Endophytes: A Treasure House of Bioactive Compounds of Medicinal Importance

Bacterial Microbiome in the Phyllo-Endosphere of Highly Specialized Rock Spleenwort

Bacteria communities associated with plants have been given increasing consideration because they are arguably beneficial to their host plants. To understand the ecological and evolutionary impact of these mutualistic associations, it is important to explore the vast unknown territory of bacterial genomic diversity and their functional contributions associated with the major branches of the tree-of-life. Arguably, this aim can be achieved by profiling bacterial communities by applying high throughput sequencing approaches, besides establishing model plant organisms to test key predictions. This study utilized the Illumina Miseq reads of bacterial 16S rRNA sequences to determine the bacterial diversity associated with the endosphere of the leaves of the highly specialized rock spleenwort Asplenium delavayi (Aspleniaceae). By documenting the bacterial communities associated with ferns collected in natural occurrence and cultivation, this study discovered the most species-rich bacterial communities associated with terrestrial ferns reported until now. Despite the substantial variations of species diversity and composition among accessions, a set of 28 bacterial OTUs was found to be shared among all accessions. Functional analyses recovered evidence to support the predictions that changes in bacterial community compositions correspond to functional differentiation. Given the ease of cultivating this species, Asplenium delavayi is introduced here as a model organism to explore the ecological and evolutionary benefits created by mutualistic associations between bacteria and ferns.

Endophytes from blueberry (Vaccinium sp.) fruit: Characterization of yeast and bacteria via label-free surface-enhanced Raman spectroscopy (SERS)

Blueberries (Vaccinium sp.) are consumed all around the globe, however, their endophytic community has not been thoroughly researched, specifically their fruit endophytes. We aimed to isolate and analyze easily cultivable blueberry fruit endophytes to help in future research, concerning probiotic microorganisms. Twelve strains were isolated in this pilot study, genetically homologous with Staphylococcus hominis, Staphylococcus cohnii, Salmonella enterica, Leuconostoc mesenteroides, and [Candida] santamariae. To determine the molecular composition of these isolates we used label-free surface-enhanced Raman spectroscopy (SERS). To our knowledge, this is the first time that SERS spectra for L. mesenteroides and C. santamariae are presented, as well as the first report of Candida yeast, isolated specifically from blueberry fruits. Our findings suggest that the differences in tested yeast and bacteria SERS spectra and subsequent differentiation are facilitated by minor shifts in spectral peak positions as well as their intensities. Moreover, we used principal component and discriminant function analyses to differentiate chemotypes within our isolate group, proving the sensitivity of the technique and its usefulness to recognize different strains in plant-associated microbe samples, which will aid to streamline future studies in biofertilizers and biocontrol agents.

The Antibacterial, Antitumor Activities, and Bioactive Constituents’ Identification of Alectra sessiliflora Bacterial Endophytes

Due to increased antimicrobial resistance against current drugs, new alternatives are sought. Endophytic bacteria associated with medicinal plants are recognized as valuable sources of novel secondary metabolites possessing antimicrobial, antitumor, insecticidal, and antiviral activities. In this study, five bacterial endophytes were isolated and identified from the medicinal plant, Alectra sessiliflora, and their antibacterial and antitumor activities were investigated. In addition, the crude extracts of the endophytes were analyzed using gas chromatography (GC) coupled with time-of-flight mass spectrometry (TOF-MS). The identified bacterial endophytes belong to three genera viz Lysinibacillus, Peribacillus, and Bacillus, with the latter as the dominant genus with three species. Ethyl acetate extracts from the endophytes were used for antimicrobial activity against eleven pathogenic strains through minimum inhibitory concentration (MIC). The antitumor activity against the Hela cervical, Hek 293 kidney, and A549 lung carcinoma cells was determined by the MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxy-phenyl)-2-(4-sulfophenyl)-2H-tetrazolium] assay. Lysinibacillus sp. strain AS_1 exhibited broad antibacterial activity against the pathogenic strains with MIC values ranging from 4 to 8 mg/ml, while Bacillus sp. strain AS_3 displayed MIC of 0.25 mg/ml. Crude extracts of Lysinibacillus sp. strain AS_1, Peribacillus sp. strain AS_2, and Bacillus sp. strain AS_3 showed growth inhibition of more than 90% against all the cancer cell lines at a concentration of 1,000 μg/ml. Untargeted secondary metabolite profiling of the crude extracts revealed the presence of compounds with reported biological activity, such as antimicrobial, antioxidant, anti-inflammatory, antitumor, and antidiabetic properties. This study reported for the first time, bacterial endophytes associated with A. sessiliflora with antibacterial and antitumor activities.

Polyhydroxylated sesquiterpenes and ergostane glycosides produced by the endophytic fungus Xylaria sp. from Azadirachta indica

The investigation of the metabolites from the endophytic fungus Xylaria sp. YM 311647 in solid fermentation resulted in the isolation of six undescribed compounds, namely xylarioxides A-F, respectively. These included one eremophilane sesquiterpene, three guaiane sesquiterpene glycosides, and two ergostane glycosides. The structures of the compounds were determined by extensive analyses of spectroscopic data, including 1D and 2D NMR, as well as HRESIMS data. The stereochemistry of xylarioxide A was confirmed by X-ray crystallographic analysis. All of the isolated compounds were assayed for their antifungal activities against seven phytopathogenic fungi and two human pathogenic fungi. Among them, xylarioxides A, E and F showed potent activities against the tested phytopathogens. Particularly, xylarioxide E exhibited the highest activity against Gibberella saubinetii, Curvularia lunata, and Colletotrichum gloeosporioides with MIC values of 4, 4, and 8 μg/mL, respectively, which were comparable to the positive control of nystatin. Interestingly, guaiane sesquiterpene glycosides have been rarely reported from fungal sources. Additionally, xylarioxide E represented an unusual naturally occurring 3,4-seco-steroidal glycoside with a seven-membered lactone in ring A.

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.

The lipopeptides Fengycin and Iturin are involved in the anticandidal activity of endophytic Bacillus sp. as determined by experimental and in-silico analysis

In this study, an endophytic Bacillus sp. strain (K7) was isolated from the medicinally important ornamental plant, Jasminum officinale. Biochemical analyses were conducted to evaluate the nature of the extracted product, which displayed strong anticandidal activity against Candida albicans SC5314, as evident from the results obtained in agar-cup diffusion tests, phase contrast microscopy, scanning electron microscopy, and minimum inhibitory concentration assays. After confirming the presence of the gene clusters encoding the lipopeptides iturins and fengycin in the genome of K7, their corresponding molecular ions were identified using MALDI-TOF-MS. 3D structures of the lipopeptides were downloaded from specific databases and molecular docking was performed against a vital C. albicans enzyme, Exo 1, 3- beta-glucanase, involved in cell wall remodeling, adhesion to polymer materials, and biofilm formation. The docking score of iturins was found to be -8.6 and -8.2 kcal mol^-1 and for fengycin it was -9.4 kcal mol^-1 , indicating a strong affinity of these cyclic lipopeptides towards Exo 1, 3- beta-glucanase. The combined in vitro and in-silico anticandidal studies suggested that these secreted lipopeptides from Bacillus sp. may be used as potential therapeutics against opportunistic and complicated infections of Candida albicans.

Phenethoxy Derivatives with Anti-inflammatory Activities from the Betelnut Endophytic Trichoderma asperellum G10

Eight new phenethoxy derivatives, trichoasperellins A-H (1-8), were isolated from the endophytic fungus Trichoderma asperellum G10 isolated from the medicinal plant Areca catechu L. The structures of these compounds were elucidated from spectroscopic data, J-based configurational analysis, and Mosher's methods. Compounds 1-4 and 6-8 bear one or two multioxidized C₇ moieties with the same carbon skeleton. The carbon skeletons of compounds 6-8 are new, all containing three moieties connected via two acetal carbons similar to those of disaccharide glycosides. Compound 4 inhibited nitric oxide production with an IC₅₀ value of 48.3 μM, comparable to that of the positive control indomethacin (IC₅₀, 42.3 μM).

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.

Metabolomics Analysis and Antioxidant Potential of Endophytic Diaporthe fraxini ED2 Grown in Different Culture Media

Endophytic fungi are a promising source of bioactive metabolites with a wide range of pharmacological activities. In the present study, MS-based metabolomics was conducted to study the metabolomes variations of endophytic Diaporthe fraxini ED2 grown in different culture media. Total phenolic content (TPC), total flavonoid content (TFC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, 2,2-azinobis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS), and ferric reducing antioxidant power (FRAP) assays were conducted to assess the antioxidant potential of the fungal extracts. Multivariate data analysis (MVDA) was employed in data analysis and interpretation to elucidate the complex metabolite profile. The supplemented culture medium of D. fraxini fungal extract stimulated the production of metabolites not occurring in the normal culture medium. Antioxidant activity studies revealed the potential of supplemented cultured fungal extract of D. fraxini as a source of antioxidants. The present findings highlight that fungal culture medium supplementation is an effective approach to unravelling the hidden metabolome in plant-associated fungal diversity.

Diversity, Antimicrobial Activity, and Antibiotic Susceptibility Pattern of Endophytic Bacteria Sourced From Cordia dichotoma L

Endophytic bacteria isolated from medicinal plants are crucial for the production of antimicrobial agents since they are capable of possessing bioactive compounds with diverse structures and activities. Cordia dichotoma, a plant of medicinal importance native to the Jammu region of India, was selected for the isolation and characterization of culturable endophytic bacteria and evaluation of their antimicrobial activities. Standardized surface sterilization methods were employed to isolate thirty-three phenotypically distinguishable endophytic bacteria from the root, stem, and leaf parts of the plant. Shannon Wiener diversity index clearly divulged diverse endophytes in roots (0.85), stem (0.61), and leaf (0.54) tissues. Physio-biochemical features of the isolates differentiated the distinct variations in their carbohydrate utilization profile and NaCl tolerance. The endophytes produced an array of enzymes, namely, catalase, oxidase, amylase, cellulase, nitrate reductase, and lipase. The bacterial isolates belong to the genera Bacillus, Pseudomonas, Paenibacillus, Acidomonas, Streptococcus, Ralstonia, Micrococcus, Staphylococcus, and Alcalignes predominantly. However, the antibiotic susceptibility pattern indicated that the isolates were mostly sensitive to erythromycin and streptomycin, while they were resistant to rifampicin, amoxicillin, and bacitracin. Interestingly, majority of the bacterial endophytes of C. dichotoma showed antimicrobial activity against Bacillus subtilis followed by Klebsiella pneumoniae. The 16S rRNA sequence of Bacillus thuringiensis has been deposited in the NCBI GenBank database under accession number OM320575. The major compounds of the crude extract derived from endophytic B. thuringiensis OM320575, according to the metabolic profile examination by GC-MS, are dibutyl phthalate, eicosane, tetrapentacontane, heneicosane, and hexadecane, which possessed antibacterial activities. In conclusion, results indicated the potential of C. dichotoma to host a plethora of bacterial endophytes that produce therapeutic bioactive metabolites.

Bioactive terpenoids derived from plant endophytic fungi: An updated review (2011-2020)

Plant endophytes have been considered as novel sources of naturally occurring compounds with various biological activities, including cytotoxic, antimicrobial, anti-inflammatory, anticancer, herbicides, antileishmanial and antioxidant. A variety of specialised products, comprising terpenoids, alkaloids, polyketides, phenolic compounds, coumarins, and quinone derivatives have been reported from various strains. An increasing number of products, especially terpenoids, are being isolated from endophytes. Herein, the isolated new terpenoids from plant endophytic fungi, their hosts, as well as biological activities, from January 2011 until the end of 2020 are reviewed. In this period, 516 terpenoids are classified into monoterpenes (5), sesquiterpenes (299), diterpenes (76), sesterterpens (22), meroterpenes (83), triterpenes (29), and other terpenoids (2), were isolated from different plant endophytic fungi species.

Diversity and antimicrobial potential of the culturable rhizobacteria from medicinal plant Baccharis trimera Less D.C

Plant microbiota is usually enriched with bacteria producers of secondary metabolites and represents a valuable source of novel species and compounds. Here, we analyzed the diversity of culturable root-associated bacteria of the medicinal native plant Baccharis trimera (Carqueja) and screened promising isolates for their antimicrobial properties. The rhizobacteria were isolated from the endosphere and rhizosphere of B. trimera from Ponta Grossa and Ortigueira localities and identified by sequencing and restriction analysis of the 16S rDNA. The most promising isolates were screened for antifungal activities and the production of siderophores and biosurfactants. B. trimera presented a diverse community of rhizobacteria, constituted of 26 families and 41 genera, with a predominance of Streptomyces and Bacillus genera, followed by Paenibacillus, Staphylococcus, Methylobacterium, Rhizobium, Tardiphaga, Paraburkholderia, Burkholderia, and Pseudomonas. The more abundant genera were represented by different species, showing a high diversity of the microbiota associated to B. trimera. Some of these isolates potentially represent novel species and deserve further examination. The communities were influenced by both the edaphic properties of the sampling locations and the plant niches. Approximately one-third of the rhizobacteria exhibited antifungal activity against Sclerotinia sclerotiorum and Colletotrichum gloeosporioides, and a high proportion of isolates produced siderophores (25%) and biosurfactants (42%). The most promising isolates were members of the Streptomyces genus. The survey of B. trimera returned a diverse community of culturable rhizobacteria and identified potential candidates for the development of plant growth-promoting and protection products, reinforcing the need for more comprehensive investigations of the microbiota of Brazilian native plants and habitats.

Prospecting potential of endophytes for modulation of biosynthesis of therapeutic bioactive secondary metabolites and plant growth promotion of medicinal and aromatic plants

Medicinal and aromatic plants possess pharmacological properties (antidiabetes, anticancer, antihypertension, anticardiovascular, antileprosy, etc.) because of their potential to synthesize a wide range of therapeutic bioactive secondary metabolites. The concentration of bioactive secondry metabolites depends on plant species, local environment, soil type and internal microbiome. The internal microbiome of medicinal plants plays the crucial role in the production of bioactive secondary metabolites, namely alkaloids, steroids, terpenoids, peptides, polyketones, flavonoids, quinols and phenols. In this review, the host specific secondry metabolites produced by endophytes, their therapeutic properties and host-endophytes interaction in relation to production of bioactive secondry metaboloites and the role of endophytes in enhancing the production of bioactive secondry metabolites is discussed. How biological nitrogen fixation, phosphorus solubilization, micronutrient uptake, phytohormone production, disease suppression, etc. can play a vital role in enhacing the plant growth and development.The role of endophytes in enhancing the plant growth and content of bioactive secondary metabolites in medicinal and aromatic plants in a sustainable mode is highlighted.

Total synthesis and stereochemical assignment of bipolamide A acetate

Asymmetric total synthesis of an acetate analogue of the endophytic unstable secondary metabolite bipolamide A has been achieved for the first time adopting a convergent approach. The key feature of this synthesis includes Evans's asymmetric ethylation, Wittig olefination, Takai olefination, stereoselective Grignard addition and intermolecular Heck coupling. This eventually developed a synthetic route of the rarely found branched amine bearing an acyloin moiety. Our synthesis finally established unambiguously the stereochemistry of the unassigned C-8 center of the naturally occurring unstable bipolamide A.

Biocontrol potential of endophytic Trichoderma citrinoviride HT-1 against root rot of Rheum palmatum through both antagonistic effects and induced systemic resistance

Some Trichoderma species have been used as biocontrol agents in agriculture. The effectiveness of T. citrinoviride HT-1, a beneficial endophyte isolated from Rheum palmatum root was explored for control of root rot and its mechanisms of induced systemic resistance. The results showed that the inhibition rate of F. oxysporum was 71.85% in dual culture. The fermentation metabolites (FM) of the T. citrinoviride HT-1 strain suppressed mycelial growth of F. oxysporum, recording an inhibition rate of 79.07%. Conidial suspensions of T. citrinoviride HT-1(1 × 10⁷ spores/mL) can suppress the root rot of R. palmatum caused by F. oxysporum to a low disease index (17.60) and had significant control effects on root rot (72.53%). The activities of induced defense-related enzymes in R. palmatum plants were significantly increased following T. citrinoviride HT-1 treatment. The RT-PCR analysis of the defense-related genes showed that T. citrinoviride HT-1 can increase the defense response-related gene expression. This study has contributed to our understanding of the biocontrol potential of T. citrinoviride HT-1 and provided a theoretical basis for the application as a bio-fungicide.

Aspen Leaves as a "Chemical Landscape" for Fungal Endophyte Diversity-Effects of Nitrogen Addition

Abiotic and biotic factors may shape the mycobiome communities in plants directly but also indirectly by modifying the quality of host plants as a substrate. We hypothesized that nitrogen fertilization (N) would determine the quality of aspen (Populus tremula) leaves as a substrate for the endophytic fungi, and that by subjecting the plants to N, we could manipulate the concentrations of positive (nutritious) and negative (antifungal) chemicals in leaves, thus changing the internal “chemical landscape” for the fungi. We expected that this would lead to changes in the fungal community composition, in line with the predictions of heterogeneity–diversity relationship and resource availability hypotheses. To test this, we conducted a greenhouse study where aspen plants were subjected to N treatment. The chemical status of the leaves was confirmed using GC/MS (114 metabolites, including amino acids and sugars), LC/MS (11 phenolics), and UV-spectrometry (antifungal condensed tannins, CTs), and the endophytic communities were characterized using culture-dependent sequencing. We found that N treatment reduced foliar concentrations of CT precursor catechin but not that of CTs. Nitrogen treatment also increased the concentrations of the amino acids and reduced the concentration of some sugars. We introduced beetle herbivores (H) as a second treatment but found no rapid changes in chemical traits nor strong effect on the diversity of endophytes induced by herbivores. A few rare fungi were associated with and potentially vectored by the beetle herbivores. Our findings indicate that in a controlled environment, the externally induced changes did not strongly alter endophyte diversity in aspen leaves.

Fungal-derived compounds and mycogenic nanoparticles with antimycobacterial activity: a review

Tuberculosis (TB) is a persistent lung infection caused by Mycobacterium tuberculosis. The disease is characterized by high mortality rates of over 1 million per year. Unfortunately, the potency and effectiveness of currently used anti-TB drugs is gradually decreasing due to the constant development of persistence and resistance by M. tuberculosis. The adverse side effects associated with current anti-TB drugs, along with anti-TB drug resistance, present an opportunity to bio-prospect novel potent anti-TB drugs from unique sources. Fundamentally, fungi are a rich source of bioactive secondary metabolites with valuable therapeutic potential. Enhancing the potency and effectiveness of fungal-based anti-TB drug leads by chemical synthesis and/or modification with nanomaterials, may result in the discovery of novel anti-TB drugs. In this review, the antimycobacterial activity of fungal-derived compounds and mycogenic nanoparticles are summarized. Numerous fungal-derived compounds as well as some mycogenic nanoparticles that exhibit strong antimycobacterial activity that is comparable to that of approved drugs, were found. If fully explored, fungi holds the promise to become key drivers in the generation of lead compounds in TB-drug discovery initiatives.

Antifungal Activity of Endophytic Aspergillus terreus Extract Against Some Fungi Causing Mucormycosis: Ultrastructural Study

Endophytes fungi are applied as favorable safe antifungal agents as well as natural bioactive compounds reservoir. In the current study, the inhibitory effect of endophytic fungus was explained by direct antifungal activity against fungi causing mucormycosis, ultrastructural, and determination of active compounds in fungal extract. Endophytic Aspergillus terreus was isolated from healthy Moringa oleifera leaves and identified morphologically and genetically, and was recorded in gene bank with accession number MW444551.1. Phytochemical analysis and gas chromatography-mass spectroscopy (GC–MS) of ethyl acetate crude extract (EACE) of A. terreus were performed. GC–MS results of EACE of A. terreus revealed that fungal extract contains 16 major bioactive compounds with extensive pharmaceutical activities. Furthermore, EACE of A. terreus revealed a promising antifungal activity against fungi causing mucormycosis as Rhizopus oryzae, Mucor racemosus, and Syncephalastrum racemosum, where inhibition zones of EACE (10 mg/ml) were 20, 37, and 18 mm, respectively. Minimum inhibitory concentration (MIC) of EACE was 0.3125 toward M. racemosus, while 1.25 and 2.5 mg/ml against R. oryzae and S. racemosum, respectively. In the same context, treated R. oryzae, M. racemosus, and S. racemosum with EACE of A. terreus revealed elevation of membrane lipid peroxidation which approves membrane leakage. Furthermore, ultrastructure changes were observed which established alteration in both sporangium and hyphal structures; cell membrane and cytoplasm leakage. In conclusion, endophytic A. terreus has an outstanding antifungal activity against fungi causing mucormycosis.

Metabolomic Insights Into Endophyte-Derived Bioactive Compounds

Among the various plant-associated microbiota, endophytes (the microbial communities inhabiting plant endosphere without causing disease symptoms) exhibit the most intimate and specific association with host plants. Endophytic microbes influence various aspects of plant responses (such as increasing availability of nutrients, tolerance against biotic and abiotic stresses, etc.) by modulating the primary and secondary metabolism of the host. Besides, endophytic microbes produce a diverse array of bioactive compounds, which have potential applications in the pharmaceutical, food, and cosmetic industries. Further, there is sufficient evidence for endophyte-derived plant metabolites, which could be pursued as alternative sources of commercially important plant metabolites. The field of bioprospecting, the discovery of novel chemistries, and endophyte-mediated production of plant metabolites have witnessed a boom with the advent of omics technologies (especially metabolomics) in endophyte research. The high throughput study of small metabolites at a particular timepoint or tissue forms the core of metabolomics. Being downstream to transcriptome and proteome, the metabolome provides the most direct reflection of the phenotype of an organism. The contribution of plant and microbial metabolomics for answering fundamental questions of plant-endophyte interaction, such as the effect of endophyte inoculation on plant metabolome, composition of metabolites on the impact of environmental stressors (biotic and abiotic), etc., have also been discussed.

Plant Growth Promotion and Biocontrol by Endophytic and Rhizospheric Microorganisms From the Tropics: A Review and Perspectives

Currently, the tropics harbor a wide variety of crops to feed the global population. Rapid population expansion and the consequent major demand for food and agriculture-based products generate initiatives for tropical forest deforestation, which contributes to land degradation and the loss of macro and micronative biodiversity of ecosystems. Likewise, the entire dependence on fertilizers and pesticides also contributes to negative impacts on environmental and human health. To guarantee current and future food safety, as well as natural resource preservation, systems for sustainable crops in the tropics have attracted substantial attention worldwide. Therefore, the use of beneficial plant-associated microorganisms is a promising sustainable way to solve issues concerning modern agriculture and the environment. Efficient strains of bacteria and fungi are a rich source of natural products that might improve crop yield in numerous biological ways, such as nitrogen fixation, hormone production, mobilization of insoluble nutrients, and mechanisms related to plant biotic and abiotic stress alleviation. Additionally, these microorganisms also exhibit great potential for the biocontrol of phytopathogens and pest insects. This review addresses research regarding endophytic and rhizospheric microorganisms associated with tropical plants as a sustainable alternative to control diseases and enhance food production to minimize ecological damage in tropical ecosystems.

Bioprospecting of fungal endophytes from Oroxylum indicum (L.) Kurz with antioxidant and cytotoxic activity

Oroxylum indicum (L.) Kurz, a medicinal plant, shows numerous pharmacological properties which may be attributed to the bioactive compounds produced by O. indicum or due to associated endophytes. In the present study, leaf of O. indicum was evaluated for the presence of associated fungal endophytes, and antioxidant and cytotoxic activities of bioactive compounds produced from them. Using culture-dependent approach, eight fungal endophytes belonging to five different genera were identified. Two endophytes Daldinia eschscholtzii and Ectophoma multirostrata have been reported for the first time from the leaf of O. indicum plant. High-performance thin-layer chromatography (HPTLC) of ethyl acetate (EA) extract of isolated fungal endophytes showed a distinct fingerprinting profile in EA extract of Colletotrichum gloeosporioides. Among identified endophytes, EA extract of C. gloeosporioides showed significant antioxidant activity against DPPH free radical, superoxide anion radical, nitric oxide radical and hydroxyl radical with EC50 values of 22.24±1.302 μg/mL, 67.46±0.576 μg/mL, 80.10±0.706 μg/mL and 61.55±1.360 μg/mL, respectively. EA extract of C. gloeosporioides exhibited potential cytotoxicity against HCT116, HeLa and HepG2 cancer cell lines with IC50 values of 76.59 μg/mL, 176.20 μg/mL and 1750.70 μg/mL, respectively. A comparative HPTLC fingerprinting and the antioxidant activity of C. gloeosporioides associated with two different hosts (leaf of O. indicum and dead twigs of other plant) showed that C. gloeosporioides produces bioactive compounds in a host-dependent manner.

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.

Predicting global numbers of teleomorphic ascomycetes

Sexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of fungi. The global diversity of teleomorphic species in Ascomycota has not been estimated. This paper estimates the species number for sexual ascomycetes based on five different estimation approaches, viz. by numbers of described fungi, by fungus:substrate ratio, by ecological distribution, by meta-DNA barcoding or culture-independent studies and by previous estimates of species in Ascomycota. The assumptions were made with the currently most accepted, “2.2–3.8 million” species estimate and results of previous studies concluding that 90% of the described ascomycetes reproduce sexually. The Catalogue of Life, Species Fungorum and published research were used for data procurement. The average value of teleomorphic species in Ascomycota from all methods is 1.86 million, ranging from 1.37 to 2.56 million. However, only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data repositories. The ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:22. Therefore, where are the undiscovered teleomorphic ascomycetes? The undescribed species are no doubt to be found in biodiversity hot spots, poorly-studied areas and species complexes. Other poorly studied niches include extremophiles, lichenicolous fungi, human pathogens, marine fungi, and fungicolous fungi. Undescribed species are present in unexamined collections in specimen repositories or incompletely described earlier species. Nomenclatural issues, such as the use of separate names for teleomorph and anamorphs, synonyms, conspecific names, illegitimate and invalid names also affect the number of described species. Interspecies introgression results in new species, while species numbers are reduced by extinctions.

Endophytic Fungal Terpenoids: Natural Role and Bioactivities

Endophytic fungi are a highly diverse group of fungi that intermittently colonize all plants without causing symptoms of the disease. They sense and respond to physiological and environmental changes of their host plant and microbiome. The inter-organism interactions are largely driven by chemical networks mediated by specialized metabolites. The balance of these complex interactions leads to healthy and strong host plants. Endophytic strains have particular machinery to produce a plethora of secondary metabolites with a variety of bioactivities and unknown functions in an ecological niche. Terpenoids play a key role in endophytism and represent an important source of bioactive molecules for human health and agriculture. In this review, we describe the role of endophytic fungi in plant health, fungal terpenoids in multiple interactions, and bioactive fungal terpenoids recently reported from endophytes, mainly from plants used in traditional medicine, as well as from algae and mangroves. Additionally, we highlight endophytic fungi as producers of important chemotherapeutic terpenoids, initially discovered in plants. Despite advances in understanding endophytism, we still have much to learn in this field. The study of the role, the evolution of interactions of endophytic fungi and their terpenoids provide an opportunity for better applications in human health and agriculture.

Comoclathrin, a novel potent skin-whitening agent produced by endophytic Comoclathris strains associated with Andalusia desert plants

As part of our screening program for the discovery of molecules of microbial origin with skin-whitening activity, 142 diverse fungal endophytes from a wide variety of Andalusia arid plants were screened, applying the OSMAC approach. The fungal strains CF-090361 and CF-090766, isolated from xerophytic plants, were selected as the most promising, while phylogenetic analysis revealed that both strains could represent a new species within the genus Comoclathris. The effect of different fermentation conditions on the production of tyrosinase inhibitory activity was examined, in order to identify the optimum cultivation conditions. LCMS based metabolomics was applied to determine significant differences between the strains and fermentation conditions, and to identify potential bioactive secondary metabolites. Bioassay-guided purification of the main active components led to the isolation of three new compounds (1-3), along with the known compounds graphostrin B (4) and brevianamide M (5). Compound 1 (Comoclathrin) demonstrated the strongest anti-tyrosinase activity (IC50 0.16 μΜ), which was 90-times higher than kojic acid (IC50 14.07 μΜ) used as positive control. Additionally, comoclathrin showed no significant cytotoxicity against a panel of cancer cell lines (HepG2, A2058, A549, MCF-7 and MIA PaCa-2) and normal BJ fibroblasts. These properties render comoclathrin an excellent development candidate as whitening agent.

Fungal Endophytes of Vitis vinifera-Plant Growth Promoters or Potentially Toxinogenic Agents?

Fungal endophytes occurring in grapevine (Vitis vinifera L.) are usually important sources of various compounds with biological activities with great potential for use in agriculture. Nevertheless, many species isolated from this plant belong to the genera Fusarium, Alternaria, or Aspergillus, all of which are well-known to produce mycotoxins. Our study is focused on the assessment of the toxinogenic potential of fungal endophytes isolated from vineyards in the Czech Republic. In total, 20 endophytic fungal species were cultivated in wine must, and 57 mycotoxins of different classes were analysed by liquid chromatography coupled with mass spectrometry. As a result, alternariol, tentoxin, meleagrin, roquefortine C, gliotoxin, and verruculogen were detected in the culture medium, of which verruculogen followed by gliotoxin were the most frequent (present in 90 and 40% of samples, respectively) and most concentrated (up to thousands ng/mL). The alternaria mycotoxins alternariol and tentoxin were detected not only in Alternaria sp. cultures, but traces of these mycotoxins were also quantified in the Diatripe and Epicoccum cultures. Meleagrin and roquefortine C were detected in Didymella sancta and Penicillium crustosum, gliotoxin was detected in Alternaria sp., Didymella sp., Aureobasidium pullulans, Cladosporium herbarum, Penicillium crustosum and Pleurophoma ossicola, and verruculogen was quantified in 99% of endophytic isolates investigated. The potential of endophytes to produce mycotoxins should be carefully checked, specifically in cases where they are intended for the purpose of V. vinifera growing.

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.

Discovering the Next-Generation Plant Protection Products: A Proof-of-Concept via the Isolation and Bioactivity Assessment of the Olive Tree Endophyte Bacillus sp. PTA13 Lipopeptides

Endophytic microorganisms (EMs) have recently attracted interest for applications in plant protection, mainly due to their bioactive compound-producing capacity. Therefore, we underwent the task of isolating olive tree EMs and investigating their bioactivity against the devastating pathogen Colletotrichum acutatum. Several EMs were isolated; however, the Bacillus sp. PTA13 isolate exhibited the highest toxicity to the phytopathogen. Bacteria of the genus Bacillus exhibit superior bioactive metabolite-producing capacity, with the lipopeptides (LPs) of surfactin, iturin, and fengycin groups being the most studied. A total LP extract and several fractions were obtained, and their bioactivity was assessed against C. acutatum strains. LPs of the major surfactin, iturin, and fengycin groups and the minor gageotetrin and bacilotetrin groups were annotated. The results confirmed the bioactivity of the major LPs, with fengycins being the most fungitoxic. Interestingly, the minor LP fraction exhibited selective toxicity to the fungicide-resistant C. acutatum isolate, an observation that highlights the significance of our approach to comprehensively mine the total LP extract. This work represents a proof of concept of the exploitation of EMs in customized olive tree plant protection and aligns well with strategies that focus on the sustainability and safety of food production via the development of next-generation plant protection products.

Isolation of Taxol and Flavin-like fluorochrome from Endophytic Fungi of Mangifera indica

Scouting for novel and plant-derived biomolecules from endophytic microbial sources draws greater focus on the discovery of novel bioactive metabolites. With this rationale, we scouted the endophytic fungi for taxol, an anticancer diterpenoid and fluorescent biomolecules. In the present study, about 31 endophytic fungal isolates recovered from the Mangifera indica leaves were screened for taxol production in M1D medium. About five isolates were shortlisted based on the thin layer chromatographic analysis of the fungal extracts. Among them Colletotrichum sp. MIP-5 has been identified as a producer of fungal taxol based on UV, FTIR, TLC and HPLC analysis. The partially purified fungal taxol showed similar spectral and chromatographic features of commercially available paclitaxel. In addition to this, we also report the production of a fluorescent compound by Penicillium sp. MIP-3. The Flavin-like compound exhibited a bright greenish-yellow fluorescence with an emission maximum in the range of 505 – 545nm. GC-MS analysis showed the occurrence of Latia luciferin, primarily associated with the bioluminescence of freshwater limpet Latia neritoides. This is the first report of this compound from Penicillium sp. In addition, therapeutically active steroid (β-Sitosterol, Stigmasterol, Campesterol), quinones (Benzo[h]quinoline, 2,4-dimethyl-) and phloroglucinol (Aspidinol) derivatives were also identified from Penicillium sp. MIP-3 based on GC-MS analysis. These molecules could potentially be used in biological and pharmaceutical applications in future.

Influence of Endophytic Bacterium, Cellulosimicrobium sp. FRR2 on Plant Growth of Amaranthus campestris L. and Bacterial Survival at Adverse Environmental Conditions

The endophytic microorganisms are believed to be an important bio-resource for modern agriculture because of their beneficial effects on plant growth promotion, biocontrol, stress tolerance, and diseases resistance. This study was focused to know the beneficial effect of endophytic bacterium (FRR2) isolated from the roots of Ficus religiosa L. on Amaranthus campestris L. and their tolerance ability against salinity and heavy metals. The strain FRR2 was recognized as Cellulosimicrobium sp. by 16s rRNA sequencing and phylogenetic study. The bacterial isolate FRR2 showed salt (at 150 mM NaCl) and metal (at 150 µM CuSO4 and 100 µM ZnSO4) tolerance ability and significantly higher growth rate of Amaranthus campestris in a green leafy vegetable might be due to the nitrogen fixation, indole acetic acid production, amylase and protease activities. In addition, the endophyte FRR2 application slightly increased the antioxidants activity than their controls. The results of this study revealed that Cellulosimicrobium sp. strain FRR2 would be an effective endophyte to increase the growth of green leafy vegetables.

Protease Produced by Endophytic Fungi: A Systematic Review

The purpose of this systematic review was to identify the available literature of production, purification, and characterization of proteases by endophytic fungi. There are few complete studies that entirely exhibit the production, characterization, and purification of proteases from endophytic fungi. This study followed the PRISMA, and the search was conducted on five databases: PubMed, PMC, Science Direct, Scopus Articles, and Web of Science up until 18 May 2021, with no time or language restrictions. The methodology of the selected studies was evaluated using GRADE. Protease production, optimization, purification, and characterization were the main evaluated outcomes. Of the 5540 initially gathered studies, 15 met the inclusion criteria after a two-step selection process. Only two studies optimized the protease production using statistical design and two reported enzyme purification and characterization. The genus Penicillium and Aspergillus were the most cited among the eleven different genera of endophytic fungi evaluated in the selected articles. Six studies proved the ability of some endophytic fungi to produce fibrinolytic proteases, demonstrating that endophytic fungi can be exploited for the further production of agents used in thrombolytic therapy. However, further characterization and physicochemical studies are required to evaluate the real potential of endophytic fungi as sources of industrial enzymes.

Sanguibacter suaedae sp. nov., isolated from the root of Suaeda aralocaspica in north-west PR China

A bacterial strain, designated YZGR15^T, was isolated from the root of an annual halophyte Suaeda aralocaspica, collected from the southern edge of the Gurbantunggut desert, north-west PR China. Cells of the isolate were Gram-stain-positive, facultatively anaerobic, irregular rods. Growth occurred at 4-42 °C (optimum, 30-37 °C), at pH 6.0-9.0 (optimum, pH 7.0-7.5) and in the presence of 0-9 % (w/v) NaCl (optimum, 2-5 %). Phylogenetic analysis using 16S rRNA gene sequences indicated that strain YZGR15^T showed the highest sequence similarity to Sanguibacter keddieii (98.27 %), Sanguibacter antarcticus (98.20 %) and Sanguibacter inulinus (98.06 %). Results of genome analyses of strain YZGR15^T indicated that the genome size was 3.16 Mb, with a genomic DNA G+C content of 71.9 mol%. Average nucleotide identity and digital DNA-DNA hybridization values between strain YZGR15^Tand three type strains were in the range of 76.5-77.8 % and 20.0-22.2 %, respectively. Analysis of the cellular component of strain YZGR15^T revealed that the primary fatty acids were anteiso-C_15 : 0, C_16 : 0, C_14 : 0 and iso-C_16 : 0 and the polar lipids included diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and two unidentified glycolipids. The cell-wall characteristic amino acids were glutamic acid, alanine and an unknown amino acid. The whole-cell sugars for the strain were mannose, ribose, rhamnose, glucose and an unidentified sugar. The predominant respiratory quinone was MK-9(H₄). Based on the results of genomic, phylogenetic, phenotypic and chemotaxonomic analyses, strain YZGR15^T represents a novel species of the genus Sanguibacter, for which the name Sanguibacter suaedae sp. nov. is proposed. The type strain is YZGR15^T (=CGMCC 1.18691^T=KCTC 49659^T).

Optimization of L-asparaginase production from endophytic Fusarium proliferatum using OFAT and RSM and its cytotoxic evaluation

L-asparaginase from endophytic Fusarium proliferatum (isolate CCH, GenBank accession no. MK685139) isolated from the medicinal plant Cymbopogon citratus (Lemon grass), was optimized for its L-asparaginase production and its subsequent cytotoxicity towards Jurkat E6 cell line. The following factors were optimized; carbon source and concentration, nitrogen source and concentration, incubation period, temperature, pH and agitation rate. Optimization of L-asparaginase production was performed using One-Factor-At-A-Time (OFAT) and Response surface methodology (RSM) model. The cytotoxicity of the crude enzyme from isolate CCH was tested on leukemic Jurkat E6 cell line. The optimization exercise revealed that glucose concentration, nitrogen source, L-asparagine concentration and temperature influenced the L-asparaginase production of CCH. The optimum condition suggested using OFAT and RSM results were consistent. As such, the recommended conditions were 0.20% of glucose, 0.99% of L-asparagine and 5.34 days incubation at 30.50 °C. The L-asparaginase production of CCH increased from 16.75 ± 0.76 IU/mL to 22.42 ± 0.20 IU/mL after optimization. The cytotoxicity of the crude enzyme on leukemic Jurkat cell line recorded IC₅₀ value at 33.89 ± 2.63% v/v. To conclude, the enzyme extract produced from Fusarium proliferatum under optimized conditions is a potential alternative resource for L-asparaginase.

Combination of Pseudo-LC-NMR and HRMS/MS-Based Molecular Networking for the Rapid Identification of Antimicrobial Metabolites From Fusarium petroliphilum

An endophytic fungal strain isolated from a seagrass endemic to the Mediterranean Sea (Posidonia oceanica) was studied in order to identify its antimicrobial constituents and further characterize the composition of its metabolome. It was identified as Fusarium petroliphilum by in-depth phylogenetic analyses. The ethyl acetate extract of that strain exhibited antimicrobial activities and an ability to inhibit quorum sensing of Staphylococcus aureus. To perform this study with a few tens of mg of extract, an innovative one-step generic strategy was devised. On one side, the extract was analyzed by UHPLC-HRMS/MS molecular networking for dereplication. On the other side, semi-preparative HPLC using a similar gradient profile was used for a single-step high-resolution fractionation. All fractions were systematically profiled by ¹H-NMR. The data were assembled into a 2D contour map, which we call “pseudo-LC-NMR,” and combined with those of UHPLC-HRMS/MS. This further highlighted the connection within structurally related compounds, facilitated data interpretation, and provided an unbiased quantitative profiling of the main extract constituents. This innovative strategy led to an unambiguous characterization of all major specialized metabolites of that extract and to the localization of its bioactive compounds. Altogether, this approach identified 22 compounds, 13 of them being new natural products and six being inhibitors of the quorum sensing mechanism of S. aureus and Pseudomonas aeruginosa. Minor analogues were also identified by annotation propagation through the corresponding HRMS/MS molecular network, which enabled a consistent annotation of 27 additional metabolites. This approach was designed to be generic and applicable to natural extracts of the same polarity range.

Cytotoxicity, Antimicrobial, and In Silico Studies of Secondary Metabolites From Aspergillus sp. Isolated From Tecoma stans (L.) Juss. Ex Kunth Leaves

Endophytes are prolific producers of privileged secondary metabolites with diverse therapeutic potential, although their anticancer and antimicrobial potential still have a room for further investigation. Herein, seven known secondary metabolites namely, arugosin C (1), ergosterol (2), iso-emericellin (3), sterigmatocystin (4), dihydrosterigmatocystin (5), versicolorin B (6), and diorcinol (7) were isolated from the rice culture of Aspergillus sp. retrieved from Tecoma stans (L.) Juss. ex Kunth leaves. Their anticancer and antimicrobial activities were evaluated in MTT and agar well diffusion assays, respectively. The cytotoxicity results showed that metabolite 3 displayed the best viability inhibition on the MCF-7 breast cancer cells with IC₅₀ = 225.21 µM, while 5 on the HepG2 hepatocellular carcinoma cells with IC₅₀ = 161.81 µM. 5 demonstrated a 60% apoptotic mode of cell death which is virtually correlated to its high docking affinity to Hsp90 ATP binding cleft (binding score −8.4 Kcal/mol). On the other side, metabolites 4 and 5 displayed promising antimicrobial activity especially on Pseudomonas aeruginosa with MIC = 125 μg/ml. The observed effect may be likely related to their excellent in silico inhibition of the bacterial DNA-gyrase kinase domain (binding score −10.28 Kcal/mol). To the best of our knowledge, this study is the first to report the promising cytotoxic and antibacterial activities of metabolites 3, 4, and 5 which needs further investigation and renovation to therapeutic leads.

Secondary Metabolite Production and Terpenoid Biosynthesis in Endophytic Fungi Cladosporium cladosporioides Isolated from Wild Cymbopogon martinii (Roxb.) Wats

Endophytic fungi Cladosporium cladosporioides (F1-MH810309) and Cladosporium tenuissimum (F2-MN715834) from the leaf of wild Cymbopogon martinii (MT90507) were isolated and selected based on the persistent occurrence during different seasons of the year. They were identified based on the morphological features and molecular characterization (ITS sequence), and later deposited at NCBI. Phytochemical studies on F1, F2 and host extracts showed the presence of alkaloids, flavonoids, phenols, terpenoids and tannins. The GC-MS of F1 extract (control) under the axenic condition revealed compounds like hexadecane, heptadecane,2,4-Ditert-butylphenol, E-14 hexadecenal, geraniol, geranyl acetate and cubenol similar to the host. The GC-MS of F2 extract (control) revealed metabolites that were unique. Further, both F1 and F2 were cultured in the supplementation of different concentrations (5%, 10%, 15% and 20%) of the host plant extract (an-axenic condition). The GC-MS of F1 extracts (test) exhibited good growth and showed the gradual increased production of terpenoid compounds whereas the F2 (test) did not show any growth. These compounds such as hyrdoxymenthol, nor-borneol, cedralacetate, α-cyclogeraniol, campesterol, β-cyclogeraniol, linalool oxide,2,3-boranediol, citronellyltiglate and 2,3-pinanediol were produced in a minor quantity and were known as biotransformed forms of the precursor compounds present in the host extract. In comparison, only F1 was able to produce terpenoids similar to the host species both in axenic and an-axenic conditions. Hence from the current study, the endophytic fungus F1 isolated from wild C. martinii for the first time can serve as a better resource for the bioprospection of an important terpenoid and its metabolites.

Bioremediation of heavy metals from industrial effluents by endophytes and their metabolic activity: Recent advances

Worldwide, heavy metals pollution is mostly caused by rapid population growth and industrial development which is accumulated in food webs causing a serious public health risk. Endophytic microorganisms have a variety of mechanisms for metal sequestration having metal biosorption capacities.Endophytic organisms like bacteria and fungi provide beneficial qualities that help plants to improve their health, reduce stress, and detoxify metals. Endophytes have a higher proclivity for improving metal and mineral solubility by cells that secrete low-molecular-weight organic acids and metal-specific ligands like siderophores, which change the pH of the soil and improve binding activity. Protein-related approaches like chromatin immunoprecipitation sequencing (ChIP-Seq) and modified enzyme-linked immunosorbent assay (ELISA test) can represent endophytic bacterial community and DNA-protein interactions during metal reduction. This review explored the role of endophytes in bioremediation approaches that can help in analyzing the potential and prospects in response to industrial effluents' detoxification.

The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications

Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.

Diversity Profiling of Seed Associated Endophytic Microbiome in Important Species of Caricaceae Family

Background: Plant associated endophytic microbes play an important role in plant’s growth and development. After seed germination, the seed associated endophytes rapidly colonize the seedlings and help in their growth and protection against pathogens. This study was aimed to understand the diversity in the endophytic microbial population associated with the seeds of papaya (Carica papaya) and its wild relatives from Vasconcellea genus (family: Caricaceae). The species of Vasconcellea genus are widely used to introgress virus resistance in cultivated varieties of papaya. Hence, the diversity of seed associated endophytic microbes and their gene functional analysis was carried out through next generation sequencing of the microbial 16S rRNA and ITS sequences. Results: The 16S rRNA amplicon analysis revealed that the number of operational taxonomic units (OTUs) was higher for the endophytic bacteria, ranging between 144–204 when compared to 41–69 OTUs for the endophytic fungi. The bacterial phylum Proteobacteria was the most abundant seed associated phylum, with 64.7–72.8% abundance, across all four species of Caricaceae family, followed by Firmicutes (13.6–26.1%), Patescibacteria (1.1–2%) and Actinobacteria (0.7–2.7%). With respect to the diversity of bacteria by abundance indices, Vasconcellea goudotiana had the highest OTUs of 204, followed by 177 in V. cauliflora, 156 in V. cundinamarcensis, and 144 in C. papaya. The alpha diversity indices and functional analysis revealed the differences in the OTUs and the functional annotations among the above four plant species. The fungal OTUs were in the range of 41–69; however, only a small fraction of them could be taxonomically classified. Conclusion: Our microbiome studies reveal the differences in the seed associated endophytic microbial community across the four plant species of Caricaceae family. This study also unravels the composition of endophytic microbial population associated with the seeds of different plant species of Caricaceae family and their gene functions. It also provides an insight into both culturable and nonculturable endophytic microbes. Further this study reveals that domestication of Carica papaya might have resulted into reduced microbial diversity when compared to their wild relatives from Vasconcellea genus.

The plant endosphere-hidden treasures: a review of fungal endophytes

The endosphere represents intracellular regions within plant tissues colonize by microbial endophytes without causing disease symptoms to host plants. Plants harbor one or two endophytic microbes capable of synthesizing metabolite compounds. Environmental factors determine the plant growth and survival as well as the kind of microorganisms associated with them. Some fungal endophytes that symbiotically colonize the endosphere of medicinal plants with the potential of producing biological products have been employed in traditional and modern medicine. The bioactive resources from endophytic fungi are promising; biotechnologically to produce cheap and affordable commercial bioactive products as alternatives to chemical drugs and other compounds. The exploration of bioactive metabolites from fungal endophytes has been found applicable in agriculture, pharmaceutical, and industries. Thus, fungal endophytes can be engineered to produce a substantive quantity of pharmacological drugs through the biotransformation process. Hence, this review shall provide an overview of fungal endophytes, ecology, their bioactive compounds, and exploration with the biosystematics approach.

Model Application of Entomopathogenic Fungi as Alternatives to Chemical Pesticides: Prospects, Challenges, and Insights for Next-Generation Sustainable Agriculture

In the past few decades, the control of pests and diseases of cultivated plants using natural and biological measures has drawn increasing attention in the quest to reduce the level of dependence on chemical products for agricultural production. The use of living organisms, predators, parasitoids, and microorganisms, such as viruses, bacteria, and fungi, has proven to be a viable and sustainable pest management technique. Among the aforementioned, fungi, most importantly the insect-pathogenic species, have been in use for more than 150years. These include the most popular strains belonging to the genera Beauveria, Metarhizium, Isaria, Hirsutella, and Lecanicillium. Their application is usually through an inundative approach, which inherently involves exposure of the fungal spores to unfavorable humidity, temperature, and solar radiation conditions. These abiotic factors reduce the persistence and efficacy of these insect-pathogenic fungi. Despite these limitations, over 170 strains have been formulated as mycopesticides and are available for commercial use. In the last few decades, numerous studies have suggested that these species of entomopathogenic fungi (EPF) offer far more benefits and have broader ecological functions than hitherto presumed. For instance, aside from their roles as insect killers, it has been well established that they also colonize various host plants and, hence, provide other benefits including plant pathogen antagonism and plant growth promotion and serve as sources of novel bioactive compounds and secondary metabolites, etc. In this light, the potential of EPF as alternatives or perhaps as supplements to chemical pesticides in plant protection is discussed in this review. The paper highlights the numerous benefits associated with endophytic fungal entomopathogen and host plant associations, the mechanisms involved in mediating plant defense against pests and pathogens, and the general limitations to the use of EPF in plant protection. A deeper understanding of these plant host-fungus-insect relationships could help unveil the hidden potentials of fungal endophytes, which would consequently increase the level of acceptance and adoption by users as an integral part of pest management programs and as a suitable alternative to chemical inputs toward sustainable crop production.

Selection of Endophytic Beauveria bassiana as a Dual Biocontrol Agent of Tomato Pathogens and Pests

Endophytic fungi (EF) can enhance both plant growth and defense barriers against pests and pathogens, contributing to the reduction of chemical pesticides and fertilizers use in agriculture. Beauveria bassiana is an entomopathogenic fungus showing endophytism in several crops, often associated with a good capacity to limit the development of pests and disease agents. However, the diversity of the protective efficacy and plant response to different strains can be remarkable and needs to be carefully assessed for the successful and predictable use of these beneficial microorganisms. This study aims to select B. bassiana strains able to colonize tomato plants as endophytes as well as to control two important disease agents, Botrytis cinerea and Alternaria alternata, and the pest aphid, Macrosiphum euphorbiae. Nine wild-type isolates and one commercial strain were screened for endophytism, then further characterized for plant-growth promotion plus inhibition of disease development and pest infestation. Four isolates proved to have a good control activity against the biotic stressors tested, but only Bb716 was also able to promote plant growth. This work provides a simple workflow for the selection of beneficial EF, paving the way towards more effective use of B. bassiana in Integrate Pest Management (IPM) of tomato.

Plant associated fungal endophytes as a source of natural bioactive compounds

Endophytes are a potent source of bioactive compounds that mimic plant-based metabolites. The relationship of host plant and endophyte is significantly associated with alteration in fungal colonisation and the extraction of endophyte-derived bioactive compounds. Screening of fungal endophytes and their relationship with host plants is essential for the isolation of bioactive compounds. Numerous bioactive compounds with antioxidant, antimicrobial, anticancer, and immunomodulatory properties are known to be derived from fungal endophytes. Bioinformatics tools along with the latest techniques such as metabolomics, next-generation sequencing, and metagenomics multilocus sequence typing can potentially fill the gaps in fungal endophyte research. The current review article focuses on bioactive compounds derived from plant-associated fungal endophytes and their pharmacological importance. We conclude with the challenges and opportunities in the research area of fungal endophytes.

Fungal Endophytes: A Promising Frontier for Discovery of Novel Bioactive Compounds

For years, fungi have served as repositories of bioactive secondary metabolites that form the backbone of many existing drugs. With the global rise in infections associated with antimicrobial resistance, in addition to the growing burden of non-communicable disease, such as cancer, diabetes and cardiovascular ailments, the demand for new drugs that can provide an improved therapeutic outcome has become the utmost priority. The exploration of microbes from understudied and specialized niches is one of the promising ways of discovering promising lead molecules for drug discovery. In recent years, a special class of plant-associated fungi, namely, fungal endophytes, have emerged as an important source of bioactive compounds with unique chemistry and interesting biological activities. The present review focuses on endophytic fungi and their classification, rationale for selection and prioritization of host plants for fungal isolation and examples of strategies that have been adopted to induce the activation of cryptic biosynthetic gene clusters to enhance the biosynthetic potential of fungal endophytes.

Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.

Microbial Metabolites: The Emerging Hotspot of Antiviral Compounds as Potential Candidates to Avert Viral Pandemic Alike COVID-19

The present global COVID-19 pandemic caused by the noble pleomorphic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a vulnerable situation in the global healthcare and economy. In this pandemic situation, researchers all around the world are trying their level best to find suitable therapeutics from various sources to combat against the SARS-CoV-2. To date, numerous bioactive compounds from different sources have been tested to control many viral diseases. However, microbial metabolites are advantageous for drug development over metabolites from other sources. We herein retrieved and reviewed literatures from PubMed, Scopus and Google relevant to antiviral microbial metabolites by searching with the keywords "antiviral microbial metabolites," "microbial metabolite against virus," "microorganism with antiviral activity," "antiviral medicine from microbial metabolite," "antiviral bacterial metabolites," "antiviral fungal metabolites," "antiviral metabolites from microscopic algae' and so on. For the same purpose, the keywords "microbial metabolites against COVID-19 and SARS-CoV-2" and "plant metabolites against COVID-19 and SARS-CoV-2" were used. Only the full text literatures available in English and pertinent to the topic have been included and those which are not available as full text in English and pertinent to antiviral or anti-SARS-CoV-2 activity were excluded. In this review, we have accumulated microbial metabolites that can be used as antiviral agents against a broad range of viruses including SARS-CoV-2. Based on this concept, we have included 330 antiviral microbial metabolites so far available to date in the data bases and were previously isolated from fungi, bacteria and microalgae. The microbial source, chemical nature, targeted viruses, mechanism of actions and IC50/EC50 values of these metabolites are discussed although mechanisms of actions of many of them are not yet elucidated. Among these antiviral microbial metabolites, some compounds might be very potential against many other viruses including coronaviruses. However, these potential microbial metabolites need further research to be developed as effective antiviral drugs. This paper may provide the scientific community with the possible secret of microbial metabolites that could be an effective source of novel antiviral drugs to fight against many viruses including SARS-CoV-2 as well as the future viral pandemics.