Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential

Reconstruction of a genome-scale metabolic model and in-silico flux analysis of Aspergillus tubingensis: a non-mycotoxinogenic citric acid-producing fungus

BACKGROUND

Aspergillus tubingensis is a citric acid-producing fungus that can utilize sugars in hydrolysate of lignocellulosic biomass such as sugarcane bagasse and, unlike A. niger, does not produce mycotoxins. To date, no attempt has been made to model its metabolism at genome scale.

RESULTS

Here, we utilized the whole-genome sequence (34.96 Mb length) and the measured biomass composition to reconstruct a genome-scale metabolic model (GSMM) of A. tubingensis DJU120 strain. The model, named iMK1652, consists of 1652 genes, 1657 metabolites and 2039 reactions distributed over four cellular compartments. The model has been extensively curated manually. This included removal of dead-end metabolites and generic reactions, addition of secondary metabolite pathways and several transporters. Several mycotoxin synthesis pathways were either absent or incomplete in the genome, providing a genomic basis for the non-toxinogenic nature of this species. The model was further refined based on the experimental phenotypic microarray (Biolog) data. The model closely captured DJU120 fermentative data on glucose, xylose, and phosphate consumption, as well as citric acid and biomass production, showing its applicability to capture citric acid fermentation of lignocellulosic biomass hydrolysate.

CONCLUSIONS

The model offers a framework to conduct metabolic systems biology investigations and can act as a scaffold for integrative modelling of A. tubingensis.

Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex

Production of secondary metabolites is controlled by a complicated regulatory network in eukaryotic cells. Several layers of regulators are involved in this process, ranging from pathway-specific regulation, to epigenetic control, to global regulation. Here, we discover that interaction of an RNA-binding protein CsdA with a regulator RsdA coordinates fungal secondary metabolism. Employing a genetic deletion approach and transcriptome analysis as well as metabolomics analysis, we reveal that CsdA and RsdA synergistically regulate fungal secondary metabolism comprehensively. Mechanistically, comprehensive genetic and biochemical studies prove that RsdA and CsdA co-localize in the nucleus and physically interact to achieve their functions. In particular, we demonstrate that CsdA mediates rsdA expression by binding specific motif "GUCGGUAU" of its pre-mRNA at a post-transcriptional level. We thus uncover a mechanism in which RNA-binding protein physically interacts with, and controls the expression level of, the RsdA to coordinate fungal secondary metabolism.

Current status of secondary metabolite pathways linked to their related biosynthetic gene clusters in Aspergillus section Nigri

Covering: up to the end of 2021Aspergilli are biosynthetically 'talented' micro-organisms and therefore the natural products community has continually been interested in the wealth of biosynthetic gene clusters (BGCs) encoding numerous secondary metabolites related to these fungi. With the rapid increase in sequenced fungal genomes combined with the continuous development of bioinformatics tools such as antiSMASH, linking new structures to unknown BGCs has become much easier when taking retro-biosynthetic considerations into account. On the other hand, in most cases it is not as straightforward to prove proposed biosynthetic pathways due to the lack of implemented genetic tools in a given fungal species. As a result, very few secondary metabolite biosynthetic pathways have been characterized even amongst some of the most well studied Aspergillus spp., section Nigri (black aspergilli). This review will cover all known biosynthetic compound families and their structural diversity known from black aspergilli. We have logically divided this into sub-sections describing major biosynthetic classes (polyketides, non-ribosomal peptides, terpenoids, meroterpenoids and hybrid biosynthesis). Importantly, we will focus the review on metabolites which have been firmly linked to their corresponding BGCs.

A Mad7 System for Genetic Engineering of Filamentous Fungi

The introduction of CRISPR technologies has revolutionized strain engineering in filamentous fungi. However, its use in commercial applications has been hampered by concerns over intellectual property (IP) ownership, and there is a need for implementing Cas nucleases that are not limited by complex IP constraints. One promising candidate in this context is the Mad7 enzyme, and we here present a versatile Mad7-CRISPR vector-set that can be efficiently used for the genetic engineering of four different Aspergillus species: Aspergillus nidulans, A. niger, A. oryzae and A. campestris, the latter being a species that has never previously been genetically engineered. We successfully used Mad7 to introduce unspecific as well as specific template-directed mutations including gene disruptions, gene insertions and gene deletions. Moreover, we demonstrate that both single-stranded oligonucleotides and PCR fragments equipped with short and long targeting sequences can be used for efficient marker-free gene editing. Importantly, our CRISPR/Mad7 system was functional in both non-homologous end-joining (NHEJ) proficient and deficient strains. Therefore, the newly implemented CRISPR/Mad7 was efficient to promote gene deletions and integrations using different types of DNA repair in four different Aspergillus species, resulting in the expansion of CRISPR toolboxes in fungal cell factories.

Epigenetic Manipulation Induced Production of Immunosuppressive Chromones and Cytochalasins from the Mangrove Endophytic Fungus Phomopsis asparagi DHS-48

A mangrove endophytic fungus Phomopsis asparagi DHS-48 was found to be particularly productive with regard to the accumulation of substantial new compounds in our previous study. In order to explore its potential to produce more unobserved secondary metabolites, epigenetic manipulation was used on this fungus to activate cryptic or silent genes by using the histone deacetylase (HDAC) inhibitor sodium butyrate and the DNA methyltransferase (DNMT) inhibitor 5-azacytidine (5-Aza). Based on colony growth, dry biomass, HPLC, and ¹H NMR analyses, the fungal chemical diversity profile was significantly changed compared with the control. Two new compounds, named phaseolorin J (1) and phomoparagin D (5), along with three known chromones (2–4) and six known cytochalasins (6–11), were isolated from the culture treated with sodium butyrate. Their structures, including their absolute configurations, were elucidated using a combination of detailed HRESIMS, NMR, and ECD and ¹³C NMR calculations. The immunosuppressive and cytotoxic activities of all isolated compounds were evaluated. Compounds 1 and 8 moderately inhibited the proliferation of ConA (concanavalin A)-induced T and LPS (lipopolysaccharide)-induced B murine spleen lymphocytes. Compound 5 exhibited significant in vitro cytotoxicity against the tested human cancer cell lines Hela and HepG2, which was comparative to the positive control adriamycin and fluorouracil. Our finding demonstrated that epigenetic manipulation should be an efficient strategy for the induction of new metabolites from mangrove endophytic fungi.

Biosynthesis of pyrroloindoline-containing natural products

Covering: up to 2022Pyrroloindoline is a privileged tricyclic indoline motif widely present in many biologically active and medicinally valuable natural products. Thus, understanding the biosynthesis of this molecule is critical for developing convenient synthetic routes, which is highly challenging for its chemical synthesis due to the presence of rich chiral centers in this molecule, especially the fully substituted chiral carbon center at the C3-position of its rigid tricyclic structure. In recent years, progress has been made in elucidating the biosynthetic pathways and enzymatic mechanisms of pyrroloindoline-containing natural products (PiNPs). This article reviews the main advances in the past few decades based on the different substitutions on the C3 position of PiNPs, especially the various key enzymatic mechanisms involved in the biosynthesis of different types of PiNPs.

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

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

New Antioxidant Active Packaging Films Based on Yeast Cell Wall and Naphtho-γ-Pyrone Extract

The main objective of this work is the development of new active films based on yeast cell wall obtained by high-pressure homogenization (YCW-H) supplemented with naphtho-γ-pyrone (CL-NGP) extract, which is a bioactive compound produced by Aspergillus tubingensis G131 with great antioxidant potential. A complete characterization of the functional properties of the bioactive films, such as their structural, colour, thermal, mechanical, hydration and water vapour transport, was carried out to evaluate the influence of the addition of the antioxidant compounds. Likewise, the antioxidant capacity of the developed materials and the specific migration of NGPs in food simulants were evaluated. The results showed that CL-NGP extract possessed an important antioxidant activity, which was maintained after incorporation in YCW-H films. The addition of 2 and 5% CL-NGPs decreased the hydration of films and consequently improved the water vapour barrier properties. It was observed that CL-NGPs migrate in fatty food simulants and retain their antioxidant capacity in the simulant. The results obtained in this work showed that bioactive films based on yeast cell walls with the addition of CL-NGPs have the potential to be used as packaging material in systems of interest in the food industry.

Chemical synthesis in competition with global genome mining and heterologous expression for the preparation of dimeric tryptophan-derived 2,5-dioxopiperazines

Covering: up to the end of 2021Within the 2,5-dioxopiperazines-containing natural products, those generated from tryptophan allow further structural diversification due to the rich chemical reactivity of the indole heterocycle. The great variety of natural products, ranging from simple dimeric bispyrrolidinoindoline dioxopiperazines and tryptophan-derived dioxopiperazine/pyrrolidinoindoline dioxopiperazine analogs to complex polycyclic downstream metabolites containing transannular connections between the subunits, will be covered. These natural products are constructed by Nature using hybrid polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) assembly lines. Mining of microbial genome sequences has more recently allowed the study of the metabolic routes and the discovery of their hidden biosynthetic potential. The competition (ideally, also the combined efforts) between their isolation from the cultures of the producing microorganisms after global genome mining and heterologous expression and the synthetic campaigns, has more recently allowed the successful generation and structural confirmation of these natural products. Their biological activities as well as their proposed biogenetic routes and computational studies on biogenesis will also be covered.

Unraveling the Genome Sequence of Plant Growth Promoting Aspergillus niger (CSR3) Provides Insight into the Synthesis of Secondary Metabolites and Its Comparative Genomics

Aspergillus niger strain CSR3 is an endophytic fungus that regulates plant endogenous hormones, secondary metabolites, and promotes plant growth during abiotic stress conditions. In this study, we sequenced the genome of A. niger (CSR3) and compared it with previously available A. niger strains. The final genome assembly was 35.8 Mb in size, consisting of 23 scaffolds with N50 scaffold length of 2.4 Mb. A total of 12,442 protein coding genes, 270 tRNA, and 57 rRNA were predicted in the CSR3 genome. We used comparative genomic analysis to provide insights into the genome’s evolution and to elucidate the adaptive genomic signatures for bioactive secondary metabolite biosynthesis, hormones biosynthesis, and plant growth promoting activities. We also analyzed the transposable elements (TEs), simple sequence repeats (SSRs), CAZymes families, genes involved in gibberellin biosynthesis, and secondary metabolite clusters in the CSR3 genome. A total of 21 secondary metabolite biosynthesis gene clusters were detected, with 18 essential enzymes involved in the mevalonate pathway (MVA). The repeat analysis revealed about 3431 SSR, 274 TEs, and 205 inverted repeats (IR). Further gene family analysis revealed that 124 gene families were gained, whereas 125 gene families were lost in CSR3 genome, compared to A. niger ASM151534V and A. niger ASM285V2 genomes. The results improve our understanding of the CSR3 genome and will assist in future investigations on the genetic basis of A. niger CSR3, including the identification of CSR3 phytostimulant properties.

Genomic Analysis and Assessment of Melanin Synthesis in Amorphotheca resinae KUC3009

This study reports the draft genome of Amorphotheca resinae KUC30009, a fungal isolate with promising industrial-scale melanin production potential. The mechanisms for melanin or melanin-related pigment formation of this strain were examined through bioinformatic and biochemical strategies. The 30.11 Mb genome of A. resinae contains 9638 predicted genes. Genomic-based discovery analyses identified 14 biosynthetic gene clusters (BGCs) associated with secondary metabolite production. Moreover, genes encoding a specific type 1 polyketide synthase and 4-hydroxynaphthalene reductase were identified and predicted to produce intermediate metabolites of dihydroxy naphthalene (DHN)-melanin biosynthesis pathway, but not to DHN-melanin. These findings were further supported by the detection of increased flaviolin concentrations in mycelia and almost unchanged morphologies of the culture grown with tricyclazole. Apart from this, the formation of melanin in the culture filtrate appeared to depend on the laccase-like activity of multi-copper oxidases. Simultaneously, concentrations of nitrogen-containing sources decreased when the melanin formed in the media. Interestingly, melanin formation in the culture fluid was proportional to laccase-like activity. Based on these findings, we proposed novel strategies for the enhancement of melanin production in culture filtrates. Therefore, our study established a theoretical and methodological basis for synthesizing pigments from fungal isolates using genomic- and biochemical-based approaches.

Genetic Diversity, Ochratoxin A and Fumonisin Profiles of Strains of Aspergillus Section Nigri Isolated from Dried Vine Fruits

We investigated ochratoxin A (OTA) contamination in raisin samples purchased from Slovak markets and determined the diversity of black-spored aspergilli as potential OTA and fumonisin (FB1 and FB2) producers. The taxonomic identification was performed using sequences of the nuclear ITS1-5.8s-ITS2 region, the calmodulin and beta-tubulin genes. We obtained 239 isolates from eight fungal genera, of which 197 belonged to Aspergillus (82%) and 42 strains (18%) to other fungal genera. OTA contamination was evidenced in 75% of the samples and its level ranged from 0.8 to 10.6 µg/kg. The combination of all three markers used enabled unambiguous identification of A. carbonarius, A. luchuensis, A. niger, A. tubingensis and A. welwitschiae. The dominant coloniser, simultaneously having the highest within-species diversity isolated from our raisin samples, was A. tubingensis. Out of all analysed strains, only A. carbonarius was found to produce OTA, but in relatively high quantity (2477–4382 µg/kg). The production of FB1 and FB2 was evidenced in A. niger strains only.

Statistical approach to evaluate effect of temperature and moisture content on the production of antioxidant naphtho-gamma-pyrones and hydroxycinnamic acids by Aspergillus tubingensis in solid-state fermentation

Non-ochratoxigenic Aspergillus tubingensis G131 is a filamentous fungus that can produce naphtho-gamma-pyrones (NγPs), polyketide pigments that exhibit interesting antioxidant properties. This study aims to investigate the effect of two critical parameters, temperature and moisture content on the fungus grown in solid-state fermentation using agricultural by-products (vine shoots and wheat bran) as sole medium. From the kinetic productions of secondary metabolites NγPs (asperpyrone E, dianhydroaurasperone C, fonsecin, fonsecin B and ustilaginoidin A), alkaloids (nigragilin and aspernigrin A), degradation products from the solid medium (β-D-glucose, p-coumaric acid and trans-ethyl ferulate), ergosterol and conidia obtained for different temperatures and moisture contents, a principal component analysis (PCA) was carried out to highlight the production patterns of these compounds. This approach allowed us to determine that fonsecin, the compound of higher interest-exhibiting the most interesting antiradical potential-is particularly more produced at 25 °C and 66% of moisture content. This study underlines the importance of temperature and moisture content on naphtho-gamma-pyrones and hydroxycinnamic acid production using solid-state fermentation and contributes to the development of agroindustrial by-product valorization.

Characterization of diketopiperazine heterodimers as potential chemical markers for discrimination of two dominant black aspergilli, Aspergillus niger and Aspergillus tubingensis

Black aspergilli are distributed worldwide and represent one of the most prolific sources of metabolites with biomedical and agrochemical interests. However, due to their similar morphological characteristics and insufficient molecular identification, the taxonomic classification of black aspergilli remains ill-defined. The production of specialised metabolites is often unique for species among black aspergilli and could be used as diagnostic chemical markers for species identification. In this study, chemical investigation of Aspergillus tubingensis OUCMBIII 143291 led to the discovery of the diagnostic chemical marker asperazine, a complex diketopiperazine heterodimer, as well as two previously undescribed analogues, asperazine B and C. In addition, an undescribed 2-benzylpyridin-4(1H)-one-containing amide, pestalamide D, along with four known related metabolites were isolated. Their chemical structures, including their absolute configurations, were established on the basis of comprehensive spectral analysis and chiral HPLC analysis of the acidic hydrolysates. Asperazines B and C can serve as potential chemical markers for distinguishing A. tubingensis from A. niger, two representative species of black aspergilli that are usually incorrectly identified. Moreover, the isolated compounds were evaluated for their antifungal activity against eight phytopathogenic fungi including Alternaria alternata, A. brassicae, Botrytis cinerea, Colletotrichum lagenarium, Fusarium oxysporum, Gaeumannomyces graminis, Penicillium digitatum, and Valsa mali. Pestalamide D exhibited significant activities against B. cinerea, C. lagenarium, and V. mali, with MIC values of 4, 8, and 8 μg/mL, respectively, compared with the positive controls carbendazim (MICs = 8, 4, and 4 μg/mL) and prochloraz (MICs = 8, 8, and 4 μg/mL). The results of this study reveal two additional chemical markers and provide a powerful tool for the rapid identification of black aspergilli.

Characterizing the Fungal Microbiome in Date (Phoenix dactylifera) Fruit Pulp and Peel from Early Development to Harvest

Date palm (Phoenix dactylifera) is considered to be a highly important food crop in several African and Middle Eastern countries due to its nutritional value and health-promoting properties. Microbial contamination of dates has been of concern to consumers, but very few works have analyzed in detail the microbial load of the different parts of date fruit. In the present work, we characterized the fungal communities of date fruit using a metagenomic approach, analyzing the data for differences between microbial populations residing in the pulp and peel of “Medjool” dates at the different stages of fruit development. The results revealed that Penicillium, Cladosporium, Aspergillus, and Alternaria were the most abundant genera in both parts of the fruit, however, the distribution of taxa among the time points and tissue types (peel vs. pulp) was very diverse. Penicillium was more abundant in the pulp at the green developmental stage (Kimri), while Aspergillus was more frequent in the peel at the brown developmental stage (Tamer). The highest abundance of Alternaria was detected at the earliest sampled stage of fruit development (Hababauk stage). Cladosporium had a high level of abundance in peel tissues at the Hababauk and yellow (Khalal) stages. Regarding the yeast community, the abundance of Candida remained stable up until the Khalal stage, but exhibited a dramatic increase in abundance at the Tamer stage in peel tissues, while the level of Metschnikowia, a genus containing several species with postharvest biocontrol activity, exhibited no significant differences between the two tissue types or stages of fruit development. This work constitutes a comprehensive metagenomic analysis of the fungal microbiome of date fruits, and has identified changes in the composition of the fungal microbiome in peel and pulp tissues at the different stages of fruit development. Notably, this study has also characterized the endophytic fungal microbiome present in pulp tissues of dates.

Aspergillus, Penicillium and Cladosporium species associated with dried date fruits collected in the Perugia (Umbria, Central Italy) market

A total of 20 dried date samples, chosen as representative among those available on the Perugia (Umbria, Central Italy) market, were analyzed for the possible occurrence of fungal species and related contamination by fungal secondary metabolites. Twenty-six isolates, representative of the total mycobiota, were obtained and morphologically identified as belonging to the genera Aspergillus, Penicillium and Cladosporium. Inside each genus, molecular characterization (by partial sequencing of ITS region and/or β-tubulin and calmodulin regions for Aspergillus and Penicillium isolates or actin region for Cladosporium isolates) and in vitro mycotoxigenic profile characterization (by LC-MS/MS analysis) showed the presence of the following species: A. flavus, A. tubingensis, P. brevicompactum, P. chrysogenum, P. crustosum, P. glabrum, P. solitum, P. venetum, C. cladosporioides, C. limoniforme and C. halotolerans, with A. tubingensis as the prevalent species and P. crustosum, P. solitum, P. venetum and C. limoniforme first reported here on dates. Date packaging and format showed an effect on the incidence of isolated fungi, with the lowest incidence recovered from whole dates and in hermetic bag packaging. These findings can be useful both for dried dates producers and consumers, guiding them towards choices of packaging and format with a lower risk of mycotoxigenic species presence. However, no fungal metabolites were detected in the dried date samples analyzed, which were therefore regarded as safe for human consumption, underlining the absence of correspondence between fungal isolation and mycotoxin contaminations.

Harnessing diverse transcriptional regulators for natural product discovery in fungi

This review covers diverse transcriptional regulators for the activation of secondary metabolism and novel natural product discovery in fungi.

Transcriptome analysis of non-ochratoxigenic Aspergillus carbonarius strains and interactions between some black aspergilli species

Aspergillus carbonarius consistently produces large amounts of ochratoxin A (OTA), a mycotoxin with nephrotoxic effects on animals and humans. In the present study, we analyzed the transcriptional changes associated to OTA production in three atypical non-ochratoxigenic strains of A. carbonarius. In addition, in vitro interactions between ochratoxigenic strains of A. carbonarius and A. niger and non-ochratoxigenic strains of A. carbonarius and A. tubingensis were studied in order to evaluate their potential for controlling OTA production. RNA-seq analysis revealed that there are 696 differentially expressed genes identified in the three non-OTA-producing strains, including 280 up-regulated and 333 down-regulated genes. A functional and gene ontology enrichment analysis revealed that the processes related to metabolic and oxidation processes, associated with functions such as oxidoreductase and hydrolase activity were down regulated. All the genes related with OTA biosynthesis in A. carbonarius were the most down-regulated genes in non-ochratoxigenic strains. We also showed that these strains possess a deleterious mutation in the AcOTApks gene required for OTA biosynthesis. Moreover, one of these strains gave the best control of OTA production resulting in an OTA reduction of 98-100% in co-inoculation with an ochratoxigenic strain of A. niger and an OTA reduction of 79-89% with an ochratoxigenic strain of A. carbonarius. Results of this study provided novel insights into the knowledge of the OTA biosynthetic pathway in these non-ochratoxigenic wild strains, and showed the biocontrol potential of these strains.

Naphtho-Gamma-Pyrones Produced by Aspergillus tubingensis G131: New Source of Natural Nontoxic Antioxidants

Seven naphtho-gamma-pyrones (NγPs), including asperpyrone E, aurasperone A, dianhydroaurasperone C, fonsecin, fonsecinone A, fonsecin B, and ustilaginoidin A, were isolated from Aspergillus tubingensis G131, a non-toxigenic strain. The radical scavenging activity of these NγPs was evaluated using ABTS assay. The Trolox equivalent antioxidant capacity on the seven isolated NγPs ranged from 2.4 to 14.6 μmol L^-1. The toxicity and ability of the NγPs to prevent H₂O₂-mediated cell death were evaluated using normal/not cancerous cells (CHO cells). This cell-based assay showed that NγPs: (1) Are not toxic or weakly toxic towards cells and (2) are able to protect cells from oxidant injuries with an IC₅₀ on H₂O₂-mediated cell death ranging from 2.25 to 1800 μmol mL^-1. Our data show that A. tubingensis G131 strain is able to produce various NγPs possessing strong antioxidant activities and low toxicities, making this strain a good candidate for antioxidant applications in food and cosmetic industries.

Impact of Spray-Drying on Biological Properties of Chitosan Matrices Supplemented with Antioxidant Fungal Extracts for Wine Applications

Black aspergilli produce many bioactive compounds: enzymes, organic acids, and secondary metabolites. One such fungus, Aspergillus tubingensis G131, isolated from French Mediterranean vineyards, produces secondary metabolites with antioxidant properties that can be extracted with ethanol. In this study, crude antioxidant extracts obtained from A. tubingensis G131 cultures were encapsulated with two types of chitosan matrix. Spray-drying was used to obtain dried particles from a dispersion of fungal crude extracts in a solution of the coating agent chitosan. This process appeared to be an efficient method for obtaining a dry extract with antioxidant activity. Three types of fungal extracts, with different antioxidant capacities, were produced: two different concentrations of crude extract and a semi-purified extract. In this study, the chitosan matrices for encapsulation were chosen on the basis of their antimicrobial activities for wine applications. Classical low molecular weight chitosan was compared with NoBrett Inside^® which is already used to prevent the development of Brettanomyces spp. in wine. The objective of this study was to confirm that both antioxidant (fungal extract) and antimicrobial (chitosan) properties were preserved after spray-drying. The combination of these two properties and the powder formulation of this entirely natural product would make it a good alternative to chemicals, such as sulfites, in the food and wine industries.

Genomic characteristics and comparative genomics analysis of the endophytic fungus Sarocladium brachiariae

BACKGROUND

Sarocladium brachiariae is a newly identified endophytic fungus isolated from Brachiaria brizantha. A previous study indicated that S. brachiariae had antifungal activity; however, limited genomic information restrains further study. Therefore, we sequenced the genome of S. brachiariae and compared it with the genome of S. oryzae to identify differences between a Sarocladium plant pathogen and an endophyte.

RESULTS

In this study, we reported a gapless genome sequence of a newly identified endophytic fungus Sarocladium brachiariae isolated from Brachiaria brizantha. The genome of S. brachiariae is 31.86 Mb, with a contig N50 of 3.27 Mb and 9903 protein coding genes. Phylogenomic analysis based on single copy orthologous genes provided insights into the evolutionary relationships of S. brachiariae and its closest species was identified as S. oryzae. Comparative genomics analysis revealed that S. brachiaria has 14.9% more plant cell wall degradation related CAZymes to S. oryzae, and 33.3% more fungal cell wall degradation related CAZymes, which could explain the antifungal activity of S. brachiaria. Based on Antibiotics & Secondary Metabolite Analysis Shell (antiSMASH) analysis, we identified a contact helvolic acid biosynthetic gene cluster (BGC) for the first time in S. oryzae. However, S. brachiaria had seven fewer terpene gene clusters, including helvolic acid BGC, compared with S. oryzae and this may be associated with adaptation to an endophytic lifestyle. Synteny analysis of polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid (PKS-NRPS) gene clusters between S. brachiariae and S. oryzae revealed that just 37.5% of tested clusters have good synteny, while 63.5% have no or poor synteny. This indicated that the S. brachiariae could potentially synthesize a variety of unknown-function secondary metabolites, which may play an important role in adaptation to its endophytic lifestyle and antifungal activity.

CONCLUSIONS

The data provided a better understanding of the Sarocladium brachiariae genome. Further comparative genomic analysis provided insight into the genomic basis of its endophytic lifestyle and antifungal activity.

Significance of Aspergillus niger aggregate species as contaminants of food products in Spain regarding their occurrence and their ability to produce mycotoxins

The Aspergillus niger aggregate contains 15 morphologically indistinguishable species which presence is related to ochratoxin A (OTA) and fumonisin B₂ (FB₂) contamination of foodstuffs. The taxonomy of this group was recently reevaluated and there is a need of new studies regarding the risk that these species might pose to food security. 258 isolates of A. niger aggregate obtained from a variety of products from Spain were classified by molecular methods being A. tubingensis the most frequently occurring (67.5%) followed by A. welwitschiae (19.4%) and A. niger (11.7%). Their potential ability to produce mycotoxins was evaluated by PCR protocols which allow a rapid detection of OTA and FB₂ biosynthetic genes in their genomes. OTA production is not widespread in A. niger aggregate since only 17% of A. niger and 6% of A. welwitschiae isolates presented the complete biosynthetic cluster whereas the lack of the cluster was confirmed in all A. tubingensis isolates. On the other hand, A. niger and A. welwitschiae seem to be important FB₂ producers with 97% and 29% of the isolates, respectively, presenting the complete cluster. The genes involved in OTA and FB₂ were overexpressed in producing isolates and their expression was related to mycotoxin synthesis.