Deep learning strategies for active secondary metabolites biosynthesis from fungi: Harnessing artificial manipulation and application

Enzyme evolution and antioxidant defense in salt-stressed Kunthali rice: A pathway to sustainable biocatalytic solutions for crop improvement

Kunthali (KTL), an indigenous rice variety from Tamil Nadu, India, was tested for its salt-tolerant capacity compared to commercial rice variety, IR64. Present study uncovered that KTL had a more effective response to salinity stress stimulus, as this cultivar uses reactive oxygen species scavenging mechanism through antioxidative enzymes like Superoxide dismutase, Catalase and Peroxidase. While KTL had lower levels of these enzymes compared to IR64, showed better modulation of total chlorophyll, carotenoids, anthocyanin, hydrogen peroxide, ascorbic acid, malondialdehyde, and proline contents also showed significant (p < 0.05) moderation upon salinity stress. In KTL, there was a significant correlation between the levels of H2O2 and antioxidant enzymes activity, which was not observed inIR64. Morphological, functional and biochemical investigations unveiled KTL as a promising candidate for salt-tolerance in TN, India. Advanced analysis using deep and machine learning techniques was used to analyze and predict the features essential for sustaining the salinity stress condition in rice. Principal component analysis and factor loadings provided a better understanding of salt-tolerant rice variables and placed apart the salt-sensitive rice. Correlation and regression charts gave a clear variable relationship between salt-tolerant and separated salt-sensitive rice. Comparatively, deep neural networks (DNN) predicted better features and models than machine learning techniques.

Optimization of fungal secondary metabolites production via response surface methodology coupled with multi-parameter optimized artificial neural network model

Filamentous fungi's secondary metabolites (SMs) possess significant application owing to their distinct structure and diverse bioactivities, yet their restricted yield levels often hinder further research and application. The study developed a response surface methodology-artificial neural network (RSM-ANN) strategy with multi-parameter optimizations of the ANN model to optimize medium for the production of two high-value fungal SMs, echinocandin E and paraherquamide A. Multi-parameter optimization of the ANN model was achieved through stratifying experimental data, fully adjusting neural network internals, and evaluating metaheuristic algorithms for optimal initial weights and biases. Experimental validation of models revealed that ANN-genetic algorithm models outperformed traditional RSM models in terms of determination coefficients, accuracy, and mean squared errors. ANN models showed outstanding robustness across a variety of fungal species, mediums, and experimental designs (Central Composite Design or Box-Behnken Design). This work refines the RSM-ANN optimization technique to increase fungal SM production efficiency, enabling industrial-scale production and applications.

Aspergillus-Penicillium co-culture: An investigation of bioagents for controlling Fusarium proliferatum-induced basal rot in onion

Fungal co-culture is a method that allows the detection of interactions between fungi, enabling the examination of bioactive novel metabolites induction that may not be produced in monocultures. Worldwide, Fusarium basal rot is a primary limitation to onion yield, being caused by different Fusarium species. Current research directions encourage biological control of plant diseases as a replacement for routine chemical treatments. The current study aimed to investigate the co-culturing technique for mining new sources of bioagents that could be used as fungicides. Aspergillus ochraceus AUMC15539 was co-cultured with Penicillium chrysogenum AUMC15504, and their ethyl acetate extract was tested in vitro and in a greenhouse against Fusarium proliferatum AUMC15541. The results showed that Aspergillus-Penicillium (AP) co-culture extract significantly inhibited the growth of F. proliferatum with an MIC value of 0.78 mg/mL and showed antioxidant efficiency with an IC50 value of 1.31 mg/mL. The brine shrimp toxicity testing showed a LC50 value of 2.77 mg/mL. In addition, the co-culture extract showed the highest phenolic content at 114.71 GAE mg/g, with a 27.82 QE mg/g flavonoid content. Profiling of AP co-culture and its monoculture extracts by HPLC revealed a change in the metabolites profile in AP co-culture. Principal component analysis verified a positive correlation between the obtained HPLC data of A. ochraceus (A), P. chrysogenum (P), and AP extracts. Greenhouse experiments demonstrated that treating infected onion plants with the AP co-culture extract significantly enhanced all growth parameters. Additionally, the co-culture extract treatment resulted in the highest levels of total pigments (3.46 mg/g), carbohydrates (52.10 mg/g dry weight), proteins (131.44 mg/g), phenolics (41.66 GAE mg/g), and flavonoids (9.43 QE mg/g) compared with other treatments. This indicates a promising potential for fungal co-cultures in discovering new bioagents with antifungal properties and growth-promoting capabilities.

Wound Healing, Metabolite Profiling, and In Silico Studies of Aspergillus terreus

Burn injuries, which significantly affect global public health, require effective treatment strategies tailored to varying severity. Fungi are considered a sustainable, easily propagated source for lead therapeutic discovery. In this study, we explored the burn wound healing potential of Aspergillus terreus through a combination of in vitro, in vivo, metabolite profiling, and in silico analysis. The in vitro scratch assays performed with human skin fibroblast cells showed promising wound healing activity. Furthermore, the burn-induced rats model showed a marked improvement in cutaneous wound healing, evidenced by an accelerated rate of wound closure and better skin regeneration after A. terreus extract treatment at 14 days. The results of this study demonstrated significant enhancements in wound closure and tissue regeneration in the treated rat model, surpassing the outcomes of standard treatments. This controlled healing process, evidenced by superior collagen synthesis and angiogenesis and confirmed by histopathological studies, suggests that A. terreus has potential beyond the traditionally studied fungal metabolites. The metabolite profiling of 27 bioactive compounds was further investigated by docking analysis for the potential inhibition of the NF-κB pathway, which has an important function in inflammation and wound repair. The compounds eurobenzophenone A (7), aspernolide D (16), asperphenalenone A (23), aspergilate D (15), kodaistatin A (18), and versicolactone A (14) showed the highest binding affinity to the target protein with a pose score of -16.86, -14.65, -12.65, -12.45, -12.19, and -12.08 kcal/mol, respectively. Drug-likeness properties were also conducted. The findings suggest the potential wound healing properties of A. terreus as a source for lead therapeutic candidate discovery.

Comparative Analysis of Microbial Diversity and Metabolic Profiles during the Spontaneous Fermentation of Jerusalem Artichoke (Helianthus tuberosus L.) Juice

Jerusalem artichoke juice is valued for its nutritional content and health benefits. Spontaneous fermentation enhances its flavor, quality, and functional components through microbial metabolic activities. This study used high-throughput sequencing to analyze microbial community changes, and LC-MS and GC-MS to detect secondary metabolites and flavor compounds during fermentation. During natural fermentation, beneficial bacteria like Lactobacillus and Pediococcus increased, promoting lactic acid production and inhibiting harmful bacteria, while environmental bacteria decreased. Similarly, fungi shifted from environmental types like Geosmithia and Alternaria to fermentation-associated Pichia and Penicillium. A total of 1666 secondary metabolites were identified, with 595 upregulated and 497 downregulated. Key metabolic pathways included phenylpropanoid biosynthesis, with significant increases in phenylalanine, tryptophan, and related metabolites. Lipid and nucleotide metabolism also showed significant changes. Flavor compounds, including 134 identified alcohols, esters, acids, and ketones, mostly increased in content after fermentation. Notable increases were seen in Phenylethyl Alcohol, Ethyl Benzenepropanoate, 3-Methylbutyl Butanoate, Ethyl 4-Methylpentanoate, 5-Ethyl-3-Hydroxy-4-Methyl-2(5H)-Furanone, Ethyl Decanoate, Hexanoic Acid, and 1-Octanol. γ-aminobutyric acid (GABA) and other functional components enhanced the health value of the juice. This study provides insights into microbial and metabolic changes during fermentation, aiding in optimizing processes and improving the quality of fermented Jerusalem artichoke juice for functional food development.

Flavonoid glycosides from Odontonema strictum leaves

Odontonema strictum (Acanthaceae) leave extract was investigated for its flavonoid content. Column chromatography was used for compound isolation and mass spectrometry was performed using electrospray ionization (ESI) in the negative ion mode for compound identification. The full characterization of luteolin 7-O-[β-D-apiofuranosyl-(1 → 2)-O-β-D-ribofuranoside], a flavone glycoside, was achieved using tandem mass spectrometry and high resolution 1D and 2D Nuclear Magnetic Resonance (NMR). Among the 10 flavonoids glycosides detected in the ethanol extract, beside the isolated one, 3 flavone glycosides with luteolin or apigenin aglycone were tentatively identified.

Oleaginous fungi: a promising source of biofuels and nutraceuticals with enhanced lipid production strategies

Oleaginous fungi have attracted a great deal of interest for their potency to accumulate high amounts of lipids (more than 20% of biomass dry weight) and polyunsaturated fatty acids (PUFAs), which have a variety of industrial and biological applications. Lipids of plant and animal origin are related to some restrictions and thus lead to attention towards oleaginous microorganisms as reliable substitute resources. Lipids are traditionally biosynthesized intra-cellularly and involved in the building structure of a variety of cellular compartments. In oleaginous fungi, under certain conditions of elevated carbon ratio and decreased nitrogen in the growth medium, a change in metabolic pathway occurred by switching the whole central carbon metabolism to fatty acid anabolism, which subsequently resulted in high lipid accumulation. The present review illustrates the bio-lipid structure, fatty acid classes and biosynthesis within oleaginous fungi with certain key enzymes, and the advantages of oleaginous fungi over other lipid bio-sources. Qualitative and quantitative techniques for detecting the lipid accumulation capability of oleaginous microbes including visual, and analytical (convenient and non-convenient) were debated. Factors affecting lipid production, and different approaches followed to enhance the lipid content in oleaginous yeasts and fungi, including optimization, utilization of cost-effective wastes, co-culturing, as well as metabolic and genetic engineering, were discussed. A better understanding of the oleaginous fungi regarding screening, detection, and maximization of lipid content using different strategies could help to discover new potent oleaginous isolates, exploit and recycle low-cost wastes, and improve the efficiency of bio-lipids cumulation with biotechnological significance.

The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applications

This review provides a comprehensive overview of the key aspects of the natural metabolite production by endophytic fungi, which has attracted significant attention due to its diverse biological activities and wide range of applications. Synthesized by various fungal species, these metabolites encompass compounds with therapeutic, agricultural, and commercial significance. We delved into strategies and advancements aimed at optimizing fungal metabolite production. Fungal cultivation, especially by Aspergillus, Penicillium, and Fusarium, plays a pivotal role in metabolite biosynthesis, and researchers have explored both submerged and solid-state cultivation processes to harness the full potential of fungal species. Nutrient optimization, pH, and temperature control are critical factors in ensuring high yields of the targeted bioactive metabolites especially for scaling up processes. Analytical methods that includes High-Performance Liquid Chromatography (HPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), Gas Chromatography-Mass Spectrometry (GC-MS), Nuclear Magnetic Resonance (NMR), and Mass Spectrometry (MS), are indispensable for the identification and quantification of the compounds. Moreover, genetic engineering and metabolic pathway manipulation have emerged as powerful tools to enhance metabolite production and develop novel fungal strains with increased yields. Regulation and control mechanisms at the genetic, epigenetic, and metabolic levels are explored to fine-tune the biosynthesis of fungal metabolites. Ongoing research aims to overcome the complexity of the steps involved to ensure the efficient production and utilization of fungal metabolites.

Anti-Staphylococcal, Anti-Candida, and Free-Radical Scavenging Potential of Soil Fungal Metabolites: A Study Supported by Phenolic Characterization and Molecular Docking Analysis

Staphylococcus and Candida are recognized as causative agents in numerous diseases, and the rise of multidrug-resistant strains emphasizes the need to explore natural sources, such as fungi, for effective antimicrobial agents. This study aims to assess the in vitro anti-staphylococcal and anti-candidal potential of ethyl acetate extracts from various soil-derived fungal isolates. The investigation includes isolating and identifying fungal strains as well as determining their antioxidative activities, characterizing their phenolic substances through HPLC analysis, and conducting in silico molecular docking assessments of the phenolics' binding affinities to the target proteins, Staphylococcus aureus tyrosyl-tRNA synthetase and Candida albicans secreted aspartic protease 2. Out of nine fungal species tested, two highly potent isolates were identified through ITS ribosomal gene sequencing: Aspergillus terreus AUMC 15447 and A. nidulans AUMC 15444. Results indicated that A. terreus AUMC 15447 and A. nidulans AUMC 15444 extracts effectively inhibited S. aureus (concentration range: 25-0.39 mg/mL), with the A. nidulans AUMC 15444 extract demonstrating significant suppression of Candida spp. (concentration range: 3.125-0.39 mg/mL). The A. terreus AUMC 15447 extract exhibited an IC50 of 0.47 mg/mL toward DPPH radical-scavenging activity. HPLC analysis of the fungal extracts, employing 18 standards, revealed varying degrees of detected phenolics in terms of their presence and quantities. Docking investigations highlighted rutin as a potent inhibitor, showing high affinity (-16.43 kcal/mol and -12.35 kcal/mol) for S. aureus tyrosyl-tRNA synthetase and C. albicans secreted aspartic protease 2, respectively. The findings suggest that fungal metabolites, particularly phenolics, hold significant promise for the development of safe medications to combat pathogenic infections.

Can we control potato fungal and bacterial diseases? - microbial regulation

The potato plant is one of the main crops in the world. However, relatively little is known about key virulence factors of major fungal and bacterial diseases in potatoes, biocontrol measures to improve activity and stability, and the core driving forces in the control process. Here, we focus on analyzing the mechanisms by which genes, proteins, or (and) metabolites of potato pathogens as key virulence factors. Then, the single strain biocontrol agents, synthetic microbial communities, microbial microcapsule strategies were introduced, and the latter two strategies can improve stability and activity in biocontrol. Meanwhile, summarized the defense mechanisms of biocontrol and their specific issues in practical applications. Furthermore, explore how potato crop management, soil management, and climate effects, as crucial driving forces affect potato biocontrol in the system. Dynamic and systematic research, excavation of biocontrol strain resources, find the causes of regional disease resistance and exploration of biocontrol mechanism will provide promising solutions for biotic stress faced by potato in the future.

Soil microbial community composition and co-occurrence network responses to mild and severe disturbances in volcanic areas

Soil physicochemical properties and vegetation types are the main factors affecting soil microorganisms, but there are few studies on the effects of the disturbance following volcanic eruption. To make up for this lack of knowledge, we used Illumina Miseq high-throughput sequencing to study the characteristics of soil microorganisms on both shores of a volcanically disturbed lake. Soil microorganisms in the two sites were subjected to different degrees of volcanic disturbance and showed significant heterogeneity. Mild volcanic disturbance area had higher enrichment of prokaryotic community. Co-occurrence network analysis showed that a total of 12 keystone taxa (9 prokaryotes and 3 fungi) were identified, suggesting that soil prokaryote may play a more significant role than fungi in overall community structure and function. Compared with severe volcanic disturbance area, the soil microbial community in mild volcanic disturbance area had the higher modular network (0.327 vs 0.291). The competition was stronger (positive/negative link ratio, P/N: 1.422 vs 1.159). Random forest analysis showed that soil superoxide dismutase was the most significant variable associated with soil microbial community. Structural equation model (SEM) results showed that keystone had a directly positive effect on prokaryotic (λ = 0.867, P < 0.001) and fungal (λ = 0.990, P < 0.001) multifunctionality while had also a directly positive effect on fungal diversity (λ = 0.553, P < 0.001), suggesting that keystone taxa played a key role in maintaining ecosystem stability. These results were important for understanding the effects of different levels of volcanic disturbance on soil ecosystems.

Evaluating the antioxidant activity of secondary metabolites of endophytic fungi from Hypericum perforatum L. by an electrochemical biosensor based on AuNPs/AC@CS composite

Due to the variety and activity of secondary metabolites of endophytic fungi (SMEF) from medicinal plants, and the operation cumbersome of existing methods for evaluating the activity, there is urgent to establish a simple, efficient and sensitive evaluation and screening technology. In this study, the prepared chitosan functionalized activated carbon (AC@CS) composite as the electrode substrate material was used to modify glassy carbon electrode (GCE), and the gold nanoparticles (AuNPs) was deposited on AC@CS/GCE by cyclic voltammetry (CV). A ds-DNA/AuNPs/AC@CS/GCE electrochemical biosensor for evaluating the antioxidant activity of SMEF from Hypericum perforatum L. (HP L.) was fabricated using the method of layer by layer assembly. The experimental conditions affecting the evaluation results of the biosensor were optimized by square wave voltammetry (SWV) using Ru(NH₃)₆³⁺ as the probe, and the antioxidant activity of various SMEF from HP L. was evaluated by the proposed biosensor. Meanwhile, the results of the biosensor were also verified by UV-vis. According to the optimized experimental results, the biosensors had a high levels of oxidative DNA damage at pH 6.0 and Fenton solution system with Fe²⁺ to OH^- ratio of 1:3 for 30 min. Among the crude extracts of SMEF from roots, stems and leaves of HP L., the crude extracts from stems presents a high antioxidant activity, but it was weaker than l-ascorbic acid. This result was consistent with the evaluation results of UV-vis spectrophotometric method, also the fabricated biosensor presents high stability and sensitivity. This study not only provides a novel, convenient and efficient way for rapid evaluating the antioxidant activity of a wide variety of SMEF from HP L., but also provides a novel evaluation strategy for the SMEF from medicinal plants.

Resveratrol biosynthesis, optimization, induction, bio-transformation and bio-degradation in mycoendophytes

Resveratrol (3,4,5-trihydroxystilbene) is a naturally occurring polyphenolic stilbene compound produced by certain plant species in response to biotic and abiotic factors. Resveratrol has sparked a lot of interest due to its unique structure and approved therapeutic properties for the prevention and treatment of many diseases such as neurological disease, cardiovascular disease, diabetes, inflammation, cancer, and Alzheimer's disease. Over the last few decades, many studies have focused on the production of resveratrol from various natural sources and the optimization of large-scale production. Endophytic fungi isolated from various types of grapevines and Polygonum cuspidatum, the primary plant sources of resveratrol, demonstrated intriguing resveratrol-producing ability. Due to the increasing demand for resveratrol, one active area of research is the use of endophytic fungi and metabolic engineering techniques for resveratrol's large-scale production. The current review addresses an overview of endophytic fungi as a source for production, as well as biosynthesis pathways and relevant genes incorporated in resveratrol biosynthesis. Various approaches for optimizing resveratrol production from endophytic fungi, as well as their bio-transformation and bio-degradation, are explained in detail.

In Vitro and In Silico Antioxidant Efficiency of Bio-Potent Secondary Metabolites From Different Taxa of Black Seed-Producing Plants and Their Derived Mycoendophytes

Oxidative stress is involved in the pathophysiology of multiple health complications, and it has become a major focus in targeted research fields. As known, black seeds are rich sources of bio-active compounds and widely used to promote human health due to their excellent medicinal and pharmaceutical properties. The present study investigated the antioxidant potency of various black seeds from plants and their derived mycoendophytes, and determined the total phenolic and flavonoid contents in different extracts, followed by characterization of major constituents by HPLC analysis. Finally, in silico docking determined their binding affinities to target myeloperoxidase enzymes. Ten dominant mycoendophytes were isolated from different black seed plants. Three isolates were then selected based on high antiradical potency and further identified by ITS ribosomal gene sequencing. Those isolated were Aspergillus niger TU 62, Chaetomium madrasense AUMC14830, and Rhizopus oryzae AUMC14823. Nigella sativa seeds and their corresponding endophyte A. niger had the highest content of phenolics in their n-butanol extracts (28.50 and 24.43 mg/g), flavonoids (15.02 and 11.45 mg/g), and antioxidant activities (90.48 and 81.48%), respectively, followed by Dodonaea viscosa and Portulaca oleracea along with their mycoendophytic R. oryzae and C. madrasense. Significant positive correlations were found between total phenolics, flavonoids, and the antioxidant activities of different tested extracts. The n-butanol extracts of both black seeds and their derived mycoendophytes showed reasonable IC50 values (0.81–1.44 mg/ml) compared to the control with significant correlations among their phytochemical contents. Overall, seventeen standard phenolics and flavonoids were used, and the compounds were detected in different degrees of existence and concentration in the examined extracts through HPLC analysis. Moreover, the investigation of the molecular simulation results of detected compounds against the myeloperoxidase enzyme revealed that, as a targeted antioxidant, rutin possessed a high affinity (−15.3184 kcal/mol) as an inhibitor. Taken together, the black seeds and their derived mycoendophytes are promising bio-prospects for the broad industrial sector of antioxidants with several valuable potential pharmaceutical and nutritional applications.

In Vitro Phytobiological Investigation of Bioactive Secondary Metabolites from the Malus domestica-Derived Endophytic Fungus Aspergillus tubingensis Strain AN103

Endophytic fungi including black aspergilli have the potential to synthesize multiple bioactive secondary metabolites. Therefore, the search for active metabolites from endophytic fungi against pathogenic microbes has become a necessity for alternative and promising strategies. In this study, 25 endophytic fungal isolates associated with Malus domestica were isolated, grown, and fermented on a solid rice medium. Subsequently, their ethyl acetate crude extracts were pretested for biological activity. One endophytic fungal isolate demonstrated the highest activity and was chosen for further investigation. Based on its phenotypic, ITS ribosomal gene sequences, and phylogenetic characterization, this isolate was identified as Aspergillus tubingensis strain AN103 with the accession number (KR184138). Chemical investigations of its fermented cultures yielded four compounds: Pyranonigrin A (1), Fonsecin (2), TMC 256 A1 (3), and Asperazine (4). Furthermore, 1H-NMR, HPLC, and LC-MS were performed for the identification and structure elucidation of these metabolites. The isolated pure compounds showed moderate-to-potent antibacterial activities against Pseudomonas aeruginosa and Escherichia coli (MIC value ranged from 31 and 121 to 14.5 and 58.3 μg/mL), respectively; in addition, the time−kill kinetics for the highly sensitive bacteria against isolated compounds was also investigated. The antifungal activity results show that (3) and (4) had the maximum effect against Fusarium solani and A. niger with inhibition zones of 16.40 ± 0.55 and 16.20 ± 0.20 mm, respectively, and (2) had the best effect against Candida albicans, with an inhibition zone of 17.8 ± 1.35 mm. Moreover, in a cytotoxicity assay against mouse lymphoma cell line L5178Y, (4) exhibited moderate cytotoxicity (49% inhibition), whereas (1−3) reported weak cytotoxicity (15, 26, and 19% inhibition), respectively. Our results reveal that these compounds might be useful to develop potential cytotoxic and antimicrobial drugs and an alternative source for various medical and pharmaceutical fields.