Optimization of process parameters for improved production of bioactive metabolite by a novel endophytic fungus Fusarium sp. DF2 isolated from Taxus wallichiana of North East India

Transcriptomic profiling of adding cobalt chloride to improve dendrobine-type total alkaloid production

Trichoderma longibrachiatum UN32 is known for its efficient production of dendrobine-type total alkaloids (DTTAs). This study aimed to determine the optimal medium composition for the UN32 strain using response surface methodology. Key factors, including glucose, beef extract, and CoCl2, were selected through the Plackett-Burman design. Subsequently, a factorial optimization approach was employed using the steepest ascent design, and 17 trial sets were completed via the Box-Behnken design. The optimal medium composition was found to consist of 29.4 g/L of glucose, 17.3 g/L of beef extract, and 0.28 mmol/L of CoCl2. This optimized medium resulted in an impressive 80.8% increase in mycelial dry weight (reaching 12.303 g/L) and a substantial 76.4% boost in DTTA production (reaching 541.63 ± 46.95 μg). Furthermore, the fermentation process was scaled up to a 5-L bioreactor, leading to a DTTA production approximately 1.95 times than the control. Transcriptome analysis of strain UN32 in response to CoCl2 supplementation revealed significant changes in the expression of critical genes associated with the TCA cycle and L-valine, L-leucine, and L-isoleucine biosynthesis changed. These alterations resulted in a heightened influx of acetyl-CoA into DTTA production. Additionally, the expression of genes related to antioxidant enzymes was modified to maintain homeostasis of reactive oxygen species (ROS). A potential mechanism for the accumulation of DTTAs based on ROS as a signal transduction was proposed. These findings provide valuable insights into the regulatory mechanisms of DTTA biosynthesis, potentially offering a method to enhance the production of secondary metabolites in the UN32 strain. KEY POINTS: • After the RSM optimization, there is a substantial increase of 80.8% in biomass production and a significant 76.4% rise in DTTA production. • Transcriptome analysis revealed that the inclusion of CoCl2 supplements resulted in an enhanced influx of acetyl-CoA. • Proposed a mechanism for the accumulation of DTTAs for the role of ROS as a signal transduction pathway.

Antifungal activity of volatile and non-volatile metabolites of endophytes of Chloranthus elatior Sw

Agriculture crops that have fungal infections suffer significant economic losses and reduced crop output. Chemical fungicides are used to tackle the problem, although this has additional detrimental side effects. There is an urgent need for safe and novel antifungals. Volatiles from plant-beneficial endophytic fungi are considered promising alternatives for the biological control of fungal pathogens as a sustainable approach in an agroecosystem. In the present investigation, a volatile-emitting sterile endophytic fungus, Diaporthe sp. CEL3 with bio-fumigation activity, was isolated from leaves of the ethnomedicinal plant Chloranthus elatior Sw., collected from the Passighat forest of North-East India. The camphor odor volatiles of CEL3 showed an inhibitory effect against eight fungal pathogens in vitro and minimized the infections of Monilinia fructicola, a causal agent of cherry fruit rot, in VOC-exposed cherry fruits. Rhizoctonia solani, Botrytis cinerea, Pythium ultimum, and M. fructicola were maximally inhibited up to 51.5%, 55.8%, 61.9%, and 78.5%, respectively, in comparison to control by the volatiles. Another isolate, CEL7, identified as Curvularia sp., synthesized non-volatile, soluble antifungal metabolites in its cell-free extracts and exhibited antifungal action. Bioassay-guided fractionation revealed the presence of imidazole compounds- (2-aminoethyl)-1H-imidazole-2-carbaldehyde, Pyrazole 4, 5 imidazole, 1-formyl 3-ethyl, phenol compounds-Phenol, 4-[2-(methylamino) ethyl]-, 6-Nitro-3-chlorophenol, Phenol, 2,4,6-tri-tert-butyl-, etc., in the cell-free extracts, with a MIC value of 250-2,000 µg ml-1. Optimum VOC emission was achieved in a modified PDA medium with instantly smashed potato (150 g L-1), dextrose (20 g L-1), wheat husk (20 g L-1), and yeast extract (20 g L-1), with additional salts. Interestingly, endophytic CEL3 emitted different types of volatiles, and trans-verbenol (32.25%), geraniol (30.32%), trans-ocimenol (12.90%), and mentha-4,8-diene (5.16%) were the prime ones. These VOCs cause lethal leakage of protein and necessary intracellular molecules from the fungal pathogens. Thus, CEL3 could potentially be used as a bio-fumigating agent to control post-harvest infections caused by fungal pathogens. This study opens a new approach to the use of endophytic fungi in biocontrol.

Optimization parameters for the production of dimer of epicatechin from an endophytic fungus Curvularia australiensis FC2AP using response surface methodology (RSM)

The search for natural therapeutic agents has intensified due to their potential to treat various diseases. Bioactive secondary metabolites from endophytes offer high therapeutic profiles and can be mass-produced after optimizing medium parameters and purification. This investigation aimed to maximize crude pigmented secondary metabolite (CPSM) production from Curvularia australiensis FC2AP by optimizing fermentation conditions statistically. The endophytic fungus produced a maximum yield of 8.81 UL/g from biomass using Sabouraud's Dextrose Broth. After screening essential factors, the Plackett-Burman design was used for factorial optimization, and the Box Behnken design was employed to investigate three significant factors. The final CPSM yield was 12.3 UL/g, approximately 4-fold higher than the preliminary growth medium. Chromatographic purification using a gradient solvent system resulted in six fractions, with the fourth fraction demonstrating the highest bioactivity profile. Structural characterization confirmed this fraction to be a dimer of epicatechin, which has anti-cancer properties, as confirmed through in vivo studies on Sprague Dawley rats. This is the first report of a epicatechin dimer produced from C. australiensis.

Developed network between taxoid and phenylpropanoid pathways in Cryptosporiopsis tarraconensis, taxan-producing endophytic fungus by Debiased Sparse Partial Correlation (DSPC) algorithm

Although bioproduction of Paclitaxel by endophytic fungi is highly considered as an alternative promising source, but its yield is usually very low in comparison with other taxoids. Different strategies i.e., chemical and physical elicitations have been developed in order to overcome the shortage of Paclitaxel production. Paclitaxel biosynthesis is started with terpenoid pathway followed by phenylpropanoid metabolism where a benzoylphenylisoserine moiety is attached to C13 of baccatin III skeleton. This point which is catalyzed by the function of PAM seems to be a bottleneck that limits the rate of Paclitaxel production. Whether phenylpropanoids pathway regulates the taxanes biosynthesis in Cryptosporiopsis tarraconensis endophytic fungus elicited with benzoic acid (BA) was hypothesized in the present paper. The involvement of certain signal molecules and key enzymes of terpenoid and phenylpropanoid metabolism were investigated. According to the results, application of BA promoted a signaling pathway which was started with increase of H2O2 and ABA and continued by increase of NO and MJ, and finally resulted in increase of both phenylpropanoids and taxanes. However, again the rate of Paclitaxel production was lower than other taxoids, and the latter was much lower than phenolics. Therefore, supplying benzoic acid provided the precursor for the common taxan ring production. It is unlikely that Paclitaxel production is merely controlled by side chain production stage. It is more likely that in C. tarraconensis endophytic fungus, similar to Taxus sp., the competition between phenylpropanoid and taxoid pathways for substrate ended in favor of the former. The interaction network which was constructed based on DSPC algorithm confirmed that most compounds with close proximity have shared metabolic pathway relationships. Therefore, it is unlikely that the feeding with a given precursor directly result in increase of a desired metabolite which is composed of different merits.

Recent advances in research for potential utilization of unexplored lichen metabolites

Several research studies have shown that lichens are productive organisms for the synthesis of a broad range of secondary metabolites. Lichens are a self-sustainable stable microbial ecosystem comprising an exhabitant fungal partner (mycobiont) and at least one or more photosynthetic partners (photobiont). The successful symbiosis is responsible for their persistence throughout time and allows all the partners (holobionts) to thrive in many extreme habitats, where without the synergistic relationship they would be rare or non-existent. The ability to survive in harsh conditions can be directly correlated with the production of some unique metabolites. Despite the potential applications, these unique metabolites have been underutilised by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability and technical challenges involved in their artificial cultivation. However, recent development of biotechnological tools such as molecular phylogenetics, modern tissue culture techniques, metabolomics and molecular engineering are opening up a new opportunity to exploit these compounds within the lichen holobiome for industrial applications. This review also highlights the recent advances in culturing the symbionts and the computational and molecular genetics approaches of lichen gene regulation recognized for the enhanced production of target metabolites. The recent development of multi-omics novel biodiscovery strategies aided by synthetic biology in order to study the heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offers a promising means for a sustainable supply of specialized metabolites.

Effect of Culture Medium Incorporated with Ocimum sanctum Extract in Enhancing Anti-MRSA activity of Endophytic Fungus, Lasiodiplodia pseudotheobromae

The effect of incorporating plant extract in the culture medium on anti-MRSA activity of Lasiodiplodia pseudotheobromae IBRL OS-64, was investigated in the present study. On disk diffusion assay, the ethyl acetate fungal extract from culture medium supplemented with host plant extract (HPE) of Ocimum sanctum leaves demonstrated good anti-MRSA activity with a diameter inhibition zone of 22.6±0.6 mm. Meanwhile, the minimal inhibition concentration (MIC) values of the extract from YES broth and YES broth incorporated with HPE were 1000 µg/mL and 250 µg/mL, respectively. The MBC values were 8000 µg/mL and 500 µg/mL, respectively. The YES + HPE extracts exerted bactericidal effect against the test bacteria since the MBC/MIC ratio was less than or equal to 4. The time-kill study revealed a 90% of growth reduction of MRSA ATCC 33591 after 16 h exposure to the fungal extract cultured in YES + HPE. Ironically, for fungal extract grown in YES broth, time-kill curve showed a regrowth pattern of bacterial cells after 24 h exposed to the extract. Therefore, the present study suggested that the addition of HPE in the culture medium could enhance the anti-MRSA activity of endophytic fungus, L. pseudotheobromae IBRL OS-64 against MRSA ATCC 33591.

Exploring endophytes for in vitro synthesis of bioactive compounds similar to metabolites produced in vivo by host plants

Endophytes represent microorganisms residing within plant tissues without typically causing any adverse effect to the plants for considerable part of their life cycle and are primarily known for their beneficial role to their host-plant. These microorganisms can in vitro synthesize secondary metabolites similar to metabolites produced in vivo by their host plants. If microorganisms are isolated from certain plants, there is undoubtedly a strong possibility of obtaining beneficial endophytes strains producing host-specific secondary metabolites for their potential applications in sustainable agriculture, pharmaceuticals and other industrial sectors. Few products derived from endophytes are being used for cultivating resilient crops and developing non-toxic feeds for livestock. Our better understanding of the complex relationship between endophytes and their host will immensely improve the possibility to explore their unlimited functionalities. Successful production of host-secondary metabolites by endophytes at commercial scale might progressively eliminate our direct dependence on high-valued vulnerable plants, thus paving a viable way for utilizing plant resources in a sustainable way.

Fungal Endophytes as Efficient Sources of Plant-Derived Bioactive Compounds and Their Prospective Applications in Natural Product Drug Discovery: Insights, Avenues, and Challenges

Fungal endophytes are well-established sources of biologically active natural compounds with many producing pharmacologically valuable specific plant-derived products. This review details typical plant-derived medicinal compounds of several classes, including alkaloids, coumarins, flavonoids, glycosides, lignans, phenylpropanoids, quinones, saponins, terpenoids, and xanthones that are produced by endophytic fungi. This review covers the studies carried out since the first report of taxol biosynthesis by endophytic Taxomyces andreanae in 1993 up to mid-2020. The article also highlights the prospects of endophyte-dependent biosynthesis of such plant-derived pharmacologically active compounds and the bottlenecks in the commercialization of this novel approach in the area of drug discovery. After recent updates in the field of 'omics' and 'one strain many compounds' (OSMAC) approach, fungal endophytes have emerged as strong unconventional source of such prized products.

Control of Foodborne Pathogenic Bacteria by Endophytic Bacteria Isolated from Ginkgo biloba L

Endophytic bacteria (EB) are a prospective source of natural and novel bioactive compounds with pharmaceutical relevance. In the present study, a total of 50 EB were isolated from the fruits and leaves of ginkgo tree (Ginkgo biloba L.), the only living species in the division Ginkgophyta and popularly known as a living fossil. All the isolated EB were screened for their antibacterial activity against five deleterious foodborne pathogenic bacteria namely Escherichia coli ATCC 43890, Salmonella Typhimurium ATCC 19586, Bacillus cereus ATCC 10876, Listeria monocytogenes ATCC19115, and Staphylococcus aureus ATCC 12600. Among the isolated EB, GbF-96, GbF-97, and GbF-98 exhibited antibacterial activity against all the pathogenic bacteria tested, with inhibition zone ranging from 33.47 to 9.55 mm. GbF-96, identified as Bacillus subtilis, exerted the highest antibacterial activity against all the tested bacteria. In contrast, the ethyl acetate extract of GbF-96 showed antibacterial activity against only B. cereus, E. coli, and Salmonella Typhimurium. Scanning electron microscopy results indicated cracked and irregular, swollen, shrunken, and lysed cell surfaces of the pathogenic bacteria treated with ethyl acetate extract of GbF-96 or B. subtilis, indicating that the metabolites of GbF-96 might penetrate the bacterial cell membranes and evoke pathways inducing cell lysis. Together, the data suggest that B. subtilis from G. biloba can be a potential candidate for controlling dreadful foodborne pathogenic bacteria, either by itself or by its metabolites.

Determination and production of antimicrobial compounds by Aspergillus clavatonanicus strain MJ31, an endophytic fungus from Mirabilis jalapa L. using UPLC-ESI-MS/MS and TD-GC-MS analysis

Endophytic fungi associated with medicinal plants are reported as potent producers of diverse classes of secondary metabolites. In the present study, an endophytic fungi, Aspergillus clavatonanicus strain MJ31, exhibiting significant antimicrobial activity was isolated from roots of Mirabilis jalapa L., was identified by sequencing three nuclear genes i.e. internal transcribed spacers ribosomal RNA (ITS rRNA), 28S ribosomal RNA (28S rRNA) and translation elongation factor 1- alpha (EF 1α). Ethyl acetate extract of strain MJ31displayed significant antimicrobial potential against Bacillus subtilis, followed by Micrococccus luteus and Staphylococcus aureus with minimum inhibitory concentrations (MIC) of 0.078, 0.156 and 0.312 mg/ml respectively. In addition, the strain was evaluated for its ability to synthesize bioactive compounds by the amplification of polyketide synthase (PKS) and non ribosomal peptide synthetase (NRPS) genes. Further, seven antibiotics (miconazole, ketoconazole, fluconazole, ampicillin, streptomycin, chloramphenicol, and rifampicin) were detected and quantified using UPLC-ESI-MS/MS. Additionally, thermal desorption-gas chromatography mass spectrometry (TD-GC-MS) analysis of strain MJ31 showed the presence of 28 volatile compounds. This is the first report on A. clavatonanicus as an endophyte obtained from M. jalapa. We conclude that A. clavatonanicus strain MJ31 has prolific antimicrobial potential against both plant and human pathogens and can be exploited for the discovery of new antimicrobial compounds and could be an alternate source for the production of secondary metabolites.

Biological Evaluation of Endophytic Fungus Chaetomium sp. NF15 of Justicia adhatoda L.: A Potential Candidate for Drug Discovery

Background

The endophytes of medicinal plants, such as Justicia adhatoda L., represent a promising and largely underexplored domain that is considered as a repository of biologically active compounds.

Objectives

The aim of present study was isolation, identification, and biological evaluation of endophytic fungi associated with the J. adhatoda L. plant for the production of antimicrobial, antioxidant, and cytotoxic compounds

Materials and Methods

Endophytic fungi associated with the J. adhatoda L. plant were isolated from healthy plant parts and taxonomically characterized through morphological, microscopic, and 18S rDNA sequencing methods. The screening for bioactive metabolite production was achieved using ethyl acetate extracts, followed by the optimization of different parameters for maximum production of bioactive metabolites. Crude and partially purified extracts were used to determine the antimicrobial, antioxidant, and cytotoxic potential

Results

Out of six endophytic fungal isolates, Chaetomium sp. NF15 showed the most promising biological activity and was selected for detailed study. The crude ethyl acetate extract of NF15 isolate after cultivation under optimized culture conditions showed promising antimicrobial activity, with significant inhibition of the clinical isolates of Staphylococcus aureus (87%, n=42), Pseudomonas aeruginosa (> 85%, n = 41), and Candida albicans (62%, n = 24).

Conclusions

The present study confirms the notion of selecting endophytic fungi of medicinal plant Justicia for the bioassay-guided isolation of its bioactive compounds, and demonstrates that endophytic fungus Chaetomium sp. NF15 could be a potential source of bioactive metabolites

Investigation of Marine-Derived Fungal Diversity and Their Exploitable Biological Activities

Marine fungi are potential producers of bioactive compounds that may have pharmacological and medicinal applications. Fungi were cultured from marine brown algae and identified using multiple target genes to confirm phylogenetic placement. These target genes included the internal transcribed spacer (ITS), the nuclear large subunit (LSU), and the β-tubulin region. Various biological activities of marine-derived fungi were evaluated, including their antifungal, antioxidant and cellulolytic enzyme activities. As a result, a total of 50 fungi was isolated from the brown algae Sargassum sp. Among the 50 isolated fungi, Corollospora angusta was the dominant species in this study. The genus Arthrinium showed a relatively strong antifungal activity to all of the target plant pathogenic fungi. In particular, Arthrinium saccharicola KUC21221 showed high radical scavenging activity and the highest activities in terms of filter paper units (0.39 U/mL), endoglucanase activity (0.38 U/mL), and β-glucosidase activity (1.04 U/mL).

Production of potent antimicrobial agent by actinomycete, Streptomyces sannanensis strain SU118 isolated from phoomdi in Loktak Lake of Manipur, India

BACKGROUND

Actinomycetes have provided a wealth of bioactive secondary metabolites with interesting activities such as antimicrobial, antiviral and anticancer. The study aims at isolation, characterization and the antimicrobial potentiality of Streptomyces sannanensis SU118 obtained from Phoomdi, a unique habitat of Loktak Lake of Manipur, India.

RESULTS

An actinomycete strain isolated from Phoomdi soil of Loktak Lake of Manipur, India was identified as Streptomyces sannanensis SU118. It is a Gram-positive filamentous bacterium which exhibits antimicrobial activity only against Gram-positive bacteria, while Gram-negative organisms were not affected. Glucose Soyabean meal broth was found to be the suitable medium for antibiotic production at 28°C for seven days of incubation. The antimicrobial agent produced by the strain was extracted with ethyl acetate as solvent and purified by thin layer chromatography. Screening and bioassay - guided fractionation of the ethyl acetate extract from the culture filtrate led to the isolation of an active potential compound (R f value 0.56) with λmax 275.0 nm which has got the lowest minimum inhibitory concentration (0.5 μg/ml) against Staphylococcus aureus MTCC 96 and Staphylococcus aureus (clinical isolate), whereas highest (3.0 μg/ml) was recorded against Mycobacterium smegmatis MTCC 6 and Bacillus circulans MTCC 8074.

CONCLUSION

This study has therefore uncovered the potential of exploring virgin untapped habitats in the Indo-Burma biodiversity hot spot region as reservoir of promising antimicrobial metabolite producer. These results highlighted the scope for further characterization of the metabolite and could be a candidate in the generation of new antimicrobial agents.

Optimization of Antioxidant Potential of Penicillium granulatum Bainier by Statistical Approaches

A three-step optimization strategy which includes one-factor-at-a-time classical method and different statistical approaches (Plackett-Burman design and response surface methodology) that were applied to optimize the antioxidant potential of Penicillium granulatum. Antioxidant activity was assayed by different procedures and compared with total phenolic content. Primarily, different carbon and nitrogen sources were screened by classical methods, which revealed sucrose and NaNO3 to be the most suitable. In second step, Plackett-Burman design also supported sucrose and NaNO3 to be the most significant. In third step, response surface analysis showed 4.5% sucrose, 0.1% NaNO3, and incubation temperature of 25°C to be the optimal conditions. Under these conditions, the antioxidant potential assayed through different procedures was 78.2%, 70.1%, and 78.9% scavenging effect for DPPH radical, ferrous ion, and nitric oxide ion, respectively. The reducing power showed an absorbance of 1.6 with 68.5% activity for FRAP assay.

Screening of endophytic fungi having ability for antioxidative and alpha-glucosidase inhibitor activities isolated from Taxus sumatrana

Endophytic microbes are considered as an important source of natural products. They show antibiotic, anticancer, antioxidative and antidiabetic activities. Therefore, there are many reports on the isolation and bioactivity screening of endophytic fungi from various plants including Taxus species. Taxus sumatrana (Miq.) de Laub is found in Indonesia. The objective of this study is to conduct an in vitro screening of 14 endophytic fungi isolated from Taxus sumatrana having antioxidative and alpha-glucosidase inhibitor activities. Each endophytic fungus was cultured for 7 days and the fungal mycelium and medium were extracted with methanol and ethyl acetate, respectively, to produce each extract. The antioxidative activity of each extract was tested by DPPH free radical scavenging activity and beta-carotene bleaching assays, whereas antidiabetic activity was tested based on alpha-glucosidase inhibitor activity. The screening results showed that fungal mycelia of TSC 13 had the best alpha-glucosidase inhibitor activity and TSC 24 had the best antioxidative activity. Isolation of bioactive compounds from TSC 13 and TSC 24 is being conducted. This is the first report that endophytic fungi isolated from T. sumatrana exhibited anti alpha-glucosidase inhibitory and anti oxidative activities.

Antioxidant Activity of Aspergillus fumigatus

The antioxidant activity of Aspergillus fumigatus was assayed by different procedures and correlated with its extracellular total phenolic contents. Different physio-chemical parameters were optimized to enhance the activity. The culture grown under stationary conditions for 10 days at 25°C at pH 7 gave the best antioxidant activity. Statistical approaches demonstrated sucrose and NaNO(3) to be the most suitable carbon and nitrogen sources, respectively. Response surface analysis showed 5% sucrose, 0.05% NaNO(3), and incubation temperature of 35°C to be the optimal conditions for best expression of antioxidant activity. Under these conditions, the antioxidant potential assayed through different procedures was 89.8%, 70.1%, and 70.2% scavenging effect for DPPH radical, ferrous ion and nitric oxide ion, respectively. The reducing power showed an absorbance of 1.0 and FRAP assay revealed the activity of 60.5%. Extracellular total phenolic content and antioxidant activity as assayed by different procedures positively correlated.

Enhancement of diepoxin ζ production by yeast extract and its fractions in liquid culture of Berkleasmium-like endophytic fungus Dzf12 from Dioscorea zingiberensis

This study was to examine the effects of yeast extract (YE) and its fractions (YE1 and YE2) on the growth and diepoxin ζ (a spirobisnaphthalene with a diversity of bioactivities) production in liquid culture of Berkleasmium-like endophytic fungus Dzf12 from Dioscorea zingiberensis. When YE was applied to the liquid medium at 10 g/L on day 3 of culture, the diepoxin ζ production was most effectively enhanced 3.2-fold (378.70 mg/L versus 120.09 mg/L in control) after another 10 days culture. Feeding with 15 g/L of YE on day 9, the mycelia biomass reached 16.44 g/L, about 2.3-fold in comparison with the control (7.15 g/L). The polysaccharide fraction (YE1) was mainly responsible for stimulating diepoxin ζ accumulation, and the non-polysaccharide fraction (YE2) was mainly responsible for promoting mycelia growth. The results showed that the diepoxin ζ production in liquid culture of endophyte Dzf12 could be effectively enhanced by YE and its fractions.