A phylogenetic analysis of Greek isolates of Aspergillus species based on morphology and nuclear and mitochondrial gene sequences

A multi-aspect analysis of two analogous aspergillus spp. belonging to section Flavi: aspergillus flavus and aspergillus oryzae

Microfungal isolates were routinely identified depending on both macro and micro morphological characteristics, sometimes, some fungal isolates appeared to be similar and such cases caused severe confusion for mycologists during the preliminary identification. During our previous studies dealing with isolation of fungi for some biotechnological applications; two mystifying species Aspergillus flavus and Aspergillus oryzae showed similar cultural and macroscopic features. Therefore, the current study aimed to easily distinguish between these two species depending on simple approaches which are routinely followed by a large segment of researchers. Investigation of the macroscopic features was performed to check the fungal growth on four different media (PDA, MEA, YES, and CYA) followed by microscopic examination using an ordinary light microscope, and scanning electron microscope SEM. Also, screening of secondary metabolites for both strains was preliminarily identified to find out the difference between their metabolic profiles. Finally, ITS rDNA was involved to clarify the molecular differences along their partial sequence. Conclusively, the BLAST strategy confirmed the similarity of ITS rDNA segments of both fungal strains that supported our hypothesis. The color of the fungal growth is a very critical factor whereas it is extensively influenced by the type of cultivation media. Accordingly, the YES medium was an inspiring tool assisting in prompt differentiation during the culture investigation step whereas A. oryzae and A. flavus appeared significant mustard yellow and olive green respectively. During the microscopic examination, the CYA medium also had a robust effect on the formation of the conidial chain whereas the knit long chain was observed in A. oryzae while the conidia appeared scattered and not in a chain in the case of A. flavus. Likewise, both two strains possessed different metabolic profiles where A. oryzae is not an Afla toxin producer, unlike A. flavus.

Storage Fungi and Mycotoxins Associated with Rice Samples Commercialized in Thailand

The study focused on the examination of the different fungal species isolated from commercial rice samples, applying conventional culture techniques, as well as different molecular and phylogenic analyses to confirm phenotypic identification. Additionally, the mycotoxin production and contamination were analyzed using validated liquid chromatography-tandem mass spectrometry (LC-MS/MS). In total, 40 rice samples were obtained covering rice berry, red jasmine rice, brown rice, germinated brown rice, and white rice. The blotting paper technique applied on the 5 different types of rice samples detected 4285 seed-borne fungal infections (26.8%) for 16,000 rice grains. Gross morphological data revealed that 19 fungal isolates belonged to the genera Penicillium/Talaromyces (18 of 90 isolates; 20%) and Aspergillus (72 of 90 isolates; 80%). To check their morphologies, molecular data (fungal sequence-based BLAST results and a phylogenetic tree of the combined ITS, BenA, CaM, and RPB2 datasets) confirmed the initial classification. The phylogenic analysis revealed that eight isolates belonged to P. citrinum and, additionally, one isolate each belonged to P. chermesinum, A. niger, A. fumigatus, and A. tubingensis. Furthermore, four isolates of T. pinophilus and one isolate of each taxon were identified as Talaromyces (T. radicus, T. purpureogenum, and T. islandicus). The results showed that A. niger and T. pinophilus were two commonly occurring fungal species in rice samples. After subculturing, ochratoxin A (OTA), generated by T. pinophilus code W3-04, was discovered using LC-MS/MS. In addition, the Fusarium toxin beauvericin was detected in one of the samples. Aflatoxin B1 or other mycotoxins, such as citrinin, trichothecenes, and fumonisins, were detected. These preliminary findings should provide valuable guidance for hazard analysis critical control point concepts used by commercial food suppliers, including the analysis of multiple mycotoxins. Based on the current findings, mycotoxin analyses should focus on A. niger toxins, including OTA and metabolites of T. pinophilus (recently considered a producer of emerging mycotoxins) to exclude health hazards related to the traditionally high consumption of rice by Thai people.

Molecular Characterization of Aspergillus flavus Strains Isolated from Animal Feeds

Aflatoxin (AF)-producing fungi such as Aspergillus flavus commonly contaminate animal feeds, causing high economic losses. A. flavus is the most prevalent and produces AFB1, a potent mutagen, and carcinogen threatening human and animal health. Aspergillaceae is a large group of closely related fungi sharing number of morphological and genetic similarities that complicate the diagnosis of highly pathogenic strains. We used here morphological and molecular assays to characterize fungal isolates from animal feeds in Southwestern Algeria. These tools helped to identify 20 out of 30 Aspergillus strains, and 15 of them belonged to the Aspergillus section Flavi. Further analyses detected four out of 15 as belonging to Aspergillus flavus-parasiticus group. PCR targeting the AF genes' aflR-aflS(J) intergenic region amplified a single 674 bp amplicon in all four isolates. The amplicons were digested with a BglII endonuclease, and three specific fragments were observed for A. flavus but A. parasitucus lacked two typical fragments. Sequencing data of four amplicons confirmed the presence of the two BglII restriction sites yielding the three fragments, confirming that all four strains were A. flavus. In addition, this analysis illustrated the genetic variability within the A. flavus strains.

Fungi composition in settled dust associated with fractional exhaled nitric oxide in school children with asthma

Fungi exposure has been significantly linked to respiratory illness. However, numerous fungi taxa that are potentially allergenic still undocumented and leave a barrier to establishing a clear connection between exposure and health risks. This study aimed to evaluate the association of fungi composition in settled dust with fractional exhaled nitric oxide (FeNO) levels among school children with doctor-diagnosed asthma. A cross-sectional study was undertaken among secondary school students in eight schools in the urban area of Hulu Langat, Selangor, Malaysia. A total of 470 school children (aged 14 years old) were randomly selected and their FeNO levels were measured and allergic skin prick tests were conducted. The settled dust samples were collected and analysed by using metagenomic technique to determine the fungi composition. The general linear regression with complex sampling was employed to determine the interrelationship. In total, 2645 fungal operational taxonomic units (OTUs) were characterised from the sequencing process which belongs to Ascomycota (60.7 %), Basidiomycota (36.4 %), Glomeromycota (2.9 %) and Chytridiomycota (0.04 %). The top five mostly abundance in all dust samples were Aspergillus clavatus (27.2 %), followed by Hyphoderma multicystidium (12.2 %), Verrucoconiothyrium prosopidis (9.4 %), Ganoderma tuberculosum (9.2 %), and Heterochaete shearii (7.2 %). The regression results indicated that A. clavatus, Brycekendrickomyces acaciae, Candida parapsilosis, Hazslinszkyomyces aloes, H. multicystidium, H. shearii, Starmerella meliponinorum, V. prosopidis were associated in increased of FeNO levels among the asthmatic group at 0.992 ppb (95 % CI = 0.34-1.68), 2.887 ppb (95 % CI = 2.09-3.76), 0.809 ppb (95 % CI = 0.14-1.49), 0.647 ppb (95 % CI = 0.36-0.94), 1.442 ppb (95 % CI = 0.29-2.61), 1.757 ppb (95 % CI = 0.59-2.87), 1.092 ppb (95 % CI = 0.43-1.75) and 1.088 ppb (95 % CI = 0.51-1.62), respectively. To our knowledge, this is a new finding. The findings pointed out that metagenomics profiling of fungi could enhance our understanding of a complex interrelation between rare and unculturable fungi with airway inflammation.

Uncovering Diagnostic Value of Mitogenome for Identification of Cryptic Species Fusarium graminearum Sensu Stricto

Fungal complexes are often composed of morphologically nearly indistinguishable species with high genetic similarity. However, despite their close relationship, they can exhibit distinct phenotypic differences in pathogenicity and production of mycotoxins. Many plant pathogenic and toxigenic fungi have been shown to consist of such cryptic species. Identification of cryptic species in economically important pathogens has added value in epidemiologic studies and provides opportunities for better control. Analysis of mitochondrial genomes or mitogenomics opens up dimensions for improved diagnostics of fungi, especially when efficient recovery of DNA is problematic. In comparison to nuclear DNA, mitochondrial DNA (mtDNA) can be amplified with improved efficacy due to its multi-copy nature. However, to date, only a few studies have demonstrated the usefulness of mtDNA for identification of cryptic species within fungal complexes. In this study, we explored the value of mtDNA for identification of one of the most important cereal pathogens Fusarium graminearum sensu stricto (F.g.). We found that homing endonucleases (HEGs), which are widely distributed in mitogenomes of fungi, display small indel polymorphism, proven to be potentially species specific. The resulting small differences in their lengths may facilitate further differentiation of F.g. from the other cryptic species belonging to F. graminearum species complex. We also explored the value of SNP analysis of the mitogenome for typing F.g. The success in identifying F.g. strains was estimated at 96%, making this tool an attractive complement to other techniques for identification of F.g.

Metagenomic characterization of indoor dust fungal associated with allergy and lung inflammation among school children

The exposure of school children to indoor air pollutants has increased allergy and respiratory diseases. The objective of this study were to determine the toxicodynamic interaction of indoor pollutants exposure, biological and chemical with expression of adhesion molecules on eosinophil and neutrophil. A self-administered questionnaire, allergy skin test, and fractional exhaled nitric oxide (FeNO) analyser were used to collect information on health status, sensitization to allergens and respiratory inflammation, respectively among school children at age of 14 years. The sputum induced were analysed to determine the expression of CD11b, CD35, CD63 and CD66b on eosinophil and neutrophil by using flow cytometry technique. The particulate matter (PM_2.5 and PM₁₀), NO₂, CO₂, and formaldehyde, temperature, and relative humidity were measured inside the classrooms. The fungal DNA were extracted from settled dust collected from classrooms and evaluated using metagenomic techniques. We applied chemometric and regression in statistical analysis. A total of 1869 unique of operational taxonomic units (OTUs) of fungi were identified with dominated at genus level by Aspergillus (15.8%), Verrucoconiothyrium (5.5%), and Ganoderma (4.6%). Chemometric and regression results revealed that relative abundance of T. asahii were associated with down regulation of CD66b expressed on eosinophil, and elevation of FeNO levels in predicting asthmatic children with model accuracy of 63.6%. Meanwhile, upregulation of CD11b expressed on eosinophil were associated with relative abundance of A. clavatus and regulated by PM_2.5. There were significant association of P. bandonii with upregulation of CD63 expressed on neutrophil and exposure to NO₂. Our findings indicate that exposure to PM_2.5, NO₂, T. asahii, P.bandonii and A.clavatus are likely interrelated with upregulation of activation and degranulation markers on both eosinophil and neutrophil.

Hydrocarbon Degradation and Enzyme Activities of Aspergillus oryzae and Mucor irregularis Isolated from Nigerian Crude Oil-Polluted Sites

Many free-living saprobic fungi are nature recruited organisms for the degradation of wastes, ranging from lignocellulose biomass to organic/inorganic chemicals, aided by their production of enzymes. In this study, fungal strains were isolated from contaminated crude-oil fields in Nigeria. The dominant fungi were selected from each site and identified as Aspergillus oryzae and Mucor irregularis based on morphological and molecular characterization, with site percentage incidences of 56.67% and 66.70%, respectively. Selected strains response/tolerance to complex hydrocarbon (used engine oil) was studied by growing them on Bushnell Haas (BH) mineral agar supplemented with the hydrocarbon at different concentrations, i.e., 5%, 10%, 15%, and 20%, with a control having dextrose. Hydrocarbon degradation potentials of these fungi were confirmed in BH broth culture filtrates pre-supplemented with 1% engine oil after 15 days of incubation using GC/MS. In addition, the presence of putative enzymes, laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) was confirmed in culture filtrates using appropriate substrates. The analyzed fungi grew in hydrocarbon supplemented medium with no other carbon source and exhibited 39.40% and 45.85% dose inhibition response (DIR) respectively at 20% hydrocarbon concentration. An enzyme activity test revealed that these two fungi produced more Lac than MnP and LiP. It was also observed through the GC/MS analyses that while A. oryzae acted on all hydrocarbon components in the used engine oil, M. irregularis only degraded the long-chain hydrocarbons and BTEX. This study confirms that A. oryzae and M. irregularis have the potential to be exploited in the bio-treatment and removal of hydrocarbons from polluted soils.

Morphological and Molecular Characterization of Toxigenic Aspergillus flavus from Groundnut Kernels in Kenya

Pathogenesis of Aspergillus flavus on important agricultural products is a key concern on human health due to the synthesis and secretion of the hazardous secondary metabolite, aflatoxin. This study identified and further characterized aflatoxigenic A. flavus from groundnuts sampled from sundry shops in Kenya using integrated morphological and molecular approaches. The groundnuts were plated on potato dextrose agar for isolation and morphological observation of A. flavus based on macroscopic and microscopic features. Molecular characterization was done through amplification and comparison of the partial sequence of the ITS1-5.8S-ITS2 region. The expression analysis of aflR, aflS, aflD, aflP, and aflQ genes in the aflatoxin biosynthesis pathways was conducted to confirm the positive identification of A. flavus. The gene expression also aided to delineate toxigenic isolates of A. flavus from atoxigenic ones. Morphologically, 18 isolates suspected to be A. flavus were identified. Out of these, 14 isolates successfully amplified the 500 bp ITS region of A. flavus or Aspergillus oryzae, while 4 isolates were not amplified. All the remaining 14 isolates expressed at least one of the aflatoxigenic genes but only 5 had all the genes expressed. Partial sequencing revealed that isolates 5, 11, 12, 13, and 15 had 99.2%, 97.6%, 98.4%, 97.5%, and 100% homology, respectively, to the A. flavus isolate LUOHE, ITS-5.8S-ITS2, obtained from the NCBI database. The five isolates were accurate identification of atoxigenic A. flavus. Precise identification of toxigenic strains of A. flavus will be useful in establishing control strategies of the fungus in food products.

Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes

Much of the mitogenome variation observed in fungal lineages seems driven by mobile genetic elements (MGEs), which have invaded their genomes throughout evolution. The variation in the distribution and nucleotide diversity of these elements appears to be the main distinction between different fungal taxa, making them promising candidates for diagnostic purposes. Fungi of the genus Fusarium display a high variation in MGE content, from MGE-poor (Fusarium oxysporum and Fusarium fujikuroi species complex) to MGE-rich mitogenomes found in the important cereal pathogens F. culmorum and F. graminearum sensu stricto. In this study, we investigated the MGE variation in these latter two species by mitogenome analysis of geographically diverse strains. In addition, a smaller set of F. cerealis and F. pseudograminearum strains was included for comparison. Forty-seven introns harboring from 0 to 3 endonucleases (HEGs) were identified in the standard set of mitochondrial protein-coding genes. Most of them belonged to the group I intron family and harbored either LAGLIDADG or GIY-YIG HEGs. Among a total of 53 HEGs, 27 were shared by all fungal strains. Most of the optional HEGs were irregularly distributed among fungal strains/species indicating ancestral mosaicism in MGEs. However, among optional MGEs, one exhibited species-specific conservation in F. culmorum. While in F. graminearum s.s. MGE patterns in cox3 and in the intergenic spacer between cox2 and nad4L may facilitate the identification of this species. Thus, our results demonstrate distinctive traits of mitogenomes for diagnostic purposes of Fusaria.

Phylogeography and Population Structure Analysis Reveal Diversity by Gene Flow and Mutation in Ustilago segetum (Pers.) Roussel tritici Causing Loose Smut of Wheat

Ustilago segetum (Pers.) Roussel tritici (UST) causes loose smut of wheat account for considerable grain yield losses globally. For effective management, knowledge of its genetic variability and population structure is a prerequisite. In this study, UST isolates sampled from four different wheat growing zones of India were analyzed using the second largest subunit of the RNA polymerase II (RPB2) and a set of sixteen neutral simple sequence repeats (SSRs) markers. Among the 112 UST isolates genotyped, 98 haplotypes were identified. All the isolates were categorized into two groups (K = 2), each consisting of isolates from different sampling sites, on the basis of unweighted paired-grouping method with arithmetic averages (UPGMA) and the Bayesian analysis of population structure. The positive and significant index of association (I_A = 1.169) and standardized index of association (rBar_D = 0.075) indicate population is of non-random mating type. Analysis of molecular variance showed that the highest variance component is among isolates (91%), with significantly low genetic differentiation variation among regions (8%) (F_st = 0.012). Recombination (R_m = 0) was not detected. The results showed that UST isolates have a clonal genetic structure with limited genetic differentiation and human arbitrated gene flow and mutations are the prime evolutionary processes determining its genetic structure. These findings will be helpful in devising management strategy especially for selection and breeding of resistant wheat cultivars.

Molecular identification of some wild Nigerian mushrooms using internal transcribed spacer: polymerase chain reaction

Identification of fungal species based on morphological characteristics is tedious, complex, prone to errors, and thus cannot be completely relied upon. In this study, internal transcribed spacers (ITS 1 and 4)-polymerase chain reaction was employed to amplify DNA of 19 mushroom isolates collected at Environmental Pollution Science and Technology farm, Ilesa, Southwest Nigeria. The PCR amplification of ITS1 and 4 of the mushrooms isolates yielded approximately 850 bp. Amplicons obtained were sequenced and identified using BLASTn in the NCBI. The BLASTn results revealed that Termitomyces aurantiacus (3), Tricholoma matsutake (8), Tricholoma robustum (2), P. ostreatus (4), Schizophyllum commune (1) and Pleurotus pulmonarius (1) were fully represented. Only Tricholoma matsutake (KT273371), Pleurotus pulmonarius (KY962469) and Tricholoma matsutake (AF438605) had 100% similarity with reference strain. However, the phylogenetic analysis of the isolates showed low genetic relatedness with reference strains. This study revealed the novelty of the mushroom strains and thus advocating the need for strict conservation measures and further investigations on their potential benefits to mankind.

Aspergillus section Nidulantes (formerly Emericella): Polyphasic taxonomy, chemistry and biology

Aspergillus section Nidulantes includes species with striking morphological characters, such as biseriate conidiophores with brown-pigmented stipes, and if present, the production of ascomata embedded in masses of Hülle cells with often reddish brown ascospores. The majority of species in this section have a sexual state, which were named Emericella in the dual name nomenclature system. In the present study, strains belonging to subgenus Nidulantes were subjected to multilocus molecular phylogenetic analyses using internal transcribed spacer region (ITS), partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequences. Nine sections are accepted in subgenus Nidulantes including the new section Cavernicolus. A polyphasic approach using morphological characters, extrolites, physiological characters and phylogeny was applied to investigate the taxonomy of section Nidulantes. Based on this approach, section Nidulantes is subdivided in seven clades and 65 species, and 10 species are described here as new. Morphological characters including colour, shape, size, and ornamentation of ascospores, shape and size of conidia and vesicles, growth temperatures are important for identifying species. Many species of section Nidulantes produce the carcinogenic mycotoxin sterigmatocystin. The most important mycotoxins in Aspergillus section Nidulantes are aflatoxins, sterigmatocystin, emestrin, fumitremorgins, asteltoxins, and paxillin while other extrolites are useful drugs or drug lead candidates such as echinocandins, mulundocandins, calbistrins, varitriols, variecolins and terrain. Aflatoxin B₁ is produced by four species: A. astellatus, A. miraensis, A. olivicola, and A. venezuelensis.

Molecular variation analysis of Aspergillus flavus using polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer rDNA region

Aspergillus flavus is the second most common disease-causing species of Aspergillus in humans. The fungus is frequently associated with life-threatening infections in immunocompromised hosts. The primary aim of the present study was to analyze the genetic variability among different isolates of A. flavus using polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP). A total of 62 A. flavus isolates were tested in the study. Molecular variability was searched for by analysis of the PCR amplification of the internal transcribed spacer (ITS) regions of ribosomal DNA using restriction enzymes. PCR using primers for ITS1 and ITS4 resulted in a product of ~600 bp. Amplicons were subjected to digestion with restriction endonucleases EcoRI, HaeIII and TaqI. Digestion of the PCR products using these restriction enzymes produced different patterns of fragments among the isolates, with different sizes and numbers of fragments, revealing genetic variability. In conclusion, ITS-RFLP is a useful molecular tool in screening for nucleotide polymorphisms among A. flavus isolates.

Genome Sequencing and Evolutionary Analysis of Marine Gut Fungus Aspergillus sp. Z5 from Ligia oceanica

Aspergillus sp. Z5, isolated from the gut of marine isopods, produces prolific secondary metabolites with new structure and bioactivity. Here, we report the draft sequence of the approximately 33.8-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Aspergillus strain isolated from marine isopod Ligia oceanica. The phylogenetic analysis supported that this strain was closely related to A. versicolor, and genomic analysis revealed that Aspergillus sp. Z5 shared a high degree of colinearity with the genome of A. sydowii. Our results may facilitate studies on discovering the biosynthetic pathways of secondary metabolites and elucidating their evolution in this species.

A genomics based discovery of secondary metabolite biosynthetic gene clusters in Aspergillus ustus

Secondary metabolites (SMs) produced by Aspergillus have been extensively studied for their crucial roles in human health, medicine and industrial production. However, the resulting information is almost exclusively derived from a few model organisms, including A. nidulans and A. fumigatus, but little is known about rare pathogens. In this study, we performed a genomics based discovery of SM biosynthetic gene clusters in Aspergillus ustus, a rare human pathogen. A total of 52 gene clusters were identified in the draft genome of A. ustus 3.3904, such as the sterigmatocystin biosynthesis pathway that was commonly found in Aspergillus species. In addition, several SM biosynthetic gene clusters were firstly identified in Aspergillus that were possibly acquired by horizontal gene transfer, including the vrt cluster that is responsible for viridicatumtoxin production. Comparative genomics revealed that A. ustus shared the largest number of SM biosynthetic gene clusters with A. nidulans, but much fewer with other Aspergilli like A. niger and A. oryzae. These findings would help to understand the diversity and evolution of SM biosynthesis pathways in genus Aspergillus, and we hope they will also promote the development of fungal identification methodology in clinic.

Phylogenetic relationship of phosphate solubilizing bacteria according to 16S rRNA genes

Phosphate solubilizing bacteria (PSB) can convert insoluble form of phosphorous to an available form. Applications of PSB as inoculants increase the phosphorus uptake by plant in the field. In this study, isolation and precise identification of PSB were carried out in Malaysian (Serdang) oil palm field (University Putra Malaysia). Identification and phylogenetic analysis of 8 better isolates were carried out by 16S rRNA gene sequencing in which as a result five isolates belong to the Beta subdivision of Proteobacteria, one isolate was related to the Gama subdivision of Proteobacteria, and two isolates were related to the Firmicutes. Bacterial isolates of 6upmr, 2upmr, 19upmnr, 10upmr, and 24upmr were identified as Alcaligenes faecalis. Also, bacterial isolates of 20upmnr and 17upmnr were identified as Bacillus cereus and Vagococcus carniphilus, respectively, and bacterial isolates of 31upmr were identified as Serratia plymuthica. Molecular identification and characterization of oil palm strains as the specific phosphate solubilizer can reduce the time and cost of producing effective inoculate (biofertilizer) in an oil palm field.

Characterization of lignocellulolytic activities from a moderate halophile strain of Aspergillus caesiellus isolated from a sugarcane bagasse fermentation

A moderate halophile and thermotolerant fungal strain was isolated from a sugarcane bagasse fermentation in the presence of 2 M NaCl that was set in the laboratory. This strain was identified by polyphasic criteria as Aspergillus caesiellus. The fungus showed an optimal growth rate in media containing 1 M NaCl at 28°C and could grow in media added with up to 2 M NaCl. This strain was able to grow at 37 and 42°C, with or without NaCl. A. caesiellus H1 produced cellulases, xylanases, manganese peroxidase (MnP) and esterases. No laccase activity was detected in the conditions we tested. The cellulase activity was thermostable, halostable, and no differential expression of cellulases was observed in media with different salt concentrations. However, differential band patterns for cellulase and xylanase activities were detected in zymograms when the fungus was grown in different lignocellulosic substrates such as wheat straw, maize stover, agave fibres, sugarcane bagasse and sawdust. Optimal temperature and pH were similar to other cellulases previously described. These results support the potential of this fungus to degrade lignocellulosic materials and its possible use in biotechnological applications.