ITS-based detection and quantification of Aspergillus ochraceus and Aspergillus westerdijkiae in grapes and green coffee beans by real-time quantitative PCR

Stability and Qualification of a Legacy Fungal Collection

Background: Microbial culture collections are valuable repositories for qualified and diverse microorganisms, playing a pivotal role in research, education, innovation, as well as in our response to current and emerging public health and societal challenges. However, such precious holdings, when not integrated in professional biobank infrastructures, may be vulnerable to major risks such as staff retirement, changes in the institutional strategy, or natural disasters. The process of preserving and rescuing "historical" collections can be long and treacherous with a loss of a part of the collection. At the Biological Resource Center of Institut Pasteur, we undertook the challenge of rescuing the dormant legacy fungal collection. Materials and Methods: A total of 64 freeze-dried strains, including yeasts and filamentous fungi, were characterized by using a polyphasic approach combining morphological features and molecular data. We assessed the viability, purity, and authenticity of selected strains isolated from multiple sources and stored for more than 20 years. Results: Our preliminary results show long-term stability of the selected strains and successful qualification in terms of purity and authentication. Moreover, based on the most recent taxonomic revisions, we updated and revised the nomenclature, where applicable. Conclusion: Our findings demonstrated the potential value of reviving historical microbial collections for biobanking and research activities and reassure us about the collection's future reopening.

Endoglucanase H from Aspergillus westerdijkiae Plays an Important Role in the Virulence on Pear Fruits

Aspergillus westerdijkiae can infect many agricultural products including cereals, grapes, and pear. Pathogenic fungi secrete diverse effectors as invasive weapons for successful invasion the host plant. During the pathogen-host interaction, 4486 differentially expressed genes were observed in A. westerdijkiae with 2773 up-regulated and 1713 down-regulated, whereas 8456 differentially expressed genes were detected in pear fruits with 4777 up-regulated and 3679 down-regulated. A total of 309 effector candidate genes were identified from the up-regulated genes in A. westerdijkiae. Endoglucanase H (AwEGH) was significantly induced during the pathogen-host interaction. Deletion of AwEGH resulted in altered fungal growth and morphology and reduced conidia production and germination compared to the wild-type. Further experiments demonstrated that AwEGH plays a role in cell wall integrity. Importantly, disruption of AwEGH significantly reduced the fungal virulence on pear fruits, and this defect can be partly explained by the impaired ability of A. westerdijkiae to penetrate host plants.

Patulin in food: A mycotoxin concern for human health and its management strategies

The mycotoxin patulin is primarily produced as a secondary metabolite by numerous fungal species and predominantly by Aspergillus, Byssochlamys, and Penicillium species. It is generally associated with fungal infected food materials. Penicillium expansum is considered the only fungal species liable for patulin contamination in pome fruits, especially in apples and apple-based products. This toxin in food poses serious health concerns and economic threat, which has aroused the need to adopt effective detection and mitigation strategies. Understanding its origin sources and biosynthetic mechanism stands essential for efficiently designing a management strategy against this fungal contamination. This review aims to present an updated outline of the sources of patulin occurrence in different foods and their biosynthetic mechanisms. It further provides information regarding the detrimental effects of patulin on human and agriculture as well as its effective detection, management, and control strategies.

Recent Advances in Mycotoxin Analysis and Detection of Mycotoxigenic Fungi in Grapes and Derived Products

Mycotoxins are secondary metabolites of filamentous fungi that can cause toxic effects in human and animal health. Most of the filamentous fungi that produce these mycotoxins belong to four genera, namely, Aspergillus, Penicillium, Fusarium, and Alternaria. Mycotoxigenic fungi, along with mycotoxins, create a constant and serious economic threat for agriculture in many terms, counting product losses due to crop contamination and food spoilage, as well malnutrition when considering nutritional quality degradation. Given the importance of robust and precise diagnostics of mycotoxins and the related producing fungi in the grape food chain, one of the most important agricultural sectors worldwide, the present review initially delivers a comprehensive presentation of mycotoxin reports on grape and derived products, including a wide range of commodities such as fresh grapes, raisins, wine, juices, and other processed products. Next, based on worldwide regulations’ requirements for mycotoxins, and referring to the relative literature, this work presents methodological approaches for mycotoxin determination, and stresses major methods for the detection of fungal species responsible for mycotoxin production. The principle of function and basic technical background on the available analytical and molecular biology techniques developed—including chromatography, mass spectrometry, immunochemical-based assays, biosensors, and molecular assays—is briefly given, and references for their application to grape and derived product testing are highlighted.

A PCR method to identify ochratoxin A-producing Aspergillus westerdijkiae strains on dried and aged foods

Ochratoxins are a group of mycotoxins that frequently occur as contaminants in agricultural commodities and foods, including dry-cured meats and cheeses. The fungus Aspergillus westerdijkiae is frequently isolated from aged foods and can produce ochratoxin A (OTA). However, individual strains of the fungus can have one of two OTA production phenotypes (chemotypes): OTA production and OTA nonproduction. Monitoring and early detection of OTA-producing fungi in food are the most effective strategies to manage OTA contamination. Therefore, we examined genome sequence data from five A. westerdijkiae strains isolated from the surface of cheese from southern Italy to identify genetic markers indicative of the twoOTA chemotypes. This analysis revealed a naturally occurring deletion of the OTA regulatory gene, otaR, in an OTA-nonproducing isolate.We used this information to design a polymerase chain reaction (PCR) method that could identify A. westerdijkiae and distinguish between the two OTA chemotypes. In this method, the PCR primers were complementary to conserved sequences flanking otaR and yielded different-sized amplicons from strains with the different chemotypes. The primers did not yield ota-region-specific amplicons from other OTA-producing species. Because the method is specific to A. westerdijkiae and can distinguish between the two OTA chemotypes, it has potential to significantly improve OTA monitoring programs.

Contamination of Wheat, Barley, and Maize Seeds with Toxigenic Fusarium Species and Their Mycotoxins in Tunisia

Background

Fusarium is a worldwide distributed fungal genus. It includes different species pathogenic to cereals among others crops. Some of these species can also produce toxic compounds toward animals and humans.

Objective

In this work, occurrence of fumonisins B1+B2, zearalenone, type A trichothecenes (T-2 and HT-2 toxins), and type B trichothecenes (deoxynivalenol[DON] and nivalenol[NIV]) was studied in 65 samples of stored and freshly harvested wheat, barley, and maize collected in Tunisia.

Methods

Mycotoxins analyses were performed by using gas chromatography for type B trichothecenes and HPLC for other mycotoxins. Obtained results were compared with the presence of mycotoxigenic species considered responsible for their synthesis by using species-specific polymerase chain reaction (PCR).

Results

Fumonisins occurred in 20.83% of wheat, 40% of barley, and 57.14% of maize samples, at levels exceeding European limits and suggesting a risk in Tunisian cereals, especially maize. Zearalenone, DON, NIV, and T-2+HT-2 toxins were detected at lower values in only wheat and barley samples. PCR protocols showed the predominance of F. verticillioides especially in maize, and occurrence of F. equiseti and F. graminearum in wheat and barley, and F. proliferatum in only two maize samples. A very consistent correlation was found between the detection of F. verticillioides and the contamination by fumonisins, as well as between the presence of F. graminearum and the contamination by zearalenone, DON, and NIV in the analyzed cereals.

Conclusions

Consequently, the detection of Fusarium species with the current PCR assays strategy in wheat, barley, and maize grains may be considered predictive of their potential mycotoxin risk in these matrices.

Highlights

This work is the first to report information on the occurrence of fumonisins, trichothecene, and ZEN, together with their potentially producing Fusarium species in wheat, barley, and maize in Tunisia. The high level of fumonisins in cereals, especially maize, stresses the importance of the control and the regularization of these mycotoxins for food safety.

Multiplex PCR assay to detect Aspergillus, Penicillium and Fusarium species simultaneously

A wide variety of mycotoxins is produced by mycotoxigenic fungi and naturally contaminates food and feed products worldwide. Synergistic effects of multi-toxins are potentially more harmful than exposure to a single compound and can induce acute and chronic toxicity to animals and humans. The aim of the present study is to timely and simultaneously identify the multiple mycotoxigenic fungi capable of causing synergistic toxicity to improve the safety level of food and feedstuff. Here, a multiplex polymerase chain reaction assay was developed for simultaneous detection of mycotoxigenic fungi belonging to the genera Aspergillus, Fusarium and Penicillium. Three pairs of genus-specific primers were designed based on internal transcribed spacer (ITS) sequences of Aspergillus and Penicillium, and Elongation factor 1 alpha (EF- 1α) of Fusarium. Amplicons of 170, 750 and 490 bp respectively for the corresponding primer pairs were detected; thus amplicon length is diagnostic for the individual fungal genus. The sensitivity of the developed method was tested with genomic DNA obtained from mould pure cultures and artificially contaminated maize grain powder. The sensitivity result showed that spore concentrations in the contaminated maize grain powder of 10² spores/mL were detected without prior incubation. This result suggests that the developed mPCR assay would allow a rapid, specific and simultaneous detection of various mycotoxigenic potential fungi based on the occurrence and size of the amplification products and thus to estimate the multi-mycotoxins contamination potential in food and feedstuff.

Home chemical and microbial transitions across urbanization

Urbanization represents a profound shift in human behavior, with significant cultural and health-associated consequences^2,3. Here we investigate chemical and microbial characteristics of houses and their human occupants across an urbanization gradient in the Amazon rainforest, from a remote Peruvian Amerindian village to the Brazilian city of Manaus. Urbanization was associated with reduced microbial outdoor exposure, increased contact with housing materials, antimicrobials, and cleaning products, and increased exposure to chemical diversity. Urbanization degree correlated with changes in house bacterial and micro-eukaryotic community composition, increased house and skin fungal diversity, and increased relative abundance of human skin-associated fungi and bacteria in houses. Overall, our results indicate large-scale effects of urbanization on chemical and microbial exposures and on the human microbiota.

Differentiation and quantification of the ochratoxin A producers Aspergillus ochraceus and Aspergillus westerdijkiae using PCR-DGGE

Ochratoxin A (OTA) is a nephrotoxic, teratogenic, immunotoxic, and carcinogenic mycotoxin which is produced in tropical zones mainly by Aspergillus carbonarius, A. niger, A. ochraceus, and A. westerdijkiae. A. ochraceus and A. westerdijkiae species are phenotypically and genomically very close but A. westerdijkiae produce OTA at a very higher level than A. ochraceus. These species have been differentiated recently. The DNA primer pairs which were drawn so far are not specific and a genomic region of the same size is amplified for both species or they are too specific, and in this case, the DNA of a single species is amplified. To help preventing OTA contamination of foodstuffs, the PCR-DGGE (Denaturing Gradient Gel Electrophoresis) method was used to discriminate between A. ochraceus and A. westerdijkiae DNA fragments of the same size but with different sequences and thus faster access to a diagnosis of the toxigenic potential of the fungal microflora. The proposed methodology was able to differentiate A. westerdijkiae from A. ochraceus with only one primer pairs in a single run. A calibration based on initial DNA content was obtained from image analysis of the DGGE gels and a method of quantification of the two strains was proposed.

Mycoflora isolation and molecular characterization of Aspergillus and Fusarium species in Tunisian cereals

Wheat, barley and maize are the mainly consumed cereals in Tunisia. This study aimed to determine the mycoflora of these cereals with special focus on the mycotoxigenic Aspergillus and Fusarium species. Freshly harvested samples and other stored samples of each type of cereal (31 and 34 samples, respectively) were collected in Tunisia and cultured for fungal isolation and identification. Identification of fungal genera was based on morphological features. Aspergillus and Fusarium species were identified by species specific PCR assays complemented with DNA sequencing. Alternaria (70.83%), Eurotium (62.50%), Aspergillus (54.17%) and Penicillium (41.67%) were the most frequent fungi isolated from wheat. Penicillium (75%), Aspergillus (70%), Eurotium (65%) and Alternaria (65%) were the most frequently recovered genera from barley. The predominant genera in maize were Aspergillus (76.19%), Eurotium (42.86%), and Penicillium (38.09%). Aspergilllus, Penicillium, Fusarium and Alternaria were detected in both stored and freshly harvested grain samples. The frequencies of contamination with Aspergillus, Fusarium and Alternaria were higher in freshly harvested samples, whereas Penicillium species were more frequent in stored samples. The predominant Aspergillus species detected were A. flavus and A. niger. The Fusarium species detected were F. equiseti, F. verticillioides, F. nygamai, and F. oxysporum. This study suggested the potential risk for Aflatoxins and, to a lesser extent, for Ochratoxin A in Tunisian cereals. This is the first survey about mycoflora associated with wheat, barley and maize in Tunisia.

Targeting Conserved Genes in Alternaria Species

Real-time polymerase chain reaction (PCR) is a molecular biology technique based on the detection of the fluorescence produced by a reporter molecule, which increases as the reaction proceeds proportionally to the accumulation of the PCR product within each amplification cycle. The fluorescent reporter molecules include dyes that bind to the double-stranded DNA (i.e., SYBR^® Green) or sequence-specific probes (i.e., Molecular Beacons or TaqMan^® Probes). Real-time PCR provides a tool for accurate and sensitive quantification of target fungal DNA. Here, we describe a TaqMan real-time PCR method for specific detection and quantification of Alternaria spp. The method uses Alternaria-specific primers and probe, targeting the internal transcribed spacer regions ITS1 and ITS2 of the rRNA gene, and a positive amplification control based on 18S rRNA gene.

Aflatoxins and ochratoxin A and their Aspergillus causal species in Tunisian cereals

Occurrence of aflatoxins (AFs) AFB1, AFB2, AFG1, AFG2 and ochra toxin A (OTA) was studied in 65 samples of stored and freshly harvested wheat, barley and maize collected in Tunisia. The mycotoxins were simultaneously extracted and quantified by high performance liquid chromatography. Determination of AF-producing (section Flavi) and OTA-producing Aspergillus species (sections Nigri and Circumdati) was conducted in these samples by species-specific polymerase chain reaction (PCR). Results showed that most of maize samples were contaminated with AFs, data after storage showing lower values than those collected at harvest. All contaminated maize samples contained AFG1 and AFG2, among which 27.78% also had AFB1 and AFB2. This AFs pattern was consistent with the A. parasiticus toxin profile. A. flavus however showed the highest frequency in maize but was also found in barley and wheat where no AFs were detected. In contrast, OTA was neither found in maize nor in barley and only one wheat sample contained OTA. A. niger was the only OTA-producing species detected.

Integrating gene expression, ecology and mycotoxin production by Fusarium and Aspergillus species in relation to interacting environmental factors

Environmental factors, such as water availability (water activity, aw), temperature and their interactions, have a significant impact on the life cycle of mycotoxigenic fungi. Growth and mycotoxin production are influenced by these interacting factors resulting in a broader range of aw × temperature conditions for germination, than growth or mycotoxin production. The biosynthetic genes are mostly clustered together and by using microarrays with sub-arrays for specific mycotoxins, such as trichothecenes, fumonisins and aflatoxins it has been possible to examine the relationship between interacting aw × temperature conditions on growth, toxin gene cluster expression and relate these to phenotypic toxin production. The data for groups of biosynthetic genes (Fusarium culmorum/Fusarium graminearum; Fusarium verticillioides; Aspergillus flavus) were integrated with data on growth and mycotoxin production under different aw × temperature conditions using a mixed growth model. This was used to correlate these factors and predict toxin levels which may be produced under different abiotic stress conditions. Indeed, the relative importance of the different genes could be examined using ternary diagrams of the relative expression of 3 genes at a time in relation to aw, temperature and mycotoxin production to identify the most important relationships. The effect of three-way interacting environmental factors representative of climate change (CC) scenarios (water stress × temperature (+2-4 °C) × elevated CO2 (350-400 vs 650 and 1000 ppm) on growth and mycotoxin production by A. flavus and by species of the Aspergillus section Circumdati and section Nigri have been determined. These studies on maize grain and coffee, respectively, suggest that while growth may not be significantly affected, mycotoxin production may be stimulated by CC factors. This approach to integrate such data sets and model the relationships could be a powerful tool for predicting the relative toxin production under extreme stress conditions, including CC scenarios.

Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

BACKGROUND

Aspergillus westerdijkiae produces ochratoxin A (OTA) in Aspergillus section Circumdati. It is responsible for the contamination of agricultural crops, fruits, and food commodities, as its secondary metabolite OTA poses a potential threat to animals and humans. As a member of the filamentous fungi family, its capacity for enzymatic catalysis and secondary metabolite production is valuable in industrial production and medicine. To understand the genetic factors underlying its pathogenicity, enzymatic degradation, and secondary metabolism, we analysed the whole genome of A. westerdijkiae and compared it with eight other sequenced Aspergillus species.

RESULTS

We sequenced the complete genome of A. westerdijkiae and assembled approximately 36 Mb of its genomic DNA, in which we identified 10,861 putative protein-coding genes. We constructed a phylogenetic tree of A. westerdijkiae and eight other sequenced Aspergillus species and found that the sister group of A. westerdijkiae was the A. oryzae - A. flavus clade. By searching the associated databases, we identified 716 cytochrome P450 enzymes, 633 carbohydrate-active enzymes, and 377 proteases. By combining comparative analysis with Kyoto Encyclopaedia of Genes and Genomes (KEGG), Conserved Domains Database (CDD), and Pfam annotations, we predicted 228 potential carbohydrate-active enzymes related to plant polysaccharide degradation (PPD). We found a large number of secondary biosynthetic gene clusters, which suggested that A. westerdijkiae had a remarkable capacity to produce secondary metabolites. Furthermore, we obtained two more reliable and integrated gene sequences containing the reported portions of OTA biosynthesis and identified their respective secondary metabolite clusters. We also systematically annotated these two hybrid t1pks-nrps gene clusters involved in OTA biosynthesis. These two clusters were separate in the genome, and one of them encoded a couple of GH3 and AA3 enzyme genes involved in sucrose and glucose metabolism.

CONCLUSIONS

The genomic information obtained in this study is valuable for understanding the life cycle and pathogenicity of A. westerdijkiae. We identified numerous enzyme genes that are potentially involved in host invasion and pathogenicity, and we provided a preliminary prediction for each putative secondary metabolite (SM) gene cluster. In particular, for the OTA-related SM gene clusters, we delivered their components with domain and pathway annotations. This study sets the stage for experimental verification of the biosynthetic and regulatory mechanisms of OTA and for the discovery of new secondary metabolites.

Fungal diversity, incidence and mycotoxin contamination in grapes from two agro-climatic Spanish regions with emphasis on Aspergillus species

BACKGROUND

Fourteen vineyards from two different agro-climatic regions in Spain were sampled in two consecutive years in order to determinate the grape mycobiota and diversity indexes with the final aim to define the potential mycotoxigenic species from both regions and their relationship.

RESULTS

The most common fungal genera encountered were Aspergillus (30.0%), Alternaria (53.2%), Cladosporium (11.9%) and Penicillium (2.9%). Black aspergilli presence in the hotter region (south) was significantly higher (P < 0.05) than in the northeast in both years. Among black aspergilli, A. tubingensis seemed to be the better adapted species to environmental conditions, while A. carbonarius was the main potentially ochratoxigenic species in both regions and years, owing to the most relevant percentage of ochratoxigenic isolates. Ochratoxin A (OTA)-positive musts were only detected from southern vineyards, although contamination was always lower than 0.1 µg L(-1) . Finally, none of black aspergilli tested produced fumonisins (FBs) on Czapek yeast extract agar (CYA), while 63% of A. niger tested produced FB2 when inoculated on CYA20S, reaching 100% of isolates from the south.

CONCLUSION

Climate change scenarios in southern Europe point to an increase in temperature and drought. This could promote particularly adapted species such as A. niger, decreasing OTA risk, but this could lead to an increase in FB2 presence.

Ochratoxin production and taxonomy of the yellow aspergilli (Aspergillus section Circumdati)

Aspergillus section Circumdati or the Aspergillus ochraceus group, includes species with rough walled stipes, biseriate conidial heads, yellow to ochre conidia and sclerotia that do not turn black. Several species are able to produce mycotoxins including ochratoxins, penicillic acids, and xanthomegnins. Some species also produce drug lead candidates such as the notoamides. A polyphasic approach was applied using morphological characters, extrolite data and partial calmodulin, β-tubulin and ITS sequences to examine the evolutionary relationships within this section. Based on this approach the section Circumdati is revised and 27 species are accepted, introducing seven new species: A. occultus, A. pallidofulvus, A. pulvericola, A. salwaensis, A. sesamicola, A. subramanianii and A. westlandensis. In addition we correctly apply the name A. fresenii (≡ A. sulphureus (nom. illeg.)). A guide for the identification of these 27 species is provided. These new species can be distinguished from others based on morphological characters, sequence data and extrolite profiles. The previously described A. onikii and A. petrakii were found to be conspecific with A. ochraceus, whilst A. flocculosus is tentatively synonymised with A. ochraceopetaliformis, despite extrolite differences between the two species. Based on the extrolite data, 13 species of section Circumdati produce large amounts of ochratoxin A: A. affinis, A. cretensis, A. fresenii, A. muricatus, A. occultus, A. ochraceopetaliformis (A. flocculosus), A. ochraceus, A. pseudoelegans, A. pulvericola, A. roseoglobulosus, A. sclerotiorum, A. steynii and A. westerdijkiae. Seven additional species produce ochratoxin A inconsistently and/or in trace amounts: A. melleus, A. ostianus, A. persii, A. salwaensis, A. sesamicola, A. subramanianii and A. westlandensis. The most important species regarding potential ochratoxin A contamination in agricultural products are A. ochraceus, A. steynii and A. westerdijkiae.

The use of real-time PCR to study Penicillium chrysogenum growth kinetics on solid food at different water activities

Fungal growth on solid foods can make them unfit for human consumption, but certain specialty foods require fungi to produce their characteristic properties. In either case, a reliable way of measuring biomass is needed to study how various factors (e.g. water activity) affect fungal growth rates on these substrates. Biochemical markers such as chitin, glucosamine or ergosterol have been used to estimate fungal growth, but they cannot distinguish between individual species in mixed culture. In this study, a real-time polymerase chain reaction (rt-PCR) protocol specific for a target fungal species was used to quantify its DNA while growing on solid food. The measured amount of DNA was then related to the biomass present using an experimentally determined DNA-to-biomass ratio. The highly sensitive rt-PCR biomass assay was found to have a wide range, able to quantify the target DNA within a six orders-of-magnitude difference. The method was used to monitor germination and growth of Penicillium chrysogenum spores on a model porous food (cooked wheat flour) at 25°C and different water activities of 0.973, 0.936, and 0.843. No growth was observed at 0.843, but lag, exponential and stationary phases were identified in the growth curves for the higher water activities. The calculated specific growth rates (μ) during the exponential phase were almost identical, at 0.075/h and 0.076/h for aw=0.973 and 0.936, respectively. The specificity of the method was demonstrated by measuring the biomass of P. chrysogenum while growing together with Aspergillus niger on solid media at aw=0.973.

Non-Botrytis grape-rotting fungi responsible for earthy and moldy off-flavors and mycotoxins

The grape microflora is complex and includes filamentous fungi, yeasts and bacteria with different physiological characteristics and effects on wine production. Most studies have focused on the wine microbiota, but a few studies have reported the ecology of grape microorganisms. Some of these organisms - such as non-Botrytis bunch rotting fungi, which greatly influence the safety or sensory quality of wine, due to the production of mycotoxins and off-flavors, respectively - are considered to be spoilage agents. We review here the diversity of filamentous fungi on grapes and the factors influencing their development, such as grape ripening stage, environmental factors (climate, rain and cultivation practices), grape variety and grape health status. We also discuss the pathways by which mycotoxins and off-flavors are produced, the control of the population, the metabolites responsible for wine spoilage and the methods for detecting and characterizing the microorganisms involved.

Contamination of barley seeds with Fusarium species and their toxins in Spain: an integrated approach

Fusarium is a globally distributed fungal genus that includes different species pathogenic to cereals among others crops. Some of these Fusarium species can also produce toxic compounds towards animals and humans. In this work, the presence of the most important Fusarium toxins was determined in barley seeds from Spain, sampled according to European Union requirements. The results obtained were compared with the presence of mycotoxigenic species considered responsible for their synthesis by using species-specific polymerase chain reaction protocols. Fumonisins B(1) and B(2), zearalenone, trichothecenes type A (T-2 and HT-2) and trichothecenes type B (deoxynivalenol and nivalenol) were analysed by using high-performance liquid chromatography. Deoxynivalenol and zearalenone were detected in 72% and 38% of the barley samples, respectively, at levels below European Union limits in all cases. However, the co-occurrence of both toxins in 34% of the samples suggested that synergistic activity of these two mycotoxins should be evaluated. Nivalenol and HT-2/T-2 were detected at low levels in 17% and 10% of the samples, respectively. Fumonisins occurred in 34% of the samples at levels up to 300 µg/kg. This suggested that they might represent a risk in Spanish barley, and to our knowledge, this is the first report on the presence of fumonisins in barley in this country. The species-specific polymerase chain reaction assays to detect mycotoxin-producing Fusarium species showed a very consistent correlation between F. verticillioides detection and fumonisin contamination as well as F. graminearum presence and zearalenone, deoxynivalenol and nivalenol contamination in barley samples. The approach used in this study provided information of mycotoxin contamination of barley together with the identification of the fungal species responsible for their production. Detection of the species with the current polymerase chain reaction assay strategy may be considered predictive of the potential mycotoxin risk in this matrix.

The relative abundance of mountain pine beetle fungal associates through the beetle life cycle in pine trees

The mountain pine beetle (MPB) is a native bark beetle of western North America that attacks pine tree species, particularly lodgepole pine. It is closely associated with the ophiostomatoid ascomycetes Grosmannia clavigera, Leptographium longiclavatum, Ophiostoma montium, and Ceratocystiopsis sp.1, with which it is symbiotically associated. To develop a better understanding of interactions between beetles, fungi, and host trees, we used target-specific DNA primers with qPCR to assess the changes in fungal associate abundance over the stages of the MPB life cycle that occur in galleries under the bark of pine trees. Multivariate analysis of covariance identified statistically significant changes in the relative abundance of the fungi over the life cycle of the MPB. Univariate analysis of covariance identified a statistically significant increase in the abundance of Ceratocystiopsis sp.1 through the beetle life cycle, and pair-wise analysis showed that this increase occurs after the larval stage. In contrast, the abundance of O. montium and Leptographium species (G. clavigera, L. longiclavatum) did not change significantly through the MPB life cycle. From these results, the only fungus showing a significant increase in relative abundance has not been formally described and has been largely ignored by other MPB studies. Although our results were from only one site, in previous studies we have shown that the fungi described were all present in at least ten sites in British Columbia. We suggest that the role of Ceratocystiopsis sp.1 in the MPB system should be explored, particularly its potential as a source of nutrients for teneral adults.

ITS-based detection and quantification of Alternaria spp. in raw and processed vegetables by real-time quantitative PCR

A TaqMan real-time polymerase chain reaction (PCR) method was developed for specific detection of Alternaria spp. in foodstuffs. The method uses Alternaria-specific primers and probe targeting the internal transcribed spacer regions ITS1 and ITS2 of the rRNA gene, and a positive amplification control based on 18S rRNA gene. The applicability of the real-time PCR protocol was assessed through analysis of 190 commercial food samples, including 80 fresh fruit and vegetable samples and 110 processed foodstuffs. The assay demonstrated the presence of Alternaria spp. DNA in 46 out of the 80 raw samples (57.5%) and in 66 out of the 110 processed samples (60%), enabling quantitative detection of Alternaria spp. DNA at levels as low as 1 CFU/g. The estimated Alternaria counts obtained by real-time PCR showed a good relationship (R(2) = 0.9006, P < 0.01) with the Alternaria counts obtained by plating on Potato Carrot Agar (PCA). The developed real-time PCR assay provides a useful tool for early detection of Alternaria spp. and could be applied as a quality and biosecurity marker of raw materials and final products in the fruits and vegetables processing industries.

Real-time PCR assays for detection and quantification of aflatoxin-producing molds in foods

Aflatoxins are among the most toxic mycotoxins. Early detection and quantification of aflatoxin-producing species is crucial to improve food safety. In the present work, two protocols of real-time PCR (qPCR) based on SYBR Green and TaqMan were developed, and their sensitivity and specificity were evaluated. Primers and probes were designed from the o-methyltransferase gene (omt-1) involved in aflatoxin biosynthesis. Fifty-three mold strains representing aflatoxin producers and non-producers of different species, usually reported in food products, were used as references. All strains were tested for aflatoxins production by high-performance liquid chromatography-mass spectrometry (HPLC-MS). The functionality of the proposed qPCR method was demonstrated by the strong linear relationship of the standard curves constructed with the omt-1 gene copy number and Ct values for the different aflatoxin producers tested. The ability of the qPCR protocols to quantify aflatoxin-producing molds was evaluated in different artificially inoculated foods. A good linear correlation was obtained over the range 4 to 1 log cfu/g per reaction for all qPCR assays in the different food matrices (peanuts, spices and dry-fermented sausages). The detection limit in all inoculated foods ranged from 1 to 2 log cfu/g for SYBR Green and TaqMan assays. No significant effect was observed due to the different equipment, operator, and qPCR methodology used in the tests of repeatability and reproducibility for different foods. The proposed methods quantified with high efficiency the fungal load in foods. These qPCR protocols are proposed for use to quantify aflatoxin-producing molds in food products.

Development of real-time PCR methods to quantify patulin-producing molds in food products

Patulin is a mycotoxin produced by different Penicillium and Aspergillus strains isolated from food products. To improve food safety, the presence of patulin-producing molds in foods should be quantified. In the present work, two real-time (RTi) PCR protocols based on SYBR Green and TaqMan were developed. Thirty four patulin producers and 28 non-producers strains belonging to different species usually reported in food products were used. The patulin production was tested by mycellar electrokinetic capillary electrophoresis (MECE) and high-pressure liquid chromatography-mass spectrometry (HPLC-MS). A primer pair F-idhtrb/R-idhtrb and the probe IDHprobe were designed from the isoepoxydon dehydrogenase (idh) gene, involved in patulin biosynthesis. The functionality of the developed method was demonstrated by the high linear relationship of the standard curves constructed with the idh gene copy number and Ct values for the different patulin producers tested. The ability to quantify patulin producers of the developed SYBR Green and TaqMan assays in artificially inoculated food samples was successful, with a minimum threshold of 10 conidia g(-1) per reaction. The developed methods quantified with high efficiency fungal load in foods. These RTi-PCR protocols, are proposed to be used to quantify patulin-producing molds in food products and to prevent patulin from entering the food chain.