrum. However, their use as raw materials for novel drug synthesis has been greatly limited by unsustainable harvesting leading to decimation of their wild populations coupled with inherent low concentrations of constituent secondary metabolites per unit mass. Thus, adding value to the medicinal plants research dynamics calls for adequate attention. In light of this, medicinal plants harbour endophytes which are believed to be contributing towards the host plant survival and bioactive metabolites through series of physiological interference. Stimulating secondary metabolite production in medicinal plants by using endophytes as plant growth regulators has been demonstrated to be one of the most effective methods for increasing metabolite syntheses. Use of endophytes as plant growth promotors could help to ensure continuous supply of medicinal plants, and mitigate issues with fear of extinction. Endophytes minimize heavy metal toxicity in medicinal plants. It has been hypothesized that when medicinal plants are exposed to harsh conditions, associated endophytes are the primary signalling channels that induce defensive reactions. Endophytes go through different biochemical processes which lead to activation of defence mechanisms in the host plants. Thus, through signal transduction pathways, endophytic microorganisms influence genes involved in the generation of secondary metabolites by plant cells. Additionally, elucidating the role of gene clusters in production of secondary metabolites could expose factors associated with low secondary metabolites by medicinal plants. Promising endophyte strains can be manipulated for enhanced production of metabolites, hence, better probability of novel bioactive metabolites through strain improvement, mutagenesis, co-cultivation, and media adjustment.

Cultivable Endophyte Resources in Medicinal Plants and Effects on Hosts

With the increasing demand for medicinal plants and the increasing shortage of resources, improving the quality and yield of medicinal plants and making more effective use of medicinal plants has become an urgent problem to be solved. During the growth of medicinal plants, various adversities can lead to nutrient loss and yield decline. Using traditional chemical pesticides to control the stress resistance of plants will cause serious pollution to the environment and even endanger human health. Therefore, it is necessary to find suitable pesticide substitutes from natural ingredients. As an important part of the microecology of medicinal plants, endophytes can promote the growth of medicinal plants, improve the stress tolerance of hosts, and promote the accumulation of active components of hosts. Endophytes have a more positive and direct impact on the host and can metabolize rich medicinal ingredients, so researchers pay attention to them. This paper reviews the research in the past five years, aiming to provide ideas for improving the quality of medicinal plants, developing more microbial resources, exploring more medicinal natural products, and providing help for the development of research on medicinal plants and endophytes.

Exploring the antimicrobial, antioxidant, anticancer, biocompatibility, and larvicidal activities of selenium nanoparticles fabricated by endophytic fungal strain Penicillium verhagenii

Herein, four endophytic fungal strains living in healthy roots of garlic were used to produce selenium nanoparticles (Se-NPs) via green synthesis. Penicillium verhagenii was found to be the most efficient Se-NPs producer with a ruby red color that showed maximum surface plasmon resonance at 270 nm. The as-formed Se-NPs were crystalline, spherical, and well-arranged without aggregation, and ranged from 25 to 75 nm in size with a zeta potential value of -32 mV, indicating high stability. Concentration-dependent biomedical activities of the P. verhagenii-based Se-NPs were observed, including promising antimicrobial activity against different pathogens (Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Staphylococcus aureus, Candida albicans, C. glabrata, C. tropicalis, and C. parapsilosis) with minimum inhibitory concentration (MIC) of 12.5-100 µg mL^-1. The biosynthesized Se-NPs showed high antioxidant activity with DPPH-scavenging percentages of 86.8 ± 0.6% at a concentration of 1000 µg mL^-1 and decreased to 19.3 ± 4.5% at 1.95 µg mL^-1. Interestingly, the Se-NPs also showed anticancer activity against PC3 and MCF7 cell lines with IC₅₀ of 225.7 ± 3.6 and 283.8 ± 7.5 µg mL^-1, respectively while it is remaining biocompatible with normal WI38 and Vero cell lines. Additionally, the green synthesized Se-NPs were effective against instar larvae of a medical insect, Aedes albopictus with maximum mortality of 85.1 ± 3.1, 67.2 ± 1.2, 62.10 ± 1.4, and 51.0 ± 1.0% at a concentration of 50 µg mL^-1 for I, II, III, and IV-instar larva, respectively. These data highlight the efficacy of endophytic fungal strains for cost-effective and eco-friendly Se-NPs synthesis with different applications.

Culturable bacterial endophytes of Aconitum carmichaelii Debx. were diverse in phylogeny, plant growth promotion, and antifungal potential

Medicinal plants harbor tremendously diverse bacterial endophytes that maintain plant growth and health. In the present study, a total of 124 culturable bacterial endophytes were isolated from healthy Aconitum carmichaelii Debx. plants. These strains were clustered into 10 genera based on full-length 16S rDNA sequences, among which Bacillus and Pseudomonas were the dominant genera. In addition, A. carmichaelii may capture 10 potential new bacterial species based on multi-locus sequence analysis of three housekeeping genes (gyrA, rpoB, and atpD). The majority of these bacterial endophytes exhibited plant growth-promoting ability through diverse actions including the production of either indole acetic acid and siderophore or hydrolytic enzymes (glucanase, cellulose, and protease) and solubilization of phosphate or potassium. A total of 20 strains inhibited hyphal growth of fungal pathogens Sclerotium rolfsii and Fusarium oxysporum in vitro on root slices of A. carmichaelii by the dual-culture method, among which Pseudomonas sp. SWUSTb-19 showed the best antagonistic activity. Field experiment confirmed that Pseudomonas sp. SWUSTb-19 significantly reduced the occurrence of southern blight and promoted plant biomass compared with non-inoculation treatment. The possible mode of actions for Pseudomonas sp. SWUSTb-19 to antagonize against S. rolfsii involved the production of glucanase, siderophore, lipopeptides, and antimicrobial volatile compounds. Altogether, this study revealed that A. carmichaelii harbored diverse plant growth-promoting bacterial endophytes, and Pseudomonas sp. SWUSTb-19 could be served as a potential biocontrol agent against southern blight.

Research progress of volatile organic compounds produced by plant endophytic bacteria in control of postharvest diseases of fruits and vegetables

Pathogen infestation results in significant losses of fruits and vegetables during handling, transportation, and storage. The use of synthetic fungicides has been a common measure for controlling plant pathogens. However, their excessive use of chemicals has led to increased environmental pollution, leaving large amounts of chemicals in agricultural products, posing a threat to human and animal health. There is now an increasing amount of research activities to explore safer and more innovative ways to control plant pathogens. In this regard, endophytic bacteria contribute significantly. Endophytic bacteria are ubiquitous in the internal tissues of plants without causing damage or disease to the host. Due to their high volatility and difficulties in residue in fruits and vegetables, volatile organic chemicals (VOCs) produced by endophytic bacteria have received a lot of attention in recent years. VOCs are a potential biofumigant for the effective control of postharvest fruits and vegetables diseases. This review focuses mainly on the recent progress in using endophytic bacteria VOCs to control post-harvest fruits and vegetables disease. This review provides a brief overview of the concept, characteristics, and summarises the types, application effect, and control mechanisms of endophytic bacterial VOCs. The research area that is being developed has great application value in agriculture and living practice.

Root endophytic bacterial community composition of Aconitum carmichaelii debx. from three main producing areas in China

Aconitum carmichaelii Debx. is famous for the bioactive aconitum alkaloids as traditional Chinese medicine. Endophytic bacteria play vital roles in plant growth, health, and the production of secondary metabolites such as alkaloids. In this study, we employed 16 S rRNA amplicon high-throughput sequencing to determine the root endophytic bacterial community of A. carmichaelii Debx. collected from three main producing areas including the geo-authentic area in China, high performance liquid chromatography to measure the contents of six bioactive alkaloids and correlation analysis to explore the relationship among environmental factors, alkaloids contents, and endophytic bacterial community. The results indicated that the root core microbiota of A. carmichaelii Debx. was dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Root endophytic bacterial community in the geo-authentic area was distinct from the other two regions. Soil nitrogen contents, organic matter, and temperature were the main factors contributing to the endophytic bacterial community structure. Significant correlation was found between alkaloids contents and some bacterial genera. Particularly, the abundance of Lactobacillus was positively correlated with the contents of benzoyl-mesaconitine and benzoyl-aconine. This study provided the first insight into the root endophytic bacterial community composition of A. carmichaelii Debx., and can direct further isolation of functional bacterial strains.

Seeds of Stevia rebaudiana Bertoni as a Source of Plant Growth-Promoting Endophytic Bacteria with the Potential to Synthesize Rebaudioside A

In this study, a new strain of Pantoea vagans, SRS89, was isolated from surface-sterilized stevia seeds. The isolate was evaluated using morphological, molecular, and biochemical methods. The bacterium was 1.5 μm long, yellowish in color, and classified as Gram-negative. Whole genome sequencing of our strain revealed the presence of a 4,610,019 bp chromosome, and genome annotation resulted in the detection of 4283 genes encoding 4204 putative coding sequences. Phylogenic analysis classified the genome of our strain close to the MP7 and LMG 24199 strains of P. vagans. Functional analysis showed that the highest number of genes within the analyzed bacterium genome were involved in transcription, amino acid transport and metabolism, and carbohydrate transport and metabolism. We also identified genes for enzymes involved in the biosynthesis of carotenoids and terpenoids. Furthermore, we showed the presence of growth regulators, with the highest amount noted for gibberellic acid A₃, indole-3-acetic acid, and benzoic acid. However, the most promising property of this strain is its ability to synthesize rebaudioside A; the estimated amount quantified using reversed-phase (RP)-HPLC was 4.39 mg/g of the dry weight of the bacteria culture. The isolated endophytic bacterium may be an interesting new approach to the production of this valuable metabolite.

Calendula officinalis-A Great Source of Plant Growth Promoting Endophytic Bacteria (PGPEB) and Biological Control Agents (BCA)

The application of beneficial bacteria may present an alternative approach to chemical plant protection and fertilization products as they enhance growth and resistance to biotic and abiotic stresses. Plant growth-promoting bacteria are found in the rhizosphere, epiphytically or endophytically (Plant Growth Promoting Endophytic Bacteria, PGPEB). In the present study, 36 out of 119 isolated endophytic bacterial strains from roots, leaves and flowers of the pharmaceutical plant Calendula officinalis were further identified and classified into Bacillus, Pseudomonas, Pantoea, Stenotrophomonas and Rhizobium genera. Selected endophytes were evaluated depending on positive reaction to different plant growth promoting (PGP) traits, motility, survival rate and inhibition of phytopathogenic fungi in vitro and ex vivo (tomato fruit). Bacteria were further assessed for their plant growth effect on Arabidopsis thaliana seedlings and on seed bio-primed tomato plantlets, in vitro. Our results indicated that many bacterial endophytes increased seed germination, promoted plant growth and changed root structure by increasing lateral root density and length and root hair formation. The most promising antagonistic PGPEB strains (Cal.r.29, Cal.l.30, Cal.f.4, Cal.l.11, Cal.f.2.1, Cal.r.19 and Cal.r.11) are indicated as effective biological control agents (BCA) against Botrytis cinerea on detached tomato fruits. Results underlie the utility of beneficial endophytic bacteria for sustainable and efficient crop production and disease control.

Screening of endophytic bacteria from potato tubers and their antagonistic activity against soil-borne potato pathogens

In order to appraise the bacterial endophyte communities that help resist disease in potato tuber, the separation, the population density, biodiversity and the antagonistic activity of endophytic bacteria, from the tuber peel of potato cultivars (Fontan90, Agria, Sante’a and Jeli89), were examined in the Fars province in Iran. In this study, the bacterial endophyte Colony Forming Units (CFU) were counted based on the most suitable dilution in petri dishes and expressed per g of wet weight of tuber tissue. The presence of bacteria was found mostly in the outer layer. A wide variety of endophyte species biodiversity was in Agria cultivar. To estimate the antagonistic effect of potato associated endophytic bacteria, 115 bacterial isolates were evaluated by dual culture method against main soil-borne potato pathogens Fusarium oxysporum, Rhizoctonia solani, Verticillium dahliae, Streptomyces scabies and Ralstonia solanacearum. Endophyte strains were identified based on physiological, morphological and chemical characteristics and the 16S rRNA gene sequence analysis. The highest degree of the inhibitory activity in all layers of potato cultivars was related to Bacillus subtilis, Bacillus mojavensis and Klebsiella variicola. Antagonistic activity of endophytic bacteria against the pathogens was significantly higher (p<0.01) in the examined strains from the outermost layer of tuber peel and decreased progressively toward the center of the tuber. In this research, Klebsiella variicola was reported as endophyte bacteria in the four commercial potatocultivars mentioned above, for the first time.

Deciphering the potential of a plant growth promoting endophyte Rhizobium sp. WYJ-E13, and functional annotation of the genes involved in the metabolic pathway

Plant growth-promoting rhizobacteria (PGPR) are well-acknowledged root endophytic bacteria used for plant growth promotion. However, which metabolites produced by PGPR could promote plant growth remains unclear. Additionally, which genes are responsible for plant growth-promoting traits is also not elucidated. Thus, as comprehensive understanding of the mechanism of endophyte in growth promotion is limited, this study aimed to determine the metabolites and genes involved in plant growth-promotion. We isolated an endophytic Rhizobium sp. WYJ-E13 strain from the roots of Curcuma wenyujin Y.H. Chen et C. Ling, a perennial herb and medicinal plant. The tissue culture experiment showed its plant growth-promoting ability. The bacterium colonization in the root was confirmed by scanning electron microscopy and paraffin sectioning. Furthermore, it was noted that the WYJ-E13 strain produced cytokinin, anthranilic acid, and L-phenylalanine by metabolome analysis. Whole-genome analysis of the strain showed that it consists of a circular chromosome of 4,350,227 bp with an overall GC content of 60.34%, of a 2,149,667 bp plasmid1 with 59.86% GC, and of a 406,180 bp plasmid2 with 58.05% GC. Genome annotation identified 4,349 putative protein-coding genes, 51 tRNAs, and 9 rRNAs. The CDSs number allocated to the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and Clusters of Orthologous Genes databases were 2027, 3,175 and 3,849, respectively. Comparative genome analysis displayed that Rhizobium sp. WYJ-E13 possesses the collinear region among three species: Rhizobium acidisoli FH23, Rhizobium gallicum R602 and Rhizobium phaseoli R650. We recognized a total set of genes that are possibly related to plant growth promotion, including genes involved in nitrogen metabolism (nifU, gltA, gltB, gltD, glnA, glnD), hormone production (trp ABCDEFS), sulfur metabolism (cysD, cysE, cysK, cysN), phosphate metabolism (pstA, pstC, phoB, phoH, phoU), and root colonization. Collectively, these findings revealed the roles of WYJ-E13 strain in plant growth-promotion. To the best of our knowledge, this was the first study using whole-genome sequencing for Rhizobium sp. WYJ-E13 associated with C. wenyujin. WYJ-E13 strain has a high potential to be used as Curcuma biofertilizer for sustainable agriculture.

Screening of Endophytic Bacteria of Leucojum aestivum 'Gravety Giant' as a Potential Source of Alkaloids and as Antagonist to Some Plant Fungal Pathogens

Leucojum aestivum is a medicinal plant belonging to the Amaryllidaceae family well known as a producer of alkaloids such as galanthamine and lycorine. However, the endophytic microbes that colonize different plant tissues without causing any damage have not been reported in this plant. Here, we explored the different endophytic bacterial communities isolated from different surface disinfected tissues of L. aestivum 'Gravety giant' and screened bacterial isolates producing alkaloids and their potential use as biocontrol agent against wheat pathogens. For that purpose, endophytic bacteria were isolated from bulbs, roots and shoots of L. aestivum. After taxonomical characterization, these microorganisms were screened for their ability to produce alkaloids using high-performance thin-layer chromatography (HPTLC) and untargeted liquid chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS) strategies. We isolated 138 bacteria belonging to four phyla and 42 genera, mainly from roots and shoots. The most abundant genera were Rahnella in shoot, Patulibacter in bulb and Bacillus in roots. Among the different bacterial isolates, the methanolic extracts of Luteibacter rhizovicinus (LaBFB3301) and Commamonas denitrificans (LaBFS2103) slightly delayed the growth of F. graminearum colonies in in vitro dual tests against F. graminearum and M. nivale strains with 15.5% and 19.9% inhibition rates, respectively. These isolates are able to produce an indolic alkaloid tryptophol (C₁₀H₁₁NO, [M + H]⁺ 162.0913). These endophytic bacteria might be investigated to characterize the plant protection effect and the plant growth promotion effect.

Isolation and identification of endophytic actinobacteria from Citrullus colocynthis (L.) Schrad and their antibacterial properties

BACKGROUND

Antibiotic resistance poses a major threat to human health globally. Consequently, new antibiotics are desperately required to discover and develop from unexplored habitats to treat life-threatening infections. Microbial natural products (NP) are still remained as primary sources for the discovery of new antibiotics. Endophytic actinobacteria (EA) which are well-known producers of bioactive compounds could provide novel antibiotic against pathogenic bacteria. This research aimed to isolate EA from the Citrullus colocynthis plant and explore the antibacterial properties of their metabolites against pathogenic bacteria.

RESULTS

The healthy samples were collected, dissected and surface-sterilized before cultured on four different selection media at 28 °C. Six endophytic actinobacteria were isolated from Citrullus colocynthis plant. They were taxonomically classified into two family namely Streptomycetaceae and Nocardiopsaceae, based on colony morphological features, scanning electron microscope analysis and molecular identification of isolates. This is the first report on the identification of EA form Citrullus colocynthis and their antibacterial activity. The strains generated a chain of vibrio-comma, cubed or cylindrical shaped spores with indenting or smooth surfaces. Three of those were reported as endophytes for the first time. The strain KUMS-C1 showed 98.55% sequence similarity to its closely related strains which constitutes as a novel species/ strain for which the name Nocardiopsis colocynthis sp. was proposed for the isolated strain. Five isolated strains had antagonist activity against S. aureus, P. aeruginosa, and E. coli. Among those, stain KUMS-C6 showed the broadest spectrum of antibacterial activity against all test bacteria, whereas the strain KUMS-C4 had no antibacterial activity.

CONCLUSIONS

NPs have a long history of safe and efficient use for development of pharmaceutical products. Our study highlights that Citrullus colocynthis is an untapped source for the isolation of EA, generating novel and bioactive metabolites by which might lead to discovery of new antibiotic(s). This study reveals the future of new antibiotic developments looks bright against multi-drug resistance diseases by mining under- or unexplored habitats.

The bacterial consortia promote plant growth and secondary metabolite accumulation in Astragalus mongholicus under drought stress

Astragalus mongholicus is a widely used Traditional Chinese Medicine. However, cultivated A. mongholicus is often threatened by water shortage at all growth stage, and the content of medicinal compounds of cultivated A. mongholicus is much lower than that of wild plants. To alleviate drought stress on A. mongholicus and improve the accumulation of medicinal components in roots of A. mongholicus, we combined different bacteria with plant growth promotion or abiotic stress resistance characteristics and evaluated the role of bacterial consortium in helping plants tolerate drought stress and improving medicinal component content in roots simultaneously. Through the determination of 429 bacterial strains, it was found that 97 isolates had phosphate solubilizing ability, 63 isolates could release potassium from potash feldspar, 123 isolates could produce IAA, 58 isolates could synthesize ACC deaminase, and 21 isolates could secret siderophore. Eight bacterial consortia were constructed with 25 bacterial isolates with more than three functions or strong growth promoting ability, and six out of eight bacterial consortia significantly improved the root dry weight. However, only consortium 6 could increase the root biomass, astragaloside IV and calycosin-7-glucoside content in roots simultaneously. Under drought challenge, the consortium 6 could still perform these functions. Compared with non-inoculated plants, the root dry weight of consortium inoculated-plants increased by 120.0% and 78.8% under mild and moderate drought stress, the total content of astragaloside IV increased by 183.83% and 164.97% under moderate and severe drought stress, calycosin-7-glucoside content increased by 86.60%, 148.56% and 111.45% under mild, moderate and severe drought stress, respectively. Meanwhile, consortium inoculation resulted in a decrease in MDA level, while soluble protein and proline content and SOD, POD and CAT activities increased. These findings provide novel insights about multiple bacterial combinations to improve drought stress responses and contribute to accumulate more medicinal compounds.

Novel Approaches for Sustainable Horticultural Crop Production: Advances and Prospects

Reduction of plant growth, yield and quality due to diverse environmental constrains along with climate change significantly limit the sustainable production of horticultural crops. In this review, we highlight the prospective impacts that are positive challenges for the application of beneficial microbial endophytes, nanomaterials (NMs), exogenous phytohormones strigolactones (SLs) and new breeding techniques (CRISPR), as well as controlled environment horticulture (CEH) using artificial light in sustainable production of horticultural crops. The benefits of such applications are often evaluated by measuring their impact on the metabolic, morphological and biochemical parameters of a variety of cultures, which typically results in higher yields with efficient use of resources when applied in greenhouse or field conditions. Endophytic microbes that promote plant growth play a key role in the adapting of plants to habitat, thereby improving their yield and prolonging their protection from biotic and abiotic stresses. Focusing on quality control, we considered the effects of the applications of microbial endophytes, a novel class of phytohormones SLs, as well as NMs and CEH using artificial light on horticultural commodities. In addition, the genomic editing of plants using CRISPR, including its role in modulating gene expression/transcription factors in improving crop production and tolerance, was also reviewed.

Advancement in the molecular perspective of plant-endophytic interaction to mitigate drought stress in plants

Change in global climate has started to show its effect in the form of extremes of temperatures and water scarcity which is bound to impact adversely the global food security in near future. In the current review we discuss the impact of drought on plants and highlight the ability of endophytes, microbes that inhabit the plants asymptomatically, to confer stress tolerance to their host. For this we first describe the symbiotic association between plant and the endophytes and then focus on the molecular and physiological strategies/mechanisms adopted by these endophytes to confer stress tolerance. These include root alteration, osmotic adjustment, ROS scavenging, detoxification, production of phytohormones, and promoting plant growth under adverse conditions. The review further elaborates on how omics-based techniques have advanced our understanding of molecular basis of endophyte mediated drought tolerance of host plant. Detailed analysis of whole genome sequences of endophytes followed by comparative genomics facilitates in identification of genes involved in endophyte-host interaction while functional genomics further unveils the microbial targets that can be exploited for enhancing the stress tolerance of the host. Thus, an amalgamation of endophytes with other sustainable agricultural practices seems to be an appeasing approach to produce climate-resilient crops.

Characterization of the Cultivable Endophytic Bacterial Community of Seeds and Sprouts of Cannabis sativa L. and Perspectives for the Application as Biostimulants

Endophytes are beneficial microorganisms exerting growth-promoting activities in plants; they are most often located within the plant intercellular spaces and can be found in all plant tissues, including roots, leaves, stems, flowers, and seeds. In this work, we investigated the cultivable bacterial community of the seeds and the two-week sprouts of the Cannabis sativa L. cultivar “Futura 75”. Endophytes were genotypically and phenotypically characterized and were exposed to different concentrations of seed extracts to verify their susceptibility. A bacterial strain among all the isolates was selected for germination tests of C. sativa in different experimental conditions. The results revealed the dominance of Firmicutes (Staphylococcus sp.) among the isolated strains. Two strains were different from the others for indole-3-acetic acid (IAA) production and for their resistance patterns towards abiotic and biotic stresses. The Sphingomonas sp. strain Can_S11 (Alphaproteobacteria) showed a potential ability to increase the nutraceutical features of its sprouts, particularly an increase in the polyphenol content and antioxidant activity. None of the isolated strains were susceptible to the seed extracts, which were previously tested as antimicrobial and antibiofilm agents against human pathogenic bacteria. The results open new perspectives for the study of the endophytes of C. sativa as possible biostimulants.

Seed Endophytic Achromobacter sp. F23KW as a Promising Growth Promoter and Biocontrol of Rhizoctonia Root Rot of Fenugreek

Root rot is one of the most significant soil and seed-borne fungal diseases, limiting the cultivation of fenugreek plants. Endophytic bacteria and their natural bioproducts have emerged as growth promoters and disease suppressors in the current era. Despite limited research, seeds are a good funder of endophytic microbiomes, which are transmitted from them to other seedling parts, thereby providing a shield against biotic and abiotic anxiety and promoting the growth at early germination and later stages. The current study evaluated the hypothesis that seed endophytic bacteria and their lytic enzymes, growth promotors, and antifungal molecules can induce growth, and inhibit root rot disease development at the same time. The isolation trial from fenugreek seeds revealed a lytic Achromobacter sp., which produces indole acetic acid, has antifungal compounds (e.g., 2-Butanol, 3,3’-oxybis-), and reduces the growth of Rhizoctonia solani by 43.75%. Under the greenhouse and natural field conditions, bacterial cells and/or supernatant improved the growth, physiology, and yield performance of fenugreek plants, and effectively suppressed the progress of root rot disease; this is the first extensive study that uses a new seed-borne endophytic bacterium as a plant-growth-promoting, and biocontrol tool against the sclerotia-forming; R. solani; the causative of fenugreek root rot.

Dendrobium officinale Endophytes May Colonize the Intestinal Tract and Regulate Gut Microbiota in Mice

Dendrobium officinale is a traditional Chinese medicine for treating gastrointestinal diseases by nourishing “Yin” and thickening the stomach lining. To study whether D. officinale endophytes can colonize the intestinal tract and regulate gut microbiota in mice, we used autoclave steam sterilizing and 60Co-γ radiation to eliminate D. officinale endophytes from its juice. Then, high-throughput ITS1-ITS2 rDNA and 16S rRNA gene amplicons were sequenced to analyze the microbial community of D. officinale endophytes and fecal samples of mice after administration of fresh D. officinale juice. Sterilization of D. officinale juice by autoclaving for 40 min (ASDO40) could more effectively eliminate the D. officinale endophytes and decrease their interference on the gut microbiota. D. officinale juice could increase beneficial gut microbiota and metabolites including short-chain fatty acids. D. officinale endophytes Pseudomonas mosselii, Trichocladium asperum, Titata maxilliformis, Clonostachys epichloe, and Rhodotorula babjevae could colonize the intestinal tract of mice and modulate gut microbiota after oral administration of the juice for 28 days. Thus, the regulatory effect of D. officinale juice on gut microbiota was observed, which provides a basis for inferring that D. officinale endophytes might colonize the intestinal tract and participate in regulating gut microbiota to treat diseases. Thus, this study further provides a new approach for the treatment of diseases by colonizing plant endophytes in the intestinal tract and regulating gut microbiota.

Large-scale microbiome analysis reveals bacterial community characteristics in typical Chinese herbal slices

Chinese herbal slices (CHSs) are closely associated to microorganisms, whether they are endophytic or epiphytic in plants, or introduced during processing. In this study, the structures and predicted functions of microbial communities in 150 batches of samples from five types of CHSs were investigated by combining pure culture and 16 S rDNA amplicon sequencing. Bile-salt-tolerant gram-negative bacteria were detected in 56.0% of samples, and Salmonella was detected in two batches of Glycyrrhiza slices and in one batch of Rheum slices. The main genera from the Enterobacteriaceae, Bacillaceae, Fibrobacteraceae, and Pseudomonadaceae families were assessed in typical colonies. Amplicon sequencing identified 1200 bacterial genera, including some pharmacopeial-controlled bacteria and many beneficial endophytes of medicinal plants. Around 65% of the genera co-occurred in all five CHSs. In clustering based on different algorithms, the samples from each CHS type were relatively clustered, with some overlap. Ranked from highest to lowest diversity, the CHSs were Rheum, Angelica, Astragalus, Codonopsis, and Glycyrrhiza. Each CHS had its indicator species. Functional annotations suggest that potential microbial transformation uses CHSs as substrates and microbial communities as transformants. Overall, it was demonstrated that, based on their complementary advantages, high-throughput sequencing technology and traditional pure-culture technology together can fully assess the microbial load of CHSs and reduce the misdetection rate. We observed large microbial communities in typical CHSs, demonstrating differences and similarities among different CHS types. These results provide a reference for establishing new microbial limit criteria for CHSs and highlight the importance of further correlating CHS microbial community structure and function.

Synergism of endophytic Bacillus subtilis and Klebsiella aerogenes modulates plant growth and bacoside biosynthesis in Bacopa monnieri

Bacopa monnieri is the main source of pharmaceutically important bacosides; however, the low content of these molecules in planta remains a limiting factor for fulfilling the industrial requirement. The accumulation of secondary metabolites can be enhanced in plants upon inoculation with endophytes. In this study, we isolated and analyzed the culturable endophytes associated with different plant parts. By analyzing their impact on plant growth parameters (in vitro and in vivo) and Bacoside A content, we found few candidates which increased bacoside accumulation significantly. Finally, two promising endophytes namely Bacillus subtilis (OK070745) and Klebsiella aerogenes (OK070774) were co-cultivated with B. monnieri cuttings singly and in combination mode to clarify their effect on bacoside biosynthesis and their accumulation in B. monnieri shoot. Consortium-inoculated plants significantly enhanced the plant biomass and Bacoside A content with respect to single inoculation. The results of real-time quantitative (RT-PCR) revealed significant accumulation of bacoside biosynthetic pathway transcripts (HMGCR, PMVK, FDPS, SQS, and β-AS) in the case of plants inoculated with microbial combination, while the single inoculation of B. subtilis diverted the plant's machinery toward the synthesis of phenylpropanoid genes like CCR, CAD, CHS, and HST. In addition, higher expression of MYB 2 and WRKY 1 transcription factors in combinational treatment points out their probable role in better physiological and developmental processes. Altogether, this is the first study on B. monnieri-endophyte interaction showing improvement in the accumulation of bacoside A by modulating various genes of metabolic pathway and thus suggests an effective "green approach" for augmenting in planta production of pharmaceutically important bacosides.

Biosynthetic Mechanisms of Secondary Metabolites Promoted by the Interaction Between Endophytes and Plant Hosts

Endophytes is a kind of microorganism resource with great potential medicinal value. The interactions between endophytes and host not only promote the growth and development of each other but also drive the biosynthesis of many new medicinal active substances. In this review, we summarized recent reports related to the interactions between endophytes and hosts, mainly regarding the research progress of endophytes affecting the growth and development of host plants, physiological stress and the synthesis of new compounds. Then, we also discussed the positive effects of multiomics analysis on the interactions between endophytes and their hosts, as well as the application and development prospects of metabolites synthesized by symbiotic interactions. This review may provide a reference for the further development and utilization of endophytes and the study of their interactions with their hosts.

Biotization of Endophytes Trichoderma asperellum and Bacillus subtilis in Mentha spicata Microplants to Promote Growth, Pathogen Tolerance and Specialized Plant Metabolites

In the present study, the effect of biotization of Mentha spicata microplants with Trichoderma asperellum and Bacillus subtilis on growth, Rhizoctonia sp., incidence, and specialized metabolites content was evaluated. Analyses of root tissues of the microplants showed 100% endophytism with both microorganisms. During the acclimatization phase, plants with the endophytes T. asperellum and B. subtilis had a survival rate of 95% and 93%, respectively, compared to 75% for control plants. Then, under greenhouse conditions, a trial was carried out with biotized plants with or without Rhizoctonia sp. inoculation, plants inoculated with Rhizoctonia sp., and endophyte- and pathogen-free control. Biotized plants with the endophytes showed higher dry biomass and the incidence of Rhizoctonia was lower (8% for T. asperellum and 10% for B. subtilis) compared to plants inoculated with the pathogen (82%). In addition, plants with T. asperellum had the highest contents of total polyphenols (280 GAE/100 mg sample) and rosmarinic acid (28 mg RA/100 g sample). Thus, this study shows the potential of the technique of using the endophytes T. asperellum and B. subtilis on M. spicata microplants to improve plant survival and growth, decrease the incidence of Rhizoctonia sp., and improve the contents of specialized metabolites, which can contribute to the sustainable management of this crop.

Synergistic Plant-Microbe Interactions between Endophytic Actinobacteria and Their Role in Plant Growth Promotion and Biological Control of Cotton under Salt Stress

Bacterial endophytes are well-acknowledged inoculants to promote plant growth and enhance their resistance toward various pathogens and environmental stresses. In the present study, 71 endophytic strains associated with the medicinal plant Thymus roseus were screened for their plant growth promotion (PGP), and the applicability of potent strains as bioinoculant has been evaluated. Regarding PGP traits, the percentage of strains were positive for the siderophore production (84%), auxin synthesis (69%), diazotrophs (76%), phosphate solubilization (79%), and production of lytic enzymes (i.e., cellulase (64%), lipase (62%), protease (61%), chitinase (34%), and displayed antagonistic activity against Verticillium dahliae (74%) in vitro. The inoculation of strain XIEG05 and XIEG12 enhanced plant tolerance to salt stress significantly (p < 0.05) through the promotion of shoot, root development, and reduced the activities of antioxidant enzymes (SOD, POD, and CAT), compared with uninoculated controls in vivo. Furthermore, inoculation of strain XIEG57 was capable of reducing cotton disease incidence (DI) symptoms caused by V. dahliae at all tested salt concentrations. The GC-MS analysis showed that many compounds are known to have antimicrobial and antifungal activity. Our findings provide valuable information for applying strains XIEG05 and XIEG12 as bioinoculant fertilizers and biological control agent of cotton under saline soil conditions.

Environmental and Human Microbiome for Health

Microorganisms are an essential part of life on the earth and can exist in association with virtually any living thing. The environmental microbiome is much more diverse than the human microbiome. It is reported that most microbes existing in the environment are difficult to culture in the laboratory. Whereas both pathogenic and beneficial microbes may be prevailing in the environment, the human body can have three categories of microbes- beneficial, pathogenic, and opportunistic pathogenic. With at least 10-fold more cells than human cells, microbes as normal flora are critical for human survival. The microbes present in the human body play a crucial role in maintaining human health, and the environmental microbiome influences the human microbiome makeup. The interaction between the environmental and human microbiome highly influences human health, however it is poorly understood. In addition, as an established infection is associated with health-seeking behavior, a large number of studies have focused on the transmission and dynamics of infectious microorganisms than the noninfectious or beneficial ones. This review will summarize how the interaction between the environmental and human microbiome affects human health and identify approaches that might be beneficial for humans to improve health by being exposed to the natural environment.

Integrated Genomic and Metabolomic Analysis Illuminates Key Secreted Metabolites Produced by the Novel Endophyte Bacillus halotolerans Cal.l.30 Involved in Diverse Biological Control Activities

The endophytic strain Cal.l.30, isolated from the medicinal plant Calendula officinalis, was selected among seven Bacillus strains with plant growth promoting activity and strong biological potential against the postharvest fungal pathogen Botrytis cinerea. Treatment by inoculating Cal.l.30 bacterial cell culture or cell free supernatant on harvested grapes and cherry tomato fruits, significantly reduced gray mold disease severity index and disease incidence. Based on 16S rRNA sequence analysis and whole genome phylogeny, Cal.l.30 was identified as Bacillus halotolerans. Genome mining revealed that B. halotolerans Cal.l.30 is endowed with a diverse arsenal of secondary metabolite biosynthetic gene clusters (SM-BGCs) responsible for metabolite production with antimicrobial properties. A sub-set of the identified SM-BGCs (mojavensin A, ‘bacillunoic acid’) appears to be the result of recent horizontal gene transfer events. Its genome was also mined for CAZymes associated with antifungal activity. Further UHPLC-HRMS analysis indicated that Cal.l.30 synthesizes and secretes secondary metabolites with antimicrobial activity, including the lipopeptides, fengycin, surfactin and mojavensin A, bacillaene isoforms, L-dihydroanticapsin and bacillibactin. Other compounds with known antimicrobial activity were also detected, such as azelaic acid, 15- hydroxypentadecanoid acid and 2-hydroxyphenylacetic acid. The genomic and metabolomic features of the B. halotolerans Cal.l.30 provided new perspectives on the exploitation of novel Bacillus sp. as a biocontrol agent.

Differences in gene expression and endophytic bacterial diversity in Atractylodes macrocephala Koidz. rhizomes from different growth years

Atractylodes macrocephala Koidz. (AMK) is widely used owing to its pharmacological activity in traditional Chinese medicine (TCM). Here, we aimed to characterize the differentially expressed genes (DEGs) of one- and three-year growth (OYG and TYG) rhizomes of AMK combined with the endophytic bacterial diversity analysis using high-throughput RNA-sequencing. 114,572 unigenes were annotated in six public databases. 3570 DEGs revealed a clear difference, of which 936 and 2634 genes were up- and down-regulated, respectively. The results of KEGG pathway analysis indicated that DEGs corresponding to the terpenoid synthesis gene were downregulated in TYG rhizomes. 414,424 sequences corresponding to the 16S rRNA gene were divided into 1267 operational taxonomic units (OTUs). Moreover, the diversity of endophytic bacteria changed with species in OYG (773) and TYG (1201) rhizomes at OTU level, and Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla. Comparison of species differences among different growth years revealed that some species were significantly different, such as Actinomycetes, Variovorax, Cloacibacterium, etc. Interestingly, the decrease in the function-related metabolism of terpenoids and polyketides was found to be correlated the low expression of terpene synthesis genes in TYG rhizomes assessed using PICRUSt2. These data provide a scientific basis for elucidating the mechanism underlying metabolite accumulation and endophytic bacterial diversity in relation to the growth years in AMK.

Analysis of Endophytic Bacterial Diversity From Different Dendrobium Stems and Discovery of an Endophyte Produced Dendrobine-Type Sesquiterpenoid Alkaloids

As the unique component of Dendrobium, dendrobine-type sesquiterpenoid alkaloids (DSAs) possess a variety of medicinal properties. It has been well documented that plant endophytes can in vitro synthesize secondary metabolites identical or similar to metabolites produced by their host plants. This study aimed to investigate the composition and distribution of endophytic bacteria of Dendrobium stems by Illumina MiSeq platform sequencing and cultivation-dependent methods and then to assess the potential for endophytic bacteria to produce DSAs. Results indicated that it was necessary to combine both cultivation-dependent and cultivation-independent methods to analyze the community structure of endophytic bacterial in plants comprehensively. The length of the Dendrobium stems influenced the endophytic bacterial community. The diversity and richness of endophytic bacteria in group J10_15cm of stems were the highest, which showed a significant difference from the other stem groups. However, there was no certain connection between the diversity and richness of endophytic bacteria and the content of dendrobine. It was most likely due to the influence of several specific endophytic bacteria genera, such as Sphingomonas and Rhodococcus. Athelia rolfsii, Myrothecium roridum, as pathogenic fungi, and Pectobacterium carotovorum subsp. actinidiae, as pathogenic bacteria of Dendrobium, were used to determine the antimicrobial activities. In these assays, six strains belonging to five genera showed antimicrobial activity against at least two phytopathogens. The strain BL-YJ10_15-29 (Paracoccus pueri THG-N2.35, 98.98%) showed the best antimicrobial activity against the three phytopathogens. In addition, 2 DSAs (6-hydroxydendrobine and nobilonine) were identified in the fermentation supernatant of the strain CM-YJ10_15-44 (Pseudomonas protegens CHA0, 99.24%), whereas the whole-genome analysis results further demonstrated that the precursors of the two DSAs [geranyl-PP and (E, E)-famesyl-PP] were synthesized mainly through the methyl-D-erythritol 4-phosphate pathway in this strain. This study provides new insight into the studies on the biosynthesis of DSAs and provides potential biocontrol bacteria.

Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia

The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10−5), Bradyhizobium (p = 1 × 10−8), and Paenibacillus (p = 1.46 × 10−6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10−3) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.

Biocontrol Potential of Endophytic Streptomyces malaysiensis 8ZJF-21 From Medicinal Plant Against Banana Fusarium Wilt Caused by Fusarium oxysporum f. sp. cubense Tropical Race 4

Banana (Musa spp.) is an important fruit crop cultivated in most tropical countries. Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is the most destructive fungal disease. Biocontrol using endophytic microorganisms is considered as a safety and sustainable strategy. Actinomycetes have a potential for the production of diverse metabolites. Isolation of endophytic actinomycetes with high efficiency and broad-spectrum antagonism is key for exploring biocontrol agents. Our previous study showed that a total of 144 endophytic actinomycetes were isolated from different tissues of medicinal plants in Hainan, China. Especially, strain 8ZJF-21 exhibited a broad-spectrum antifungal activity. Its morphological, physiological, and biochemical characteristics were consistent with the genus Streptomyces. The phylogenetic tree demonstrated that strain 8ZJF-21 formed a distinct clade with Streptomyces malaysiensis. Average nucleotide identity (ANI) was 98.49% above the threshold of novel species. The pot experiment revealed that endophytic Streptomyces malaysiensis 8ZJF-21 could improve the plant resistance to Foc TR4 by enhancing the expression levels of defense-related and antioxidant enzyme genes. It also promoted the plant growth by producing several extracellular enzymes and metabolites. Antifungal mechanism assays showed that S. malaysiensis 8ZJF-21 extract inhibited mycelial growth and spore germination of Foc TR4 in vitro. Pathogenic cells occurred cytoplasmic heterogeneity, disappeared organelles, and ruptured ultrastructure. Sequencing and annotation of genome suggested that S. malaysiensis 8ZJF-21 had a potential of producing novel metabolites. Nineteen volatile organic compounds were obtained from the extract by Gas Chromatography-Mass Spectrometry (GC-MS). Hence, endophytic Streptomyces strains will become essential biocontrol agents of modern agricultural practice.

Dynamic Changes in Endophytic Microorganisms and Metabolites During Natural Drying of Licorice

The method of drying licorice is an important factor affecting the quality of the final product. To determine the best processing method of licorice postharvest, we investigated the interaction of increasing aridity between the endophytic microorganisms and the accumulation of metabolites. Samples from the roots of licorice growing along an aridity gradient during the natural drying process were collected, and the metabolic components, the content of the main active substances and the dynamic changes of the endophytic microbial community were assessed. The glycyrrhizic acid and liquiritin contents decreased slightly or remained flat during natural drying, whereas those of liquiritigenin and isoliquiritigenin increased slightly. Moreover, the Shannon index of endophytic microbial diversity of licorice was the highest in the fresh period and showed a downward trend during the drying process. When the licorice were fresh, Cladosporiaceae and Burkholderiaceae were the dominant family present, but after drying, Nectriaceae and Enterobacteriaceae were the dominant families. A similar trend was also found in which the differential metabolites of licorice were reduced during natural drying. Furthermore, correlation analysis between dominant families and differential metabolites showed that there was a correlation between the two. Therefore, fresh processing is an effective drying method to ensure the quality of licorice. This study revealed the relationship of endophytic microbiota and changes in the licorice metabolites during different stages of drying, which provided a scientific basis for the drying method of licorice.