Composition, diversity and bioactivity of culturable bacterial endophytes in mountain-cultivated ginseng in Korea

Plant beneficial traits of endophytic bacteria associated with fennel (Foeniculum vulgare Mill.)

In this study, we used 16S rRNA gene sequence analysis to describe the diversity of cultivable endophytic bacteria associated with fennel (Foeniculum vulgare Mill.) and determined their plant-beneficial traits. The bacterial isolates from the roots of fennel belonged to four phyla: Firmicutes (BRN1 and BRN3), Proteobacteria (BRN5, BRN6, and BRN7), Gammaproteobacteria (BRN2), and Actinobacteria (BRN4). The bacterial isolates from the shoot of fennel represented the phyla Proteobacteria (BSN1, BSN2, BSN3, BSN5, BSN6, BSN7, and BSN8), Firmicutes (BSN4, BRN1, and BRN3), and Actinobacteria (BRN4). The bacterial species Bacillus megaterium, Bacillus aryabhattai, and Brevibacterium frigoritolerans were found both in the roots and shoots of fennel. The bacterial isolates were found to produce siderophores, HCN, and indole-3-acetic acid (IAA), as well as hydrolytic enzymes such as chitinase, protease, glucanase, and lipase. Seven bacterial isolates showed antagonistic activity against Fusarium culmorum, Fusarium solani, and Rhizoctonia. solani. Our findings show that medicinal plants with antibacterial activity may serve as a source for the selection of microorganisms that exhibit antagonistic activity against plant fungal infections and may be considered as a viable option for the management of fungal diseases. They can also serve as an active part of biopreparation, improving plant growth.

Age-induced Changes in Ginsenoside Accumulation and Primary Metabolic Characteristics of Panax Ginseng in Transplantation Mode

Background

Ginseng (Panax ginseng Mayer) is an important natural medicine. However, a long culture period and challenging quality control requirements limit its further use. Although artificial cultivation can yield a sustainable medicinal supply, research on the association between the transplantation and chaining of metabolic networks, especially the regulation of ginsenoside biosynthetic pathways, is limited.

Methods

Herein, we performed Liquid chromatography tandem mass spectrometry based metabolomic measurements to evaluate ginsenoside accumulation and categorise differentially abundant metabolites (DAMs). Transcriptome measurements using an Illumina Platform were then conducted to probe the landscape of genetic alterations in ginseng at various ages in transplantation mode. Using pathway data and crosstalk DAMs obtained by MapMan, we constructed a metabolic profile of transplantation Ginseng.

Results

Accumulation of active ingredients was not obvious during the first 4 years (in the field), but following transplantation, the ginsenoside content increased significantly from 6-8 years (in the wild). Glycerolipid metabolism and Glycerophospholipid metabolism were the most significant metabolic pathways, as Lipids and lipid-like molecule affected the yield of ginsenosides. Starch and sucrose were the most active metabolic pathways during transplantation Ginseng growth.

Conclusion

This study expands our understanding of metabolic network features and the accumulation of specific compounds during different growth stages of this perennial herbaceous plant when growing in transplantation mode. The findings provide a basis for selecting the optimal transplanting time.

Comparative transcriptome analysis on wild-simulated ginseng of different age revealed possible mechanism of ginsenoside accumulation

Panax ginseng is one of the most famous pharmaceutical plants in Asia. Ginseng plants grown in mountain have longer longevity which ensures higher accumulation of ginsenoside components than those grown in farms. However, wild-simulated ginseng over certain age cannot be easily distinguished in morphology. To identify transcriptomic mechanism of ginsenoside accumulation in older wild-simulated ginseng without large phenotype change, we performed comparative transcriptome analysis for leaf, shoot, and root tissues of 7-yr-old and 13yr-old wild-simulated ginseng. Of 559 differentially expressed genes (DEGs) in comparison between 7-yr-old and 13yr-old wild-simulated ginseng, 280 leaf-, 103 shoot-, and 164 root-mainly expressing genes were found to be changed in transcript level according to age. Functional analysis revealed that pentose-phosphate shunt and abscisic acid responsive genes were up-regulated in leaf tissues of 7-yr-old ginseng while defense responsive genes were up-regulated in root tissues of 13-yr-old ginseng. Quantitative real-time PCR revealed that jasmonic acid responsive genes, ERDL6, and some UGTs were up-regulated in 13-yr-old ginseng in higher order lateral root tissues. These data suggest that bacterial stimulation in mountain region can enhance the expression of several genes which might support minor ginsenoside biosynthesis.

Growth-Promoting Characteristics of Fungal and Bacterial Endophytes Isolated from a Drought-Tolerant Mint Species Endostemon obtusifolius (E. Mey. ex Benth.) N. E. Br

Endophytes are primarily endosymbiotic bacteria and fungi that colonize the interior tissues of their host plant. They enhance the host plant's growth and attenuate adverse effects of biological stress. Endophytic species of many indigenous plants are an untapped resource of plant growth-promoting microorganisms that can mitigate abiotic stress effects. Thus, this study aimed to isolate endophytes from the roots and leaves of the medicinal plant Endostemon obtusifolius to evaluate their in vitro growth-promoting capacities and drought tolerance and to characterize the most promising species. Twenty-six endophytes (fourteen bacteria and twelve fungi) were isolated and cultured from the roots and leaves of E. obtusifolius. All 26 endophytes produced flavonoids, and 14 strains produced phenolic compounds. Of the 11 strains that displayed good free radical scavenging capability (low IC₅₀) in the 1-1-diphenyl-1-picryhydrazyl radical scavenging assay, only three strains could not survive the highest drought stress treatment (40% polyethylene glycol). These 11 strains were all positive for ammonia and siderophore production and only one strain failed to produce hydrogen cyanide and solubilize phosphate. Seven isolates showed aminocyclopropane-1-carboxylate deaminase activity and differentially synthesized indole-3-acetic acid. Using molecular tools, two promising symbiotic, drought stress tolerant, and plant growth-enhancing endophytic species (EORB-2 and EOLF-5) were identified as Paenibacillus polymyxa and Fusarium oxysporum. The results of this study demonstrate that P. polymyxa and F. oxysporum should be further investigated for their drought stress mitigation and plant growth enhancement effects as they have the potential to be developed for use in sustainable agricultural practices.

New Insights on Endophytic Microbacterium-Assisted Blast Disease Suppression and Growth Promotion in Rice: Revelation by Polyphasic Functional Characterization and Transcriptomics

Plant growth-promoting endophytic microbes have drawn the attention of researchers owing to their ability to confer fitness benefits in many plant species. Here, we report agriculturally beneficial traits of rice-leaf-adapted endophytic Microbacterium testaceum. Our polyphasic taxonomic investigations revealed its identity as M. testaceum. The bacterium displayed typical endophytism in rice leaves, indicated by the green fluorescence of GFP-tagged M. testaceum in confocal laser scanning microscopy. Furthermore, the bacterium showed mineral solubilization and production of IAA, ammonia, and hydrolytic enzymes. Tobacco leaf infiltration assay confirmed its non-pathogenic nature on plants. The bacterium showed antifungal activity on Magnaporthe oryzae, as exemplified by secreted and volatile organic metabolome-mediated mycelial growth inhibition. GC-MS analysis of the volatilome of M. testaceum indicated the abundance of antimicrobial compounds. Bacterization of rice seedlings showed phenotypic traits of MAMP-triggered immunity (MTI), over-expression of OsNPR1 and OsCERK, and the consequent blast suppressive activity. Strikingly, M. testaceum induced the transcriptional tradeoff between physiological growth and host defense pathways as indicated by up- and downregulated DEGs. Coupled with its plant probiotic features and the defense elicitation activity, the present study paves the way for developing Microbacterium testaceum-mediated bioformulation for sustainably managing rice blast disease.

Analysis of endophyte diversity of Rheum palmatum among different tissues and ages

Rheum palmatum, a well-known Traditional Chinese Medicines (TCM), has been used for medical purposes for thousand years in China. However, endophyte diversity of R. palmatum among different tissues and ages is still not revealed. In this study, we used 16S and ITS amplicon sequencing and combined with PICRUSt and FUNGuild to compare endophyte diversity and ecological function among different tissues and ages of R. palmatum. The results showed that the diversity and OTUs (Operational taxonomic units) abundance of endophytic fungi and bacteria of R. palmatum differed among different tissues and ages. The predictive function analysis showed that metabolism was main function of endophytic bacteria in different tissue and year samples, while saprotroph was dominant trophic mode of endophytic fungi in different year samples. The dominant trophic modes of endophytic fungi were saprotroph, pathotroph-symbiotroph and symbiotroph, and relative abundances differed in the different tissue samples. Our results elucidated the comprehensive diversity and composition profiles of endophytes in different tissues and year of R. palmatum. Our data offered pivotal information to clarify the role of endophytes in the production of R. palmatum and its important metabolites.

Different factors drive the assembly of pine and Panax notoginseng-associated microbiomes in Panax notoginseng-pine agroforestry systems

Land-use conversion affects the composition and assembly of plant-associated microbiomes, which in turn affects plant growth, development, and ecosystem functioning. However, agroforestry systems, as sustainable land types, have received little attention regarding the dynamics of different plant-associated microbes. In this study, we used high-throughput sequencing technology to analyze the assembly mechanisms and the driving factors of pine- and Panax notoginseng (P.n.)-associated microbiomes during the conversion of different pine forests (Pinus kesiya var. langbianensis and Pinus armandii) into P.n.-pine agroforestry systems. The results showed that the conversion of pure pine forest into P.n.-pine agroforestry systems significantly altered the diversity of pine-associated fungi rather than the community structure, and the community structure of P.n.-associated fungi rather than the diversity. Additionally, plant-associated fungi were more responsive to land-use change than bacteria. Main effect analysis revealed that compartment rather than genotype was the driving factor of pine- and P.n.-associated microbiomes, but P.n. cultivation also significantly affected the assembly of pine-associated microbiomes. In addition, there was a transfer of P.n. endophytes to pine trees in agroforestry systems and the beneficial microbiomes (Massilia, Marmoricola, Herbaspirillum, etc.) were enlarged in pine roots. Therefore, the diversity of the assembly mechanisms of P.n.- and pine-associated microbiomes played an important role in the P.n.--pine agroforestry systems and were the basis for the sustainable development of the P.n.--pine agroforestry systems.

The Bacterial and Fungal Microbiota of the Mexican Rubiaceae Family Medicinal Plant Bouvardia ternifolia

Bouvardia ternifolia is a medicinal plant considered a source of therapeutic compounds, like the antitumoral cyclohexapeptide bouvardin. It is known that large number of secondary metabolites produced by plants results from the interaction of the host and adjacent or embedded microorganisms. Using high-throughput DNA sequencing of V3-16S and V5-18S ribosomal gene libraries, we characterized the endophytic, endophytic + epiphyte bacterial, and fungal communities associated to flowers, leaves, stems, and roots, as well as the rhizosphere. The Proteobacteria (average 80.7%) and Actinobacteria (average 14.7%) were the most abundant bacterial phyla, while Leotiomycetes (average 54.8%) and Dothideomycetes (average 27.4%) were the most abundant fungal classes. Differential abundance for the bacterial endophyte group showed a predominance of Erwinia, Propionibacterium, and Microbacterium genera, while Sclerotinia, Coccomyces, and Calycina genera predominated for fungi. The predictive metagenome analysis for bacteria showed significative abundance of pathways for secondary metabolite production, while a FUNguild analysis revealed the presence of pathotroph, symbiotroph, and saprotrophs in the fungal community. Intra and inter copresence and mutual exclusion interactions were identified for bacterial and fungal kingdoms in the endophyte communities. This work provides a description of the diversity and composition of bacterial and fungal microorganisms living in flowers, leaves, stems, roots, and the rhizosphere of this medicinal plant; thus, it paves the way towards an integral understanding in the production of therapeutic metabolites.

Wild Panax plants adapt to their thermal environment by harboring abundant beneficial seed endophytic bacteria

The seed microbiome of crop wild relatives is a potential reservoir of beneficial traits that potentially improve their host plant resilience to fluctuating environments and pathogenic threats. Herein, we studied the seed microbiome of three species of the medicinal genus Panax (P. vietnamensis, P. japonicas, and P. stipuleanatus) collected from seven locations in Southwest China. We used qPCR and metabarcoding high-throughput sequencing to target both endophytic bacteria and fungi. Seed bacterial absolute abundance (1.1 × 109∼1.0 × 107 gene copy numbers per gram seed) was substantially higher than that of fungi (7.6 × 105∼3.7 × 102). Host plant genotype was the main driver of seed microbiome composition for both bacteria and fungi. Panax growing hypothermal environments significantly shaped their seed endophytic bacterial but not fungal microbiota. The three Panax species’ seeds harbored unique microbes [averaged ∼150 amplicon sequence variants (ASVs)], sharing only 12 bacterial ASVs (half affiliated to Halomonas) and four fungal ASVs. Network analysis showed that the Panax seed endophytic bacteria tend to form inter-weaved functional modules that are majorly connected by core members from the genus Halomonas, Pseudomonas, and Pantoea. These genera have been associated with nutrient cycling, plant, disease suppression, and tolerance to environmental fluctuation. Together, these novel insights may shade light on the ecological strategies of wild Panax plants adaptation to their thermal environment by possessing abundant beneficial seed endophytic bacteria.

Anti-Inflammatory Effects of Limosilactobacillus fermentum KGC1601 Isolated from Panax ginseng and Its Probiotic Characteristics

We investigated the potential probiotic properties of Limosilactobacillus fermentum KGC1601 isolated from Panax ginseng. Ginseng cultivated in an experimental field of the Korea Ginseng Research Institute was fermented, followed by single colony selection from MRS agar. We performed 16s-rRNA sequencing and whole-genome analysis to identify L. fermentum and evaluate the biosafety parameters of this strain, respectively. We confirmed this strain was susceptible to six antibiotics, as proposed by the European Food Safety Authority, did not produce biogenic amines, and did not exhibit any hemolytic activity. Acid resistance and bile salt tolerance, which are essential properties of a probiotic agent, were investigated. Notably, distinguishing properties of this strain were that it exhibited excellent bile salt tolerance and anti-inflammatory effects. The excellent bile salt tolerance was confirmed by scanning electron microscopy. Through qRT-PCR and ELISA studies, it was revealed that L. fermentum KGC1601 pre-treatment up-regulates anti-inflammatory cytokines and down-regulates pro-inflammatory cytokines in RAW 264.7 cells. Consequently, we suggested that L. fermentum KGC1601 can be safely used as a potential anti-inflammatory functional probiotic agent.

In-Depth Characterization of Plant Growth Promotion Potentials of Selected Alkanes-Degrading Plant Growth-Promoting Bacterial Isolates

The use of plant growth-promoting rhizobacteria (PGPR) as a bioremediation enhancer in plant-assisted phytoremediation requires several steps, consisting of the screening, selection, and characterization of isolates. A subset of 50 bacterial isolates representing a wide phylogenetic range were selected from 438 morphologically different bacteria that were originally isolated from a petroleum hydrocarbon (PHC)-polluted site of a former petrochemical plant. Selected candidate bacteria were screened using six conventional plant growth-promoting (PGP) traits, complemented with the genetic characterization of genes involved in alkane degradation, as well as other pertinent functions. Finally, the bacterial isolates were subjected to plant growth promotion tests using a gnotobiotic approach under normal and stressed conditions. Our results indicated that 35 bacterial isolates (70%) possessed at least four PGP traits. Twenty-nine isolates (58%) were able to utilize n-hexadecane as a sole carbon source, whereas 43 isolates (86%) were able to utilize diesel as the sole carbon source. The presence of catabolic genes related to hydrocarbon degradation was assessed using endpoint PCR, with the alkane monooxygenase (alkB) gene found in 34 isolates, the cytochrome P450 hydroxylase (CYP153) gene found in 24 isolates, and the naphthalene dioxygenase (nah1) gene found to be present in 33 isolates. Thirty-six strains (72%) promoted canola root elongation in the growth pouch assay. After several rounds of screening, seven bacterial candidates (individually or combined in a consortium) were tested for canola root and shoot growth promotion in substrates amended by different concentrations of n-hexadecane (0%, 1%, 2%, and 3%) under gnotobiotic conditions. Our results showed that Nocardia sp. (WB46), Pseudomonas plecoglossicida (ET27), Stenotrophomonas pavanii (EB31), and Gordonia amicalis (WT12) significantly increased the root length of canola grown in 3% n-hexadecane compared with the control treatment, whereas Nocardia sp. (WB46) and Bacillus megaterium (WT10) significantly increased shoot length compared to control treatment at the same concentration of n-hexadecane. The consortium had a significant enhancement effect on root length compared to all isolates inoculated individually or to the control. This study demonstrates that the combination of PGPR traits and the PHC degradation potential of bacteria can result in an enhanced beneficial effect in phytoremediation management, which could lead to the development of innovative bacterial inoculants for plants to remediate PHC-contaminated soils.

Analysis of endophyte diversity of two Gentiana plants species and the association with secondary metabolite

Background

The influence of external environmental factors on secondary metabolites of medicinal plants has always been studied. However, little is known about the relationships between endophytes and host metabolites, especially the relationship differences between different plant species. Thus, we used high-throughput sequencing methods to compare endophyte diversity from roots of two closely related species, Gentiana officinalis and G. siphonantha, from the same production area, and analyze the association with four secondary metabolites (Gentiopicroside, Loganic acid, Swertiamarine and Sweroside).

Results

The fungal and bacteria communities’ richness and diversity of G. siphonantha was higher than G. officinalis. Ascomycota and Proteobacteria were dominant fungal and bacterial phylum of the two closely related species. At the genus level, Tetracladium and Cadophora were dominant fungal genus in G. officinalis and G. siphonantha samples, respectively. While Pseudomonas was dominant bacterial genus in two closely related species, with relative abundances were 8.29 and 8.05%, respectively. Spearman analysis showed that the content of loganic acid was significantly positively correlated with endophytic fungi, the content of gentiopicroside, swertiamarine and sweroside were significantly positively correlated with endophytic bacteria in the two related species. PICRUSt and FUNGuild predictive analysis indicated that metabolism and saprotroph was primary function of endophytic bacteria and fungi in the two related species.

Conclusion

Our results will expand the knowledge on relationships of plant-microbe interactions and offer pivotal information to reveal the role of endophytes in the production of Gentiana plant and its important secondary metabolite.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02510-4.

Endophytic bacterial and fungal community compositions in different organs of ginseng (Panax ginseng)

Panax ginseng (Panax ginseng C. A. Mey.) is a perennial herb of the genus ginseng, which is used as medicine with dried roots and rhizomes. With the deepening of research on ginseng, the chemical components and pharmacological effects of ginseng have gradually been discovered. Endophytes are beneficial to host plants. However, the composition of endophytes in different organs from ginseng is poorly elucidated. The report of ginsenoside production by endophytic microbes isolated from Panax sp., motivated us to explore the endophytic microbial diversity related to the roots, stems, and leaves. In this study, the V5-V7 variable region of endophytic bacteria 16S rRNA gene and V1 variable region of endophytic fungi ITS gene in different organs were analyzed by high-throughput sequencing. The diversity and abundance of endophytic microbes in the three organs are different and are affected by the organs. For example, the most abundant endophytic bacterial genus in roots was Mycobacterium, while, the stems and leaves were Ochrobactrum. Similarly, the fungal endophytes, Coniothyrium and Cladosporium, were also found in high abundance in stems, in comparison to roots and leaves. The Shannon index shows that the diversity of endophytic bacteria in roots is the highest, and the richness of endophytic bacterial was root > stem (p < 0.05). Principal coordinate analysis showed that there were obvious microbial differences among the three groups, and the endophytic bacterial composition of the leaves was closer to that of the roots. This study provides an important reference for the study of endophytic microorganisms in ginseng.

The Endosphere Microbiome of Ginseng

The endosphere of ginseng contains a variety of fungal, bacterial, archaeal and viral endophytes. Bacterial endophytes are primarily members of the Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, and fungal endophytes are primarily members of the Ascomycota, Zygomycota and Basidiomycota. Although archaea and viruses have been detected in symptomless ginseng plants, little is known about them. Many but not all studies have shown roots having the highest abundance and diversity of bacterial and fungal endophytes, with some endophytes showing specificity to above or belowground tissues. Abundance often increases with root age, although diversity can decrease, possibly related to increases in potential latent fungal pathogen infections. The descriptions of many endophytes that can metabolize ginsenosides indicate an adaptation of the microbes to the unique combination of secondary metabolites found in ginseng tissues. Most research on the benefits provided by bacterial and fungal endophytes has concentrated on improved plant nutrition, growth promotion and increased disease resistance, but little on their ability to increase abiotic stress resistance. Some other areas where more research is needed is field trials with endophyte-treated plants grown in various environments, genomic/metagenomic analysis of endophytes, and the effects of endophytes on induced disease resistance and abiotic stress tolerance.

Drops join to make a stream: high-throughput nanoscale cultivation to grasp the lettuce root microbiome

Root endospheres house complex and diverse bacterial communities, of which many strains have not been cultivated yet by means of the currently available isolation techniques. The Prospector® (General Automation Lab Technologies, San Carlos, CA, USA), an automated and high-throughput bacterial cultivation system, was applied to analyse the root endomicrobiome of lettuce (Lactuca sativa L.). By using deep sequencing, we compared the results obtained with the Prospector and the traditional solid medium culturing and extinction methods. We found that the species richness did not differ and that the amount of previously uncultured bacteria did not increase, but that the bacterial diversity isolated by the three methods varied. In addition, the tryptic soy broth and King's B media provided a lower, but different, diversity of bacteria than that of Reasoner's 2A (R2A) medium when used within the Prospector system and the number of unique bacterial strains did not weigh up against those isolated with the R2A medium. Thus, to cultivate as broad a variety of bacteria as possible, divergent isolation techniques should be used in parallel. Thanks to its speed and limited manual requirements, the Prospector is a valuable system to enlarge root microbiome culture collections.

Bacterial endophytes from ginseng and their biotechnological application

Ginseng has been well-known as a medicinal plant for thousands of years. Bacterial endophytes ubiquitously colonize the inside tissues of ginseng without any disease symptoms. The identification of bacterial endophytes is conducted through either the internal transcribed spacer region combined with ribosomal sequences or metagenomics. Bacterial endophyte communities differ in their diversity and composition profile, depending on the geographical location, cultivation condition, and tissue, age, and species of ginseng. Bacterial endophytes have a significant effect on the growth of ginseng through indole-3-acetic acid (IAA) and siderophore production, phosphate solubilization, and nitrogen fixation. Moreover, bacterial endophytes can protect ginseng by acting as biocontrol agents. Interestingly, bacterial endophytes isolated from Panax species have the potential to produce ginsenosides and bioactive metabolites, which can be used in the production of food and medicine. The ability of bacterial endophytes to transform major ginsenosides into minor ginsenosides using β-glucosidase is gaining increasing attention as a promising biotechnology. Recently, metabolic engineering has accelerated the possibilities for potential applications of bacterial endophytes in producing beneficial secondary metabolites.

Plant growth-promoting properties of bacterial endophytes isolated from roots of Thymus vulgaris L. and investigate their role as biofertilizers to enhance the essential oil contents

The main objective of the current study was to improve the essential oil contents of Thymus vulgaris L. using bio-inoculation with bacterial endophytes. Therefore, out of fourteen endophytic bacterial isolates obtained from roots of T. vulgaris, five isolates were selected based on the highest nitrogen-fixation and phosphate solubilization activity and identified as: Bacillus haynesii T9r, Citrobacter farmeri T10r, Bacillus licheniformis T11r, Bacillus velezensis T12r, and Bacillus velezensis T13r. These five strains have been recorded as ammonia, hydrogen cyanide (HCN), siderophores, and indole-3-acetic acid (IAA) producers. These strains have the efficacy to fix-nitrogen by reduction of acetylene with values of 82.133±1.4-346.6±1.4 n-mole-C₂H₄/ml/24 h. The IAA, gibberellic acid, abscisic acid, benzyl, kinten, and ziaten production were confirmed using HPLC. Two strains of T11r and T13r showed the highest plant growth-promoting properties and were selected for bio-inoculation of T. vulgaris individually or in a consortium with different mineral fertilization doses (0, 50, 75, and 100%) under field conditions. The highest growth performance was attained with the endophytic consortium (T11r+T13r) in the presence of 100% mineral fertilization. The GC-MS analysis of thyme oil contents showed the presence of 23 various compounds with varying percentages and the thymol fraction represented the highest percentages (39.1%) in the presence of the bacterial consortium.

Tissue-specific diversity of bacterial endophytes in Mexican husk tomato plants (Physalis ixocarpa Brot. ex Horm.), and screening for their multiple plant growth-promoting activities

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Endophytic bacterial diversity of root, stem, and leaf tissues of Physalis ixocarpa was deciphered.

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Unique and shared species were found for each plant compartment analyzed.

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Extensive screening of various isolates exhibited antagonism against fungal pathogens.

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Diverse endophytes stimulated the growth of Physalis ixocarpa seedlings.

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Neobacillus drentensis CH23 stood out as an excellent plant growth-promoting bacterium.

The endophytic bacterial diversity of root, stem, and leaf tissues of Mexican husk tomato plants (Physalis ixocarpa) was compared and deciphered, and screened for their plant growth-promoting activity and antagonism against fungal phytopathogens. Total 315 isolates (108 roots, 102 stems, and 105 leaves) were obtained and characterized by 16S ribosomal gene sequencing. The most abundant genera were Bacillus, Microbacterium, Pseudomonas, and Stenotrophomonas. Unique species were found for each tissue analyzed, along with B. thuringiensis, B. toyonensis, Neobacillus drentensis, Paenibacillus castaneae, P. fluorescens, P. poae, and S. maltophilia present throughout the plant. Biodiversity indices did not show significant differences, but root tissues showed the highest abundance of bacterial endophytes. Several isolates showed excellent promotion activities in Physalis ixocarpa seedlings, increasing the length and weight of the root, total biomass, and chlorophyll content. Various isolates also exhibited antagonism against fungal pathogens. Among screened isolates, Neobacillus drentensis CH23 was found in all plant compartments, exhibiting growth-promoting activity and fungal antagonism. Strain CH23 and other endophytes showed the production of indoleacetic acid, siderophores, proteases, and solubilization of phosphates. These results demonstrate that the husk tomato plant endobiome has a high potential as a bioinoculating agent for agriculturally important crops.

Diversity of the Bacterial Microbiome Associated With the Endosphere and Rhizosphere of Different Cassava (Manihot esculenta Crantz) Genotypes

Root-associated microbial communities play important roles in plant growth and development. However, little attention has been paid to the microbial community structures associated with cassava, which is a staple food for approximately 800 million people worldwide. Here, we studied the diversity and structure of tuber endosphere and rhizosphere bacterial communities in fourteen cassava genotypes: SC5, SC8, SC9, SC205, KU50, R72, XL1, FX01, SC16, 4612, 587, 045, S0061, and 1110. The results of bacterial 16S rDNA sequencing showed that the richness and diversity of bacteria in the rhizosphere were higher than those in the tuber endosphere across the 14 cassava genotypes. After sequencing, 21 phyla and 310 genera were identified in the tuberous roots, and 36 phyla and 906 genera were identified in the rhizosphere soils. The dominant phylum across all tuber samples was Firmicutes, and the dominant phyla across all rhizosphere samples were Actinobacteria, Proteobacteria, and Acidobacteria. The numbers of core bacterial taxa within the tuber endospheres and the rhizospheres of all cassava genotypes were 11 and 236, respectively. Principal coordinate analysis and hierarchical cluster analysis demonstrated significant differences in the compositions of rhizosphere soil microbiota associated with the different cassava genotypes. Furthermore, we investigated the metabolic changes in tuber roots of three genotypes, KU50, SC205, and SC9. The result showed that the abundances of Firmicutes, Proteobacteria, and Actinobacteria in tuber samples were positively correlated with organic acids and lipids and negatively correlated with vitamins and cofactors. These results strongly indicate that there are clear differences in the structure and diversity of the bacterial communities associated with different cassava genotypes.

Arnebia euchroma, a Plant Species of Cold Desert in the Himalayas, Harbors Beneficial Cultivable Endophytes in Roots and Leaves

The endophytic mutualism of plants with microorganisms often leads to several benefits to its host including plant health and survival under extreme environments. Arnebia euchroma is an endangered medicinal plant that grows naturally in extreme cold and arid environments in the Himalayas. The present study was conducted to decipher the cultivable endophytic diversity associated with the leaf and root tissues of A. euchroma. A total of 60 bacteria and 33 fungi including nine yeasts were isolated and characterized at the molecular level. Among these, Proteobacteria was the most abundant bacterial phylum with the abundance of Gammaproteobacteria (76.67%) and genus Pseudomonas. Ascomycota was the most abundant phylum (72.73%) dominated by class Eurotiales (42.42%) and genus Penicillium among isolated fungal endophytes. Leaf tissues showed a higher richness (S_chao1) of both bacterial and fungal communities as compared to root tissues. The abilities of endophytes to display plant growth promotion (PGP) through phosphorus (P) and potassium (K) solubilization and production of ACC deaminase (ACCD), indole acetic acid (IAA), and siderophores were also investigated under in vitro conditions. Of all the endophytes, 21.51% produced ACCD, 89.25% solubilized P, 43.01% solubilized K, 68.82% produced IAA, and 76.34% produced siderophores. Six bacteria and one fungal endophyte displayed all the five PGP traits. The study demonstrated that A. euchroma is a promising source of beneficial endophytes with multiple growth-promoting traits. These endophytes can be used for improving stress tolerance in plants under nutrient-deficient and cold/arid conditions.

Global Trends in Research on Wild-Simulated Ginseng: Quo Vadis?

To the best of our knowledge, no study has systematically reviewed and analyzed the research trends of wild-simulated ginseng (WSG) used for food or medicinal purposes in many countries. WSG, a non-timber forest product, has been traditionally produced using agroforestry practices, and it has been consumed in various ways for a long time. WSG has a great demand in the market due to its medicinal effects, particularly in improving forest livelihoods and human health. Due to the significance of WSG, we conducted this research to explore the global research trends on WSG using systematic review methodology and keyword analysis. We used two international academic databases, the Web of Science and SCOPUS, to extract 115 peer-reviewed articles published from 1982 to 2020. The research subjects, target countries, and keywords were analyzed. Our results indicate four categories of WSG research subjects, namely growth conditions, components, effects on humans/animals, and the environment of WSG, and the case studies were mainly from the Republic of Korea, China, and the USA. Through topic modelling, research keywords were classified into five groups, namely medicinal effects, metabolite analysis, genetic diversity, cultivation conditions, and bioactive compounds. We observed that the research focus on WSG changed from the biological properties and cultivation conditions of WSG to the precise identification and characterization of bioactive metabolites of WSG. This change indicates an increased academic interest in the value-added utilization of WSG.

Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India

Bacterial endophytes are found in the internal tissues of plants and have intimate associations with their host. However, little is known about the diversity of medicinal plant endophytes (ME) or their capability to produce specialised metabolites that may contribute to therapeutic properties. We isolated 75 bacterial ME from 24 plant species of the Western Ghats, India. Molecular identification by 16S rRNA gene sequencing grouped MEs into 13 bacterial genera, with members of Gammaproteobacteria and Firmicutes being the most abundant. To improve taxonomic identification, 26 selected MEs were genome sequenced and average nucleotide identity (ANI) used to identify them to the species-level. This identified multiple species in the most common genus as Bacillus. Similarly, identity of the Enterobacterales was also distinguished within Enterobacter and Serratia by ANI and core-gene analysis. AntiSMASH identified non-ribosomal peptide synthase, lantipeptide and bacteriocin biosynthetic gene clusters (BGC) as the most common BGCs found in the ME genomes. A total of five of the ME isolates belonging to Bacillus, Serratia and Enterobacter showed antimicrobial activity against the plant pathogen Pectobacterium carotovorum. Using molecular and genomic approaches we have characterised a unique collection of endophytic bacteria from medicinal plants. Their genomes encode multiple specialised metabolite gene clusters and the collection can now be screened for novel bioactive and medicinal metabolites.

Grazing Affects Bacterial and Fungal Diversities and Communities in the Rhizosphere and Endosphere Compartments of Leymus chinensis through Regulating Nutrient and Ion Distribution

Plant-associated endophytic microorganisms are essential to developing successful strategies for sustainable agriculture. Grazing is an effective practice of grassland utilization through regulating multitrophic relationships in natural grasslands. This study was conducted for exploring the effects of grazing on the diversities and communities of bacteria and fungi presented in rhizosphere soils, roots, stems, and leaves of Leymus chinensis (L. chinensis), based on high-throughput sequencing. Grazing increased bacterial diversity but reduced fungal diversity in plant leaves. Further analysis confirmed that the abundance of Chloroflexi, Gemmatimonadota, Nitrospirota, Sordariales, and Pezizales in plant leaves was increased by grazing. The Bray-Curtis similarities of microbial communities in the endosphere were higher under grazing plots than non-grazing plots. Moreover, the bacterial communities were significantly correlated with ions, while the nutrient and negative ions exhibited strong influence on fungal communities. We concluded that grazing-induced changes of microbial diversities and communities in different compartments of a dominant perennial grass (L. chinensis) could be attributed to the nutrient and ion distribution in host plant. The current study highlights the importance of livestock in mediating diversities and communities of endophytic microbes, and will be useful for better understanding the complexity of multitrophic interactions in a grassland ecosystem.

Advances in the Production of Minor Ginsenosides Using Microorganisms and Their Enzymes

Abstract Minor ginsenodes are of great interest due to their diverse pharmacological activities such as their anti-cancer, anti-diabetic, neuroprotective, immunomodulator, and anti-inflammatory effects. The miniscule amount of minor ginsenosides in ginseng plants has driven the development of their mass production methods. Among the various production methods for minor ginsenosides, the utilization of microorganisms and their enzymes are considered as highly specific, safe, and environmentally friendly. In this review, various minor ginsenosides production strategies, namely utilizing microorganisms and recombinant microbial enzymes, for biotransforming major ginsenosides into minor ginsenoside, as well as constructing synthetic minor ginsenosides production pathways in yeast cell factories, are described and discussed. Furthermore, the present challenges and future research direction for producing minor ginsenosides using those approaches are discussed.

Bacterial endophytes from Lycoris radiata promote the accumulation of Amaryllidaceae alkaloids

Lycoris radiata is the major source of Amaryllidaceae alkaloids, having various medicinal activities. However, the low content of these alkaloids in planta limits their pharmaceutical development and utilization. In this study, the ability of bacterial endophytes to enhance the accumulation of five important Amaryllidaceae alkaloids was investigated. A total of 188 bacterial endophytes were isolated from L. radiata and their composition and diversity were analyzed. Fourteen ones were demonstrated to significantly increase the concentration of the alkaloids of interest in different organs, up to 11.1-fold over the control level, with no adverse influence on the plant growth. An additional 3 bacterial endophytes were found to significantly increase the dry weight of L. radiata with no adverse influence on the concentration of the alkaloids in planta, so the total yield of alkaloids in planta was increased up to 2.4-fold over the control level. Considering the plant growth-promoting abilities of these bacterial endophytes, it is speculated that the indole-3-acetic acid and siderophore secreted by them, combined with their nitrogen fixation ability, may contribute to the enhanced plant growth and the increased alkaloid accumulation in L. radiata. To our knowledge, this work is firstly defining the diversity of culturable bacterial endophytes in L. radiata and determining which species promoted the accumulation of Amaryllidaceae alkaloids. It provides several valuable bacterial inoculants that can be further applied to improve alkaloid production in L. radiata and broadens our understanding of the interactions between a medicinal plant and the bacterial endophytes.

Endophytic bacterial and fungal microbiota in different cultivars of cassava (Manihot esculenta Crantz)

Endophytes colonize tissues of healthy host plants and play a crucial role in plant growth and development. However, little attention has been paid to the endophytes of tuber crops such as cassava, which is used as a staple food by approximately 800 million people worldwide. This study aimed to elucidate the diversity and composition of endophytic bacterial and fungal communities in different cassava cultivars using high-throughput sequencing. Although no significant differences in richness or diversity were observed among the different cassava cultivars, the community compositions were diverse. Two cultivars (SC124 and SC205) tolerant to root rot exhibited similar community compositions, while two other cultivars (SC10 and SC5), which are moderately and highly susceptible to root rot, respectively, harboured similar community compositions. Proteobacteria, Firmicutes, and Ascomycota dominated the endophyte assemblages, with Weissella, Serratia, Lasiodiplodia, Fusarium, and Diaporthe being the predominant genera. The differentially abundant taxonomic clades between the tolerant and susceptible cultivars were mainly rare taxa, such as Lachnoclostridium_5, Rhizobium, Lampropedia, and Stenotrophomonas. These seemed to be key genera that affected the susceptibility of cassava to root rot. Moreover, the comparison of KEGG functional profiles revealed that 'Environmental adaptation' category was significantly enriched in the tolerant cultivars, while 'Infectious diseases: Parasitic' category was significantly enriched in the susceptible cultivars. The present findings open opportunities for further studies on the roles of endophytes in the susceptibility of plants to diseases.

Rhizosphere Microbiome Assembly and Its Impact on Plant Growth

Microorganisms colonizing the plant rhizosphere provide a number of beneficial functions for their host. Although an increasing number of investigations clarified the great functional capabilities of rhizosphere microbial communities, the understanding of the precise mechanisms underlying the impact of rhizosphere microbiome assemblies is still limited. Also, not much is known about the various beneficial functions of the rhizosphere microbiome. In this review, we summarize the current knowledge of biotic and abiotic factors that shape the rhizosphere microbiome as well as the rhizosphere microbiome traits that are beneficial to plants growth and disease-resistance. We give particular emphasis on the impact of plant root metabolites on rhizosphere microbiome assemblies and on how the microbiome contributes to plant growth, yield, and disease-resistance. Finally, we introduce a new perspective and a novel method showing how a synthetic microbial community construction provides an effective approach to unravel the plant-microbes and microbes-microbes interplays.

Comparison of Ginsenoside Components of Various Tissues of New Zealand Forest-Grown Asian Ginseng (Panax Ginseng) and American Ginseng (Panax Quinquefolium L.)

Asian ginseng (Panax ginseng) and American ginseng (Panax quinquefolium L.) are the two most important ginseng species for their medicinal properties. Ginseng is not only popular to consume, but is also increasingly popular to cultivate. In the North Island of New Zealand, Asian ginseng and American ginseng have been grown in Taupo and Rotorua for more than 15 years. There are no publications comparing the chemical constituents between New Zealand-grown Asian ginseng (NZPG) and New Zealand-grown American ginseng (NZPQ). In this study, fourteen ginsenoside reference standards and LC-MS2 technology were employed to analyze the ginsenoside components of various parts (fine root, rhizome, main root, stem, and leaf) from NZPG and NZPQ. Fifty and 43 ginsenosides were identified from various parts of NZPG and NZPQ, respectively, and 29 ginsenosides were found in both ginseng species. Ginsenoside concentrations in different parts of ginsengs were varied. Compared to other tissues, the fine roots contained the most abundant ginsenosides, not only in NZPG (142.49 ± 1.14 mg/g) but also in NZPQ (115.69 ± 3.51 mg/g). For the individual ginsenosides of both NZPG and NZPQ, concentration of Rb1 was highest in the underground parts (fine root, rhizome, and main root), and ginsenoside Re was highest in the aboveground parts (stem and leaf).

Diversity and bioactivities of fungal endophytes from Distylium chinense, a rare waterlogging tolerant plant endemic to the Three Gorges Reservoir

BACKGROUND

The present study involves diversity and biological activities of the endophytic fungal community from Distylium chinense, a rare waterlogging tolerant plant endemic to the Three Gorges Reservoir. This study has been conducted hypothesizing that the microbial communities in the TGR area would contribute to the host plant tolerating a range of abiotic stress such as summer flooding, infertility, drought, salinity and soil erosion etc., and they may produce new metabolites, which may possess plentiful bioactive property, especially antioxidant activity. Therefore in the current study, the antioxidant, antimicrobial and anticancer activities of 154 endophytes recovered from D. chinense have been investigated. Furthermore, the active metabolites of the most broad-spectrum bioactive strain have also been studied.

RESULTS

A total of 154 fungal endophytes were isolated from roots and stems. They were categorized into 30 morphotypes based on cultural characteristics and were affiliated with 27 different taxa. Among these, the most abundant fungal orders included Diaporthales (34.4%) and Botryosphaeriales (30.5%), which were predominantly represented by the species Phomopsis sp. (24.7%) and Neofusicoccum parvum (23.4%). Fermentation extracts were evaluated, screening for antioxidant, antimicrobial and anticancer activities. Among the 154 isolates tested, 99 (64.3%) displayed significant antioxidant activity, 153 (99.4%) exhibited inclusive antimicrobial activity against at least one tested microorganism and 27 (17.5%) showed exclusive anticancer activity against one or more cancer cell lines. Specifically, the crude extract of Irpex lacteus DR10-1 exhibited note-worthy bioactivities. Further chemical investigation on DR10-1 strain resulted in the isolation and identification of two known bioactive metabolites, indole-3-carboxylic acid (1) and indole-3-carboxaldehyde (2), indicating their potential roles in plant growth promotion and human medicinal value.

CONCLUSION

These results indicated that diverse endophytic fungal population inhabits D. chinense. One of the fungal isolate DR10-1 (Irpex lacteus) exhibited significant antioxidant, antimicrobial and anticancer potential. Further, its active secondary metabolites 1 and 2 also showed antioxidant, antimicrobial and anticancer potential.

Phylogenetic characterization of bacterial endophytes from four Pinus species and their nematicidal activity against the pine wood nematode

Recently, bacterial endophytes (BEs) have gained importance in the agricultural sector for their use as biocontrol agents to manage plant pathogens. Outbreak of the pine wilt disease (PWD) in Korea has led researchers to test the feasibility of BEs in controlling the pine wood nematode (PWN) Bursaphelenchus xylophilus. In this study, we have reported the diversity and biocontrol activity of BEs against the PWN. By employing a culture-dependent approach, 1,622 BEs were isolated from the needle, stem, and root tissues of P. densiflora, P. rigida, P. thunbergii, and P. koraiensis across 18 sampling sites in Korea. We classified 389 members based on 16S rDNA analysis and taxonomic binning, of which, 215 operational taxonomic units (OTUs) were determined. Using Shannon’s indices, diversity across the Pinus species and tissues was estimated to reveal the composition of BEs and their tissue-specific preferences. When their ethyl acetate crude extracts were analysed for biocontrol activity, 44 candidates with nematicidal activity were obtained. Among these, Stenotrophomonas and Bacillus sp. exhibited significant inhibitory activity against PWN during their developmental stages. Altogether, our study furnishes a basic comprehension of bacterial communities found in the Pinus species and highlights the potential of BEs as biocontrol agents to combat PWD.

Distribution and diversity of bacterial endophytes from four Pinus species and their efficacy as biocontrol agents for devastating pine wood nematodes

In this study, we isolated a total of 238 culturable putative bacterial endophytes from four Pinus species (Pinus densiflora, P. koraiensis, P. rigida, and P. thunbergii) across 18 sampling sites in Korea. The samples were cultured in de Man Rogosa Sharpe and humic acid-vitamin agar media. These selective media were used to isolate lactic acid bacteria and Actinobacteria, respectively. Analysis using 16S ribosomal DNA sequencing grouped the isolated putative bacterial endophytes into 107 operational taxonomic units (OTUs) belonging to 48 genera. Gamma-proteobacteria were the most abundant bacteria in each sampling site and three tissues (needle, stem and root). The highest OTU richness and diversity indices were observed in the roots, followed by stem and needle tissues. Total metabolites extracted from three isolates (two isolates of Escherichia coli and Serratia marcescens) showed significant nematicidal activity against the pine wood nematode (Bursaphelenchus xylophilus). Our findings demonstrated the potential use of bacterial endophytes from pine trees as alternative biocontrol agents against pine wood nematodes.

Metagenomic analysis of bacterial endophyte community structure and functions in Panax ginseng at different ages

This study investigated the root-associated bacterial endophytes of Panax ginseng at different ages by shotgun metagenomic analysis. After mapping metagenome data to the complete ginseng genome to identify unmapped sequences, we predicted the structure and functions of ginseng bacterial endophytes by metagenomic rapid annotation using subsystems technology analysis. While Proteobacteria and Actinobacteria were the predominant phyla in all samples (2-6-year-old roots), class Alphaproteobacteria was most abundant in 3-, 4-, and 5-year-old plants. We found that 3-year-old P. ginseng had a 0.66% unmapped rate against the whole ginseng genome and showed the greatest diversity of endophytic bacteria (α diversity = 299). Prediction of endophytic bacterial functions at different ages by SEED subsystem analysis revealed that siderophore and auxin-related traits-which are known to promote plant growth-were most highly represented in 3-year-old plants. This was supported by a gene frequency analysis of plant growth-promoting genes, including those responsible for solubilization of phosphate and nitrogen metabolism, using BLASTn. These results suggest that endophytic bacteria of the P. ginseng root affect plant growth. Furthermore, the isolation and purification of plant growth-promoting endophytes identified in this study could promote sustainable cultivation of ginseng in the future.

Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl

Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, and E) and one from Fuqin (F) in the Fujian province, China in the months of April, July, and October (represented by 1, 2 and 3), indicating spring, summer, and early winter, respectively. Results from 16s rDNA sequences revealed 10,844,124 effective sequences. The highest OTUs (Operational taxonomic units) was highest in the A1 sample (1086), while the lowest was in C2 (509). Our observations showed that samples taken in October had the highest diversity of endophytes as indicated by the Shannon index (B3 = 5.3337), Chao1 (E3 = 1233.10), abundance-based coverage estimator (ACE) (A3 = 1764.72), and the Simpson indices of diversity (C3 = 0.1655) irrespective of the species. The order of the endophytes richness in the samples was April > July > October. The Ribosomal Database Project (RDP) classifier showed that the obtained sequences belonged to nine major phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Acidobacteria, Planctomycetes, Chloroflexi, and Fusobacteria. Proteobacteria accounted for the highest proportion in each sample, ranging from 35.15% to 89.72%. These sequences belonged mainly to 10 orders: Rhizobiales, Clostridiales, Peseudomonadales, Burkholderiales, Bacteroidales, Enterobacteriales, Rhodocyclales, Sphingomonadales, Lactobacillales, and Bacillales. Also, other taxa with possible taxonomic statuses, which were unclassified, were present.

Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities

Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.

Inside the plant: addressing bacterial endophytes in biotic stress alleviation

Bacterial endophytes are the internal association of bacteria with the plants, cherished whole or any part of their life cycle inside the plant. They are reported to improve plant health against the biotic stresses via de novo synthesis of structural compounds and stimulation of plant immunity. They are found to be vital in development of host resistance against phytopathogens and capable in reducing and elimination of deleterious effects of plant pathogens. Fungal-, bacterial-, viral-, insect- and nematode-associated negative effect can be reduced by the bacterial endophytes. They are also reported to control plant pathogens through several defense mechanisms such as by producing antimicrobial compounds and antibiotics, de novo synthesis of structural compounds, keeping out of pathogens by niche competition and induction of plant immunity or induced systemic resistance. In this review, an effort is made to summarize the exploitation of endophytic bacteria as a biological substitute to control biotic stresses in agricultural practices.

Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants

The aims of this study were to isolate, identify and characterize culturable endophytic bacteria from chickpea (Cicer arietinum L.) roots grown in different soils. In addition, the effects of rhizobial inoculation, soil and stress on the functionality of those culturable endophytic bacterial communities were also investigated. Phylogenetic analysis based on partial 16S rRNA gene sequences revealed that the endophytic bacteria isolated in this work belong to the phyla Proteobacteria, Firmicutes and Actinobacteria, with Enterobacter and Pseudomonas being the most frequently observed genera. Production of indoleacetic acid and ammonia were the most widespread plant growth-promoting features, while antifungal activity was relatively rare among the isolates. Despite the fact that the majority of bacterial endophytes were salt- and Mn-tolerant, the isolates obtained from soil with Mn toxicity were generally more Mn-tolerant than those obtained from the same soil amended with dolomitic limestone. Several associations between an isolate's genus and specific plant growth-promoting mechanisms were observed. The data suggest that soil strongly impacts the Mn tolerance of endophytic bacterial communities present in chickpea roots while rhizobial inoculation induces significant changes in terms of isolates' plant growth-promoting abilities. In addition, this study also revealed chickpea-associated endophytic bacteria that could be exploited as sources with potential application in agriculture.

Diversity of bacterial endophytes in Panax ginseng and their protective effects against pathogens

Although endophytic bacteria are known to colonize Panax ginseng, little is known about their diversity and roles. We addressed in the present study by comparing endophytic bacterial populations in P. ginseng plants of different ages (2-6 years) and in various tissue types (root, stem, leaf, and flower stalk). A total of 116 strains assigned to 42 species were identified by 16S rDNA sequencing. The predominant phylum was Firmicutes. Two-year-old ginseng plants and root tissues showed the greatest diversity of endophytic bacteria, with Bacillales being the predominant order. The antifungal activity of isolates against two pathogens, Cylindrocarpon destructans and/or Botrytis cinerea, was evaluated in dual-culture assays. In total, 28 strains showed antifungal activity with PgBE14 (Bacillus amyloliquefaciens), PgBE40 (B. megaterium), PgBE39, PgBE45 (Pseudomonas frederiksbergensis), and PgBE42 (Staphylococcus saprophyticus) inhibiting both pathogens. These results improve our understanding of the structure and diversity of endophytic bacterial communities of P. ginseng and identify strains with antifungal activity that have potential applications as biocontrol agents.

Endophytic Bacterial Community Structure and Function of Herbaceous Plants From Petroleum Hydrocarbon Contaminated and Non-contaminated Sites

Bacterial endophytes (BEs) are non-pathogenic residents of healthy plant tissues that can confer benefits to plants. Many Bacterial endophytes have been shown to contribute to plant growth and health, alleviation of plant stress and to in-planta contaminant-degradation. This study examined the endophytic bacterial communities of plants growing abundantly in a heavily hydrocarbon contaminated site, and compared them to those found in the same species at a non-contaminated. We used culture- dependent and independent methods to characterize the community structure, hydrocarbon degrading capabilities, and plant growth promoting traits of cultivable endophytes isolated from Achillea millefolium, Solidago Canadensis, and Daucus carota plants from these two sites. Culture- dependent and independent analyses revealed class Gammaproteobacteria predominated in all the plants regardless of the presence of petroleum hydrocarbon, with Pantoea spp. as largely dominant. It was interesting to note a >50% taxonomic overlap (genus level) of 16s rRNA high throughput amplicon sequences with cultivable endophytes. PERMANOVA analysis of TRFLP fragments revealed significant structural differences between endophytic bacterial communities from hydrocarbon-contaminated and non-contaminated soils-however, there was no marked difference in their functional capabilities. Pantoea spp. demonstrated plant beneficial characteristics, such as P solubilization, indole-3-acetic acid production and presence of 1-aminocyclopropane-1-carboxylate deaminase. Our findings reveal that functional capabilities of bacterial isolates being examined were not influenced by the presence of contamination; and that the stem endosphere supports ubiquitous BEs that were consistent throughout plant hosts and sites.

Diversity and composition of bacterial endophytes among plant parts of Panax notoginseng

Background

Bacterial endophytes are widespread inhabitants inside plant tissues that play crucial roles in plant growth and biotransformation. This study aimed to offer information for the exploitation of endophytes by analyzing the bacterial endophytes in different parts of Panax notoginseng.

Methods

We used high-throughput sequencing methods to analyze the diversity and composition of bacterial endophytes from different parts of P. notoginseng.

Results

A total of 174,761 classified sequences were obtained from the analysis of 16S ribosomal RNA in different parts of P. notoginseng. Its fibril displayed the highest diversity of bacterial endophytes. Principal coordinate analysis revealed that the compositions of the bacterial endophytes from aboveground parts (flower, leaf, and stem) differed from that of underground parts (root and fibril). The abundances of Conexibacter, Gemmatimonas, Holophaga, Luteolibacter, Methylophilus, Prosthecobacter, and Solirubrobacter were significantly higher in the aboveground parts than in the underground parts, whereas the abundances of Bradyrhizobium, Novosphingobium, Phenylobacterium, Sphingobium, and Steroidobacter were markedly lower in the aboveground parts.

Conclusions

Our results elucidated the comprehensive diversity and composition profiles of bacterial endophytes in different parts of 3-year-old P. notoginseng. Our data offered pivotal information to clarify the role of endophytes in the production of P. notoginseng and its important metabolites.

Computational and experimental characterization of estrogenic activities of 20(S, R)-protopanaxadiol and 20(S, R)-protopanaxatriol

Background

As the main metabolites of ginsenosides, 20(S, R)-protopanaxadiol [PPD(S, R)] and 20(S, R)-protopanaxatriol [PPT(S, R)] are the structural basis response to a series of pharmacological effects of their parent components. Although the estrogenicity of several ginsenosides has been confirmed, however, the underlying mechanisms of their estrogenic effects are still largely unclear. In this work, PPD(S, R) and PPT(S, R) were assessed for their ability to bind and activate human estrogen receptor α (hERα) by a combination of in vitro and in silico analysis.

Methods

The recombinant hERα ligand-binding domain (hERα-LBD) was expressed in E. coli strain. The direct binding interactions of ginsenosides with hERα-LBD and their ERα agonistic potency were investigated by fluorescence polarization and reporter gene assays, respectively. Then, molecular dynamics simulations were carried out to simulate the binding modes between ginsenosides and hERα-LBD to reveal the structural basis for their agonist activities toward receptor.

Results

Fluorescence polarization assay revealed that PPD(S, R) and PPT(S, R) could bind to hERα-LBD with moderate affinities. In the dual luciferase reporter assay using transiently transfected MCF-7 cells, PPD(S, R) and PPT(S, R) acted as agonists of hERα. Molecular docking results showed that these ginsenosides adopted an agonist conformation in the flexible hydrophobic ligand-binding pocket. The stereostructure of C-20 hydroxyl group and the presence of C-6 hydroxyl group exerted significant influence on the hydrogen bond network and steric hindrance, respectively.

Conclusion

This work may provide insight into the chemical and pharmacological screening of novel therapeutic agents from ginsenosides.

Genomic Insights into Nematicidal Activity of a Bacterial Endophyte, Raoultella ornithinolytica MG against Pine Wilt Nematode

Pine wilt disease, caused by the nematode Bursaphelenchus xylophilus, is one of the most devastating conifer diseases decimating several species of pine trees on a global scale. Here, we report the draft genome of Raoultella ornithinolytica MG, which is isolated from mountain-cultivated ginseng plant as an bacterial endophyte and shows nematicidal activity against B. xylophilus. Our analysis of R. ornithinolytica MG genome showed that it possesses many genes encoding potential nematicidal factors in addition to some secondary metabolite biosynthetic gene clusters that may contribute to the observed nematicidal activity of the strain. Furthermore, the genome was lacking key components of avermectin gene cluster, suggesting that nematicidal activity of the bacterium is not likely due to the famous anthelmintic agent of wide-spread use, avermectin. This genomic information of R. ornithinolytica will provide basis for identification and engineering of genes and their products toward control of pine wilt disease.

Endophytic Trichoderma citrinoviride isolated from mountain-cultivated ginseng (Panax ginseng) has great potential as a biocontrol agent against ginseng pathogens

Background

Ginseng (Panax ginseng Meyer) is an invaluable medicinal plant containing various bioactive metabolites (e.g., ginsenosides). Owing to its long cultivation period, ginseng is vulnerable to various biotic constraints. Biological control using endophytes is an important alternative to chemical control.

Methods

In this study, endophytic Trichoderma citrinoviride PG87, isolated from mountain-cultivated ginseng, was evaluated for biocontrol activity against six major ginseng pathogens. T. citrinoviride exhibited antagonistic activity with mycoparasitism against all ginseng pathogens, with high endo-1,4-β-D-glucanase activity.

Results

T. citrinoviride inoculation significantly reduced the disease symptoms caused by Botrytis cinerea and Cylindrocarpon destructans and induced ginsenoside biosynthesis in ginseng plants. T. citrinoviride was formulated as dustable powder and granules. The formulated agents also exhibited significant biocontrol activity and induced ginsenosides production in the controlled environment and mountain area.

Conclusion

Our results revealed that T. citrinoviride has great potential as a biological control agent and elicitor of ginsenoside production.