The Emergence of Endophytic Microbes and Their Biological Promise

Harnessing Trichoderma spp.: A Promising Approach to Control Apple Scab Disease

Apple scab, caused by the pathogenic fungus Venturia inaequalis, can result in significant economic losses. The frequent use of fungicidal products has led to the emergence of isolates resistant to commonly used active substances. Therefore, biological control offers a sustainable alternative for managing apple scab. In this study, eight Trichoderma isolates were evaluated against five different isolates of V. inaequalis isolated from the Fes-Meknes region. The biocontrol potential of these Trichoderma isolates had previously been demonstrated against other pathogens. The results indicated that the inhibition rate of mycelial growth of V. inaequalis obtained with Trichoderma spp. isolates ranged from 50% to 81%, with significant differences observed among the pathogenic isolates after 5 and 12 days of incubation. In addition, the in vitro tests with Trichoderma cell-free filtrates showed inhibition rates ranging from 2% to 79%, while inhibition rates ranged from 5% to 78% for volatile compound tests. Interestingly, the inhibition of spore germination and elongation was approximately 40-50%, suggesting the involvement of antifungal metabolites in their biocontrol activities. The in vivo bioassay on detached apple leaves confirmed the biocontrol potential of these Trichoderma isolates and demonstrated their ability to preventively control apple scab disease. However, their efficacies were still lower than those of the fungicidal product difenoconazole. These findings could contribute to the development of an effective biofungicide based on these Trichoderma isolates for reliable and efficient apple scab control.

Impact of Irpex lenis and Schizophyllum commune endophytic fungi on Perilla frutescens: enhancing nutritional uptake, phytochemicals, and antioxidant potential

BACKGROUND

Endophytic fungi (EF) reside within plants without causing harm and provide benefits such as enhancing nutrients and producing bioactive compounds, which improve the medicinal properties of host plants. Selecting plants with established medicinal properties for studying EF is important, as it allows a deeper understanding of their influence. Therefore, the study aimed to investigate the impact of EF after inoculating the medicinal plant Perilla frutescens, specifically focusing on their role in enhancing medicinal properties.

RESULTS

In the current study, the impact of two EF i.e., Irpex lenis and Schizophyllum commune isolated from A. bracteosa was observed on plant Perilla frutescens leaves after inoculation. Plants were divided into four groups i.e., group A: the control group, group B: inoculated with I. lenis; group C: inoculated with S. commune and group D: inoculated with both the EF. Inoculation impact of I. lenis showed an increase in the concentration of chlorophyll a (5.32 mg/g), chlorophyll b (4.46 mg/g), total chlorophyll content (9.78 mg/g), protein (68.517 ± 0.77 mg/g), carbohydrates (137.886 ± 13.71 mg/g), and crude fiber (3.333 ± 0.37%). Furthermore, the plants inoculated with I. lenis showed the highest concentrations of P (14605 mg/kg), Mg (4964.320 mg/kg), Ca (27389.400 mg/kg), and Mn (86.883 mg/kg). The results of the phytochemical analysis also indicated an increased content of total flavonoids (2.347 mg/g), phenols (3.086 mg/g), tannins (3.902 mg/g), and alkaloids (1.037 mg/g) in the leaf extract of P. frutescens inoculated with I. lenis. Thus, overall the best results of inoculation were observed in Group B i.e. inoculated with I. lenis. GC-MS analysis of methanol leaf extract showed ten bioactive constituents, including 9-Octadecenoic acid (Z)-, methyl ester, and hexadecanoic acid, methyl ester as major constituents found in all the groups of P. frutescens leaves. The phenol (gallic acid) and flavonoids (rutin, kaempferol, and quercetin) were also observed to increase after inoculation by HPTLC analysis. The enhancement in the phytochemical content was co-related with improved anti-oxidant potential which was analyzed by DPPH (% Inhibition: 83.45 µg/ml) and FRAP (2.980 µM Fe (II) equivalent) assay as compared with the control group.

CONCLUSION

Inoculation with I. lenis significantly enhances the uptake of nutritional constituents, phytochemicals, and antioxidant properties in P. frutescens, suggesting its potential to boost the therapeutic properties of host plants.

Endophytic fungi: A future prospect for breast cancer therapeutics and drug development

Globally, breast cancer is a primary contributor to cancer-related fatalities and illnesses among women. Consequently, there is a pressing need for safe and effective treatments for breast cancer. Bioactive compounds from endophytic fungi that live in symbiosis with medicinal plants have garnered significant interest in pharmaceutical research due to their extensive chemical composition and prospective medicinal attributes. This review underscores the potentiality of fungal endophytes as a promising resource for the development of innovative anticancer agents specifically tailored for breast cancer therapy. The diversity of endophytic fungi residing in medicinal plants, success stories of key endophytic bioactive metabolites tested against breast cancer and the current progress with regards to in vivo studies and clinical trials on endophytic fungal metabolites in breast cancer research forms the underlying theme of this article. A thorough compilation of putative anticancer compounds sourced from endophytic fungi that have demonstrated therapeutic potential against breast cancer, spanning the period from 1990 to 2022, has been presented. This review article also outlines the latest trends in endophyte-based drug discovery, including the use of artificial intelligence, machine learning, multi-omics approaches, and high-throughput strategies. The challenges and future prospects associated with fungal endophytes as substitutive sources for developing anticancer drugs targeting breast cancer are also being highlighted.

Xylatolides A and B, new 10-membered macrolides from the endophytic fungus Xylaria sp

Chemical investigation of the fungal endophyte Xylaria sp. isolated from leaves of Moringa oleifera, collected in Cameroon, resulted in the previously undescribed 10-membered macrolide, and two known natural products. The structures of the xylatolides A and B were unambiguously identified by their mass spectra and by extensive 1D and 2D NMR spectroscopic analysis, featuring a 10-membered lactone core structure with oxygenated substituents and an unsubstituted 10-alkyl chain presenting seven carbon atoms. Compounds were screened for their cytotoxic potential against the human HepG2 hepatocellular carcinoma cells and HCT-116 cells (human colon carcinoma cell line). Moreover, the isolated compounds were also assayed against a small panel of sensitive strains including the bacterial species Escherichia coli, Staphylococcus aureus, and Mycobacterium tuberculosis as well as against the fungal species Candida albicans. However, no significant activities were found.

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.

Molecular authentication, metabolite profiling and in silico-in vitro cytotoxicity screening of endophytic Penicillium ramusculum from Withania somnifera for breast cancer therapeutics

In the present study, we isolated a potent endophytic fungus from the roots of Withania somnifera. The endophytic fungal strain was authenticated as Penicillium ramusculum SVWS3 based on morphological and molecular sequencing using four gene data and phylogenetic analyses. In vitro cytotoxicity studies unveiled the remarkable cytotoxic potential of the crude extract derived from P. ramusculum, exhibiting dose-dependent effects on MDA-MB-468 and MCF-7 cells. At a concentration of 100 µg/mL, the crude extract resulted in cell viability of 29.78% for MDA-MB-468 cells and 14.61% for MCF-7 cells. The IC50 values were calculated as 62.83 ± 0.93 µg/mL and 17.23 ± 1.43 µg/mL, respectively for MDA-MB-468 and MCF-7 cells. Caspase activation assay established the underlying mechanism of the crude extract depicting the activation of caspases 3 and 7, indicating the induction of apoptosis in MCF-7 cells. Chemotaxonomic profiling elucidated the ability of P. ramusculum to synthesize a diverse array of bioactive compounds, including Fasoracetam, Tryprostatin B, Odorinol, Thyronine, Brevianamide F, Proglumide, Perlolyrine, Tyrphostin B48, Baptifoline, etc. Molecular docking studies inferred that Baptifoline, Brevianamide F, Odorinol, Perlolyrine, Thyronine, Tryphostin B48, and Tryprostatin B were the lead compounds that could effectively interact with the five selected target receptors of breast cancer, further surpassing the positive controls analyzed. Pharmacokinetic profiling revealed that Baptifoline, Odorinol, and Thyronine depicted an excellent therapeutic profile of druggability. These findings collectively substantiate the anticancer activity of bioactive metabolites synthesized by P. ramusculum SVWS3. Hence, the endophytic P. ramusculum SVWS3 can be an authentic source for developing novel chemotherapeutic drug formulations.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03906-3.

Isolation and Identification of Pigment-Producing Endophytic Fungi from the Amazonian Species Fridericia chica

Pigments of fungal origin have aroused increasing interest in the food dye and cosmetic industries since the global demand for natural dyes has grown. Endophytic microorganisms are a source of bioactive compounds, and Amazonian plant species can harbor fungi with a wide range of biotechnological applications. Popularly known in Brazil as crajiru, Fridericia chica is a medicinal plant that produces a red pigment. In this study, a total of 121 fungi were isolated in potato dextrose agar from three plants. We identified nine pigment-producing endophytic fungi isolated from branches and leaves of F. chica. The isolates that showed pigment production in solid media were molecularly identified via multilocus analysis as Aspergillus welwitschiae, A. sydowii, Curvularia sp., Diaporthe cerradensis (two strains), Hypoxylon investiens, Neoscytalidium sp. (two strains) and Penicillium rubens. These isolates were subjected to submerged fermentation in two culture media to obtain metabolic extracts. The extracts obtained were analyzed in terms of their absorbance between 400 and 700 nm. The pigmented extract produced by H. investiens in medium containing yeast extract showed maximum absorbance in the red absorption range (UA700 = 0.550) and significant antioxidant and antimicrobial activity. This isolate can thus be considered a new source of extracellular pigment.

In Planta Detection of Beauveria bassiana (Ascomycota: Hypocreales) Strains as Endophytes in Bean (Phaseolus vulgaris L.)

Beauveria bassiana (B. bassiana) is a significant entomopathogenic fungus (EPF) in agriculture as a sprayable biocontrol agent. It has the potential to be established as an endophyte (ENP) in various crops, resulting in beneficial effects for the host plants, including resistance to pest insects and increased growth and yield. However, it is not known whether a B. bassiana strain has such a favorable impact on the plant, since it is a common soil microorganism. Therefore, techniques that allow strain monitoring will be advantageous. To date, methods for detecting or monitoring a specific EPF strain after external application are scarce. In the present study, an in planta nested PCR technique was standardized to differentiate between three B. bassiana strains (GHA, PTG4, and BB37) established as endophytes in bean plants under laboratory conditions by detecting the insertion profile of four group I introns located in the 28S gene of B. bassiana ribosomal DNA. This technique recognized a distinct pattern of bands of different sizes for each strain, with a sensitivity of 1 pg per 10 ng of plant DNA. This molecular approach may be more effective monitoring B. bassiana strains after application to evaluate their significance on crops.

Fungus-based bioherbicides on circular economy

This review aimed to show that bioherbicides are possible in organic agriculture as natural compounds from fungi and metabolites produced by them. It is discussed that new formulations must be developed to improve field stability and enable the commercialization of microbial herbicides. Due to these bottlenecks, it is crucial to advance the bioprocesses behind the formulation and fermentation of bio-based herbicides, scaling up, strategies for field application, and the potential of bioherbicides in the global market. In this sense, it proposed insights for modern agriculture based on sustainable development and circular economy, precisely the formulation, scale-up, and field application of microbial bioherbicides.

Endophytic bacteria Klebsiella spp. and Bacillus spp. from Alternanthera philoxeroides in Madiwala Lake exhibit additive plant growth-promoting and biocontrol activities

BACKGROUND

The worldwide increase in human population and environmental damage has put immense pressure on the overall global crop production making it inadequate to feed the entire population. Therefore, the need for sustainable and environment-friendly practices to enhance agricultural productivity is a pressing priority. Endophytic bacteria with plant growth-promoting ability and biocontrol activity can strongly enhance plant growth under changing environmental biotic and abiotic conditions. Herein, we isolated halotolerant endophytic bacteria from an aquatic plant, Alternanthera philoxeroides, from the polluted waters of Madiwala Lake in Bangalore and studied their plant growth promotion (PGP) and biocontrol ability for use as bioinoculant.

RESULTS

The isolated bacterial endophytes were screened for salt tolerance ranging from 5 to 15% NaCl concentration. Klebsiella pneumoniae showed halotolerant up to 10% NaCl and Bacillus amyloliquefaciens and Bacillus subtilis showed up to 15%. All three strains demonstrated good PGP abilities such as aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, phosphate solubilization, ammonia production, and nitrogen fixation. In addition, K. pneumoniae also exhibited high indoleacetic acid (IAA) production (195.66 ± 2.51 µg/ml) and potassium solubilization (2.13 ± 0.07 ppm). B. amyloliquefaciens and B. subtilis showed good extracellular enzyme production against cellulase, lipase, protease, and amylase. Both the isolates showed a broad spectrum of antimicrobial activity against the tested organisms. The optimization of IAA production by K. pneumoniae was done by the response surface methodology (RSM) tool. Characterization of IAA produced by the isolate was done by gas chromatography-mass spectrometry (GCMS) analysis. The enhanced plant growth-promoting ability of K. pneumoniae was also demonstrated using various growth parameters in a pot trial experiment using the seeds of Vigna unguiculata.

CONCLUSION

The isolated bacterial endophytes reported in this study can be utilized as PGP promotion and biocontrol agents in agricultural applications, to enhance crop yield under salinity stress. The isolate K. pneumoniae may be used as a biofertilizer in sustainable agriculture and more work can be done to optimize the best formulations for its application as a microbial inoculant for crops.

A novel endophytic fungus strain of Cladosporium: its identification, genomic analysis, and effects on plant growth

INTRODUCTION

Endophytic microorganisms are bacteria or fungi that inhabit plant internal tissues contributing to various biological processes of plants. Some endophytic microbes can promote plant growth, which are known as plant growth-promoting endophytes (PGPEs). There has been an increasing interest in isolation and identification of PGPEs for sustainable production of crops. This study was undertaken to isolate PGPEs from roots of a halophytic species Sesuvium portulacastrum L. and elucidate potential mechanisms underlying the plant growth promoting effect.

METHODS

Surface-disinfected seeds of S. portulacastrum were germinated on an in vitro culture medium, and roots of some germinated seedlings were contaminated by bacteria and fungi. From the contamination, an endophytic fungus called BF-F (a fungal strain isolated from bacterial and fungal contamination) was isolated and identified. The genome of BF-F strain was sequenced, its genome structure and function were analyzed using various bioinformatics software. Additionally, the effect of BF-F on plant growth promotion were investigated by gene cluster analyses.

RESULTS

Based on the sequence homology (99%) and phylogenetic analysis, BF-F is likely a new Cladosporium angulosum strain or possibly a new Cladosporium species that is most homologous to C. angulosum. The BF-F significantly promoted the growth of dicot S. portulacastrum and Arabidopsis as well as monocot rice. Whole genome analysis revealed that the BF-F genome has 29,444,740 bp in size with 6,426 annotated genes, including gene clusters associated with the tryptophan synthesis and metabolism pathway, sterol synthesis pathway, and nitrogen metabolism pathway. BF-F produced indole-3-acetic acid (IAA) and also induced the expression of plant N uptake related genes.

DISCUSSION

Our results suggest that BF-F is a novel strain of Cladosporium and has potential to be a microbial fertilizer for sustainable production of crop plants. The resulting genomic information will facilitate further investigation of its genetic evolution and its function, particularly mechanisms underlying plant growth promotion.

Evaluation of drought-tolerant endophytic fungus Talaromyces purpureogenus as a bioinoculant for wheat seedlings under normal and drought-stressed circumstances

The present work is aimed to hypothesize that fungal endophytes associated with wheat (Triticum aestivum L.) plants can play a variety of roles in biotechnology including plant growth. Out of 67 fungal isolates, five maximum drought-tolerant isolates were used to check their various plant growth-promoting traits, antioxidants, and antifungal activities under secondary screening. Fungal isolate #8TAKS-3a exhibited the maximum drought tolerance capacity and potential to produce auxin, gibberellic acid, ACC deaminase, phosphate, zinc solubilization, ammonia, siderophore, and extracellular enzyme activities followed by #6TAKR-1a isolate. In terms of antioxidant activities, #8TAKS-3a culture also showed maximum DPPH scavenging, total antioxidant, and NO-scavenging activities. However, #6TAKR-1a exhibited maximum total flavonoid content, total phenolic content, and Fe-reducing power and also the highest growth inhibition of Aspergillus niger (ITCC 6152) and Colletotrichum sp. (ITCC 6152). Based on morphological characters and multi-locus phylogenetic analysis of the nuc rDNA internal transcribed spacer region (ITS1-5.8S-ITS2 = ITS), β-tubulin (TUB 2), and RNA polymerase II second largest subunit (RPB2) genes, potent fungal isolate #8TAKS-3a was identified as Talaromyces purpureogenus. Under the in vitro conditions, T. purpureogenus (#8TAKS-3a) was used as a bioinoculant that displayed a significant increase in various physio-biochemical growth parameters under normal and stressed conditions (p < 0.05). Our results indicate that drought stress-tolerant T. purpureogenus can be further used for field testing as a growth promoter.

Persephacin Is a Broad-Spectrum Antifungal Aureobasidin Metabolite That Overcomes Intrinsic Resistance in Aspergillus fumigatus

Fungi pose a persistent threat to humankind with worrying indications that emerging and re-emerging pathogens (e.g., Candida auris, Coccidioides spp., drug-resistant Aspergilli, and more) exhibit resistance to the limited number of approved antifungals. To address this problem, our team is exploring endophytic fungi as a resource for the discovery of new antifungal natural products. The rationale behind this decision is based on evidence that endophytes engage with plants in mutualistic relationships wherein some fungi actively participate by producing chemical defense measures that suppress pathogenic microorganisms. To improve the odds of bioactive metabolite discovery, we developed a new hands-free laser-cutting system capable of generating >50 plant samples per minute that, in turn, enabled our team to prepare and screen large numbers of endophytic fungi. One of the fungal isolates obtained in this way was identified as an Elsinoë sp. that produced a unique aureobasidin analogue, persephacin (1). Some distinctive features of 1 are the absence of both phenylalanine residues combined with the incorporation of a novel amino acid residue, persephanine (9). Compound 1 exhibits potent antifungal effects against a large number of pathogenic yeast (including several clinical C. auris strains), as well as phylogenetically diverse filamentous fungi (e.g., Aspergillus fumigatus). In an ex vivo eye infection model, compound 1 outperformed standard-of-care treatments demonstrating the ability to suppress fluconazole-resistant Candida albicans and A. fumigatus at a concentration (0.1% solution) well below the clinically recommended levels used for fluconazole and natamycin (2% and 5% solutions, respectively). In 3D tissue models for acute dermal and ocular safety, 1 was found to be nontoxic and nonirritating at concentrations required to elicit antifungal activity. Natural product 1 appears to be a promising candidate for further investigation as a broad-spectrum antifungal capable of controlling a range of pathogens that negatively impact human, animal, and plant health.

Antimicrobial and Antioxidant Activities of Endophytic Fungi Associated with Arrabidaea chica (Bignoniaceae)

The endophytic fungal community of the Amazonian medicinal plant Arrabidaea chica (Bignoniaceae) was evaluated based on the hypothesis that microbial communities associated with plant species in the Amazon region may produce metabolites with interesting bioactive properties. Therefore, the antimicrobial and antioxidant activities of the fungal extracts were investigated. A total of 107 endophytic fungi were grown in liquid medium and the metabolites were extracted with ethyl acetate. In the screening of fungal extracts for antimicrobial activity, the fungus identified as Botryosphaeria mamane CF2-13 was the most promising, with activity against E. coli, S. epidermidis, P. mirabilis, B. subtilis, S. marcescens, K. pneumoniae, S. enterica, A. brasiliensis, C. albicans, C. tropicalis and, especially, against S. aureus and C. parapsilosis (MIC = 0.312 mg/mL). Screening for antioxidant potential using the DPPH elimination assay showed that the Colletotrichum sp. CG1-7 endophyte extract exhibited potential activity with an EC50 of 11 µg/mL, which is equivalent to quercetin (8 µg/mL). The FRAP method confirmed the antioxidant potential of the fungal extracts. The presence of phenolic compounds and flavonoids in the active extracts was confirmed using TLC. These results indicate that two of the fungi isolated from A. chica exhibit significant antimicrobial and antioxidant potential.

Biocontrol potential of endophytic fungi originated from grapevine leaves for management of anthracnose disease caused by Colletotrichum gloeosporioides

In the present study, 51 fungal endophytes (FEs) were isolated, purified and identified from the healthy leaf segments of ten grapevine varieties based on the spore and colony morphologies and ITS sequence information. The FEs belonged to the Ascomycota division comprising eight genera viz., Alternaria, Aspergillus, Bipolaris, Curvularia, Daldinia, Exserohilum, Fusarium and Nigrospora. The in vitro direct confrontation assay against Colletotrichum gloeosporioides revealed that six isolates viz., VR8 (70%), SB2 (83.15%), CS2 (88.42%), MN3 (88.42%), MS5 (78.94%) and MS15 (78.94%) inhibited the mycelial growth of test pathogen. The remaining 45 fungal isolates showed 20-59.9% growth inhibition of C. gloeosporioides. Indirect confrontation assay manifested that the isolates MN1 and MN4a showed 79.09% and 78.18% growth inhibition of C. gloeosporioides followed by MM4 (73.63%) and S5 (71.81%) isolates. Isolate S5 and MM4 were found to produce azulene and 1,3-Cyclopentanedione, 4,4-dimethyl as antimicrobial volatile organic compounds, respectively. The 38 FEs showed PCR amplification using internal transcribed spacer universal primers. The BLAST search revealed highest similarity with the existing sequences in the database. The phylogenetic analysis revealed the occurrence of seven distinct clusters each corresponding to single genus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03675-z.

Biocontrol Screening of Endophytes: Applications and Limitations

The considerable loss of crop productivity each year due to plant disease or pathogen invasion during pre- or post-harvest storage conditions is one of the most severe challenges to achieving the goals of food security for the rising global population. Although chemical pesticides severally affect the food quality and health of consumers, a large population relies on them for plant disease management. But currently, endophytes have been considered one of the most suitable biocontrol agents due to better colonization and acclimatization potential. However, a very limited number of endophytes have been used commercially as biocontrol agents. Isolation of endophytes and their screening to represent potential characteristics as biocontrol agents are considered challenging by different procedures. Through a web search using the keywords "endophytes as biocontrol agents" or "biocontrol mechanism of endophytes," we have succinctly summarised the isolation strategies and different in vitro and in vivo biocontrol screening methods of endophytic biocontrol agents in the present review. In this paper, biocontrol mechanisms of endophytes and their potential application in plant disease management have also been discussed. Furthermore, the registration and regulatory mechanism of the endophytic biocontrol agents are also covered.

The Influence of Cone Age and Urbanisation on the Diversity and Community Composition of Culturable Seed Fungal Endophytes within Native Australian Banksia ericifolia L.f. subsp. ericifolia

Seed fungal endophytes play a crucial role in assisting the overall health and success of their host plant; however, little is known about the factors that influence the diversity and composition of these endophytes, particularly with respect to how they change over time and within urban environments. Using culturing techniques, morphological analyses, and Sanger sequencing, we identified the culturable seed fungal endophytes of Banksia ericifolia at two urban and two natural sites in Sydney, New South Wales, Australia. A total of 27 Operational Taxonomic Units were obtained from 1200 seeds. Older cones were found to contain, on average, more colonised endophytes than younger cones. Species richness was also significantly influenced by cone age, with older cones being more speciose. Between urban and natural sites, the overall community composition did not change, although species richness and diversity were greatest at urban sites. Understanding how these endophytes vary in time and space may help provide an insight into the transmission pathways used and the potential role they play within the development and survival of the seed. This knowledge may also be crucial for restoration purposes, especially regarding the need to consider endophyte viability in ex situ seed collection and storage in seed-banking practices.

Fungal Endophytes: Microfactories of Novel Bioactive Compounds with Therapeutic Interventions; A Comprehensive Review on the Biotechnological Developments in the Field of Fungal Endophytic Biology over the Last Decade

The seminal discovery of paclitaxel from endophytic fungus Taxomyces andreanae was a milestone in recognizing the immense potential of endophytic fungi as prolific producers of bioactive secondary metabolites of use in medicine, agriculture, and food industries. Following the discovery of paclitaxel, the research community has intensified efforts to harness endophytic fungi as putative producers of lead molecules with anticancer, anti-inflammatory, antimicrobial, antioxidant, cardio-protective, and immunomodulatory properties. Endophytic fungi have been a valuable source of bioactive compounds over the last three decades. Compounds such as taxol, podophyllotoxin, huperzine, camptothecin, and resveratrol have been effectively isolated and characterized after extraction from endophytic fungi. These findings have expanded the applications of endophytic fungi in medicine and related fields. In the present review, we systematically compile and analyze several important compounds derived from endophytic fungi, encompassing the period from 2011 to 2022. Our systematic approach focuses on elucidating the origins of endophytic fungi, exploring the structural diversity and biological activities exhibited by these compounds, and giving special emphasis to the pharmacological activities and mechanism of action of certain compounds. We highlight the tremendous potential of endophytic fungi as alternate sources of bioactive metabolites, with implications for combating major global diseases. This underscores the significant role that fungi can play in the discovery and development of novel therapeutic agents that address the challenges posed by prevalent diseases worldwide.

Microbial Endophytes: Emerging Trends and Biotechnological Applications

A plethora of knowledge on the role of endophytic microorganisms has been reported in recent years. The cooperative chemistry between the endophytes and the internal host tissue has turned them into a crucial aid for biotechnological applications. Microbial endophytes are ubiquitous among most plant species on earth and contribute to the benefit of host plants by generating a wide range of metabolites that provide the plant with survival value. Endophytes can either directly stimulate plant growth by producing phytohormones or indirectly stimulate plant growth by increasing the availability of soil nutrients to plants. Endophytes may also help suppress diseases in plants directly by neutralizing environmental toxic elements, and by inhibiting plant pathogens by antagonistic action, or indirectly by stimulating induced plant systemic resistance. Several natural compounds produced by endophytes as secondary metabolites are beneficial to both plants and humans. This is why endophytes are regarded as a significant source of novel natural products of value in modern medicine, agriculture, and industry. Endophytes are known for producing pigments, bioactive compounds, and industrially important enzymes, like glucanase, amylase, laccase, etc. Some endophytes can also produce nanoparticles that potentially have numerous applications in a variety of fields. They also play an important role in biodegradation and bioremediation, both of which are beneficial to the environment and ecology. In this review, we highlighted potential biotechnological applications of endophytic microbes, as well as their diverse importance in plant growth and public health.

In vivo and In vitro evaluation of the antifungal activity of the PGPR Bacillus amyloliquefaciens RaSh1 (MZ945930) against Alternaria alternata with growth promotion influences on Capsicum annuum L. plants

Alternaria alternata that threatens pepper production and causes major economic harm is responsible for the leaf spot/blight disease. Chemical fungicides have been widely employed; unfortunately, fungicidal resistance is a current concern. Therefore, finding new environmentally friendly biocontrol agents is a future challenge. One of these friendly solutions is the use of bacterial endophytes that have been identified as a source of bioactive compounds. The current study investigates the in vivo and in vitro fungicidal potential of Bacillus amyloliquefaciens RaSh1 (MZ945930) against pathogenic A. alternata. In vitro, the results revealed that RaSh1 exhibited strong antagonistic activity against A. alternata. In addition to this, we inoculated pepper (Capsicum annuum L.) plants with B. amyloliquefaciens RaSh1 and infected them with A. alternata. As a result of A. alternata infection, which generated the highest leaf spot disease incidence (DI), the plant's growth indices and physio-biochemical characteristics significantly decreased, according to our findings. Our results also showed the abnormal and deformed cell structure using light and electron microscopy of A. alternata-infected leaves compared with other treatments. However, DI was greatly reduced with B. amyloliquefaciens RaSh1 application (40%) compared to pepper plants infected with A. alternata (80%), and this led to the largest increases in all identified physio-biochemical parameters, including the activity of the defense-related enzymes. Moreover, inoculation of pepper plants with B. amyloliquefaciens RaSh1 decreased electrolyte leakage by 19.53% and MDA content by 38.60% as compared to A. alternata infected ones. Our results show that the endophyte B. amyloliquefaciens RaSh1 has excellent potential as a biocontrol agent and positively affects pepper plant growth.

Endophytic species of Induratia from coffee and carqueja plants from Brazil and its potential for the biological control of toxicogenic fungi on coffee beans by means of antimicrobial volatiles

Several endophytic fungi have been reported to have produced bioactive metabolites. Some of them, including the Induratia species, have the capacity to emit volatile compounds with antimicrobial properties with broad spectrum against human and plant pathogens. The present study aimed to prospect the Induratia species producing volatile organic compounds (VOCs), in carqueja plants used in alternative medicine and coffee plants in Brazil. A total of 11 fungal isolates producing volatile metabolites were obtained by a parallel growth technique, using I. alba 620 as a reference strain. Phylogenetic relationships revealed the presence of at least three distinct species, I. coffeana, I. yucatanensis, and Induratia sp. SPME/GC/MS analyses of the VOCs in the headspace above the mycelium from Induratia species cultured for 10 days on PDA revealed the volatile profile emitted by I. coffeana CCF 572, I. coffeana COAD 2055, I. yucatanensis COAD 2062, and Induratia sp. COAD 2059. Volatile organic compounds produced by I. coffeana isolates presented antimicrobial activity against Aspergillus ochraceus, A. sclerotiorum, A. elegans, A. foetidus, A. flavus, A. tamari, A. tubingensis, A. sydowii, A. niger, A. caespitosus, A. versicolor, and A. expansum, sometimes by decreasing the growth rate or, mainly, by fully inhibiting colony growth. Fifty-eight percent of the target species died after 6 days of exposure to VOCs emitted by I. coffeana CCF 572. In addition, VOCs emitted by the same fungus inhibited the growth in A. ochraceus inoculated into coffee beans, which indicates that plants which have I. coffeana as an endophyte may be protected from attacks by this plant pathogen.

Brassicaceae Fungi and Chromista Diseases: Molecular Detection and Host–Plant Interaction

Brassicaceae plants cover a large number of species with great economic and nutritional importance around the world. The production of Brassica spp. is limited due to phytopathogenic fungal species causing enormous yield losses. In this scenario, precise and rapid detection and identification of plant-infecting fungi are essential to facilitate the effective management of diseases. DNA-based molecular methods have become popular methods for accurate plant disease diagnostics and have been used to detect Brassicaceae fungal pathogens. Polymerase chain reaction (PCR) assays including nested, multiplex, quantitative post, and isothermal amplification methods represent a powerful weapon for early detection of fungal pathogens and preventively counteract diseases on brassicas with the aim to drastically reduce the fungicides as inputs. It is noteworthy also that Brassicaceae plants can establish a wide variety of relationships with fungi, ranging from harmful interactions with pathogens to beneficial associations with endophytic fungi. Thus, understanding host and pathogen interaction in brassica crops prompts better disease management. The present review reports the main fungal diseases of Brassicaceae, molecular methods used for their detection, review studies on the interaction between fungi and brassicas plants, and the various mechanisms involved including the application of omics technologies.

Taxonomic Study of Three Novel Paenibacillus Species with Cold-Adapted Plant Growth-Promoting Capacities Isolated from Root of Larix gmelinii

Exploration of the novel species of the genus Paenibacillus with plant-growth promoting characteristics at the low-temperature environment is of great significance for the development of psychrotolerant biofertilizer in forestry and agriculture. During the course of isolation of root endophytes of Larix gmelinii in the island frozen soil, three strains designated as T3-5-0-4, N1-5-1-14 and N5-1-1-5 were isolated. The three strains showed plant growth-promoting properties at the low temperature, such as phosphate solubilization, indole-3-acetic acid biosynthesis and siderophore production. According to pairwise sequence analyses of the 16S rRNA genes, the three strains represent putatively novel taxa within the genus Paenibacillus. The strains have typical chemotaxonomic characteristics of the genus Paenibacillus by having meso-diaminopimelic acid as diagnostic diamino acid, anteiso-C15:0 as the predominant fatty acid and MK-7 as the predominant menaquinone. The polar lipid profiles of all strains contained diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The sizes of the genomes of the stains ranged from 5.66 to 9.07 Mb and the associated G+C contents ranged from 37.9% to 44.7%. Polyphasic taxonomic study including determination of genome relatedness indices revealed that the strains are representatives of three novel species in the genus Paenibacillus. Consequently, isolates T3-5-0-4, N1-5-1-14 and N5-1-1-5 are proposed as novel species for which the names of Paenibacillus endoradicis sp. nov. (CFCC15691T = KCTC43441T), Paenibacillus radicibacter sp. nov, (CFCC15694T = KCTC43442T) and Paenibacillus radicis sp. nov. (CFCC15710T = KCTC43173T), respectively. Moreover, analysis for biosynthetic genes showed that the strains have potential for plant growth-promoting characteristics, plant rhizospheres colonization and low-temperature adaption, most of which are consistent with the results of the bioactivity test.

Minimally processed fruits as vehicles for foodborne pathogens

The consumption of minimally processed fruit (MPF) has increased over the last decade due to a novel trend in the food market along with the raising consumers demand for fresh, organic, convenient foods and the search for healthier lifestyles. Although represented by one of the most expanded sectors in recent years, the microbiological safety of MPF and its role as an emergent foodborne vehicle has caused great concern to the food industry and public health authorities. Such food products may expose consumers to a risk of foodborne infection as they are not subjected to prior microbial lethal methods to ensure the removal or destruction of pathogens before consumption. A considerable number of foodborne disease cases linked to MPF have been reported and pathogenic strains of Salmonella enterica, Escherichia coli, Listeria monocytogenes, as well as Norovirus accounted for the majority of cases. Microbial spoilage is also an issue of concern as it may result in huge economic losses among the various stakeholders involved in the manufacturing and commercialization of MPF. Contamination can take place at any step of production/manufacturing and identifying the nature and sources of microbial growth in the farm-to-fork chain is crucial to ensure appropriate handling practices for producers, retailers, and consumers. This review aims to summarize information about the microbiological hazards associated with the consumption of MPF and also highlight the importance of establishing effective control measures and developing coordinated strategies in order to enhance their safety.

Biostimulation of tomato growth and biocontrol of Fusarium wilt disease using certain endophytic fungi

BACKGROUND

Tomato plant (Solanum lycopersicum L.) suffers from numerous fungal pathogens that cause damage to yeild production qualitatively and quantitatively. One of the most destructive disease of tomato is Fusarium wilt that caused by soil borne fungus called F. oxysporum.

METHODS

In this study, the anti-Fusarium capabilities of the foliar application of fungal endophytes extracts have been investigated on tomato under Fusarium challenges. Antifungal assay, inhibition of conidial germination, disease severity, photosynthetic pigments, osmolytes, secondary metabolites, oxidative stress, peroxidase (POD) and polyphenol oxidases (PPO) isozymes were tested for potential resistance of tomato growing under Fusarium infection.

RESULTS

Ethyl acetate extracts of A. flavus MZ045563, A. fumigatus MZ045562 and A. nidulans MZ045561 exhibited antifungal activity toward F. oxysporum where inhibition zone diameters were 15, 12 and 20 mm, respectively. Moreover, extracts of all fungal isolates at concentration 7.5 mg/mL reduced conidia germination from 94.4 to 100%. Fusarium infection caused a destructive effects on tomato plant, high severity desiese index 84.37%, reduction in growth parameters, photosynthetic pigments, and soluble protein. However, contents of proline, total phenol, malondialdehyde (MDA), hydrogen peroxide (H₂O₂) and antioxidant enzymes activity were increased in tomato plants grown under Fusarium wilt. Treatment of healthy or infected tomato plants by ethyl acetate fungal extracts showed improvements in morphological traits, photosynthetic pigments, osmolytes, total phenol and antioxidant enzymes activity. Besides, the harmful impacts of Fusarium wilt disease on tomato plants have also been reduced by lowering MDA and H₂O₂ levels. Also, treated tomato plants showed different responses in number and density of POD and PPO isozymes.

CONCLUSION

It could be suggested that application of ethyl acetate extracts of tested fungal endophytes especially combination of A. flavus, A. nidulans and A. fumigatus could be commercially used as safe biostimulation of tomato plants as well as biofungicide against tomato Fusarium wilt disease.

Monilinia fructigena Suppressing and Plant Growth Promoting Endophytic Pseudomonas spp. Bacteria Isolated from Plum

Brown rot caused by Monilinia spp. fungi causes substantial losses in stone and pome fruit production. Reports suggest that up to 90% of the harvest could be lost. This constitutes an important worldwide issue in the food chain that cannot be solved by the use of chemical fungicides alone. Biocontrol agents (BCAs) based on microorganisms are considered a potential alternative to chemical fungicides. We hypothesized that endophytic bacteria from Prunus domestica could exhibit antagonistic properties towards Monilinia fructigena, one of the main causative agents of brown rot. Among the bacteria isolated from vegetative buds, eight isolates showed antagonistic activity against M. fructigena, including three Pseudomonas spp. isolates that demonstrated 34% to 90% inhibition of the pathogen's growth when cultivated on two different media in vitro. As the stimulation of plant growth could contribute to the disease-suppressing activity of the potential BCAs, plant growth promoting traits (PGPTs) were assessed for bacterial isolates with M. fructigena-suppressing activity. While all isolates were capable of producing siderophores and indole-3-acetic acid (IAA), fixating nitrogen, mineralizing organic phosphate, and solubilizing inorganic phosphate and potassium, only the Pseudomonas spp. isolates showed 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity. Overall, our study paves the way for the development of an eco-friendly strategy for managing M. fructigena pathogens by using BCAs including Pseudomonas spp. bacteria, which could also serve as growth stimulators.

Overview of Bioactive Fungal Secondary Metabolites: Cytotoxic and Antimicrobial Compounds

Microorganisms are known as important sources of natural compounds that have been studied and applied for different purposes in distinct areas. Specifically, in the pharmaceutical area, fungi have been explored mainly as sources of antibiotics, antiviral, anti-inflammatory, enzyme inhibitors, hypercholesteremic, antineoplastic/antitumor, immunomodulators, and immunosuppressants agents. However, historically, the high demand for new antimicrobial and antitumor agents has not been sufficiently attended by the drug discovery process, highlighting the relevance of intensifying studies to reach sustainable employment of the huge world biodiversity, including the microorganisms. Therefore, this review describes the main approaches and tools applied in the search for bioactive secondary metabolites, as well as presents several examples of compounds produced by different fungi species with proven pharmacological effects and additional examples of fungal cytotoxic and antimicrobial molecules. The review does not cover all fungal secondary metabolites already described; however, it presents some reports that can be useful at any phase of the drug discovery process, mainly for pharmaceutical applications.

Apple Endophytic fungi and their antagonism against apple scab disease

Endophytic fungi are microorganisms with the ability to colonize plants for the entire or at least a significant part of their life cycle asymptomatically, establishing a plant-fungus association. They play an important role in balancing ecosystems, as well as benefiting host through increasing plant growth, and protecting the host plants from abiotic and biotic stresses using various strategies. In the present study, endophytic fungi were isolated from wild and endemic apple cultivars, followed by characterizing their antifungal effect against Venturia inaequalis. To characterize the endophytic fungi, 417 fungal strains were separated from 210 healthy fruit, leaf, and branch samples collected from the north of Iran. Among the purified fungal isolates, 33 fungal genera were identified based on the morphological characteristics, of which 38 species were detected according to the morphological features and molecular data of ITS, tef-1α, and gapdh genomic regions (related to the genus). The results represented that most of the endophytic fungi belonged to Ascomycota (67.8%), 31.4% of isolates were mycelia sterilia, while the others were Basidiomycota (0.48%) and Mucoromycota (0.24%). Additionally, Alternaria, Cladosporium, and Nigrospora were determined as the dominant genera. The antifungal properties of the identified isolates were evaluated against V. inaequalis in vitro to determine the release of media-permeable metabolites, Volatile Organic Compounds (VOCs), chitinase, and cellulase as antifungal mechanisms, as well as producing phosphate solubilisation as growth-promoting effect. Based on the results of metabolite and VOC tests, the six isolates of Acremonium sclerotigenum GO13S1, Coniochaeta endophytica 55S2, Fusarium lateritium 61S2, Aureobasidium microstictum 7F2, Chaetomium globosum 2S1 and Ch. globosum 3 L2 were selected for greenhouse tests. Further, Co. endophytica 55S2 and F. lateritium 61S2 could solubilize inorganic phosphate. All isolates except Ch. globosum 3 L2 exhibited cellulase activity, while chitinase activity was observed in Ch. globosum 2S1, Ch. globosum 3 L2, and F. lateritium 61S2. Finally, Co. endophytica 55S2 and Ch. globosum 2S1 completely controlled the disease on the apple seedling leaves under greenhouse conditions.

Combined Biological and Chemical/Physicochemical Pretreatment Methods of Lignocellulosic Biomass for Bioethanol and Biomethane Energy Production—A Review

Lignocellulosic biomass is a low-cost and environmentally-friendly resource that can be used to produce biofuels such as bioethanol and biogas, which are the leading candidates for the partial substitution of fossil fuels. However, the main challenge of using lignocellulosic materials for biofuel production is the low accessibility to cellulose for hydrolysis of enzymes and microorganisms, which can be overcome by pretreatment. Biological and chemical pretreatments have their own disadvantages, which could be reduced by combining the two methods. In this article, we review biological–chemical combined pretreatment strategies for biogas and bioethanol production. The synergy of fungal/enzyme–NaOH pretreatment is the only biological–chemical combination studied for biogas production and has proven to be effective. The use of enzyme, which is relatively expensive, has the advantage of hydrolysis efficiency compared to fungi. Nonetheless, there is vast scope for research and development of other chemical–biological combinations for biogas production. With respect to ethanol production, fungal–organosolv combination is widely studied and can achieve a maximum of 82% theoretical yield. Order of pretreatment is also important, as fungi may reduce the accessibility of cellulose made available by prior chemical strategies and suppress lignin degradation. The biofuel yield of similarly pretreated biomass can vary depending on the downstream process. Therefore, new strategies, such as bioaugmentation and genetically engineered strains, could help to further intensify biofuel yields.

Diversity and antibacterial activity of endophytic bacteria associated with medicinal plant, Scrophularia striata

To search endophytic bacteria diversity and evaluate their antibacterial activity, healthy medicinal plant of Scrophularia striata was chosen in this study. One hundred endophytic bacteria were isolated from surface-sterilized tissues (root, stem and leaf) of S. striata. Using sequence analysis targeting 16S rRNA gene, eight genera, including Agrococcus, Arthrobacter, Bacillus, Chryseobacterium, Delftia, Kocuria, Pseudomonas and Sphingomonas were identified. Antibacterial activity of endophytic bacteria was examined against some test bacteria, employing agar well diffusion method. Out of 31 endophytic bacterial isolates, 24(77.42%) isolates showed significant antimicrobial activity against Bacillus cereus, 17(54.84%) isolates exhibited maximum activity against Staphylococcus aureus, 14(45.16%) isolates against Escherichia coli and 5(16.13%) isolates showed positive activity against Proteus mirabilis.The results obtained in this study suggested that the medicinal plant, S. striatais is a potent source of endophytic bacteria with antibacterial activity and offers promise for discovery of more impressive biological compounds.

Plant-Endophyte Interaction during Biotic Stress Management

Plants interact with diverse microbial communities and share complex relationships with each other. The intimate association between microbes and their host mutually benefit each other and provide stability against various biotic and abiotic stresses to plants. Endophytes are heterogeneous groups of microbes that live inside the host tissue without showing any apparent sign of infection. However, their functional attributes such as nutrient acquisition, phytohormone modulation, synthesis of bioactive compounds, and antioxidant enzymes of endophytes are similar to the other rhizospheric microorganisms. Nevertheless, their higher colonization efficacy and stability against abiotic stress make them superior to other microorganisms. In recent studies, the potential role of endophytes in bioprospecting has been broadly reported. However, the molecular aspect of host–endophyte interactions is still unclear. In this study, we have briefly discussed the endophyte biology, colonization efficacy and diversity pattern of endophytes. In addition, it also summarizes the molecular aspect of plant–endophyte interaction in biotic stress management.

Fungal endophytes of Brassicaceae: Molecular interactions and crop benefits

Brassicaceae family includes an important group of plants of great scientific interest, e.g., the model plant Arabidopsis thaliana, and of economic interest, such as crops of the genus Brassica (Brassica oleracea, Brassica napus, Brassica rapa, etc.). This group of plants is characterized by the synthesis and accumulation in their tissues of secondary metabolites called glucosinolates (GSLs), sulfur-containing compounds mainly involved in plant defense against pathogens and pests. Brassicaceae plants are among the 30% of plant species that cannot establish optimal associations with mycorrhizal hosts (together with other plant families such as Proteaceae, Chenopodiaceae, and Caryophyllaceae), and GSLs could be involved in this evolutionary process of non-interaction. However, this group of plants can establish beneficial interactions with endophytic fungi, which requires a reduction of defensive responses by the host plant and/or an evasion, tolerance, or suppression of plant defenses by the fungus. Although much remains to be known about the mechanisms involved in the Brassicaceae-endophyte fungal interaction, several cases have been described, in which the fungi need to interfere with the GSL synthesis and hydrolysis in the host plant, or even directly degrade GSLs before they are hydrolyzed to antifungal isothiocyanates. Once the Brassicaceae-endophyte fungus symbiosis is formed, the host plant can obtain important benefits from an agricultural point of view, such as plant growth promotion and increase in yield and quality, increased tolerance to abiotic stresses, and direct and indirect control of plant pests and diseases. This review compiles the studies on the interaction between endophytic fungi and Brassicaceae plants, discussing the mechanisms involved in the success of the symbiosis, together with the benefits obtained by these plants. Due to their unique characteristics, the family Brassicaceae can be seen as a fruitful source of novel beneficial endophytes with applications to crops, as well as to generate new models of study that allow us to better understand the interactions of these amazing fungi with plants.

Plant-associated fungi affect above- and belowground pest responses to soybean plants

AIM

The objective of this research was to screen fungal isolates originally isolated from cotton plants and measure their effects on the interactions between soybean and two aboveground pests (cabbage looper; Trichoplusia ni and soybean looper; Chrysodeixis includens) as well as a belowground pest (soybean cyst nematode; Heterodera glycines).

METHODS AND RESULTS

For aboveground pests, we measured the leaf area consumed and larval weight. For our belowground pest tests, we measured shoot height, shoot fresh weight, root fresh weight and number of cysts. Out of the 50 fungal isolates tested, we tested 30 fungi in the interaction with cabbage looper, 36 for soybean looper, 41 for soybean cyst nematode. We tested 23 isolates against all pests and identified multiple isolates that significantly changed the response of pests on inoculated soybean plants versus controls.

CONCLUSIONS

We identified three fungal isolates that significantly reduced both leaf area consumed aboveground by caterpillars and number of cysts produced belowground by nematodes. These isolates were an Epicoccum italicum, a Chaetomium undulatum and a Stemphylium majusculum.

SIGNIFICANCE AND IMPACT OF STUDY

Overall, this study provides important insights into plant-fungal interactions and their effect on both above- and belowground pests. This study also highlights an important first step towards harnessing the potential of microbial inoculates as a tool for integrated pest management in soybeans.

Succession of endophytic bacterial community and its contribution to cinnamon oil production during cinnamon shade-drying process

Cinnamon oil is a blend of secondary metabolites and is widely used as spice. Endophytic bacteria are always related to the secondary metabolites production. However, the potential of endophytic bacteria communities for cinnamon oil production during cinnamon shade-drying process is still not clear. In this study, we investigated the composition and metabolic function of endophytic bacterial community during 80-day shade-drying process. The temporal dynamics of essential oil content and its dominant constituents were analyzed. The succession of endophytic bacterial community from d0 to d80 was identified. The influence of endophytic bacterial community evolution on cinnamon oil is significant positive. Predictive functional analysis indicated that shade-drying process was rich in Saccharopolyspora that produce enzymes for the conversion of phenylalanine to cinnamaldehyde. These findings enhance our understanding of the functional bacterial genera and functional genes involved in the production of cinnamon oil during cinnamon shade-drying process.

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.

Endophytic fungi and their bioactive secondary metabolites in medicinal leguminosae plants: Nearly untapped medical resources

There are many species of Chinese traditional leguminosae family plants that are well known for their medicinal applications, such as Astragalus membranaceus, Catsia tora, Glycyrrhiza uralensis, Sophora flavescens and Albacia acacia. Their unique bioactive composition and internal phenological environment contribute to the formation of specific and unique endophytic fungal communities, which are important resources for new compounds used in a variety of pharmacological activities. Nonetheless, they have not been systematically studied. In the last decade, nearly 64 genera and thousands of species of endophytic fungi have been discovered from leguminosae plants, as well as 138 secondary metabolites (with 34 new compounds) including flavonoid, alkaloids, phenol, anthraquinone, macrolide, terpenoid, phytohormone and many more. They were shown to have diverse applications and benefits, such as antibacterial, antitumor, antioxidative, immunoregulatory and neuroprotective properties. Here, we provide a summarized overview with the aim of raising awareness of endophytic fungi from medicinal leguminosae plants and providing a comprehensive review of the discoveries of new natural products that may be of medicinal and pharmaceutical importance.

Production and Functionalities of Specialized Metabolites from Different Organic Sources

Medicinal plants are rich sources of specialized metabolites that are of great importance to plants, animals, and humans. The usefulness of active biological compounds cuts across different fields, such as agriculture, forestry, food processing and packaging, biofuels, biocatalysts, and environmental remediation. In recent years, research has shifted toward the use of microbes, especially endophytes (bacteria, fungi, and viruses), and the combination of these organisms with other alternatives to optimize the production and regulation of these compounds. This review reinforces the production of specialized metabolites, especially by plants and microorganisms, and the effectiveness of microorganisms in increasing the production/concentration of these compounds in plants. The study also highlights the functions of these compounds in plants and their applications in various fields. New research areas that should be explored to produce and regulate these compounds, especially in plants and microbes, have been identified. Methods involving molecular studies are yet to be fully explored, and next-generation sequencing possesses an interesting and reliable approach.

Enhancing the Discovery of Bioactive Secondary Metabolites From Fungal Endophytes Using Chemical Elicitation and Variation of Fermentation Media

Endophytic microorganisms are an important source of bioactive secondary metabolites. In this study, fungal endophytes obtained from A*STAR’s Natural Product Library (NPL) and previously isolated from different habitats of Singapore were investigated for their diversity, antimicrobial, and cytotoxic activities. A total of 222 fungal strains were identified on the basis of sequence analysis of ITS region of the rDNA gene. The identified fungal strains belong to 59 genera distributed in 20 orders. Majority of the identified strains (99%; 219 strains) belong to the phylum Ascomycota, while two strains belonged to the phylum Basidiomycota, and only one strain was from Mucoromycota phylum. The most dominant genus was Colletotrichum accounting for 27% of all the identified strains. Chemical elicitation using 5-azacytidine and suberoylanilide hydroxamic acid (SAHA) and variation of fermentation media resulted in the discovery of more bioactive strains. Bioassay-guided isolation and structure elucidation of active constituents from three prioritized fungal strains: Lophiotrema sp. F6932, Muyocopron laterale F5912, and Colletotrichum tropicicola F10154, led to the isolation of a known compound; palmarumycin C₈ and five novel compounds; palmarumycin CP₃₀, muyocopronol A-C and tropicicolide. Tropicicolide displayed the strongest antifungal activity against Aspergillus fumigatus with an IC₅₀ value of 1.8 μg/ml but with a weaker activity against the Candida albicans presenting an IC₅₀ of 7.1 μg/ml. Palmarumycin C₈ revealed the best antiproliferative activity with IC₅₀ values of 1.1 and 2.1 μg/ml against MIA PaCa-2 and PANC-1 cells, respectively.

Jasmonic acid pathway is required in the resistance induced by Acremonium sclerotigenum in tomato against Pseudomonas syringae

The use of fungal endophytes is considered as a new tool to confer resistance in plants against stresses. However, the mechanisms involved in colonization as well as in the induction of resistance by the endophytes are usually unclear. In this work, we tested whether a fungal endophyte isolated from an ancestor of wheat could induce resistance in plants of a different class from the ones that were isolated from the beginning. Seeds of Solanum lycopersicum were inoculated with Acremonium sclerotigenum and after four weeks, seedlings were inoculated with the bacterium Pseudomonas syringae pv tomato. Plants inoculated with endophytes showed significantly lower symptoms of infection as well as lower levels of colony forming units compared with control plants. Moreover, the presence of the endophytes induced an enhancement of Jasmonic acid (JA) upon inoculation with P. syringae compared with endophyte free plants. To ascertain the implication of JA in the resistance induced by A. sclerotigenum, two mutants defective in JA were tested. Results showed that the endophyte is not able to induce resistance in the mutant spr2, which is truncated in the first step of JA biosynthesis. On the contrary, acx1 mutant plants, which are unable to synthesize JA from OPC8, show a phenotype similar to wild type plants. Moreover, experiments with GFP-tagged endophytes showed no differences in the colonization in both mutants. In conclusion, the jasmonic acid pathway is required for the resistance mediated by the endophyte A. sclerotigenum in tomato against the biotrophic bacterium P. syringae but is not necessary for the colonization.

Phytostimulating Potential of Endophytic Bacteria from Ethnomedicinal Plants of North-East Indian Himalayan Region

North-East Indian Himalayan Region has a humid subtropical climate having diverse ecosystems. The majority of the population of the region depends on agriculture for sustainable livelihood. However, it can produce only 1.5% of the country’s food grains, thereby importing from other parts of the country for consumption. To feed the increase in the population of the region, there is an urgent need to augment the agricultural and allied products to sustain the population and uplift the economic conditions. Plant beneficial endophytes isolated from ethnomedicinal plants of North-East India play an important role as a plant growth promoter by the production of phytohormones, solubilization and mobilization of mineral nutrients. It also indirectly promotes growth by protecting the plants from diseases through the production of antibiotics, enzymes and volatile compounds. The bacteria also have the potential to induce systemic resistance against various abiotic stresses. Since the region has various agro-climatic conditions, the plants are continuously affected by abiotic stress particularly, acidity, drought and waterlogging, there is a need to explore the indigenous endophytes that can mitigate the stress and enhance the sustainable development of agricultural products.

Comprehensive Review of Fungi on Coffee

Coffee is grown in more than 80 countries as a cash crop and consumed worldwide as a beverage and food additive. It is susceptible to fungal infection during growth, processing and storage. Fungal infections, in particular, can seriously affect the quality of coffee and threaten human health. The data for this comprehensive review were collected from the United States Department of Agriculture, Agricultural Research Service (USDA ARS) website and published papers. This review lists the fungal species reported on coffee based on taxonomy, life mode, host, affected plant part and region. Five major fungal diseases and mycotoxin-producing species (post-harvest diseases of coffee) are also discussed. Furthermore, we address why coffee yield and quality are affected by fungi and propose methods to control fungal infections to increase coffee yield and improve quality. Endophytic fungi and their potential as biological control agents of coffee disease are also discussed.

Endophytic Fungi: An Effective Alternative Source of Plant-Derived Bioactive Compounds for Pharmacological Studies

Plant-associated fungi (endophytic fungi) are a biodiversity-rich group of microorganisms that are normally found asymptomatically within plant tissues or in the intercellular spaces. Endophytic fungi promote the growth of host plants by directly producing secondary metabolites, which enhances the plant's resistance to biotic and abiotic stresses. Additionally, they are capable of biosynthesizing medically important "phytochemicals" that were initially thought to be produced only by the host plant. In this review, we summarized some compounds from endophyte fungi with novel structures and diverse biological activities published between 2011 and 2021, with a focus on the origin of endophytic fungi, the structural and biological activity of the compounds they produce, and special attention paid to the exploration of pharmacological activities and mechanisms of action of certain compounds. This review revealed that endophytic fungi had high potential to be harnessed as an alternative source of secondary metabolites for pharmacological studies.

Root Endophytic Fungi Regulate Changes in Sugar and Medicinal Compositions of Polygonum cuspidatum

Polygonum cuspidatum Sieb. et Zucc is an important industrial crop because it contains a large amount of medicinal secondary metabolites (such as polydatin, resveratrol, chrysophanol, and emodin). However, it is unclear whether root endophytic fungi increase the content of secondary metabolites in the plant. This study aimed to analyze the effects of Funneliformis mosseae (Fm) and Piriformospora indica (Pi) alone or in combination on plant growth, root morphology, thirteen sugars concentrations, and six secondary metabolites (physcion, chrysophanol, emodin, aloe-emodin, polydatin, and resveratrol) concentrations of P. cuspidatum. After 11 weeks of the fungal inoculation, the roots could be colonized by Fm and Pi single or in combination, along with the higher root colonization frequency of Fm > Pi > Fm + Pi in the descending order. In addition, Fm and Pi improved plant growth performance (plant height, stem diameter, leaf number, and shoot and root biomass) and root morphology (average diameter, maximum diameter, total length, area, and volume) to varying degrees, depending on fungal inoculations, in which Pi displayed a relatively better effect on plant growth. Single Fm and Pi inoculation significantly increased three disaccharides (sucrose, maltose, and trehalose) accumulation, while dual inoculum (Fm + Pi) only elevated sucrose concentrations. Most monosaccharides concentrations, such as D-arabinose, D-galactose, D-sorbitol, D-fructose, glucose, and L-rhamnose were not altered or inhibited by the endophytic fungi, except the increase in L-fucose and inositol. All fungal treatments significantly increased root chrysophanol and resveratrol concentrations, while decreased aloe-emodin concentrations. In addition, single Pi and dual Fm + Pi increased emodin concentrations, and single Fm and dual Fm + Pi elevated physcion and polydatin concentrations. It was concluded that Fm and Pi promoted the growth of P. cuspidatum, and the combination of Fm and Pi was more conducive to the production of some secondary metabolites than single inoculation.

Wheat endophytes and their potential role in managing abiotic stress under changing climate

Wheat (Triticum aestivum L.) cultivation differs considerably in respect of soil type, temperature, pH, organic matter, moisture regime, etc. Among these, rising atmospheric temperature due to global warming is most important as it affects grain yield drastically. Studies have shown that for every 1°C rise in temperature above wheat's optimal growing temperature range of 20-25°C, there is a decrease in 2.8 days and 1.5 mg in the grain filling period and kernel weight, respectively, resulting in wheat yield reduction by 4-6 quintal per hectare. Growing demand for food and multidimensional issues of global warming may further push wheat crop to heat stress environments that can substantially affect heading duration, percent grain setting, maturity duration, grain growth rate and ultimately total grain yield. Considerable genetic variation exists in wheat gene pool with respect to various attributes associated with high temperature and stress tolerance; however, only about 15% of the genetic variability could be incorporated into cultivated wheat so far. Thus, alternative strategies have to be explored and implemented for sustainable, more productive and environment friendly agriculture. One of the feasible and environment friendly option is to look at micro-organisms that reside inside the plant without adversely affecting its growth, known as 'endophytes', and these colonize virtually all plant organs such as roots, stems, leaves, flowers and grains. The relationship between plant and endophytes is vital to the plant health, productivity and overall survival under abiotic stress conditions. Thus, it becomes imperative to enlist the endophytes (bacterial and fungal) isolated till date from wheat cultivars, their mechanism of ingression and establishment inside plant organs, genes involved in ingression, the survival advantages they confer to the plant under abiotic stress conditions and the potential benefits of their use in sustainable wheat cultivation.

Shifting Perspectives of Translational Research in Bio-Bactericides: Reviewing the Bacillus amyloliquefaciens Paradigm

Simple Summary

The continuous reduction of approved conventional microbicides, due to health concerns and the development of plant-pathogen resistance, has been urged for the use of safe alternatives in crop protection. Several beneficial bacterial species, termed biological control agents, are currently used in lieu of chemical pesticides. The approach to select such bacterial species and manufacture commercial products has been based on their biocontrol effect under optimal growth conditions, which is far from the real nutrient-limited field conditions of plant niches. It’s important to determine the complex interactions that occur among BCAs, plant host and niche microbiome to fully understand and exploit the potential of biological control agents. Furthermore, it’s crucial to acknowledge the environmental impact of their long-term use.

Abstract

Bacterial biological control agents (BCAs) have been increasingly used against plant diseases. The traditional approach to manufacturing such commercial products was based on the selection of bacterial species able to produce secondary metabolites that inhibit mainly fungal growth in optimal media. Such species are required to be massively produced and sustain long-term self-storage. The endpoint of this pipeline is large-scale field tests in which BCAs are handled as any other pesticide. Despite recent knowledge of the importance of BCA-host-microbiome interactions to trigger plant defenses and allow colonization, holistic approaches to maximize their potential are still in their infancy. There is a gap in scientific knowledge between experiments in controlled conditions for optimal BCA and pathogen growth and the nutrient-limited field conditions in which they face niche microbiota competition. Moreover, BCAs are considered to be safe by competent authorities and the public, with no side effects to the environment; the OneHealth impact of their application is understudied. This review summarizes the state of the art in BCA research and how current knowledge and new biotechnological tools have impacted BCA development and application. Future challenges, such as their combinational use and ability to ameliorate plant stress are also discussed. Addressing such challenges would establish their long-term use as centerfold agricultural pesticides and plant growth promoters.

Scaling-up production of plant endophytes in bioreactors: concepts, challenges and perspectives

The benefit of microorganisms to humans, animals, insects and plants is increasingly recognized, with intensified microbial endophytes research indicative of this realization. In the agriculture industry, the benefits are tremendous to move towards sustainable crop production and minimize or circumvent the use of chemical fertilizers and pesticides. The research leading to the identification of potential plant endophytes is long and arduous and for many researchers the challenge is ultimately in scale-up production. While many of the larger agriculture and food industries have their own scale-up and manufacturing facilities, for many in academia and start-up companies the next steps towards production have been a stumbling block due to lack of information and understanding of the processes involved in scale-up fermentation. This review provides an overview of the fermentation process from shake flask cultures to scale-up and the manufacturing steps involved such as process development optimization (PDO), process hazard analysis (PHA), pre-, in- and post-production (PIP) challenges and finally the preparation of a technology transfer package (TTP) to transition the PDO to manufacturing. The focus is on submerged liquid fermentation (SLF) and plant endophytes production by providing original examples of fungal and bacterial endophytes, plant growth promoting Penicillium sp. and Streptomyces sp. bioinoculants, respectively. We also discuss the concepts, challenges and future perspectives of the scale-up microbial endophyte process technology based on the industrial and biosafety research platform for advancing a massive production of next-generation biologicals in bioreactors.

Genome In Silico and In Vitro Analysis of the Probiotic Properties of a Bacterial Endophyte, Bacillus Paranthracis Strain MHSD3

Spore-forming Bacillus species are gaining interest in human health recently, due to their ability to withstand the harsh environment of the gastrointestinal tract. The present study explores probiotic features of Bacillus paranthracis strain MHSD3 through genomic analysis and in vitro probiotic assays. The draft genome of strain MHSD3 contained genes associated with tolerance to gastrointestinal stress and adhesion. Cluster genes responsible for the synthesis of antimicrobial non-ribosomal peptide synthetases, bacteriocins, and linear azole-containing peptides were identified. Additionally, strain MHSD3 was able to survive in an acidic environment, had the tolerance to bile salt, and exhibited the capability to tolerate gastric juices. Moreover, the isolate was found to possess strong cell surface traits such as high auto-aggregation and hydrophobicity indices of 79 and 54%, respectively. Gas chromatography-mass spectrometry analysis showed that the strain produced secondary metabolites such as amino acids, phenolic compounds, and organic acid, known to exert health-promoting properties, including the improvement of gastrointestinal tract health.