Metabolomic Insights Into Endophyte-Derived Bioactive Compounds

Endophytic Penicillium oxalicum AUMC 14898 from Opuntia ficus-indica: A Novel Source of Tannic Acid Inhibiting Virulence and Quorum Sensing of Extensively Drug-Resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa is a harmful pathogen that causes a variety of acute and chronic infections through quorum sensing (QS) mechanisms. The increasing resistance of this bacterium to numerous antibiotics has created a demand for new medications that specifically target QS. Endophytes can be the source of compounds with antibacterial properties. This research is the first to examine tannic acid (TA) produced by endophytic fungus as a potential biotherapeutic agent. A novel endophytic fungal isolate identified as Penicillium oxalicum was derived from the cladodes of Opuntia ficus-indica (L.). The species identification for this isolate was confirmed through sequencing of the internal transcribed spacer region. The metabolites from the culture of this isolate were extracted using ethyl acetate, then separated and characterized using chromatographic methods. This led to the acquisition of TA, a compound that shows strong anti-QS and excellent antibacterial effects against extensively drug-resistant P. aeruginosa strains. Furthermore, it was shown that treating P. aeruginosa with the obtained TA reduced the secretion of virulence factors controlled by QS in a dose-dependent manner, indicating that TA inhibited the QS characteristics of P. aeruginosa. Simultaneously, TA significantly inhibited the expression of genes associated with QS, including rhlR/I, lasR/I, and pqsR. In addition, in silico virtual molecular docking showed that TA could efficiently bind to QS receptor proteins. Our results showed that P. oxalicum could be a new source of TA for the treatment of infections caused by extensively drug-resistant P. aeruginosa.

Biodiversity and Bioprospecting of Fungal Endophytes from Houttuynia cordata Thunb. as a Potential Antibacterial and Anticancer Agent

Endophytic fungi are considered a new source of bioactive compounds that have important applications in agriculture and medicine. This study aims to investigate the biodiversity and potential of endophytic fungi isolated from Houttuynia cordata Thunb. as antimicrobials and anticancer agents. Out of ten isolated endophytes, four species have never been reported to be associated with H. cordata: Ceratobasidium sp., Cladosporium sp., Phomopsis sp., and Fusarium sp. The antibacterial activity assay revealed that the ethyl acetate extract of Ceratobasidium sp. HCS-3 possessed most potent antibacterial activity against Escherichia coli and Staphylococcus aureus. In addition, its cytotoxic activity test showed the promising anticancer activity on lung cancer A549, osteosarcoma MG-63, and cervical cancer HeLa cells with IC50 of 4.55±1.16, 32.14±2.78, and 1.54±0.66 ppm, respectively. Furthermore, metabolite profiling identified 66 compounds suggesting that benzoic acid, farnesol, and cyclopeptides may contribute to the antibacterial activity, while 4-methoxycinnamic acid may have anticancer potential.

Genomic and Chemical Evidence on Biosynthesis of Taxane Diterpenoids in Alternaria Isolates from Cupressaceae

Alternaria species (Deuteromycetes, Ascomycota) as ubiquitous fungi and prolific producers of a variety of toxic compounds are a part of microbiomes of plants, humans, and animals, mainly causing disease, allergic reactions, and toxicosis. However, some species have also been reported as endophytic microorganisms with highly bioactive metabolites. Our previous results indicate that potentially endophytic Alternaria species from Cupressaceae produce bioactive metabolites that possibly contribute to plant holobiont's health. Here, a possible mechanism behind this bioactivity is elucidated. As some endophytic fungi are reported to produce cytotoxic taxane diterpenoids, eight potentially endophytic Alternaria isolates from our collection were analyzed for the presence of the key genes of the paclitaxel (Taxol) biosynthetic pathway, i.e., taxadin synthase (ts), 10-deacetylbaccatin III-10-O-acetyltransferase (dbat), and C-13-phenylpropanoid side-chain CoA acyltransferase (bapt). The presence of all genes, i.e., ts, dbat, and bapt, was detected by PCR in six isolates and dbat and bapt in two isolates. Chemical analyses of the fermentation broths by TLC and HPLC chromatography and IR spectroscopy indicated the synthesis of the final product, i.e., paclitaxel. So, we introduce the synthesis of taxane diterpenoids as a possible mechanism by which Alternaria occupies the plant niches and protects the plant holobiont in the presence of competing microorganisms.

In Vivo and Real-Time Metabolic Profiling of Plant-Microbe Interactions in Leaves, Stems, and Roots of Bacterially Inoculated Chardonnay Plantlets using SpiderMass

There is growing interest in limiting the use of fungicides and implementing innovative, environmentally friendly strategies, such as the use of beneficial bacteria-triggered immunity, to protect grapevines from natural pathogens. Therefore, we need rapid and innovative ways to translate the knowledge of the molecular mechanisms underlying the activation of grapevine defenses against pathogens to induced resistance. Here, we have implemented an in vivo minimally invasive approach to study the interaction between plants and beneficial bacteria based on metabolic signatures. Paraburkholderia phytofirmans strain PsJN and PsJN-grapevine were used as bacterial and plant-bacterium interaction models, respectively. Using an innovative tool, SpiderMass, based on water-assisted laser desorption ionization with an IR microsampling probe, we simultaneously detect metabolic and lipidomic species. A metabolomic spectrum was thus generated, which was used to build a library and identify the most variable and discriminative peaks between the two conditions. We then showed that caftaric acid (m/z 311.04), caftaric acid dimer (m/z 623.09), derived caftaric acid (m/z 653.15), and quercetin-O-glucuronide tended to accumulate in grapevine leaves after root bacterization with PsJN. In addition, together with these phenolic messengers, we identified lipid biomarkers such as palmitic acid, linoleic acid, and α-linoleic acid as important messengers of enhanced defense mechanisms in Chardonnay plantlets. Taken together, SpiderMass is the next-generation methodology for studying plant-microorganism metabolic interactions with the prospect of in vivo real-time analysis in viticulture.

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.

Comparative metabolic profiling of the mycelium and fermentation broth of Penicillium restrictum from Peucedanum praeruptorum rhizosphere

Microorganisms in the rhizosphere, particularly arbuscular mycorrhiza, have a broad symbiotic relationship with their host plants. One of the major fungi isolated from the rhizosphere of Peucedanum praeruptorum is Penicillium restrictum. The relationship between the metabolites of P. restrictum and the root exudates of P. praeruptorum is being investigated. The accumulation of metabolites in the mycelium and fermentation broth of P. restrictum was analysed over different fermentation periods. Non-targeted metabolomics was used to compare the differences in intracellular and extracellular metabolites over six periods. There were significant differences in the content and types of mycelial metabolites during the incubation. Marmesin, an important intermediate in the biosynthesis of coumarins, was found in the highest amount on the fourth day of incubation. The differential metabolites were screened to obtain 799 intracellular and 468 extracellular differential metabolites. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the highly enriched extracellular metabolic pathways were alanine, aspartate and glutamate metabolism, glyoxylate and dicarboxylate metabolism, and terpenoid backbone biosynthesis. In addition, the enrichment analysis associated with intracellular and extracellular ATP-binding cassette transporter proteins revealed that some ATP-binding cassette transporters may be involved in the transportation of certain amino acids and carbohydrates. Our results provide some theoretical basis for the regulatory mechanisms between the rhizosphere and the host plant and pave the way for the heterologous production of furanocoumarin.

Actinomycetes are a natural resource for sustainable pest control and safeguarding agriculture

Actinomycetes, a diverse group of bacteria with filamentous growth characteristics, have long captivated researchers and biochemists for their prolific production of secondary metabolites. Among the myriad roles played by actinomycete secondary metabolites, their historical significance in the field of biocontrol stands out prominently. The fascinating journey begins with the discovery of antibiotics, where renowned compounds like streptomycin, tetracycline, and erythromycin revolutionized medicine and agriculture. The history of biocontrol traces its roots back to the early twentieth century, when scientists recognized the potential of naturally occurring agents to combat pests and diseases. The emergence of synthetic pesticides in the mid-twentieth century temporarily overshadowed interest in biocontrol. However, with growing environmental concerns and the realization of the negative ecological impacts of chemical pesticides, the pendulum swung back towards exploring sustainable alternatives. Beyond their historical role as antibiotics, actinomycete-produced secondary metabolites encompass a rich repertoire with biopesticide potential. The classification of these compounds based on chemical structure and mode of action is highlighted, demonstrating their versatility against both plant pathogens and insect pests. Additionally, this review provides in-depth insights into how endophytic actinomycete strains play a pivotal role in biocontrol strategies. Case studies elucidate their effectiveness in inhibiting Spodoptera spp. and nematodes through the production of bioactive compounds. By unraveling the multifunctional roles of endophytic actinomycetes, this review contributes compelling narrative knowledge to the field of sustainable agriculture, emphasizing the potential of these microbial allies in crafting effective, environmentally friendly biocontrol strategies for combating agricultural pests.

Antimicrobials from endophytes as novel therapeutics to counter drug-resistant pathogens

The rapid increase in antimicrobial resistance (AMR) projects a "global emergency" and necessitates a need to discover alternative resources for combating drug-resistant pathogens or "superbugs." One of the key themes in "One Health Concept" is based on the fact that the interconnected network of humans, the environment, and animal habitats majorly contribute to the rapid selection and spread of AMR. Moreover, the injudicious and overuse of antibiotics in healthcare, the environment, and associated disciplines, further aggravates the concern. The prevalence and persistence of AMR contribute to the global economic burden and are constantly witnessing an upsurge due to fewer therapeutic options, rising mortality statistics, and expensive healthcare. The present decade has witnessed the extensive exploration and utilization of bio-based resources in harnessing antibiotics of potential efficacies. The discovery and characterization of diverse chemical entities from endophytes as potent antimicrobials define an important yet less-explored area in natural product-mediated drug discovery. Endophytes-produced antimicrobials show potent efficacies in targeting microbial pathogens and synthetic biology (SB) mediated engineering of endophytes for yield enhancement, forms a prospective area of research. In keeping with the urgent requirements for new/novel antibiotics and growing concerns about pathogenic microbes and AMR, this paper comprehensively reviews emerging trends, prospects, and challenges of antimicrobials from endophytes and their effective production via SB. This literature review would serve as the platform for further exploration of novel bioactive entities from biological organisms as "novel therapeutics" to address AMR.

Unveiling Metal Tolerance Mechanisms in Leersia hexandra Swartz under Cr/Ni Co-Pollution by Studying Endophytes and Plant Metabolites

Heavy metal pollution poses significant environmental challenges, and understanding how plants and endophytic bacteria interact to mitigate these challenges is of utmost importance. In this study, we investigated the roles of endophytic bacteria, particularly Chryseobacterium and Comamonas, in Leersia hexandra Swartz (L. hexandra) in response to chromium and nickel co-pollution. Our results demonstrated the remarkable tolerance of Chryseobacterium and Comamonas to heavy metals, and their potential to become dominant species in the presence of co-pollution. We observed a close relationship between these endophytic bacteria and the significant differences in metabolites, particularly carbohydrates, flavonoids, and amino acids in L. hexandra. These findings shed light on the potential of endophytic bacteria to promote the production of aspartic acid and other metabolites in plants as a response to abiotic stressors. Furthermore, our study presents a new direction for plant and bioremediation strategies in heavy metal pollution and enhances our understanding of L. hexandra's mechanisms for heavy metal tolerance.

Molecular mechanism of endophytic bacteria DX120E regulating polyamine metabolism and promoting plant growth in sugarcane

Introduction

Sugarcane endophytic nitrogen-fixing bacterium Klebsiella variícola DX120E displayed broad impact on growth, but the exact biological mechanism, especially polyamines (PAs) role, is still meager.

Methods

To reveal this relationship, the content of polyamine oxidase (PAO), PAs, reactive oxygen species (ROS)-scavenging antioxidative enzymes, phytohormones, 1-aminocyclopropane-1-carboxylic synthase (ACS), chlorophyll content, and biomass were determined in sugarcane incubated with the DX120E strain. In addition, expression levels of the genes associated with polyamine metabolism were measured by transcriptomic analysis.

Results

Genomic analysis of Klebsiella variícola DX120E revealed that 39 genes were involved in polyamine metabolism, transport, and the strain secrete PAs in vitro. Following a 7-day inoculation period, DX120E stimulated an increase in the polyamine oxidase (PAO) enzyme in sugarcane leaves, however, the overall PAs content was reduced. At 15 days, the levels of PAs, ROS-scavenging antioxidative enzymes, and phytohormones showed an upward trend, especially spermidine (Spd), putrescine (Put), catalase (CAT), auxin (IAA), gibberellin (GA), and ACS showed a significant up-regulation. The GO and KEGG enrichment analysis found a total of 73 differentially expressed genes, involving in the cell wall (9), stimulus response (13), peroxidase activity (33), hormone (14) and polyamine metabolism (4).

Discussion

This study demonstrated that endophytic nitrogen-fixing bacteria stimulated polyamine metabolism and phytohormones production in sugarcane plant tissues, resulting in enhanced growth. Dual RNA-seq analyses provided insight into the early-stage interaction between sugarcane seedlings and endophytic bacteria at the transcriptional level. It showed how diverse metabolic processes selectively use distinct molecules to complete the cell functions under present circumstances.

Xenomyrothecium tongaense PTS8: a rare endophyte of Polianthes tuberosa with salient antagonism against multidrug-resistant pathogens

Introduction

Endophytes refer to microorganisms residing within the endosphere of plants, particularly perennials, without inflicting noticeable injury or inducing obvious morphological variations to their host plant or host organism. Endophytic fungi, although often overlooked microorganisms, have garnered interest due to their significant biological diversity and ability to produce novel pharmacological substances.

Methods

In this study, fourteen endophytic fungi retrieved were from the stem of the perennial plant Polianthes tuberosa of the Asparagaceae family. These fungal crude metabolites were tested for antagonistic susceptibility to Multi-Drug Resistant (MDR) pathogens using agar well diffusion, Minimum Inhibitory Concentration (MIC), and Minimum Bactericidal Concentration (MBC) assays. The chequerboard test was used to assess the synergistic impact of active extract.

Results and discussion

In early antibacterial screening using the Agar plug diffusion test, three of fourteen endophytes demonstrated antagonism against Methicillin-resistant Staphylococcus aureus (MRSA) and Vancomycin-resistant Enterococcus (VRE). Three isolates were grown in liquid medium and their secondary metabolites were recovered using various organic solvents. Eight extracts from three endophytic fungi displayed antagonism against one or more human pathogens with diameters ranging from 11 to 24 mm. The highest antagonistic effect was obtained in ethyl acetate extract for PTS8 isolate against two MRSA (ATCC 43300, 700699) with 20 ± 0.27 and 22 ± 0.47 mm zones of inhibition, respectively, among different solvent extracts. The extract had MICs of 3.12 ± 0.05 and 1.56 ± 0.05 μg/mL, and MBCs of 50 ± 0.01 and 12.5 ± 0.04 μg/mL, respectively. Antagonism against VRE was 18 ± 0.23 mm Zone of Inhibition (ZOI) with MIC and MBC of 6.25 ± 0.25 and 25 ± 0.01 μg/mL. When ethyl acetate extract was coupled with antibiotics, the chequerboard assay demonstrated a synergistic impact against MDR bacteria. In an antioxidant test, it had an inhibitory impact of 87 ± 0.5% and 88.5 ± 0.5% in 2,2-Diphenyl-1-Picrylhydrazyl and reducing power assay, respectively, at 150 μg/mL concentration. PTS8 was identified as a Xenomyrothecium tongaense strain by 18S rRNA internal transcribed spacer (ITS) sequencing. To our insight, it is the foremost study to demonstrate the presence of an X. tongaense endophyte in the stem of P. tuberosa and the first report to study the antibacterial efficacy of X. tongaense which might serve as a powerful antibacterial source against antibiotic-resistant human infections.

A cyclic dipeptide for salinity stress alleviation and the trophic flexibility of endophyte provide insights into saltmarsh plant-microbe interactions

In response to climate change, the nature of endophytes and their applications in sustainable agriculture have attracted the attention of academics and agro-industries. This work focused on the endophytic halophiles of the endangered Taiwanese salt marsh plant, Bolboschoenus planiculmis, and evaluated the functions of these isolates through in planta salinity stress alleviation assay using Arabidopsis. The endophytic strain Priestia megaterium BP01R2, which can promote plant growth and salinity tolerance, was further characterized through multi-omics approaches. The transcriptomics results suggested that BP01R2 could function by tuning hormone signal transduction, energy-producing metabolism, multiple stress responses, etc. In addition, the cyclodipeptide cyclo(L-Ala-Gly), which was identified by metabolomics analysis, was confirmed to contribute to the alleviation of salinity stress in stressed plants via exogenous supplementation. In this study, we used multi-omics approaches to investigate the genomics, metabolomics, and tropisms of endophytes, as well as the transcriptomics of plants in response to the endophyte. The results revealed the potential molecular mechanisms underlying the occurrence of biostimulant-based plant-endophyte symbioses with possible application in sustainable agriculture.

Chemical constituents from the medicinal herb-derived fungus Chaetomium globosum Km1226

BACKGROUND

Endophytic fungi have proven to be a rich source of novel natural products with a wide-array of biological activities and higher levels of structural diversity.

RESULTS

Chemical investigation on the liquid- and solid-state fermented products of Chaetomium globosum Km1226 isolated from the littoral medicinal herb Atriplex maximowicziana Makino resulted in the isolation of compounds 1-14. Their structures were determined by spectroscopic analysis as three previously undescribed C13-polyketides, namely aureonitol C (1), mollipilins G (2), and H (3), along with eleven known compounds 4-14. Among these, mollipilin A (5) exhibited significant nitric oxide production inhibitory activity in LPS-induced BV-2 microglial cells with an IC50 value of 0.7 ± 0.1 µM, and chaetoglobosin D (10) displayed potent anti-angiogenesis property in human endothelial progenitor cells (EPCs) with an IC50 value of 0.8 ± 0.3 µM.

CONCLUSIONS

Three previously unreported compounds 1-3 were isolated and identified. Mollipilin A (5) and chaetoglobosin D (10) could possibly be developed as anti-inflammatory and anti-angiogenic lead drugs, respectively.

Fungal and mycotoxin contaminants in cannabis and hemp flowers: implications for consumer health and directions for further research

Medicinal and recreational uses of Cannabis sativa, commonly known as cannabis or hemp, has increased following its legalization in certain regions of the world. Cannabis and hemp plants interact with a community of microbes (i.e., the phytobiome), which can influence various aspects of the host plant. The fungal composition of the C. sativa phytobiome (i.e., mycobiome) currently consists of over 100 species of fungi, which includes phytopathogens, epiphytes, and endophytes, This mycobiome has often been understudied in research aimed at evaluating the safety of cannabis products for humans. Medical research has historically focused instead on substance use and medicinal uses of the plant. Because several components of the mycobiome are reported to produce toxic secondary metabolites (i.e., mycotoxins) that can potentially affect the health of humans and animals and initiate opportunistic infections in immunocompromised patients, there is a need to determine the potential health risks that these contaminants could pose for consumers. This review discusses the mycobiome of cannabis and hemp flowers with a focus on plant-infecting and toxigenic fungi that are most commonly found and are of potential concern (e.g., Aspergillus, Penicillium, Fusarium, and Mucor spp.). We review current regulations for molds and mycotoxins worldwide and review assessment methods including culture-based assays, liquid chromatography, immuno-based technologies, and emerging technologies for these contaminants. We also discuss approaches to reduce fungal contaminants on cannabis and hemp and identify future research needs for contaminant detection, data dissemination, and management approaches. These approaches are designed to yield safer products for all consumers.

Harnessing the action mechanisms of microbial endophytes for enhancing plant performance and stress tolerance: current understanding and future perspectives

Microbial endophytes are microorganisms that reside within plant tissues without causing any harm to their hosts. These microorganisms have been found to confer a range of benefits to plants, including increased growth and stress tolerance. In this review, we summarize the recent advances in our understanding of the mechanisms by which microbial endophytes confer abiotic and biotic stress tolerance to their host plants. Specifically, we focus on the roles of endophytes in enhancing nutrient uptake, modulating plant hormones, producing secondary metabolites, and activating plant defence responses. We also discuss the challenges associated with developing microbial endophyte-based products for commercial use, including product refinement, toxicology analysis, and prototype formulation. Despite these challenges, there is growing interest in the potential applications of microbial endophytes in agriculture and environmental remediation. With further research and development, microbial endophyte-based products have the potential to play a significant role in sustainable agriculture and environmental management.

Temporal dynamics of endophytic bacterial and fungal communities during spike development in Piper longum L

The female spikes (fruits) of Piper longum are widely used in Ayurvedic, Siddha and Unani medicine systems to treat respiratory and digestive disorders. The spikes are rich in piperine, a pharmacologically active amide alkaloid and a potent bioavailability enhancer, which accumulates to the highest level during the dark-green stage of spike development. Plant-associated microbiota influence the plant's fitness, response, and production of economically important metabolites. Considering the economic importance of piperine and other spike-derived alkaloids, understanding microbial community dynamics during spike development would be key to bioprospecting for economically important metabolites. In the present study, the structural diversity of microbial communities associated with early (SI), mid (SII), and late (SIII) stages of spike development in P. longum has been analysed by Illumina-based amplicon sequencing of 16S rRNA gene and ITS region. Results revealed that spike development significantly drives the diversity and abundance of spike-associated microbiota, especially bacterial communities. Cyanobacteria and Ascomycota constituted the most abundant bacterial and fungal phyla, respectively, across all stages of spike development. Interestingly, Halomonas, Kushneria and Haererehalobacter were found to be exclusively associated with SIII (corresponding to economically important) stage of spike development. Sphingomonas, Mortierella, Cladosporium and Vishniacozyma constituted the core microbiome of the spike. Besides, PICRUSt analysis revealed that amino acid metabolism was the most dominant metabolic function attributed to spike-associated bacterial communities. To the best of our knowledge, this is the first study to investigate the endomicrobiome dynamics during spike development in a medicinal plant species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01352-2.

Biochemical and Biotechnological Insights into Fungus-Plant Interactions for Enhanced Sustainable Agricultural and Industrial Processes

The literature is full of studies reporting environmental and health issues related to using traditional pesticides in food production and storage. Fortunately, alternatives have arisen in the last few decades, showing that organic agriculture is possible and economically feasible. And in this scenario, fungi may be helpful. In the natural environment, when associated with plants, these microorganisms offer plant-growth-promoting molecules, facilitate plant nutrient uptake, and antagonize phytopathogens. It is true that fungi can also be phytopathogenic, but even they can benefit agriculture in some way-since pathogenicity is species-specific, these fungi are shown to be useful against weeds (as bioherbicides). Finally, plant-associated yeasts and molds are natural biofactories, and the metabolites they produce while dwelling in leaves, flowers, roots, or the rhizosphere have the potential to be employed in different industrial activities. By addressing all these subjects, this manuscript comprehensively reviews the biotechnological uses of plant-associated fungi and, in addition, aims to sensitize academics, researchers, and investors to new alternatives for healthier and more environmentally friendly production processes.

Towards further understanding the applications of endophytes: enriched source of bioactive compounds and bio factories for nanoparticles

The most significant issues that humans face today include a growing population, an altering climate, an growing reliance on pesticides, the appearance of novel infectious agents, and an accumulation of industrial waste. The production of agricultural goods has also been subject to a great number of significant shifts, often known as agricultural revolutions, which have been influenced by the progression of civilization, technology, and general human advancement. Sustainable measures that can be applied in agriculture, the environment, medicine, and industry are needed to lessen the harmful effects of the aforementioned problems. Endophytes, which might be bacterial or fungal, could be a successful solution. They protect plants and promote growth by producing phytohormones and by providing biotic and abiotic stress tolerance. Endophytes produce the diverse type of bioactive compounds such as alkaloids, saponins, flavonoids, tannins, terpenoids, quinones, chinones, phenolic acids etc. and are known for various therapeutic advantages such as anticancer, antitumor, antidiabetic, antifungal, antiviral, antimicrobial, antimalarial, antioxidant activity. Proteases, pectinases, amylases, cellulases, xylanases, laccases, lipases, and other types of enzymes that are vital for many different industries can also be produced by endophytes. Due to the presence of all these bioactive compounds in endophytes, they have preferred sources for the green synthesis of nanoparticles. This review aims to comprehend the contributions and uses of endophytes in agriculture, medicinal, industrial sectors and bio-nanotechnology with their mechanism of action.

Plants as the Extended Phenotype of Endophytes-The Actual Source of Bioactive Compounds

For thousands of years, plants have been used for their medicinal properties. The industrial production of plant-beneficial compounds is facing many drawbacks, such as seasonal dependence and troublesome extraction and purification processes, which have led to many species being on the edge of extinction. As the demand for compounds applicable to, e.g., cancer treatment, is still growing, there is a need to develop sustainable production processes. The industrial potential of the endophytic microorganisms residing within plant tissues is undeniable, as they are often able to produce, in vitro, similar to or even the same compounds as their hosts. The peculiar conditions of the endophytic lifestyle raise questions about the molecular background of the biosynthesis of these bioactive compounds in planta, and the actual producer, whether it is the plant itself or its residents. Extending this knowledge is crucial to overcoming the current limitations in the implementation of endophytes for larger-scale production. In this review, we focus on the possible routes of the synthesis of host-specific compounds in planta by their endophytes.

Effect of Arbuscular Mycorrhizal Fungi on Nitrogen and Phosphorus Uptake Efficiency and Crop Productivity of Two-Rowed Barley under Different Crop Production Systems

Arbuscular Mycorrhizal Fungi (AMF) constitute a ubiquitous group of soil microorganisms, affecting plant and soil microorganism growth. Various crop management practices can have a significant impact on the AM association. This study investigated the AMF inoculation contribution on growth and productivity of two-rowed barley crop by identifying the underlying mechanisms both in conventional and organic cropping systems. A two-year field trial was set up as a split-plot design with 2 main plots [AMF inoculation: with (AMF+) and without (AMF-)] and five sub-plots (fertilization regimes: untreated, 100% recommended dose of fertilizer in organic and inorganic form, and 60% recommended dose of fertilizer in organic and inorganic form) in three replications. According to the results, AMF+ plants presented higher plant height and leaf area index (LAI), resulting in increased biomass and, as a result, higher seed yield. With regard to the quality traits, including the nitrogen and phosphorus uptake and their utilization indices, the AMF inoculated plants showed higher values. Furthermore, the level of fertilization, particularly in an inorganic form, adversely affected AMF root colonization. Consequently, it was concluded that substitution of inorganic inputs by organic, as well as inputs reduction, when combined with AMF inoculation, can produce excellent results, thus making barley crop cultivation sustainable in Mediterranean climates.

Analysis of the molecular and biochemical mechanisms involved in the symbiotic relationship between Arbuscular mycorrhiza fungi and Manihot esculenta Crantz

INTRODUCTION

Plants and arbuscular mycorrhizal fungi (AMF) mutualistic interactions are essential for sustainable agriculture production. Although it is shown that AMF inoculation improves cassava physiological performances and yield traits, the molecular mechanisms involved in AM symbiosis remain largely unknown. Herein, we integrated metabolomics and transcriptomics analyses of symbiotic (Ri) and asymbiotic (CK) cassava roots and explored AM-induced biochemical and transcriptional changes.

RESULTS

Three weeks (3w) after AMF inoculations, proliferating fungal hyphae were observable, and plant height and root length were significantly increased. In total, we identified 1,016 metabolites, of which 25 were differentially accumulated (DAMs) at 3w. The most highly induced metabolites were 5-aminolevulinic acid, L-glutamic acid, and lysoPC 18:2. Transcriptome analysis identified 693 and 6,481 differentially expressed genes (DEGs) in the comparison between CK (3w) against Ri at 3w and 6w, respectively. Functional enrichment analyses of DAMs and DEGs unveiled transport, amino acids and sugar metabolisms, biosynthesis of secondary metabolites, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interactions as the most differentially regulated pathways. Potential candidate genes, including nitrogen and phosphate transporters, transcription factors, phytohormone, sugar metabolism-related, and SYM (symbiosis) signaling pathway-related, were identified for future functional studies.

DISCUSSION

Our results provide molecular insights into AM symbiosis and valuable resources for improving cassava production.

Comparison of the diversity and structure of the rhizosphere microbial community between the straight and twisted trunk types of Pinus yunnanensis

Background

Pinus yunnanensis is a major silvicultural species in Southwest China. Currently, large areas of twisted-trunk Pinus yunnanensis stands severely restrict its productivity. Different categories of rhizosphere microbes evolve alongside plants and environments and play an important role in the growth and ecological fitness of their host plant. However, the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types-straight and twisted-remain unclear.

Methods

We collected the rhizosphere soil of 5 trees with the straight and 5 trees with the twisted trunk type in each of three sites in Yunnan province. We assessed and compared the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types by Illumina sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions.

Results

The available phosphorus in soil differed significantly between P. yunnanensis with straight and twisted trunks. Available potassium had a significant effect on fungi. Chloroflexi dominated the rhizosphere soils of the straight trunk type, while Proteobacteria was predominant in the rhizosphere soils of the twisted trunk type. Trunk types significantly explained 6.79% of the variance in bacterial communities.

Conclusion

This study revealed the composition and diversity of bacterial and fungal groups in the rhizosphere soil of P. yunnanensis with straight and twisted trunk types, providing proper microbial information for different plant phenotypes.

Investigations of specialised metabolites of endophyte Diaporthe destruens hosted in Illigera orbiculata C. Y. Wu

A chemical investigation of the endophytic fungus Diaporthe destruens from the Hernandiaceae plant Illigera orbiculata C. Y. Wu collected from southern Yunnan Province, China, led to the isolation of six undescribed compounds, including two azaphilone analogs, which are a pair of epimers (13R-hydroxy-chermesinone A and 13S-hydroxy-chermesinone A); a pyrrole derivative (1-(4-(methoxymethyl)-1H-pyrrol-3-yl)ethan-1-one); an isoindolone derivative (4-hydroxy-6-methoxyisoindolin-1-one); a benzylbenzene derivative (destruensine A) and a conjectural fragment of polyketide ((2R,4R)-2-(methoxymethyl)pentane-1,4-diol) along with nine known compounds. Their structures were elucidated by spectroscopic methods and HRESIMS, and the absolute configurations were further confirmed by electronic circular dichroism (ECD) and chemical derivatization. The antimicrobial activities, anti-acetylcholinesterase activities, antiproliferation, and NO production inhibitory effects of compounds 1-15 were evaluated.

Microbial endophytes: application towards sustainable agriculture and food security

Microbial endophytes are ubiquitous and exist in each recognised plant species reported till date. Within the host plant, the entire community of microbes lives non-invasively within the active internal tissues without causing any harm to the plant. Endophytes interact with their host plant via metabolic communication enables them to generate signal molecules. In addition, the host plant's genetic recombination with endophytes helps them to imitate the host's physicochemical functions and develop identical active molecules. Therefore, when cultured separately, they begin producing the host plant phytochemicals. The fungal species Penicillium chrysogenum has portrayed the glory days of antibiotics with the invention of the antibiotic penicillin. Therefore, fungi have substantially supported social health by developing many bioactive molecules utilised as antioxidant, antibacterial, antiviral, immunomodulatory and anticancerous agents. But plant-related microbes have emanated as fountainheads of biologically functional compounds with higher levels of medicinal perspective in recent years. Researchers have been motivated by the endless need for potent drugs to investigate alternate ways to find new endophytes and bioactive molecules, which tend to be a probable aim for drug discovery. The current research trends with these promising endophytic organisms are reviewed in this review paper. KEY POINTS: • Identified 54 important bioactive compounds as agricultural relevance • Role of genome mining of endophytes and "Multi-Omics" tools in sustainable agriculture • A thorough description and graphical presentation of agricultural significance of plant endophytes.

Broad-Spectrum Antimicrobial Action of Cell-Free Culture Extracts and Volatile Organic Compounds Produced by Endophytic Fungi Curvularia Eragrostidis

Endophytes are the mutualistic microorganisms that reside within the host plant and promote plant growth in adverse conditions. Plants and their endophytes are engaged in a symbiotic relationship that enables endophytes to access bioactive genes of the ethnomedicinal plants, and, as a result, endophytes are constantly addressed in the sector of pharmaceuticals and agriculture for their multidomain bio-utility. The gradual increase of antimicrobial resistance can be effectively countered by the endophytic metabolites. In these circumstances, in the present investigation, endophytic Curvularia eragrostidis HelS1 was isolated from an ethnomedicinally valuable plant Helecteris isora from East India's forests. The secondary volatile and non-volatile metabolites are extracted from HelS1 and are found to be effective broad-spectrum antimicrobials. A total of 26 secondary metabolites (9 volatiles and 17 non-volatiles) are extracted from the isolate, which exhibits effective antibacterial [against six Gram-positive and seven Gram-negative pathogens with a minimum inhibitory concentrations (MIC) value ranging from 12.5 to 400 μg ml-1] and antifungal (against seven fungal plant pathogens) activity. The secondary metabolite production was optimised by one variable at a time technique coupled with the response surface methodology. The results revealed that there was a 34% increase in antibacterial activity in parameters with 6.87 g L-1 of fructose (as a carbon source), 3.79 g L-1 of peptone (as a nitrogen source), pH 6.75, and an inoculation period of 191.5 h for fermentation. The volatile metabolite production was also found to be optimum when the medium was supplemented with yeast extract and urea (0.2 g L-1) along with dextrose (40 g L-1). Amongst extracted volatile metabolites, 1-H-indene 1 methanol acetate, tetroquinone, N, N-diphenyl-2-nitro-thio benzamide, Trans 1, 2-diethyl-trans-2-decalinol, naphthalene, and azulene are found to be the most effective. Our investigation opens up opportunities in the sector of sustainable agriculture as well as the discovery of novel antimicrobials against dreadful phyto and human pathogens.

Endophytic Fungal and Bacterial Microbiota Shift in Rice and Barnyardgrass Grown under Co-Culture Condition

Although barnyardgrass (Echinochloa crus-galli L.) is more competitive than rice (Oryza sativa L.) in the aboveground part, little is known about whether barnyardgrass is still competitive in recruiting endophytes and the root microbiota composition variation of rice under the barnyardgrass stress. Here, by detailed temporal characterization of root-associated microbiomes of rice plants during co-planted barnyardgrass stress and a comparison with the microbiomes of unplanted soil, we found that the bacterial community diversity of rice was dramatically higher while the fungal community richness was significantly lower than that of barnyardgrass at BBCH 45 and 57. More importantly, rice recruited more endophytic bacteria at BBCH 45 and 57, and more endophytic fungi at BBCH 17, 24, 37 to aginst the biotic stress from barnyardgrass. Principal coordinates analysis (PCoA) showed that rice and barnyardgrass had different community compositions of endophytic bacteria and fungi in roots. The PICRUSt predictive analysis indicated that majority of metabolic pathways of bacteria were overrepresented in barnyardgrass. However, eleven pathways were significantly presented in rice. In addition, rice and barnyardgrass harbored different fungal trophic modes using FUNGuild analysis. A negative correlation between bacteria and fungi in rice and barnyardgrass roots was found via network analysis. Actinobacteria was the vital bacteria in rice, while Proteobacteria dominated in barnyardgrass, and Ascomycota was the vital fungi in each species. These findings provided data and a theoretical basis for the in-depth understanding of the competition of barnyardgrass and endophytes and have implications relevant to weed prevention and control strategies using root microbiota.

The Multifunctions and Future Prospects of Endophytes and Their Metabolites in Plant Disease Management

Endophytes represent a ubiquitous and magical world in plants. Almost all plant species studied by different researchers have been found to harbor one or more endophytes, which protect host plants from pathogen invasion and from adverse environmental conditions. They produce various metabolites that can directly inhibit the growth of pathogens and even promote the growth and development of the host plants. In this review, we focus on the biological control of plant diseases, aiming to elucidate the contribution and key roles of endophytes and their metabolites in this field with the latest research information. Metabolites synthesized by endophytes are part of plant disease management, and the application of endophyte metabolites to induce plant resistance is very promising. Furthermore, multi-omics should be more fully utilized in plant–microbe research, especially in mining novel bioactive metabolites. We believe that the utilization of endophytes and their metabolites for plant disease management is a meaningful and promising research direction that can lead to new breakthroughs in the development of more effective and ecosystem-friendly insecticides and fungicides in modern agriculture.