Secretome of the Coprophilous Fungus Doratomyces stemonitis C8, Isolated from Koala Feces

Diversity of Cellulolytic Microorganisms Associated with the Subterranean Termite Reticulitermes grassei

Reticulitermes grassei is a subterranean termite species that forages on woody structures of the Iberian Peninsula, and is often a building and crops pest. A total of 23 microorganisms associated with the activity of R. grassei were isolated from colonized ecosystems in southern Spain. They were morphologically and molecularly characterized, with fungi being the most prevalent ones. The fungi showed high values of optimum growth temperature, suggesting that they could be able to survive and develop in warm regions. Their cellulolytic activity was tested in carboxymethylcellulose (CMC) agar, concluding that all fungal isolates produce cellulases, and the enzymatic index (EI) was revealed in CMC agar with Gram’s iodine solution, with Penicillium citrinum showing the highest EI and Trichoderma longibrachiatum the highest mycelial growth rate on CMC. A preliminary microorganism dispersion assay was carried out with the termites, concluding that these insects may have a positive influence on fungal dispersion and the subsequent colonization of new substrates. Our study suggests that fungi associated with R. grassei may potentially be of interest in biotechnological fields such as biofuel production and the food industry.

Effect of the Crude Extract of Coprophilous Fungi on Some Bacterial Species Isolated from Cases of Mastitis

Coprophilous fungi are a large group of fungi mostly found in herbivore dung and have an exclusive life cycle. This group of fungi produces many important metabolites which can be consumed in medicine or agriculture. The present study aimed to investigate the antibacterial effects of these fungi on bacterial mastitis. A total of 50 dung samples were collected from four herbivores (cows, buffalos, sheep, and camels) from different areas of Basra. The moist chamber method was used for each sample to establish a fungal fruiting body and detect the type of the fungi. The coprophilous fungi included Aspergillus sp. (A. niger, A. fumigatus, A. flavus, A. terrus), Chaetomium sp., Sordaria sp., and Podospora sp. which belong to the Ascomycetes class. PCR test was performed using the ITS region for confirmatory detection of species. The highest and the lowest number of isolated species was associated with cow dung and camel dung, respectively. The antimicrobial property of three different partitioned extracts (petroleum ether [F1], ethanol [F2], and water [F3]) prepared from some fungal mycelia was evaluated in vitro. All fractions were tested to detect antimicrobial activity using the disc diffusion assay against five pathogenic bacteria Staphylococcus aureus, Streptococcus Enterobacter, Proteus mirabilis, and E. coli. which is isolated from bovine mastitis. Data revealed that all fractions could inhibit the tested bacteria. However, inhibitory activity was found to be dependent on (6i) the used fungal strains; (ii) the extracted solvent; and (iii) the tested bacteria. In general, the petroleum ether extracts (F1) derived from all fungi displayed the highest inhibitory activity against the testing bacteria. In conclusion, the present study concluded that the extracts prepared from the fungal mycelia contain bioactive compounds with antibacterial properties. This study was first conducted in Iraq and further studies are required to develop new treatments.

Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review

The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.

Pharmaceutical biotechnological potential of filamentous fungi isolated from textile industry

The need for more effective drugs for the treatment of infectious diseases as well as for general applications including wound healing and burn surgery, has guided efforts for the discovery of new compounds of medical interest. Microorganisms found in textile industrial waste have the ability to produce a variety of enzymes and/or secondary metabolites including molecules of pharmaceutical interest. The present work investigated the biotechnological potential of filamentous fungi isolated from textile industry wastewater for the production of collagenase and antimicrobial metabolites. From 28 isolates assayed, Sarocladium sp. ITF33 showed specific collagenolytic activity with values of 7.62 and 9.04 U mg^-1 for the intracellular and extracellular fractions, respectively. The isolate Penicillium sp. ITF28 showed the best antimicrobial activity, reaching MIC ranging from 1.0 to 0.0625 mg mL^-1 against five pathogenic bacteria. Molecular analyzes suggest that the isolate Sarocladium sp. ITF 33 can be considered a species not yet described. The results of the present work encourage studies of characterization and purification of the enzymes and secondary metabolites produced by the isolates found aiming future applications in the medical and pharmaceutical fields.

Anti-cryptococcal activity of preussolides A and B, phosphoethanolamine-substituted 24-membered macrolides, and leptosin C from coprophilous isolates of Preussia typharum

Cryptococcus neoformans is a serious human pathogen with limited options for treatment. We have interrogated extracts from fungal fermentations to find Cryptococcus-inhibiting natural products using assays for growth inhibition and differential thermosensitivity. Extracts from fermentations of four fungal strains from wild and domestic animal dung from Arkansas and West Virginia, USA were identified as Preussia typharum. The extracts exhibited two antifungal regions. Purification of one region yielded new 24-carbon macrolides incorporating both a phosphoethanolamine unit and a bridging tetrahydrofuran ring. The structures of these metabolites were established mainly by analysis of high-resolution mass spectrometry and 2D NMR data. Relative configurations were assigned using NOESY data, and the structure assignments were supported by NMR comparison with similar compounds. These new metabolites are designated preussolides A and B. The second active region was caused by the cytotoxin, leptosin C. Genome sequencing of the four strains revealed biosynthetic gene clusters consistent with those known to encode phosphoethanolamine-bearing polyketide macrolides and the biosynthesis of dimeric epipolythiodioxopiperazines. All three compounds showed moderate to potent and selective antifungal activity toward the pathogenic yeast C. neoformans.

An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in the most diverse environments and stressful conditions and have been selected and exploited for multiple aims by humans. The characteristic features intrinsic of Fungi have required evolutionary changes and adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, and proteomics have enormously advanced the way to understand fungal diversity at diverse taxonomic levels, under changeable conditions and in still under-investigated environments. These approaches can be applied both on environmental communities and on individual organisms, either in nature or in axenic culture and have led the traditional morphology-based fungal systematic to increasingly implement molecular-based approaches. The advent of next-generation sequencing technologies was key to boost advances in fungal genomics and proteomics research. Much effort has also been directed towards the development of methodologies for optimal genomic DNA and protein extraction and separation. To date, the amount of proteomics investigations in Ascomycetes exceeds those carried out in any other fungal group. This is primarily due to the preponderance of their involvement in plant and animal diseases and multiple industrial applications, and therefore the need to understand the biological basis of the infectious process to develop mechanisms for biologic control, as well as to detect key proteins with roles in stress survival. Here we chose to present an overview as much comprehensive as possible of the major advances, mainly of the past decade, in the fields of genomics (including phylogenomics) and proteomics of Ascomycota, focusing particularly on those reporting on opportunistic pathogenic, extremophilic, polyextremotolerant and lichenized fungi. We also present a review of the mostly used genome sequencing technologies and methods for DNA sequence and protein analyses applied so far for fungi.

Fungal Pretreatments on Non-Sterile Solid Digestate to Enhance Methane Yield and the Sustainability of Anaerobic Digestion

Fungi can run feedstock pretreatment to improve the hydrolysis and utilization of recalcitrant lignocellulose-rich biomass during anaerobic digestion (AD). In this study, three fungal strains (Coprinopsis cinerea MUT 6385, Cyclocybe aegerita MUT 5639, Cephalotrichum stemonitis MUT 6326) were inoculated in the non-sterile solid fraction of digestate, with the aim to further (re)use it as a feedstock for AD. The application of fungal pretreatments induced changes in the plant cell wall polymers, and different profiles were observed among strains. Significant increases (p < 0.05) in the cumulative biogas and methane yields with respect to the untreated control were observed. The most effective pretreatment was carried out for 20 days with C. stemonitis, causing the highest hemicellulose, lignin, and cellulose reduction (59.3%, 9.6%, and 8.2%, respectively); the cumulative biogas and methane production showed a 182% and 214% increase, respectively, compared to the untreated control. The increase in AD yields was ascribable both to the addition of fungal biomass, which acted as an organic feedstock, and to the lignocellulose transformation due to fungal activity during pretreatments. The developed technologies have the potential to enhance the anaerobic degradability of solid digestate and untap its biogas potential for a further digestion step, thus allowing an improvement in the environmental and economic sustainability of the AD process and the better management of its by-products.

Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger

Efficient deconstruction of plant biomass is a major barrier to the development of viable lignocellulosic biofuels. Pretreatment with ionic liquids reduces lignocellulose recalcitrance to enzymatic hydrolysis, increasing yields of sugars for conversion into biofuels. However, commercial cellulases are not compatible with many ionic liquids, necessitating extensive water washing of pretreated biomass prior to hydrolysis. To circumvent this issue, previous research has demonstrated that several thermophilic bacterial cellulases can efficiently deconstruct lignocellulose in the presence of the ionic liquid, 1-ethyl-3-methylimadizolium acetate. As promising as these enzymes are, they would need to be produced at high titer in an industrial enzyme production host before they could be considered a viable alternative to current commercial cellulases. Aspergillus niger has been used to produce high titers of secreted enzymes in industry and therefore, we assessed the potential of this organism to be used as an expression host for these ionic liquid-tolerant cellulases. We demonstrated that 29 of these cellulases were expressed at detectable levels in a wild-type strain of A. niger, indicating a basic level of compatibility and potential to be produced at high levels in a host engineered to produce high titers of enzymes. We then profiled one of these enzymes in detail, the β-glucosidase A5IL97, and compared versions expressed in both A. niger and Escherichia coli. This comparison revealed the enzymatic activity of A5IL97 purified from E. coli and A. niger is equivalent, suggesting that A. niger could be an excellent enzyme production host for enzymes originally characterized in E. coli, facilitating the transition from the laboratory to industry.

Production of rice straw hydrolysis enzymes by the fungi Trichoderma reesei and Humicola insolens using rice straw as a carbon source

Rice straw was evaluated as a carbon source for the fungi, Trichoderma reesei and Humicola insolens, to produce enzymes for rice straw hydrolysis. The enzyme activity of T. reesei and H. insolens cultivated in medium containing non-treated rice straw were almost equivalent to the enzyme of T. reesei cultivated in Avicel medium, a form of refined cellulose. The enzyme activity of T. reesei cultivated in medium containing NH₄OH-treated rice straw was 4-fold higher than enzyme from cultures grown in Avicel medium. In contrast, H. insolens enzyme from cultures grown in NH₄OH-treated rice straw had significantly lower activity compared with non-treated rice straw or Avicel. The combined use of T. reesei and H. insolens enzymes resulted in a significant synergistic enhancement in enzymatic activity. Our data suggest that rice straw is a promising low-cost carbon source for fungal enzyme production for rice straw hydrolysis.

Characterization of cattle fecal Streptomyces strains converting cellulose and hemicelluloses into reducing sugars

To characterize Streptomyces isolated from cattle feces for converting lignocellulose into reducing sugars, five Streptomyces strains were screened. All the strains could convert lignocellulose into reducing sugars. The strain A16 accumulate 3.3-folds more reducing sugars on cottonseed shells treated with ethanol than without the treatment (P < 0.05). The five strains did not accumulate more reducing sugars on rice straws and wheat brans than those on cottonseed shells. Compared with A10 alone, the microbial combination of F1 + A10 accumulated 19, 61, and 25 % less reducing sugars on cottonseed shell, rice straw, and wheat bran than those by A10 solely, respectively (P < 0.05). Further studies indicated that the activities of avicelase and xylanase were not correlated with the reducing sugar amount accumulated by the test strains. Strain A7 could produce more cellular lipids with xylose and glucose as the sole carbon sources. This study shows the potential for Streptomyces strains from herbivore feces to convert lignocelluloses into lipids and reducing sugars for fuel production.

Characterization of fibrolytic and lipid accumulating fungi isolated from fresh cattle feces

To characterize coprophilous fungi for converting lignocellulose into lipids, four fungal strains utilizing cellulose microcrystalline and xylan were screened. The fungi were identified as Cladosporium sp. F1, Circinella sp. F6, Mycocladus sp. F49, and Byssochlamys sp. F52 based on the ITS1-5.8S-ITS2 sequence similarity. The strain F52 accumulated 336.0 mg/L reducing sugars on cottonseed shells treated with ethanol. The combination of F1+F52 increased the reducing sugar accumulating rates. However, the activities of avicelase and xylanase were not correlated with the reducing sugars accumulated by the test strains. Strains F6 and F52 produced higher cellular lipids (above 530.7 mg/L) than other strains. However, the strain F52 could produce more cellular lipids with xylose and mannose as the sole carbon sources. The results indicated that the reducing sugar contents accumulated by the different strains were influenced by the fungal taxa and ligocellulosic types. With fibrolytic and lipid accumulating activities, diverse fungi harboring in herbivore feces need to be further characterized.

Comparative analyses of Podospora anserina secretomes reveal a large array of lignocellulose-active enzymes

The genome of the coprophilous fungus Podospora anserina harbors a large and highly diverse set of putative lignocellulose-acting enzymes. In this study, we investigated the enzymatic diversity of a broad range of P. anserina secretomes induced by various carbon sources (dextrin, glucose, xylose, arabinose, lactose, cellobiose, saccharose, Avicel, Solka-floc, birchwood xylan, wheat straw, maize bran, and sugar beet pulp (SBP)). Compared with the Trichoderma reesei enzymatic cocktail, P. anserina secretomes displayed similar cellulase, xylanase, and pectinase activities and greater arabinofuranosidase, arabinanase, and galactanase activities. The secretomes were further tested for their capacity to supplement a T. reesei cocktail. Four of them improved significantly the saccharification yield of steam-exploded wheat straw up to 48 %. Fine analysis of the P. anserina secretomes produced with Avicel and SBP using proteomics revealed a large array of CAZymes with a high number of GH6 and GH7 cellulases, CE1 esterases, GH43 arabinofuranosidases, and AA1 laccase-like multicopper oxidases. Moreover, a preponderance of AA9 (formerly GH61) was exclusively produced in the SBP condition. This study brings additional insights into the P. anserina enzymatic machinery and will facilitate the selection of promising targets for the development of future biorefineries.

Amylase production by Preussia minima, a fungus of endophytic origin: optimization of fermentation conditions and analysis of fungal secretome by LC-MS

Background

Environmental screening programs are used to find new enzymes that may be utilized in large-scale industrial processes. Among microbial sources of new enzymes, the rationale for screening fungal endophytes as a potential source of such enzymes relates to the hypothesised mutualistic relationship between the endophyte and its host plant. There is a need for new microbial amylases that are active at low temperature and alkaline conditions as these would find industrial applications as detergents.

Results

An α-amylase produced by Preussia minima, isolated from the Australian native plant, Eremophilia longifolia, was purified to homogeneity through fractional acetone precipitation and Sephadex G-200 gel filtration, followed by DEAE-Sepharose ion exchange chromatography. The purified α-amylase showed a molecular mass of 70 kDa which was confirmed by zymography. Temperature and pH optima were 25°C and pH 9, respectively. The enzyme was activated and stabilized mainly by the metal ions manganese and calcium. Enzyme activity was also studied using different carbon and nitrogen sources. It was observed that enzyme activity was highest (138 U/mg) with starch as the carbon source and L-asparagine as the nitrogen source. Bioreactor studies showed that enzyme activity was comparable to that obtained in shaker cultures, which encourages scale-up fermentation for enzyme production. Following in-gel digestion of the purified protein by trypsin, a 9-mer peptide was sequenced and analysed by LC-ESI-MS/MS. The partial amino acid sequence of the purified enzyme presented similarity to α-amylase from Magnaporthe oryzae.

Conclusions

The findings of the present study indicate that the purified α-amylase exhibits a number of promising properties that make it a strong candidate for application in the detergent industry. To our knowledge, this is the first amylase isolated from a Preussia minima strain of endophytic origin.

A gene encoding a new cold-active lipase from an Antarctic isolate of Penicillium expansum

Cold-active lipases are of significant interest as biocatalysts in industrial processes. We have identified a lipase that displayed activity towards long carbon-chain-p-nitrophenyl substrates (C12-C18) at 25 °C from the culture supernatant of an Antarctic Penicillium expansum strain assigned P. expansum SM3. Zymography revealed a protein band of around 30 kDa with activity towards olive oil. DNA fragments of a lipase gene designated as lipPE were isolated from the genomic DNA of P. expansum SM3 by genomic walking PCR. Subsequently, the complete genomic lipPE gene was amplified using gene-specific primers designed from the 5'- and 3'-regions. Reverse transcription PCR was used to amplify the lipPE cDNA. The deduced amino acid sequence consisted of 285 residues that included a predicted signal peptide. Three peptides identified by LC/MS/MS analysis of the proteins in the culture supernatant of P. expansum were also present in the deduced amino acid sequence of the lipPE gene suggesting that this gene encoded the lipase identified by initial zymogram activity analysis. Full analysis of the nucleotide and the deduced amino acid sequences indicated that the lipPE gene encodes a novel P. expansum lipase. The lipPE gene was expressed in E. coli for further characterization of the enzyme with a view of assessing its suitability for industrial applications.

Bioinformatics tools for secretome analysis

Over recent years, analyses of secretomes (complete sets of secreted proteins) have been reported in various organisms, cell types, and pathologies and such studies are quickly gaining popularity. Fungi secrete enzymes can break down potential food sources; plant secreted proteins are primarily parts of the cell wall proteome; and human secreted proteins are involved in cellular immunity and communication, and provide useful information for the discovery of novel biomarkers, such as for cancer diagnosis. Continuous development of methodologies supports the wide identification and quantification of secreted proteins in a given cellular state. The role of secreted factors is also investigated in the context of the regulation of major signaling events, and connectivity maps are built to describe the differential expression and dynamic changes of secretomes. Bioinformatics has become the bridge between secretome data and computational tasks for managing, mining, and retrieving information. Predictions can be made based on this information, contributing to the elucidation of a given organism's physiological state and the determination of the specific malfunction in disease states. Here we provide an overview of the available bioinformatics databases and software that are used to analyze the biological meaning of secretome data, including descriptions of the main functions and limitations of these tools. The important challenges of data analysis are mainly related to the integration of biological information from dissimilar sources. Improvements in databases and developments in software will likely substantially contribute to the usefulness and reliability of secretome studies. This article is part of a Special Issue entitled: An Updated Secretome.

Analytical constraints for the analysis of human cell line secretomes by shotgun proteomics

Human cell line secretome represents a valuable source of therapeutic targets and candidate biomarkers. Secreted proteins found in biological fluids or culture media are by essence highly diluted. Secretome investigation with proteomic approaches is hardly compatible with the high content of proteins found in complete cell culture media. Therefore, many studies are currently done with media containing few or no protein. Such conditions may perturb cell metabolism and proliferation. Here, we compared seventeen different compositions of culture media for the human bronchial epithelial BEAS-2B cell line. Cell viability, proliferation rate and initial protein charge were systematically compared. We have shown that an important difficulty for the proteomic analysis is due to the presence of detergents such as Pluronic F-68 which hinders peptide mass spectrometry. The high glucose containing DMEM medium which is free of proteins was shown to preserve a good viability and proliferation of cells. With this conditioning medium, we identified 81 extracellular proteins in the secretome of BEAS-2B cells. Moreover, to illustrate this approach, we exposed BEAS-2B cells to a low toxic dose of CoCl(2,) and found 24 extracellular proteins modulated by cobalt. This study highlights the possible contribution of such proteomic approach in the field of toxicology.