Genomic and Metabolomic Analyses of the Marine Fungus Emericellopsis cladophorae: Insights into Saltwater Adaptability Mechanisms and Its Biosynthetic Potential

Comparative genomic and metabolomic analysis reveals the potential of a newly isolated Enterococcus faecium B6 involved in lipogenic effects

Evidence has indicated that Enterococcus plays a vital role in non-alcoholic fatty liver disease (NAFLD) development. However, the microbial genetic basis and metabolic potential in the disease are yet unknown. We previously isolated a bacteria Enterococcus faecium B6 (E. faecium B6) from children with NAFLD for the first time. Here, we aim to systematically investigate the potential of strain B6 in lipogenic effects. The lipogenic effects of strain B6 were explored in vitro and in vivo. The genomic and functional characterizations were investigated by whole-genome sequencing and comparative genomic analysis. Moreover, the metabolite profiles were unraveled by an untargeted metabolomic analysis. We demonstrated that strain B6 could effectively induce lipogenic effects in the liver of mice. Strain B6 contained a circular chromosome and two circular plasmids and posed various functions. Compared to the other two probiotic strains of E. faecium, strain B6 exhibited unique functions in pathways of ABC transporters, phosphotransferase system, and amino sugar and nucleotide sugar metabolism. Moreover, strain B6 produced several metabolites, mainly enriched in the protein digestion and absorption pathway. The unique potential of strain B6 in lipogenic effects was probably associated with glycolysis, fatty acid synthesis, and glutamine and choline transport. This study pioneeringly revealed the metabolic characteristics and specific detrimental traits of strain B6. The findings provided new insights into the underlying mechanisms of E. faecium in lipogenic effects, and laid essential foundations for further understanding of E. faecium-related disease.

Aspergillus nidulans gfdB, Encoding the Hyperosmotic Stress Protein Glycerol-3-phosphate Dehydrogenase, Disrupts Osmoadaptation in Aspergillus wentii

The genome of the osmophilic Aspergillus wentii, unlike that of the osmotolerant Aspergillus nidulans, contains only the gfdA, but not the gfdB, glycerol 3-phosphate dehydrogenase gene. Here, we studied transcriptomic changes of A. nidulans (reference strain and ΔgfdB gene deletion mutant) and A. wentii (reference strain and An-gfdB expressing mutant) elicited by high osmolarity. A. nidulans showed a canonic hyperosmotic stress response characterized by the upregulation of the trehalose and glycerol metabolism genes (including gfdB), as well as the genes of the high-osmolarity glycerol (HOG) map kinase pathway. The deletion of gfdB caused only negligible alterations in the transcriptome, suggesting that the glycerol metabolism was flexible enough to compensate for the missing GfdB activity in this species. A. wentii responded differently to increased osmolarity than did A. nidulans, e.g., the bulk upregulation of the glycerol and trehalose metabolism genes, along with the HOG pathway genes, was not detected. The expression of An-gfdB in A. wentii did not abolish osmophily, but it reduced growth and caused much bigger alterations in the transcriptome than did the missing gfdB gene in A. nidulans. Flexible glycerol metabolism and hence, two differently regulated gfd genes, may be more beneficial for osmotolerant (living under changing osmolarity) than for osmophilic (living under constantly high osmolarity) species.

Hidden Treasure: Halophilic Fungi as a Repository of Bioactive Lead Compounds

The pressing demand for novel compounds to address contemporary health challenges has prompted researchers to venture into uncharted territory, including extreme ecosystems, in search of new natural pharmaceuticals. Fungi capable of tolerating extreme conditions, known as extremophilic fungi, have garnered attention for their ability to produce unique secondary metabolites crucial for defense and communication, some of which exhibit promising clinical significance. Among these, halophilic fungi thriving in high-salinity environments have particularly piqued interest for their production of bioactive molecules. This review highlights the recent discoveries regarding novel compounds from halotolerant fungal strains isolated from various saline habitats. From diverse fungal species including Aspergillus, Penicillium, Alternaria, Myrothecium, and Cladosporium, a plethora of intriguing molecules have been elucidated, showcasing diverse chemical structures and bioactivity. These compounds exhibit cytotoxicity against cancer cell lines such as A549, HL60, and K-562, antimicrobial activity against pathogens like Escherichia coli, Bacillus subtilis, and Candida albicans, as well as radical-scavenging properties. Notable examples include variecolorins, sclerotides, alternarosides, and chrysogesides, among others. Additionally, several compounds display unique structural motifs, such as spiro-anthronopyranoid diketopiperazines and pentacyclic triterpenoids. The results emphasize the significant promise of halotolerant fungi in providing bioactive compounds for pharmaceutical, agricultural, and biotechnological uses. However, despite their potential, halophilic fungi are still largely unexplored as sources of valuable compounds.

Influence of Salinity on the Extracellular Enzymatic Activities of Marine Pelagic Fungi

Even though fungi are ubiquitous in the biosphere, the ecological knowledge of marine fungi remains rather rudimentary. Also, little is known about their tolerance to salinity and how it influences their activities. Extracellular enzymatic activities (EEAs) are widely used to determine heterotrophic microbes' enzymatic capabilities and substrate preferences. Five marine fungal species belonging to the most abundant pelagic phyla (Ascomycota and Basidiomycota) were grown under non-saline and saline conditions (0 g/L and 35 g/L, respectively). Due to their sensitivity and specificity, fluorogenic substrate analogues were used to determine hydrolytic activity on carbohydrates (β-glucosidase, β-xylosidase, and N-acetyl-β-D-glucosaminidase); peptides (leucine aminopeptidase and trypsin); lipids (lipase); organic phosphorus (alkaline phosphatase), and sulfur compounds (sulfatase). Afterwards, kinetic parameters such as maximum velocity (Vmax) and half-saturation constant (Km) were calculated. All fungal species investigated cleaved these substrates, but some species were more efficient than others. Moreover, most enzymatic activities were reduced in the saline medium, with some exceptions like sulfatase. In non-saline conditions, the average Vmax ranged between 208.5 to 0.02 μmol/g biomass/h, and in saline conditions, 88.4 to 0.02 μmol/g biomass/h. The average Km ranged between 1553.2 and 0.02 μM with no clear influence of salinity. Taken together, our results highlight a potential tolerance of marine fungi to freshwater conditions and indicate that changes in salinity (due to freshwater input or evaporation) might impact their enzymatic activities spectrum and, therefore, their contribution to the oceanic elemental cycles.

Identification and Characterization of Peptaibols as the Causing Agents of Pseudodiploöspora longispora Infecting the Edible Mushroom Morchella

Pseudodiploöspora longispora (previously known as Diploöspora longispora) is a pathogenic fungus of Morchella mushrooms. The molecular mechanism underlying the infection of P. longispora in fruiting bodies remains unknown. In this study, three known peptaibols, alamethicin F-50, polysporin B, and septocylindrin B (1-3), and a new analogue, longisporin A (4), were detected and identified in the culture of P. longispora and the fruiting bodies of M. sextelata infected by P. longispora. The primary amino sequence of longisporin A is defined as Ac-Aib1-Pro2-Aib3-Ala4-Aib5-Aib6-Gln7-Aib8-Val9-Aib10-Glu11-Leu12-Aib13-Pro14-Val15-Aib16-Aib17-Gln18-Gln19-Phaol20. The peptaibols 1-4 greatly suppressed the mycelial growth of M. sextelata. In addition, treatment with alamethicin F-50 produced damage on the cell wall and membrane of M. sextelata. Compounds 1-4 also exhibited inhibitory activities against human pathogens including Aspergillus fumigatus, Candida albicans, methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus, and plant pathogen Verticillium dahlia. Herein, peptaibols are confirmed as virulence factors involved in the invasion of P. longispora on Morchella, providing insights into the interaction between pathogenic P. longispora and mushrooms.

Release of cell-free enzymes by marine pelagic fungal strains

Fungi are ubiquitous organisms that secrete different enzymes to cleave large molecules into smaller ones so that can then be assimilated. Recent studies suggest that fungi are also present in the oceanic water column harboring the enzymatic repertoire necessary to cleave carbohydrates and proteins. In marine prokaryotes, the cell-free fraction is an important contributor to the oceanic extracellular enzymatic activities (EEAs), but the release of cell-free enzymes by marine fungi remains unknown. Here, to study the cell-free enzymatic activities of marine fungi and the potential influence of salinity on them, five strains of marine fungi that belong to the most abundant pelagic phyla (Ascomycota and Basidiomycota), were grown under non-saline and saline conditions (0 g/L and 35 g/L, respectively). The biomass was separated from the medium by filtration (0.2 μm), and the filtrate was used to perform fluorogenic enzymatic assays with substrate analogues of carbohydrates, lipids, organic phosphorus, sulfur moieties, and proteins. Kinetic parameters such as maximum velocity (Vmax) and half-saturation constant (Km) were obtained. The species studied were able to release cell-free enzymes, and this represented up to 85.1% of the respective total EEA. However, this differed between species and enzymes, with some of the highest contributions being found in those with low total EEA, with some exceptions. This suggests that some of these contributions to the enzymatic pool might be minimal compared to those with higher total EEA. Generally, in the saline medium, the release of cell-free enzymes degrading carbohydrates was reduced compared to the non-saline medium, but those degrading lipids and sulfur moieties were increased. For the remaining substrates, there was not a clear influence of the salinity. Taken together, our results suggest that marine fungi are potential contributors to the oceanic dissolved (i.e., cell-free) enzymatic pool. Our results also suggest that, under salinity changes, a potential effect of global warming, the hydrolysis of organic matter by marine fungal cell-free enzymes might be affected and hence, their potential contribution to the oceanic biogeochemical cycles.

Haloalkalitolerant Fungi from Sediments of the Big Tambukan Saline Lake (Northern Caucasus): Diversity and Antimicrobial Potential

We have performed a characterization of cultivated haloalkalitolerant fungi from the sediments of Big Tambukan Lake in order to assess their biodiversity and antimicrobial activity. This saline, slightly alkaline lake is known as a source of therapeutic sulfide mud used in sanatoria of the Caucasian Mineral Waters, Russia. Though data on bacteria and algae observed in this lake are available in the literature, data on fungi adapted to the conditions of the lake are lacking. The diversity of haloalkalitolerant fungi was low and represented by ascomycetes of the genera Acremonium, Alternaria, Aspergillus, Chordomyces, Emericellopsis, Fusarium, Gibellulopsis, Myriodontium, Penicillium, and Pseudeurotium. Most of the fungi were characterized by moderate alkaline resistance, and they tolerated NaCl concentrations up to 10% w/v. The analysis of the antimicrobial activity of fungi showed that 87.5% of all strains were active against Bacillus subtilis, and 39.6% were also determined to be effective against Escherichia coli. The majority of the strains were also active against Aspergillus niger and Candida albicans, about 66.7% and 62.5%, respectively. These studies indicate, for the first time, the presence of polyextremotolerant fungi in the sediments of Big Tambukan Lake, which probably reflects their involvement in the formation of therapeutic muds.

Biodeterioration and Chemical Corrosion of Concrete in the Marine Environment: Too Complex for Prediction

Concrete is the most utilized construction material worldwide. In the marine environment, it is subject to chemical degradation through reactions with chloride (the most important ion), and sulfate and magnesium ions in seawater, and to biodeterioration resulting from biological (initially microbiological) activities, principally acid production. These two types of corrosions are reviewed and the failure of attempts to predict the degree of deterioration resulting from each is noted. Chemical (abiotic) corrosion is greatest in the splash zone of coastal constructions, while phenomenological evidence suggests that biodeterioration is greatest in tidal zones. There have been no comparative experiments to determine the rates and types of microbial biofilm formation in these zones. Both chemical and microbiological concrete deteriorations are complex and have not been successfully modeled. The interaction between abiotic corrosion and biofilm formation is considered. EPS can maintain surface hydration, potentially reducing abiotic corrosion. The early marine biofilm contains relatively specific bacterial colonizers, including cyanobacteria and proteobacteria; these change over time, producing a generic concrete biofilm, but the adhesion of microorganisms to concrete in the oceans has been little investigated. The colonization of artificial reefs is briefly discussed. Concrete appears to be a relatively prescriptive substrate, with modifications necessary to increase colonization for the required goal of increasing biological diversity.

GC-MS Based Characterization, Antibacterial, Antifungal and Anti-Oncogenic Activity of Ethyl Acetate Extract of Aspergillus niger Strain AK-6 Isolated from Rhizospheric Soil

Rhizospheric soil is the richest niche of different microbes that produce biologically active metabolites. The current study investigated the antimicrobial, antifungal and anticancer activities of ethyl acetate extract of the potent rhizospheric fungus Aspergillus niger AK6 (AK-6). A total of six fungal isolates were isolated, and isolate AK-6 was selected based on primary screening. Further, it exhibited moderate antimicrobial activity against pathogens such as Klebsiella pneumonia, Candida albicans, Escherichia coli, Shigella flexneri, Bacillus subtilis and Staphylococcus aureus. The morphological and molecular characterization (18S rRNA) confirmed that the isolate AK-6 belonged to Aspergillus niger. Further, AK-6 showed potent antifungal activity with 47.2%, 59.4% and 64.1% of inhibition against Sclerotium rolfsii, Cercospora canescens and Fusarium sambucinum phytopathogens. FT-IR analysis displayed different biological functional groups. Consequently, the GC-MS analysis displayed bioactive compounds, namely, n-didehydrohexacarboxyl-2,4,5-trimethylpiperazine (23.82%), dibutyl phthalate (14.65%), e-5-heptadecanol (8.98%), and 2,4-ditert-butylphenol (8.60%), among the total of 15 compounds isolated. Further, the anticancer activity of AK-6 was exhibited against the MCF-7 cell line of human breast adenocarcinoma with an IC₅₀ value of 102.01 μg/mL. Furthermore, flow cytometry depicted 17.3%, 26.43%, and 3.16% of early and late apoptosis and necrosis in the AK-6 extarct treated MCF-7 cell line, respectively. The results of the present analysis suggest that the isolated Aspergillus niger strain AK-6 extract has the potential to be explored as a promising antimicrobial, antifungal and anticancer drug for medical and agricultural applications.

Evaluation of Lipid Extracts from the Marine Fungi Emericellopsis cladophorae and Zalerion maritima as a Source of Anti-Inflammatory, Antioxidant and Antibacterial Compounds

Marine environments occupy more than 70% of the earth's surface, integrating very diverse habitats with specific characteristics. This heterogeneity of environments is reflected in the biochemical composition of the organisms that inhabit them. Marine organisms are a source of bioactive compounds, being increasingly studied due to their health-beneficial properties, such as antioxidant, anti-inflammatory, antibacterial, antiviral, or anticancer. In the last decades, marine fungi have stood out for their potential to produce compounds with therapeutic properties. The objective of this study was to determine the fatty acid profile of isolates from the fungi Emericellopsis cladophorae and Zalerion maritima and assess the anti-inflammatory, antioxidant, and antibacterial potential of their lipid extracts. The analysis of the fatty acid profile, using GC-MS, showed that E. cladophorae and Z. maritima possess high contents of polyunsaturated fatty acids, 50% and 34%, respectively, including the omega-3 fatty acid 18:3 n-3. Emericellopsis cladophorae and Z. maritima lipid extracts showed anti-inflammatory activity expressed by the capacity of their COX-2 inhibition which was 92% and 88% of inhibition at 200 µg lipid mL^-1, respectively. Emericellopsis cladophorae lipid extracts showed a high percentage of inhibition of COX -2 activity even at low concentrations of lipids (54% of inhibition using 20 µg lipid mL^-1), while a dose-dependent behaviour was observed in Z. maritima. The antioxidant activity assays of total lipid extracts demonstrated that the lipid extract from E. cladophorae did not show antioxidant activity, while Z. maritima gave an IC₂₀ value of 116.6 ± 6.2 µg mL^-1 equivalent to 92.1 ± 4.8 µmol Trolox g^-1 of lipid extract in the DPPH• assay, and 101.3 ± 14.4 µg mL^-1 equivalent to 106.6 ± 14.8 µmol Trolox g^-1 of lipid extract in the ABTS•⁺ assay. The lipid extract of both fungal species did not show antibacterial properties at the concentrations tested. This study is the first step in the biochemical characterization of these marine organisms and demonstrates the bioactive potential of lipid extracts from marine fungi for biotechnological applications.

Metabologenomics analysis of Pseudomonas sp. So3.2b, an Antarctic strain with bioactivity against Rhizoctonia solani

Introduction

Phytopathogenic fungi are a considerable concern for agriculture, as they can threaten the productivity of several crops worldwide. Meanwhile, natural microbial products are acknowledged to play an important role in modern agriculture as they comprehend a safer alternative to synthetic pesticides. Bacterial strains from underexplored environments are a promising source of bioactive metabolites.

Methods

We applied the OSMAC (One Strain, Many Compounds) cultivation approach, in vitro bioassays, and metabolo-genomics analyses to investigate the biochemical potential of Pseudomonas sp. So3.2b, a strain isolated from Antarctica. Crude extracts from OSMAC were analyzed through HPLC-QTOF-MS/MS, molecular networking, and annotation. The antifungal potential of the extracts was confirmed against Rhizoctonia solani strains. Moreover, the whole-genome sequence was studied for biosynthetic gene clusters (BGCs) identification and phylogenetic comparison.

Results and Discussion

Molecular networking revealed that metabolite synthesis has growth media specificity, and it was reflected in bioassays results against R. solani. Bananamides, rhamnolipids, and butenolides-like molecules were annotated from the metabolome, and chemical novelty was also suggested by several unidentified compounds. Additionally, genome mining confirmed a wide variety of BGCs present in this strain, with low to no similarity with known molecules. An NRPS-encoding BGC was identified as responsible for producing the banamides-like molecules, while phylogenetic analysis demonstrated a close relationship with other rhizosphere bacteria. Therefore, by combining -omics approaches and in vitro bioassays, our study demonstrates that Pseudomonas sp. So3.2b has potential application to agriculture as a source of bioactive metabolites.

Marine fungi showing multifunctional activity against human pathogenic microbes and cancer

Multifunctional drugs have shown great promise in biomedicine. Organisms with antimicrobial and anticancer activity in combination with antioxidant activity need further research. The Red Sea and the Arabian Gulf coasts were randomly sampled to find fungi with multifunctional activity. One hundred strains (98 fungi and 2 lichenized forms) were isolated from 15 locations. One-third of the isolates inhibited clinical bacterial (Staphylococcus aureus, Bacillus subtilis, Vibrio cholerae, Salmonella typhi, S. paratyphi) and fungal pathogens (Talaromycets marneffei, Malassezia globose, Cryptococcus neoformans, Candida albicans, Aspergillus fumigatus) and four cancer cell lines (Hep G2 liver, A-549 lung, A-431skin, MCF 7 breast cancer). Bacterial and cancer inhibition was often accompanied by a high antioxidant activity, as indicated by the principal component analysis (PCA). PCA also indicated that fungal and bacterial pathogens appeared to be inhibited mostly by different marine fungal isolates. Strains with multifunctional activity were found more from the Rea Sea than from the Arabian Gulf coasts. The highest potential for multifunctional drugs were observed for Acremonium sp., Acrocalymma sp., Acrocalymma africana, Acrocalymma medicaginis (activity reported for the first time), Aspergillus sp. Cladosporium oxysporum, Emericellopsis alkaline, Microdochium sp., and Phomopsis glabrae. Lung, skin, and breast cancers were inhibited 85%-97% by Acremonium sp, while most of the isolates showed low inhibition (ca 20%). The highest antifungal activity was observed for Acremonium sp., Diaporthe hubeiensis, Lasiodiplodia theobromae, and Nannizia gypsea. One Acremonium sp. is of particular interest to offer a multifunctional drug; it displayed both antifungal and antibacterial activity combined with high antioxidant activity (DPPH scavenging 97%). A. medicaginis displayed combined antibacterial, anticancer, and antioxidant activity being of high interest. Several genera and some species included strains with both high and low biological activities pointing out the need to study several isolates to find the most efficient strains for biomedical applications.

Exploring Peptaibol's Profile, Antifungal, and Antitumor Activity of Emericellipsin A of Emericellopsis Species from Soda and Saline Soils

Features of the biochemical adaptations of alkaliphilic fungi to exist in extreme environments could promote the production of active antibiotic compounds with the potential to control microorganisms, causing infections associated with health care. Thirty-eight alkaliphilic and alkalitolerant Emericellopsis strains (E. alkalina, E. cf. maritima, E. cf. terricola, Emericellopsis sp.) isolated from different saline soda soils and belonging to marine, terrestrial, and soda soil ecological clades were investigated for emericellipsin A (EmiA) biosynthesis, an antifungal peptaibol previously described for Emericellopsis alkalina. The analysis of the Emericellopsis sp. strains belonging to marine and terrestrial clades from chloride soils revealed another novel form with a mass of 1032.7 Da, defined by MALDI-TOF Ms/Ms spectrometers, as the EmiA lacked a hydroxyl (dEmiA). EmiA displayed strong inhibitory effects on cell proliferation and viability of HCT 116 cells in a dose- and time-dependent manners and induced apoptosis.