Morphological and molecular characterisation of Penicillium roqueforti and P. paneum isolated from baled grass silage

Analysis of Whole-Genome for Identification of Seven Penicillium Species with Significant Economic Value

The Penicillium genus exhibits a broad global distribution and holds substantial economic value in sectors including agriculture, industry, and medicine. Particularly in agriculture, Penicillium species significantly impact plants, causing diseases and contamination that adversely affect crop yields and quality. Timely detection of Penicillium species is crucial for controlling disease and preventing mycotoxins from entering the food chain. To tackle this issue, we implement a novel species identification approach called Analysis of whole GEnome (AGE). Here, we initially applied bioinformatics analysis to construct specific target sequence libraries from the whole genomes of seven Penicillium species with significant economic impact: P. canescens, P. citrinum, P. oxalicum, P. polonicum, P. paneum, P. rubens, and P. roqueforti. We successfully identified seven Penicillium species using the target we screened combined with Sanger sequencing and CRISPR-Cas12a technologies. Notably, based on CRISPR-Cas12a technology, AGE can achieve rapid and accurate identification of genomic DNA samples at a concentration as low as 0.01 ng/µL within 30 min. This method features high sensitivity and portability, making it suitable for on-site detection. This robust molecular approach provides precise fungal species identification with broad implications for agricultural control, industrial production, clinical diagnostics, and food safety.

How do Time, Tannin, and Moisture Content Influence Toxicogenic Fungal Populations during the Storage of Sorghum Grains?

ABSTRACT

Cereal grains are usually ensiled to improve their nutritional value and are one of the main sources of feed for dairy cattle. However, during storage, grains can be contaminated with toxicogenic fungi. Sorghum is one of the most economically important cereals in the world. Therefore, the aim of this work was to evaluate the influence of storage duration and tannin and moisture content (MC) on toxicogenic fungal populations in sorghum grain storage. Samples that were prepared with varieties high in tannins (genotypes Morgan 108 and ACA 558, >5 g/kg dry matter) and with varieties low in tannin content (genotypes Flash 10 and ACA 546, <1 g/kg dry matter) were collected and manually compacted in experimental laboratory silos where they received different MC treatments: low (15 to 25%), medium (26 to 32%), and high (33 to 42%). Freshly harvested grains were analyzed at time 0, and stored grains were analyzed at 30, 90, and 180 days. Fungal isolation and identification were performed following conventional mycological methods. Penicillium citrinum (34%), Aspergillus flavus (60%), and Fusarium nygamai (68%) were the most abundant species. Rapid detection of aflatoxins and fumonisins in each sample was performed using enzyme-linked immunosorbent assay according to the AOAC method, and the quantification of aflatoxin B1 was performed using high-performance liquid chromatography. In four samples of pre- and poststorage grains, aflatoxins were detected with levels of 6.7 to 28.8 μg/kg and aflatoxin B1 with a level of 2 to 14 μg/kg. Fumonisins were only detected in two freshly harvested samples, with levels of 500 to 900 μg/kg. In general, storage time favored the increase of Penicillium populations and reduced Aspergillus and Fusarium. Conversely the abundance of the three populations was not affected by the MC. The results of this study show that fungal populations must be analyzed at different times.

HIGHLIGHTS

Fungal species and mycotoxins in mouldy spots of grass and maize silages in Austria

Fungi and mycotoxins in silage can have detrimental consequences for both cattle and human health. This pilot study identified, via the routinary direct plating method, the dominant cultivable fungi in mouldy grass silages (GS) (n = 19) and maize silages (MS) (n = 28) from Austria. The profiles of regulated, modified, and emerging mycotoxins together with other fungal metabolites were analysed via LC-(ESI)MS/MS. Penicillium roqueforti, Saccharomyces spp., Geotrichum candidum, Aspergillus fumigatus and Monascus ruber were the most frequent fungal organisms identified. Other species including Mucor circinelloides, Fusarium spp. and Paecilomyces niveus were detected at lower frequencies. The presence of complex mixtures of toxic and potentially toxic compounds was evidenced by high levels and occurrences (≥ 50%) of Penicillium-produced compounds such as mycophenolic acid (MPA), roquefortines (ROCs), andrastins (ANDs) and marcfortine A. Mouldy silages contained toxins commonly produced by genus Fusarium (e.g. zearalenone (ZEN) and trichothecenes), Alternaria (like tenuazonic acid (TeA) and alternariol (AHO)) and Aspergillus (such as sterigmatocystin (STC)). Compared to those in GS, mouldy spots in MS presented significantly higher fungal counts and more diverse toxin profiles, in addition to superior levels of Fusarium spp., Penicillium spp. and total fungal metabolites. Generally, no correlation between mould counts and corresponding metabolites was detected, except for the counts of P. roqueforti, which were positively correlated with Penicillium spp. metabolites in mouldy MS. This study represents a first assessment of the fungal diversity in mouldy silage in Austria and highlights its potential role as a substantial contributor to contamination with complex mycotoxin mixtures in cattle diets.

Propionic Acid and Sodium Benzoate Affected Biogenic Amine Formation, Microbial Community, and Quality of Oat Silage

Investigating the microbial communities and biogenic amine (BA) formation in silage is of vital for improving the quality and safety of oat silage. The present study evaluated the effects of propionic acid (P) and sodium benzoate (SB) on the quality properties, microbial communities, and BA formation in oat silage. Oat was harvested at boot stage and ensiled using P and SB as additives in mini silos, followed by 14 days of aerobic exposure. The results showed that P and SB improved fermentation quality of oat silage, increased the lactic acid content, and decreased pH value and ammonia nitrogen content. Putrescine, cadaverine, and tyramine were the dominant BAs in oat silage; spermidine and spermine were not detected. The control silage had the highest content of total biogenic amine (TBA, 2506.7 mg kg^–1 DM), and decreased by 51.1 and 57.7% after adding P and SB, respectively. Moreover, a lower putrescine, cadaverine, and tyramine content and undesirable microbes, such as Caproiciproducens, Stenotrophomonas, Herbinix, and Enterobacter genera, were observed in P and SB silages, which was beneficial for oat silage quality. The fungal community of P silage was dominated by Monascus fuliginosus, and the temperature, pH and ammonia nitrogen content increased after exposure to air. Sedimentibacter, Herbinix, Caproiciproducens, Enterobacter, and Escherichia-Shigella were found to be positively correlated with BA formation in oat silage. Overall, P and SB effectively inhibit the undesirable microbes and BA formation in oat silage, the P silage exhibited lower aerobic stability than the SB silage.

Differentiation of Penicillium roqueforti from Closely Related Species Contaminating Cheeses and Dairy Environment

Currently, Penicillium roqueforti and the closely related P. carneum and P. paneum are identified based on their macromorphology, micromorphology, and molecular properties, the determination of which involves time-consuming procedures. Culture collections focused on dairy isolates of P. roqueforti require quick and efficient tools for routine applications to identify the (a) taxonomy affiliation and (b) morphological properties of strains that influence the sensory properties of blue-veined cheeses. Here, we assessed the morphological variability of P. roqueforti, P. carneum, P. paneum, and P.crustosum on artificial, Edam-like, and Roquefort-like media. Molecular tools were used to test P. roqueforti strains and clones effectively. A novel primer, PrsF, was tested for specificity within strains and isolates of P. roqueforti compared to P. carneum, P. paneum, and P. crustosum. The results reveal that PrsF was specific to the P. roqueforti samples and did not amplify the other tested Penicillium species. Identification based simultaneously on the specificity of the PrsF primer pair and cultivation of P. roqueforti strains on Roquefort-like medium represents an effective method for expanding the collections and practical use of P. roqueforti in the dairy industry.

Testing selectivity of bacterial and fungal culture media compared to original silage samples using next generation sequencing

Plate counts using selective culture media is still the most frequently used method for the enumeration of the different microbial groups that colonize silage, including lactic acid bacteria, yeasts and molds. Since different culture media have specific composition, they may allow the growth of specific populations. To date, no study has used next generation sequencing technology to compare the selective capacity of these different culture media although this approach could provide comprehensive insight into the relevance of using one culture medium over another. Sequencing of the 16S rDNA and ITS amplicon were performed to compare the selectivity of different culture media used in silage microbiology. Corn silage, grass-alfalfa silage and total mixed ration extracts were plated on five selective media for lactic acid bacteria, incubated under aerobic and anaerobic conditions, and on eight selective media for yeast and molds to compare their selectivity. Ensiling provided a pre-selection environment for specific microorganisms over forage and reduced the number of observed OTUs: only 12 OTUs of bacteria were observed in corn silage sampled in the center of a bunker silo, while the mean number of OTUs identified in samples taken closer to the side of the silo, influenced by higher oxygen and humidity level, increased to 79. Still, MRS and Rogosa plates had less than 12 different OTUs in the center and 24 at the side, mainly Lactobacillaceae, Acetobacteraceae, and Leuconostocaceae. Incubating the plates under anaerobic conditions was selective against Acetobacteraceae. MRS supplemented with acetic acid increased selectivity of lactic acid bacteria. When plated on culture media specific for yeast and molds, from 17 to 68 different OTUs were observed in corn silage. Mixed grass-alfalfa silage and total mixed ration samples usually had more observed OTUs and the diversity profile of the corresponding culture media was similar to that of the original samples. For yeasts and molds, Dichloran Rose Bengal Chloramphenicol Agar revealed a diversity profile close to the that of the corn silage.

Antibacterial and antifungal activity of crude and freeze-dried bacteriocin-like inhibitory substance produced by Pediococcus pentosaceus

Pediococcus pentosaceus LBM 18 has shown potential as producer of an antibacterial and antifungal bacteriocin-like inhibitory substance (BLIS). BLIS inhibited the growth of spoilage bacteria belonging to Lactobacillus, Enterococcus and Listeria genera with higher activity than Nisaplin used as control. It gave rise to inhibition halos with diameters from 9.70 to 20.00 mm, with Lactobacillus sakei being the most sensitive strain (13.50-20.00 mm). It also effectively suppressed the growth of fungi isolated from corn grain silage for up to 25 days and impaired morphology of colonies by likely affecting fungal membranes. These results point out that P. pentosaceus BLIS may be used as a new promising alternative to conventional antibacterial and antifungal substances, with potential applications in agriculture and food industry as a natural bio-controlling agent. Moreover, cytotoxicity and cell death induction tests demonstrated cytotoxicity and toxicity of BLIS to human colon adenocarcinoma Caco-2cells but not to peripheral blood mononuclear cells, with suggests possible applications of BLIS also in medical-pharmaceutical applications.

Dynamics of fungal community during silage fermentation of elephant grass (Pennisetum purpureum) produced in northern Vietnam

Objective

This study aimed to gain deeper insights into the dynamic changes in spoilage fungi populations during fermentation and the influence of traditional additives on silage quality.

Methods

Elephant grass (Pennisetum purpureum) was prepared without any additive (control), and with the addition of 0.5% salt, and 0.5% salt−0.2% sugar mixture. The fungal community was then determined using a classic culturing method and high-throughput sequencing at 0, 5, 15, and 60 days after ensiling.

Results

The results showed that the fungal community of elephant grass silage varied significantly between the natural fermentation without any additive and the two additive groups. The diversity and relative abundance of spoilage molds in the control group were much higher than those in the two treatment groups (p<0.05). Three species of yeasts (Candida sp., Pichia sp., Trichosporon sp.) and four spoilage molds (Fusarium sp., Aspergillus sp., Muco sp. and Penicillin sp.) were the predominant fungi in elephant grass during natural fermentation from 0 to 60 days, which were found to be significantly decreased in salt and sugar additive groups (p<0.05). Meanwhile, the diversity and relative abundance of undesirable molds in the 0.5%-salt additive group were the lowest among all groups.

Conclusion

Adding salt and sugar, particularly 0.5% salt, is a promising effective approach to reduce the amount of undesirable fungi thus, improving the silage quality of elephant grass in northern Vietnam.

Bacillus velezensis as antagonist towards Penicillium roqueforti s.l. in silage: in vitro and in vivo evaluation

AIMS

The present study was conducted to evaluate the antagonistic effect of Bacillus velezensisNRRL B-23189 towards Penicillium roqueforti s.s. and Penicillium paneum (designated together as P. roqueforti s.l.) in silage conditions.

METHODS AND RESULTS

Corn silage conditions were simulated in vitro, and the impact of B. velezensis culture supernatant or cell suspension on P. roqueforti s.l. growth and roquefortine C production was evaluated. The antagonism was promising, but growth of B. velezensis in corn silage infusion was poor. Additionally, an in vivo experiment was carried out with mini-silos containing a mixture of perennial ryegrass and white clover inoculated with P. roqueforti s.l. The applied B. velezensis cell suspension was unsuccessful in reducing P. roqueforti s.l. numbers, but did not compromise the silage acidification.

CONCLUSIONS

Although the antagonism observed in vitro was promising, the applied B. velezensis cell suspension could not live up to the expectations in vivo.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, the present study is the first one evaluating the antagonistic properties of B. velezensis towards toxigenic moulds in silage conditions, offering a good base for further research.

Examination of the taxonomic position of Penicillium strains used in blue cheese production based on the partial sequence of β-tubulin

Penicillium roqueforti is a well known starter used for blue cheese production. Two closely related species, P. carneum and P. paneum, were previously classified as varieties of P. roqueforti. Penicillium roqueforti does not produce patulin, a mycotoxin harmful for human health, whereas both P. carneum and P. paneum actively produce this toxin. From the viewpoint of food safety, it is thus important to confirm that P. carneum and P. paneum are not used for cheese production. In the present study, the taxonomic position of Penicillium strains used for blue cheese production was examined on the basis of the partial sequence of β-tubulin. Twenty-eight Penicillium strains isolated from blue cheeses were investigated. All the examined strains belonged to P. roqueforti. Therefore, the Penicillium strains used for production of the blue cheese samples examined here do not negatively impact on human health.

Light-scattering sensor for real-time identification of Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio cholerae colonies on solid agar plate

The three most common pathogenic species of Vibrio, Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus, are of major concerns due to increased incidence of water‐ and seafood‐related outbreaks and illness worldwide. Current methods are lengthy and require biochemical and molecular confirmation. A novel label‐free forward light‐scattering sensor was developed to detect and identify colonies of these three pathogens in real time in the presence of other vibrios in food or water samples. Vibrio colonies grown on agar plates were illuminated by a 635 nm laser beam and scatter‐image signatures were acquired using a CCD (charge‐coupled device) camera in an automated BARDOT (BActerial Rapid Detection using Optical light‐scattering Technology) system. Although a limited number of Vibrio species was tested, each produced a unique light‐scattering signature that is consistent from colony to colony. Subsequently a pattern recognition system analysing the collected light‐scatter information provided classification in 1−2 min with an accuracy of 99%. The light‐scattering signatures were unaffected by subjecting the bacteria to physiological stressors: osmotic imbalance, acid, heat and recovery from a viable but non‐culturable state. Furthermore, employing a standard sample enrichment in alkaline peptone water for 6 h followed by plating on selective thiosulphate citrate bile salts sucrose agar at 30°C for ∼ 12 h, the light‐scattering sensor successfully detected V. cholerae, V. parahaemolyticus and V. vulnificus present in oyster or water samples in 18 h even in the presence of other vibrios or other bacteria, indicating the suitability of the sensor as a powerful screening tool for pathogens on agar plates.

Penicillium simile sp. nov. revealed by morphological and phylogenetic analysis

The morphology of three phenetically identical Penicillium isolates, collected from the bioaerosol in a restoration laboratory in Italy, displayed macro- and microscopic characteristics that were similar though not completely ascribable to Penicillium raistrickii. For this reason, a phylogenetic approach based on DNA sequencing analysis was performed to establish both the taxonomic status and the evolutionary relationships of these three peculiar isolates in relation to previously described species of the genus Penicillium. We used four nuclear loci (both rRNA and protein coding genes) that have previously proved useful for the molecular investigation of taxa belonging to the genus Penicillium at various evolutionary levels. The internal transcribed spacer region (ITS1–5.8S–ITS2), domains D1 and D2 of the 28S rDNA, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and sequenced. Analysis of the rRNA genes and of the benA and cmd sequence data indicates the presence of three isogenic isolates belonging to a genetically distinct species of the genus Penicillium, here described and named Penicillium simile sp. nov. (ATCC MYA-4591T  = CBS 129191T). This novel species is phylogenetically different from P. raistrickii and other related species of the genus Penicillium (e.g. Penicillium scabrosum), from which it can be distinguished on the basis of morphological trait analysis.

Sex in Penicillium series Roqueforti

Various fungi were isolated during the course of a survey in a cold-store of apples in the Netherlands. One of these fungi belongs to the genus Penicillium and produces cleistothecia at 9 and 15 °C. A detailed study using a combination of phenotypic characters, sequences and extrolite patterns showed that these isolates belong to a new species within the series Roqueforti. The formation of cleistothecia at low temperatures and the inability to produce roquefortine C, together with a unique phylogenetic placement, make these isolates a novel entity in the Roqueforti series. The name Penicillium psychrosexualis sp. nov. (CBS 128137^T) is proposed here for these isolates.

Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing

We report the development of 17 microsatellite markers in the cheese fungi Penicillium camemberti and P. roqueforti, using an enrichment protocol. Polymorphism and cross-amplification were explored using 23 isolates of P. camemberti, 26 isolates of P. roqueforti, and 2 isolates of each of the P. chrysogenum and P. nalgiovense species, used to produce meat fermented products. The markers appeared useful for differentiating species, both using their amplification sizes and the sequences of their flanking regions. The microsatellite locus PC4 was particularly suitable for distinguishing contaminant species closely related to P. camemberti and for clarifying the phylogenetic relationship of this species with its supposed ancestral form, P. commune. We analyzed 22 isolates from different culture collections assigned to the morphospecies P. commune, most of them occurring as food spoilers, mainly from the cheese environment. None of them exhibited identical sequences with the ex-type isolate of the species P. commune. They were instead distributed into two other distinct lineages, corresponding to the old species P. fuscoglaucum and P. biforme, previously synonymized respectively with P. commune and P. camemberti. The ex-type isolate of P. commune was strictly identical to P. camemberti at all the loci examined. P. caseifulvum, a non toxinogenic species described as a new candidate for cheese fermentation, also exhibited sequences identical to P. camemberti. The microsatellite locus PC4 may therefore be considered as a useful candidate for the barcode of these economically important species.