Antifungal Metabolites Produced by Chaetomium globosum No.04, an Endophytic Fungus Isolated from Ginkgo biloba

Construction of an Efficient Engineered Strain for Chaetoglobosin A Bioresource Production from Potato Starch Industrial Waste

Chaetoglobosin A (CheA), a typical structure of the cytochalasin family, exhibits outstanding efficacy against a variety of tumor cells and plant pathogens. However, its low yield and high production cost are major obstacles limiting its wide application. In order to increase CheA yield, an engineered strain was established by overexpressing CgMfs, the gene encoding the MFS family's efflux pump, on chassis cells lacking CgXpp1, which have been shown to act as a negative regulator of CheA biosynthesis. As expected, the engineered strain significantly boosted CheA production from 63.19 to 265.93 mg/L after incubation in PDA medium for 10 d, whereas the yield of the engineered strain was remarkably enhanced 2.93-fold compared with the wild type, following 10 d of cultivation utilizing potato starch industrial waste. The addition of metal ions had a positive effect on CheA production, with Cu2+ being the most effective and improving production to 176.92 mg/L. The optimal fermentation conditions were determined by response surface optimization, and under the optimal conditions, the engineered strain could stably produce CheA with a yield of 197.58 mg/L. This study provided the conditions for reducing production costs while increasing CheA production, as well as new strategies and insights for the production of the target compound.

Revealing culturable fungal microbiome communities from the Arabian Peninsula desert representing a unique source of biochemicals for drug discovery and biotechnology

Background

Microbes living at extremes evolve unique survival strategies to adapt to challenging environmental conditions. Among these strategies is their distinctive metabolic potential and ability to produce specialized metabolites enabling them to compete for limited resources and defend against predators. These metabolites have significant potential in pharmaceutical and industrial applications, particularly in the development of drugs and biochemicals.

Objectives

This study aimed to investigate the culturable fungal communities associated with four desert plants and their surrounding soils in the Arabian Peninsula desert to identify their bioactive properties.

Methods

A total of 12 distinct fungal species were isolated from the plants and soils. Each plant hosted a unique set of fungi, demonstrating the diversity of desert-adapted fungal communities. Biological activities of the fungal extracts were evaluated through various assays, including antimicrobial, antifungal, anticancer, and antioxidant properties.

Results

Panicum turgidum harbors the most diverse fungal community, dominated by genera such as Mucor, Aspergillus, Colletotrichum, Alternaria, and Chaetomium. Aspergillus species comprise 33% of the total isolates, followed by Fusarium at 16%. All extracts exhibit diverse activities, with Aspergillus species demonstrating the highest antioxidant activities and total phenolic and flavonoid content. Fungi from P. turgidum, particularly Mucor sp., Aspergillus sp., and Curvularia sp., display potent activity against Staphylococcus aureus, while Mucor sp., Chaetomium sp., and Curvularia sp. exhibit moderate inhibition against Pseudomonas aeruginosa.

Conclusion

This study highlights the importance of exploring extremophilic microorganisms, such as those found in desert ecosystems, as they offer a wealth of compounds that could address current challenges in drug discovery and biotechnology.

Plant secondary metabolites involved in the stress tolerance of long-lived trees

Ancient trees are natural wonders because of their longevity, having lived for hundreds or thousands of years, and their ability to withstand changing environments and a variety of stresses. These long-lived trees have sophisticated defense mechanisms, such as the production of specialized plant metabolites (SPMs). In this review, we provide an overview of the major biotic and abiotic stresses that long-lived trees often face, as well as an analysis of renowned ancient tree species and their unique protective SPMs against environmental stressors. We also discuss the synthesis and accumulation of defensive SPMs induced by environmental factors and endophytes in these trees. Furthermore, we conducted a comparative genomic analysis of 17 long-lived tree species and discovered significant expansions of SPM biosynthesis gene families in these species. Our comprehensive review reveals the crucial role of SPMs in high resistance in long-lived trees, providing a novel natural resource for plant defense, crop improvement and even the pharmaceutical industry.

Diversity and Advantages of Culturable Endophytic Fungi from Tea (Camellia sinensis)

Sordariomycetes, Dothideomycetes, and Eurotioycetes are three classes of endophytes that colocalize with tea (Camellia sinensis). Overall, the diversity indexes in this study indicated a greater abundance of fungal endophytes in roots and stems. Taking the production system into account, conventional tea plantations exhibit lower diversity compared to organic tea plantations. Notably, the influence of agrochemicals had the largest impact on the fungal endophyte communities within roots and young leaves. Despite the limited fungal diversity in conventional plantations, three fungal endophytes were isolated from tea in this culture system: Diaporthe sp., YI-005; Diaporthe sp., SI-007; and Eurotium sp., RI-008. These isolated endophytes exhibited high antagonistic activity (93.00-97.00% inhibition of hypha growth) against Stagonosporopsis cucurbitacearum, the causal agent of gummy stem blight disease. On the other hand, endophytic fungi isolated from tea in an organic system-Pleosporales sp., SO-006 and Pleosporales sp., RO-013-established the ability to produce indole-3-acetic acid (IAA; 0.65 ± 0.06 µg/mL) and assist the solubilizing phosphorus (5.17 ± 1.03 µg/mL) from the soil, respectively. This suggested that the level of diversity, whether at the tissue level or within the farming system, did not directly correlate with the discovery of beneficial fungi. More importantly, these beneficial fungi showed the potential to develop into biological agents to control the devastating diseases in the cucurbit family and the potential for use as biofertilizers with a wide range of applications in plants. Therefore, it can be concluded that there are no restrictions limiting the use of fungal endophytes solely to the plant host from which they were originally isolated.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Characterization and development of transcriptome-derived novel EST-SSR markers to assess genetic diversity in Chaetomium globosum

Chaetomium globosum Kunze, an internationally recognized biocontrol fungus. It mycoparasitizes various plant pathogens and produce antifungal metabolites to suppress the growth of pathogenic fungi. Lack of detailed genome level diversity studies has delimited the development and utilization of potential C. globosum strains. The present study was taken to reveal the distribution, identification, and characterization of expressed sequence tag-simple sequence repeats (EST-SSRs) in C. globosum. RNA-Seq experiment was performed for C. globosum potential isolate Cg2 (AY429049) using Illumina HiSeq 2500. Reference-guided de novo assembly yielded 45,582 transcripts containing 27,957 unigenes. We generated a new set of 8485 EST-SSR markers distributed in 5908 unigene sequences with one SSR locus distribution density per 6.1 kb. Six distinct classes of SSR repeat motifs were identified. The most abundant were mononucleotide repeats (51.67%), followed by tri-nucleotides (36.61%). Out of 5034 EST-SSR primers, 50 primer pairs were selected and validated for the polymorphic study of 15 C. globosum isolates. Twenty-two SSR markers showed average genetic polymorphism among C. globosum isolates. The number of alleles (Na) per marker ranges from 2 to 4, with a total of 74 alleles detected for 22 markers with a mean polymorphism information content (PIC) value of 0.4. UPGMA hierarchical clustering analysis generated three main clusters of C. globosum isolates and exhibited a lower similarity index range from 0.59 to 0.85. Thus, the newly developed EST-SSR markers could replace traditional methods for determining diversity. The study will also enhance the genomic research in C. globosum to explore its biocontrol potential against phytopathogens.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03794-7.

Chaetoglobosin A Contributes to the Antagonistic Action of Chaetomium globosum Strain 61239 Toward the Apple Valsa Canker Pathogen Cytospora mali

Apple Valsa canker (AVC) weakens apple trees and significantly reduces apple production in China and other East Asian countries. Thus far, very few AVC-targeting biocontrol resources have been described. Here, we present a thorough description of a fungal isolate (Chaetomium globosum, 61239) that has strong antagonistic action toward the AVC causal agent Cytospora mali. Potato dextrose broth culture filtrate of strain 61239 completely suppressed the mycelial growth of C. mali on potato dextrose agar, and strongly constrained the development of AVC lesions in in vitro infection assays. ultra-performance liquid chromatography (UPLC) and HPLC-MS/MS investigations supported the conclusion that strain 61239 produces chaetoglobosin A, an antimicrobial metabolite that inhibits C. mali. Using genome sequencing, we discovered a gene cluster in strain 61239 that may be responsible for chaetoglobosin A production. Two of the cluster's genes-cheA, a PKS-NRPS hybrid enzyme, and cheB, an enoyl reductase-were individually silenced, which significantly decreased chaetoglobosin A accumulation as well as the strain's antagonistic activity against C. mali. Together, the findings of our investigation illustrate the potential use of Chaetomium globosum for the management of AVC disease and emphasize the significant contribution of chaetoglobosin A to the antagonistic action of strain 61239.

Long-term effects of chloropicrin fumigation on soil microbe recovery and growth promotion of Panax notoginseng

Introduction

Panax notoginseng is a precious Chinese medicinal material. Soil fumigation can control soil-borne disease and overcome the continuous cropping obstacles of P. notoginseng. However, chloropicrin (CP) fumigation can kill non-target soil microorganisms and reduce microbial diversity, but the long-time impacts of CP fumigation on soil microbial are less reported.

Methods

We studied the long-term effects of CP fumigation on soil microbes with high-throughput gene sequencing, and correlated the changes in the composition of microbial communities with environmental factors like soil physicochemical properties and soil enzyme activities. This study mainly focuses on the recovery characteristics of soil microbe after soil fumigation by evaluating the ecological restoration of P. notoginseng soil, its sustained control effect on plant diseases, and its promotion effect on crop growth by focusing on the CP fumigation treatment.

Results

The results showed that CP fumigation significantly increased soil available phosphorus (P) to 34.6 ~ 101.6 mg/kg and electrical conductivity (EC) by 18.7% ~ 34.1%, respectively. High-throughput gene sequencing showed that soil fumigation with CP altered the relative abundance of Trichoderma, Chaetomium, Proteobacteria, and Chloroflexi in the soil while inhibiting a lot of Fusarium and Phytophthora. The inhibition rate of Phytophthora spp. was still 75.0% in the third year after fumigation. Fumigation with CP enhanced P. notoginseng's survival rate and stimulated plant growth, ensuring P. notoginseng's healthy in the growth period. The impact of fumigation on microbial community assembly and changes in microbial ecological niches were characterized using normalized stochasticity ratio (NST) and Levins' niche breadth index. Stochasticity dominated bacterial community assembly, while the fungal community was initially dominated by stochasticity and later by determinism. Fumigation with CP reduced the ecological niches of both fungi and bacteria.

Conclusion

In summary, the decrease in microbial diversity and niche caused by CP fumigation could be recovered over time, and the control of soil pathogens by CP fumigation remained sustainable. Moreover, CP fumigation could overcome continuous cropping obstacles of P. notoginseng and promote the healthy growth of P. notoginseng.

Caryophyllene Sesquiterpenes from a Chaetomium globosum Endophyte of the Canadian Medicinal Plant Empetrum nigrum

Punctaporonins T (1) and U (2), new caryophyllene sesquiterpenes, were isolated with three known punctaporonins, A (3), B (4), and C (5), from the endophytic fungus Chaetomium globosum (TC2-041). The structures and relative configurations of punctaporonins T and U were elucidated based on a combination of HRESIMS, 1D/2D NMR spectroscopic analysis, and X-ray diffraction analysis, while their absolute configuration is presumed to be consistent with the co-isolated 3-5 on biogenetic arguments. Compound 1 showed weak inhibitory activity against both Mycobacterium tuberculosis and Staphylococcus aureus.

Chemical diversity and biological activities of specialized metabolites from the genus Chaetomium: 2013-2022

Chaetomium (Chaetomiaceae), a large fungal genus consisting of at least 400 species, has been acknowledged as a promising resource for the exploration of novel compounds with potential bioactivities. Over the past decades, emerging chemical and biological investigations have suggested the structural diversity and extensive potent bioactivity of the specialized metabolites in the Chaetomium species. To date, over 500 compounds with diverse chemical types have been isolated and identified from this genus, including azaphilones, cytochalasans, pyrones, alkaloids, diketopiperazines, anthraquinones, polyketides, and steroids. Biological research has indicated that these compounds possess a broad range of bioactivities, including antitumor, anti-inflammatory, antimicrobial, antioxidant, enzyme inhibitory, phytotoxic, and plant growth inhibitory activities. This paper summarizes current knowledge referring to the chemical structure, biological activity, and pharmacologic potency of the specialized metabolites in the Chaetomium species from 2013 to 2022, which might provide insights for the exploration and utilization of bioactive compounds in this genus both in the scientific field and pharmaceutical industry.

First Report of Clonostachys rosea as a Mycoparasite on Sclerotinia sclerotiorum Causing Head Rot of Cabbage in India

Clonostachys rosea, an ascomycetous, omnipresent, cellulose-decaying soil fungus, has been reported to be a well-known mycoparasitic biological control agent. In this study, we isolated C. rosea, a mycoparasitic fungus for the first time in India from sclerotia of the notorious plant pathogen Sclerotinia sclerotiorum, causing head rot disease in cabbage. A total of five mycoparasitic fungi were isolated from the sclerotial bodies of S. sclerotiorum (TNAU-CR 01, 02, 03, 04 and 05). All the isolates were tested under morpho-molecular characterization. Among them, TNAU-CR 02 showed the greatest mycelial inhibition of 79.63% over the control. Similarly, the SEM imaging of effective C. rosea isolates indicated the presence of numerous conidia destroying the outer cortex layers of sclerotia. Metabolite fingerprinting of C. rosea TNAU-CR 02 identified 18 chemical compounds using GC-MS analysis. The crude antibiotics of C. rosea TNAU-CR 02 were verified for their antifungal activity against S. sclerotiorum and the results revealed 97.17% mycelial inhibition compared with the control. Similarly, foliar application of TNAU-CR 02 at 5 mL/litre on 30, 45 and 60 days after transplanting showed the lowest disease incidence of 15.1 PDI compared to the control. This discovery expands our understanding of the biology and the dissemination of C. rosea, providing a way for the exploitation of C. rosea against cabbage head rot pathogens.

Antioxidant, Cytotoxic, and DNA Damage Protection Activities of Endophytic Fungus Pestalotiopsis neglecta Isolated from Ziziphus spina-christi Medicinal Plant

Fungal endophytes are friendly microorganisms that colonize plants and are important in the interactions between plants and their environment. They generate valuable secondary metabolites that are valuable to both plants and humans. Endophytic fungi with bioactivities were isolated from the leaves of the medicinal plant Ziziphus spina-christi. An efficient isolate was selected and identified as Pestalotiopsis neglecta based on nucleotide sequencing of the internal transcribed spacer region (ITS 1-5.8S-ITS 2) of the 18S rRNA gene (NCBI accession number OP529850); the 564 bp had 99 to 100% similarity with P. neglecta MH860161.1, AY682935.1, KP689121.1, and MG572407.1, according to the BLASTn analysis, following preliminary phytochemical and antifungal screening. The biological activities of this fungus' crude ethyl acetate (EtOAc) extract were assessed. With an efficient radical scavenging activity against 2,2'-diphenyl-1-picrylhydrazyl and an IC₅₀ value of 36.6 µg mL^-1, P. neglecta extract has shown its potential as an antioxidant. Moreover, it displayed notable cytotoxic effects against MCF-7 (breast carcinoma, IC₅₀ = 22.4 µg mL^-1), HeLa (cervical carcinoma, IC₅₀ = 28.9 µg mL^-1) and HepG-2 (liver carcinoma, IC₅₀ = 28.9 µg mL^-1). At 10 µg mL^-1, EtOAc demonstrated significant DNA protection against hydroxyl radical-induced damage. Based on FT-IR and GC-MS spectral analysis, it was detected that the EtOAc of P. neglecta product contains multiple bioactive functional groups. Subsequently, this validated the features of major different potent compounds; tolycaine, 1H-pyrazol, 1,3,5-trimethyl-, eugenol, 2,5-cyclohexadiene-1,4-dione, 2,6-bis(1,1-dimethyl), and bis(2-ethylhexyl) phthalate. Since these compounds are biologically relevant in various aspects, and distinct biological activities of fungal extract were acceptable in vitro, this suggests that endophytic fungus P. neglecta may be a viable source of bioactive natural products. This could be a good starting point for pharmaceutical applications.

Key insights into secondary metabolites from various Chaetomium species

Endophytic fungi have proved to be a major source of secondary metabolites, wherein the genus Chaetomium has emerged as a source of multifarious bioactive natural compounds belonging to diverse classes such as chaetoglobosins, epipolythiodioxopiperazines, azaphilones, xanthones, anthraquinone, chromones, depsidones, terpenoids, and steroids. The objective of this review is to encapsulate recent findings on various Chaetomium strains, such as C. globosum, C. cupreum, C. elatum, C. subspirale, C. olivaceum, C. indicum, and C. nigricolor known for production of beneficial secondary metabolites, with an insight into their origin and function. A thorough literature survey was conducted for obtaining Chaetomium-derived secondary metabolites, with a scope of future application into drug development efforts. More than 100 secondary metabolites, with various beneficial properties such as antitumor, cytotoxic, antimalarial, and enzyme inhibitory activities, were enlisted. We believe this review will enhance the understanding of beneficial effects conferred by various Chaetomium-derived secondary metabolites and emphasize their potential in serving novel drug development efforts. KEY POINTS: • Identified Chaetomium-derived metabolites with potential for drug development. • More than 100 beneficial metabolites are enlisted. • Benefits include anti-cancerous, antimalarial, and anti-enzymatic properties.

New insight into the production improvement and resource generation of chaetoglobosin A in Chaetomium globosum

Chaetoglobosin A is a complex macrocyclic alkaloid with potent antimycotic, antiparasitic and antitumor properties. However, the low output and high cost of chaetoglobosin A biosynthesis have hampered the application and commercialization of chaetoglobosin A in agriculture and biomedicine. Here, the CgMfs1 gene, which encodes the major facilitator superfamily secondary transporter, was identified based on bioinformatics analysis, and an intensive study of its effects on chaetoglobosin A biosynthesis and secretion was performed using CgMfs1‐silencing and CgMfs1‐overexpression strategies. Inactivation of CgMfs1 caused a notable decrease in chaetoglobosin A yield from 58.66 mg/L to 19.95 mg/L (MFS1–3) and 17.13 mg/L (MFS1–4). The use of an efficient expression plasmid in Chaetomium globosum W7 to generate the overexpression mutant OEX13 resulted in the highest chaetoglobosin A increase to 298.77 mg/L. Interestingly, the transcription level of the polyketide synthase gene significantly fluctuated with the change in CgMfs1, confirming that the predicted efflux gene CgMfs1 could play a crucial role in chaetoglobosin A transportation. Effective efflux of chaetoglobosin A could possibly alleviate feedback inhibition, resulting in notable increase in the expression of the polyketide synthase gene. Furthermore, we utilized cornstalk as the fermentation substrate to produce chaetoglobosin A, and scanning electron microscopy and Fourier transform‐infrared spectroscopy revealed that the strain OEX13 could well degrade cornstalk, presenting significant increases in the chaetoglobosin A yield, when compared with that produced by the wild‐type strain (from 40.32 to 191.90 mg/L). Thus, this research provides a novel analogous engineering strategy for the construction of high‐yielding strain and offers new insight into large‐scale chaetoglobosin A production.

Mechanisms in Growth-Promoting of Cucumber by the Endophytic Fungus Chaetomium globosum Strain ND35

Endophytic fungi are effective in plant growth and development by secreting various kinds of plant hormones and nutrients. However, the cellular and molecular interactions between the endophytic fungi and plant growth-promoting have remained less explored. The present study was designed to explore the effects of the infection and colonization events of Chaetomium globosum strain ND35 on cucumber growth and the expression pattern of some metabolically important genes in development of the cucumber radicle. The results demonstrated that strain ND35 can infect and colonize the outer layers (cortical cells) of cucumber root and form a symbiotic structure with the host cell, similar to a periarbuscular membrane and establish chemical communication with the plant. Through transcriptome analysis, we found the differentially expressed genes (DEGs) caused by strain ND35 were mainly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, plant-pathogen interaction and photosynthesis. Correspondingly, the contents of reactive oxygen species (ROS), hydrogen peroxide (H₂O₂), indole-3-acetic acid (IAA), gibberellin (GA), zeatin (ZT), salicylic acid (SA), jasmonic acid (JA) and the activity of phenylalanine ammonia lyase (PAL), 4-coumarate-CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD) in ND35-colonized seedlings were generally higher than those of non-inoculated seedlings. Overall, the infection and colonization events of C. globosum strain ND35 increased cucumber growth through complex regulation of plant hormones biosynthesis and metabolism. Furthermore, although the endophytic fungus strain ND35 produced IAA, GA, ZT, and ergosterol in the fermentation broth, and there are enabled to promote growth of cucumber, it is uncertain whether there are ND35-derived microbial hormones in plants. This study of the interaction between cucumber and strain ND35 contributes to a better understanding of the plant-endophytic fungi interactions, and may help to develop new strategies for crop production.

Cytotoxic and antibacterial depsidones from the endophytic fungus Chaetomium brasiliense isolated from Thai rice

Four new depsidones, mollicellins V-Y (1-4), together with eight known depsidones (5-12) were isolated from the endophytic fungus, Chaetomium brasiliense, detached from stems of Thai rice. Their structures were determined by extensive spectroscopic methods. Mollicellins X, H, and F (3, 8 and 10) showed potent cytotoxicity against the human oral epidermoid carcinoma (KB) cell line, and mollicellin F (10) also showed a potent cytotoxicity against the human hepatocellular carcinoma (HepG2) cell line. Besides, mollicellin B (11) exhibited cytotoxicity against the colorectal adenocarcinoma (HT-29) cell line. Moreover, most of the isolated depsidones displayed potent antibacterial activity against Gram-positive bacteria, Bacillus cereus and Bacillus subtilis, and several of them showed moderate activity against Methicillin-resistant Staphylococcus aureus (MRSA) and clinical isolates of S. aureus. In addition, a few of them also showed moderate activity against a Gram-negative bacteria Pseudomonas aeruginosa.

Transcriptome Profiling Provides Insights Into Potential Antagonistic Mechanisms Involved in Chaetomium globosum Against Bipolaris sorokiniana

Chaetomium globosum Kunze is recognized as a potential biocontrol fungus against spot blotch of wheat caused by Bipolaris sorokiniana. Its molecular mechanism of biocontrol activity and the biosynthetic pathways involved have not been yet elucidated. Here, global transcriptome profiling of C. globosum strain Cg2 during interaction with B. sorokiniana isolate BS112 using RNA-seq was performed in order to gain insights into the potential mechanisms of antagonism. The Illumina HiSeq platform (2 × 150 bp) yielded an average of 20-22 million reads with 50-58% GC. De novo assembly generated 45,582 transcripts with 27,957 unigenes. Transcriptome analysis displayed distinct expression profiles in the interaction (Cg2-BS112), out of which 6,109 unique differentially expressed genes were present. The predominant transcripts classified as genes involved in "catalytic activity" constituted 45.06%, of which 10.02% were associated with "hydrolytic activity" (GO:0008152), and similarly, in the biological process, 29.18% of transcripts were involved in "metabolic activity" (GO:0004096 and GO:0006979). Heat map and cluster categorization suggested an increase in the expression levels of genes encoding secondary metabolites like polyketide synthase (GO:0009058), S-hydroxymethyl glutathione dehydrogenase (GO:0006069), terpene cyclase (EC 4.2.3.-), aminotran_1_2 domain-containing protein (GO:0009058), and other hydrolytic CAZYmes such as the glycosyl hydrolase (GH) family (GH 13, GH 2, GH 31, and GH 81; GO:0005975), cellulase domain-containing protein, chitinases, β-1, 3-glucanases (GO:0004565), glucan endo-1,3-beta-glucanase (GO:0052861), and proteases (GO:0004177). The obtained RNA-seq data were validated by RT-qPCR using 20 randomly chosen genes, showing consistency with the RNA-seq results. The present work is worldwide the first effort to unravel the biocontrol mechanism of C. globosum against B. sorokiniana. It generated a novel dataset for further studies and facilitated improvement of the gene annotation models in the C. globosum draft genome.

Alkaloids from Marine Fungi: Promising Antimicrobials

Resistance of pathogenic microorganisms against antimicrobials is a major threat to contemporary human society. It necessitates a perpetual influx of novel antimicrobial compounds. More specifically, Gram⁻ pathogens emerged as the most exigent danger. In our continuing quest to search for novel antimicrobial molecules, alkaloids from marine fungi show great promise. However, current reports of such newly discovered alkaloids are often limited to cytotoxicity studies and, moreover, neglect to discuss the enigma of their biosynthesis. Yet, the latter is often a prerequisite to make them available through sufficiently efficient processes. This review aims to summarize novel alkaloids with promising antimicrobial properties discovered in the past five years and produced by marine fungi. Several discovery strategies are summarized, and knowledge gaps in biochemical production routes are identified. Finally, links between the structure of the newly discovered molecules and their activity are proposed. Since 2015, a total of 35 new antimicrobial alkaloids from marine fungi were identified, of which 22 showed an antibacterial activity against Gram⁻ microorganisms. Eight of them can be classified as narrow-spectrum Gram⁻ antibiotics. Despite this promising ratio of novel alkaloids active against Gram⁻ microorganisms, the number of newly discovered antimicrobial alkaloids is low, due to the narrow spectrum of discovery protocols that are used and the fact that antimicrobial properties of newly discovered alkaloids are barely characterized. Alternatives are proposed in this review. In conclusion, this review summarizes novel findings on antimicrobial alkaloids from marine fungi, shows their potential as promising therapeutic candidates, and hints on how to further improve this potential.

Recent advances in inducing endophytic fungal specialized metabolites using small molecule elicitors including epigenetic modifiers

Today when the quest of new lead molecules to supply the development pipeline is driving the course of drug discovery, endophytic fungi with their outstanding biosynthetic potential seem to be highly promising avenues for natural product scientists. However, challenges such as the production of inadequate quantities of compounds, the attenuation or loss of ability of endophytes to produce the compound of interest when grown in culture and the inability of fungal endophytes to express their full biosynthetic potential in laboratory conditions have been the major constraints. These have led to the application of small chemical elicitors that induce epigenetic changes in fungi to activate their silent gene clusters optimizing the amount of metabolites of interest or inducing the synthesis of hitherto undescribed compounds. In this respect small molecular weight compounds which are known to function as inhibitors of histone deacetylase (HDAC), DNA methyltransferase (DNMT) and proteasome have proven their efficacy in enhancing or inducing the production of specialized metabolites by fungi. Moreover, organic solvents, metals and plants extracts are also acknowledged for their ability to cause shifts in fungal metabolism. We highlight the successful studies from the past two decades reporting the ability of structurally diverse small molecular weight compounds to elicit the production of previously undescribed metabolites from endophytic fungi grown in culture. This mini review argues in favor of chemical elicitation as an effective strategy to optimize the production of fungal metabolites and invigorate the pipeline of drug discovery with new chemical entities.

Response of the wood-decay fungus Schizophyllum commune to co-occurring microorganisms

Microorganisms are constantly interacting in a given environment by a constant exchange of signaling molecules. In timber, wood-decay fungi will come into contact with other fungi and bacteria. In naturally bleached wood, dark, pigmented lines arising from confrontation of two fungi often hint at such interactions. The metabolites (and pigment) exchange was investigated using the lignicolous basidiomycete Schizophyllum commune, and co-occurring fungi and bacteria inoculated directly on sterilized wood, or on media. In interactions with competitive wood degrading fungi, yeasts or bacteria, different competition strategies and communication types were observed, and stress reactions, as well as competitor-induced enzymes or pigments were analyzed. Melanin, indole, flavonoids and carotenoids were shown to be induced in S. commune interactions. The induced genes included multi-copper oxidases lcc1, lcc2, mco1, mco2, mco3 and mco4, possibly involved in both pigment production and lignin degradation typical for wood bleaching by wood-decay fungi.

Bioactivities and Future Perspectives of Chaetoglobosins

Chaetoglobosins belonging to cytochalasan alkaloids represent a large class of fungal secondary metabolites. To date, around 100 chaetoglobosins and their analogues have been isolated and identified over the years from a variety of fungi, mainly from the fungus Chaetomium globosum. Studies have found that chaetoglobosins possess a broad range of biological activities, including antitumor, antifungal, phytotoxic, fibrinolytic, antibacterial, nematicidal, anti-inflammatory, and anti-HIV activities. This review will comprehensively summarize the biological activities and mechanisms of action of nature-derived chaetoglobosins.

Effects of multi-year biofumigation on soil bacterial and fungal communities and strawberry yield

Biofumigation is an effective, non-chemical method to control soil-borne pests and diseases and to maximize crop yield. We studied the responses of soil bacterial and fungal communities, the soil's nutritional state and strawberry yield, when the soil was biofumigated each year for five consecutive years using fresh chicken manure (BioFum). BioFum significantly increased the soil's NH₄⁺-N, NO₃^--N, available P and K and organic matter. Fusarium spp. and Phytophthora spp. which are known to cause plant disease, were significantly decreased after BioFum. In addition, Biofum increased the soil's temperature, enhanced chlorophyll levels in the leaves of strawberry plants, and the soluble sugar and ascorbic acid content in strawberry fruit. We used high-throughput gene sequencing to monitor changes in the soil's bacterial and fungal communities. Although BioFum significantly decreased the diversity of these communities, it increased the relative abundance of some biological control agents in the phylum Actinobacteria and the genera Pseudomonas, Bacillus and Chaetomium. An increase in these biological control agents would reduce the incidence of soil-borne pathogens and plant disease. Although strawberry marketable yield using BioFum was higher in the first three years, the decline in the final two years could be due to the accumulation of P and K which may have delayed flowering and fruiting. Methods to overcome yield losses using BioFum need to be developed in the future. Our research, however, showed that BioFum enhanced soil fertility, reduced the presence of soil pathogens, increased the relative abundance of beneficial bacteria and fungi and improved strawberry quality. Unlike chemical soil treatments that can cause pest and disease resistance when used continuously over many years, our multi-year research program on BioFum showed that this treatment provided significant benefits to the soil, plant and strawberry fruit.

Endophytes from Ginkgo biloba and their secondary metabolites

Ginkgo biloba is a medicinal plant which contains abundant endophytes and various secondary metabolites. According to the literary about the information of endophytics from Ginkgo biloba, Chaetomium, Aspergillus, Alternaria, Penicillium and Charobacter were isolated from the root, stem, leaf, seed and bark of G. biloba. The endophytics could produce lots of phytochemicals like flavonoids, terpenoids, and other compounds. These compounds have antibacteria, antioxidation, anticardiovascular, anticancer, antimicrobial and some novel functions. This paper set forth the development of active extracts isolated from endophytes of Ginkgo biloba and will help to improve the resources of Ginkgo biloba to be used in a broader field.

Antioxidant compounds extracted from Diaporthe schini using supercritical CO2 plus cosolvent

Endophytic fungi have been highlight in the production of secondary metabolites with different bioactive properties, such as in the production of the antioxidant compounds. Therefore, the objective of this work was the extraction of the antioxidant compounds from the biomass of Diaporthe schini using supercritical carbon dioxide (CO₂) without and with ethanol as cosolvent. The biomass was produced by submerged fermentation and the parameters evaluated in the extraction process were: pressure (150-250 bar), temperature (40-60 ºC) and cosolvent [biomass: cosolvent ratio, 1:0, 1:0.75 and 1:1.5 (w/v)]. Extraction yield, antioxidant activity and chemical composition of the extracts were determined. The highest extraction yield (3.24 wt.%) and the best antioxidant activity against the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical (96.62%) were obtained at 40 ºC, 250 bar and biomass:cosolvent ratio of 1:1.5 (w/v). The chemical compounds 1,4-diaza-2,5-dioxo-3-isobutyl bicyclo[4.3.0]nonane and benzeneethanol identified in GC/MS could be responsible for the antioxidant activity found in this study.

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.

New Metabolites from Endophytic Fungus Chaetomium globosum CDW7

Five metabolites including two new ones, prochaetoviridin A (1) and chaetoindolin A (2), were isolated from the endophytic fungus Chaetomium globosum CDW7. Compounds 1 and 2 were characterized as an isocoumarin and an indole alkaloid derivative, respectively, with their structures elucidated by comprehensive spectroscopic analyses including high-resolution electrospray ionization mass spectrometry (HR-ESI-MS), NMR, and circular dichroism (CD) comparison. Compounds 3–5 were identified as chaetoviridin A, chaetoglobosin R, and chaetoglobosin T, respectively. Chaetoviridin A (3) exhibited antifungal activity against Sclerotinia sclerotiorum with an EC₅₀ value of 1.97 μg/mL. In vivo test showed that 3 displayed a protective efficacy of 64.3% against rape Sclerotinia rot at the dosage of 200 μg/mL, comparable to that of carbendazim (69.2%).

Genome-Based Discovery of Polyketide-Derived Secondary Metabolism Pathways in the Barley Pathogen Ramularia collo-cygni

Ramularia collo-cygni causes Ramularia leaf spot (RLS) disease of barley. The fungus develops asymptomatically within its host until late in the growing season, when necrotic lesions become visible on upper leaves. Fungal secondary metabolites (SM) have been proposed as important factors in RLS lesion formation but the biosynthetic pathways involved remain largely unknown. Mining the R. collo-cygni genome revealed the presence of 10 polyketide synthases (PKS), 10 nonribosomal peptide synthetases (NRPS), and 3 hybrid PKS-NRPS (HPS) identified within clusters of genes with predicted functions associated with secondary metabolism. SM core genes along with their predicted transcriptional regulators exhibited transcriptional coexpression during infection of barley plants. Moreover, their expression peaked during early stages of host colonization and preceded or overlapped with the appearance of disease symptoms, suggesting that SM may manipulate the host to promote colonization or protect R. collo-cygni from competing organisms. Accordingly, R. collo-cygni inhibited the growth of several fungi in vitro, indicating that it synthesized and excreted antifungal agents. Taken together, these findings demonstrate that the R. collo-cygni genome contains the genetic architecture to synthesize a wide range of SM and suggests that coexpression of PKS and HPS is associated with competitive colonization of the host and early symptom development.

Endophytic Fungi: A Source of Potential Antifungal Compounds

The emerging and reemerging forms of fungal infections encountered in the course of allogeneic bone marrow transplantations, cancer therapy, and organ transplants have necessitated the discovery of antifungal compounds with enhanced efficacy and better compatibility. A very limited number of antifungal compounds are in practice against the various forms of topical and systemic fungal infections. The trends of new antifungals being introduced into the market have remained insignificant while resistance towards the introduced drug has apparently increased, specifically in patients undergoing long-term treatment. Considering the immense potential of natural microbial products for the isolation and screening of novel antibiotics for different pharmaceutical applications as an alternative source has remained largely unexplored. Endophytes are one such microbial community that resides inside all plants without showing any symptoms with the promise of producing diverse bioactive molecules and novel metabolites which have application in medicine, agriculture, and industrial set ups. This review substantially covers the antifungal compounds, including volatile organic compounds, isolated from fungal endophytes of medicinal plants during 2013⁻2018. Some of the methods for the activation of silent biosynthetic genes are also covered. As such, the compounds described here possess diverse configurations which can be a step towards the development of new antifungal agents directly or precursor molecules after the required modification.

Penochalasin K, a new unusual chaetoglobosin from the mangrove endophytic fungus Penicillium chrysogenum V11 and its effective semi-synthesis

A new chaetoglobosin, penochalasin K (1) bearing an unusual six-cyclic 6/5/6/5/6/13 fused ring system, along with the known analogues, chaetoglobosin C (2), penochalasin I (3), and chaetoglobosin A (4) were isolated from the solid culture of the mangrove endophytic fungus Penicillium chrysogenum V11. Their structures were elucidated by 1D, 2D NMR spectroscopic analysis and high resolution mass spectroscopic data. The absolute configuration of compound 1 was determined by comparing the theoretical and experimental electronic circular dichroism curves. Compound 1 displayed significant inhibitory activities against Colletotrichum gloeosporioides and Rhizoctonia solani (MICs=6.13, 12.26μM, respectively), which was better than those of carbendazim, and exhibited potent cytotoxicity against MDA-MB-435, SGC-7901 and A549 cells (IC₅₀<10μM). An effective biomimetic transformation of chaetoglobosin C (2)/chaetoglobosin A (4) into penochalasin K (1)/penochalasin I (3) was developed, which provided a simple method for the semi-synthesis of chaetoglobosins with a six-cyclic 6/5/6/5/6/13 fused system formed by the connectivity of C-5 and C-2' from their corresponding epoxide analogues.

Fungal endophytes isolated from Protium heptaphyllum and Trattinnickia rhoifolia as antagonists of Fusarium oxysporum

Control of fungal pathogens is mainly addressed by the use of chemically synthesized fungicides which result in environmental pollution, developing resistance after prolonged use. In this context, endophytes have been recognized as potential biocontrollers, and also as a promising source of antifungal metabolites. Therefore, as part of our research on phytopathogen controllers, 355 fungal endophytes were isolated from Protium heptaphyllum and Trattinnickia rhoifolia (Burseraceae), both ethnobotanically important tree species that produce secondary metabolites of agronomic and industrial interest. Endophytes were tested by in vitro dual culture against Fusarium oxysporum, a phytopathogen of agronomic importance. Five endophytes exerted at least 40% inhibition on F. oxysporum growth. Ethyl acetate (EtOAc) extracts were obtained from the most active antagonistic fungi, after growing them in three different liquid media. The extracts were tested against a conidial suspension of F. oxysporum by direct bioautography. Two extracts derived from fungi identified as Chaetomium globosum, F211_UMNG and Meyerozima sp. F281_UMNG showed inhibition of pathogen growth. Isolate C. globosum, F211_UMNG was selected for a chemical analysis by RP-HPLC-DAD-ESI-MS and antifungal molecules such as cladosporin, chaetoatrosin A and chaetoviridin A were annotated and identified based on their MS data.

New production process of the antifungal chaetoglobosin A using cornstalks

Chaetoglobosin A is an antibacterial compound produced by Chaetomium globosum, with potential application as a biopesticide and cancer treatment drug. The aim of this study was to evaluate the feasibility of utilizing cornstalks to produce chaetoglobosin A by C. globosum W7 in solid-batch fermentation and to determine an optimal method for purification of the products. The output of chaetoglobosin A from the cornstalks was 0.34 mg/g, and its content in the crude extract was 4.80%. Purification conditions were optimized to increase the content of chaetoglobosin A in the crude extract, including the extract solvent, temperature, and pH value. The optimum process conditions were found to be acetone as the extractant, under room temperature, and at a pH value of 13. Under these conditions, a production process of the antifungal chaetoglobosin A was established, and the content reached 19.17%. Through further verification, cornstalks could replace crops for the production of chaetoglobosin A using this new production process. Moreover, the purified products showed great inhibition against Rhizoctonia solani, with chaetoglobosin A confirmed as the main effective constituent (IC₅₀ = 3.88 μg/mL). Collectively, these results demonstrate the feasibility of using cornstalks to synthesize chaetoglobosin A and that the production process established in this study was effective.

Bioactive Chaetoglobosins from the Mangrove Endophytic Fungus Penicillium chrysogenum

A novel chaetoglobosin named penochalasin I (1) with a unprecedented six-cyclic 6/5/6/5/6/13 fused ring system, and another new chaetoglobosin named penochalasin J (2), along with chaetoglobosins G, F, C, A, E, armochaetoglobosin I, and cytoglobosin C (3–9) were isolated from the culture of Penicillium chrysogenum V11. Their structures were elucidated by 1D, 2D NMR spectroscopic analysis and high resolution mass spectroscopic data. The absolute configuration of compounds 1 and 2 were determined by comparing the theoretical electronic circular dichroism (ECD) calculation with the experimental CD. Compound 1 was the first example, with a six-cyclic fused ring system formed by the connection of C-5 and C-2′ of the chaetoglobosin class. Compounds 5–8 remarkably inhibited the plant pathogenic fungus R. solani (minimum inhibitory concentrations (MICs) = 11.79–23.66 μM), and compounds 2, 6, and 7 greatly inhibited C. gloeosporioides (MICs = 23.58–47.35 μM), showing an antifungal activity higher than that of carbendazim. Compound 1 exhibited marked cytotoxicity against MDA-MB-435 and SGC-7901 cells (IC₅₀ < 10 μM), and compounds 6 and 9 showed potent cytotoxicity against SGC-7901 and A549 cells (IC₅₀ < 10 μM).