Use of pyrosequencing to quantify incidence of a specific Aspergillus flavus strain within complex fungal communities associated with commercial cotton crops

Structure of Aspergillus flavus populations associated with maize in Greece, Spain, and Serbia: Implications for aflatoxin biocontrol on a regional scale

Aspergillus flavus is the most frequently identified producer of aflatoxins. Non-aflatoxigenic members of the A. flavus L strains are used in various continents as active ingredients of bioprotectants directed at preventing aflatoxin contamination by competitive displacement of aflatoxin producers. The current research examined the genetic diversity of A. flavus L strain across southern Europe to gain insights into the population structure and evolution of this species and to evaluate the prevalence of genotypes closely related to MUCL54911, the active ingredient of AF-X1. A total of 2173L strain isolates recovered from maize collected across Greece, Spain, and Serbia in 2020 and 2021 were subjected to simple sequence repeat (SSR) genotyping. The analysis revealed high diversity within and among countries and dozens of haplotypes shared. Linkage disequilibrium analysis indicated asexual reproduction and clonal evolution of A. flavus L strain resident in Europe. Moreover, haplotypes closely related to MUCL54911 were found to belong to the same vegetative compatibility group (VCG) IT006 and were relatively common in all three countries. The results indicate that IT006 is endemic to southern Europe and may be utilized as an aflatoxin mitigation tool for maize across the region without concern for potential adverse impacts associated with the introduction of an exotic microorganism.

Multiple Year Influences of the Aflatoxin Biocontrol Product AF-X1 on the A. flavus Communities Associated with Maize Production in Italy

AF-X1 is a commercial aflatoxin biocontrol product containing the non-aflatoxigenic (AF-) strain of Aspergillus flavus MUCL54911 (VCG IT006), endemic to Italy, as an active ingredient. The present study aimed to evaluate the long-term persistence of VCG IT006 in the treated fields, and the multi-year influence of the biocontrol application on the A. flavus population. Soil samples were collected in 2020 and 2021 from 28 fields located in four provinces in north Italy. A vegetative compatibility analysis was conducted to monitor the occurrence of VCG IT006 on the total of the 399 isolates of A. flavus that were collected. IT006 was present in all the fields, mainly in the fields treated for 1 yr or 2 consecutive yrs (58% and 63%, respectively). The densities of the toxigenic isolates, detected using the aflR gene, were 45% vs. 22% in the untreated and treated fields, respectively. After displacement via the AF- deployment, a variability from 7% to 32% was noticed in the toxigenic isolates. The current findings support the long-term durability of the biocontrol application benefits without deleterious effects on each fungal population. Nevertheless, based on the current results, as well as on previous studies, the yearly applications of AF-X1 to Italian commercial maize fields should continue.

Quantification of the Aflatoxin Biocontrol Strain Aspergillus flavus AF36 in Soil and in Nuts and Leaves of Pistachio by Real-Time PCR

The species Aspergillus flavus and A. parasiticus are commonly found in the soils of nut-growing areas in California. Several isolates can produce aflatoxins that occasionally contaminate nut kernels, conditioning their sale. Strain AF36 of A. flavus, which does not produce aflatoxins, is registered as a biocontrol agent for use in almond, pistachio, and fig crops in California. After application in orchards, AF36 displaces aflatoxin-producing Aspergillus spp. and thus reduces aflatoxin contamination. Vegetative compatibility assays (VCAs) have traditionally been used to track AF36 in soils and crops where it has been applied. However, VCAs are labor intensive and time consuming. Here, we developed a quantitative real-time PCR (qPCR) protocol to quantify proportions of AF36 accurately and efficiently in different substrates. Specific primers to target AF36 and toxigenic strains of A. flavus and A. parasiticus were designed based on the sequence of aflC, a gene essential for aflatoxin biosynthesis. Standard curves were generated to calculate proportions of AF36 based on threshold cycle values. Verification assays using pure DNA and conidial suspension mixtures demonstrated a significant relationship by regression analysis between known and qPCR-measured AF36 proportions in DNA (R² = 0.974; P < 0.001) and conidia mixtures (R² = 0.950; P < 0.001). Tests conducted by qPCR in pistachio leaves, nuts, and soil samples demonstrated the usefulness of the qPCR method to precisely quantify proportions of AF36 in diverse substrates, ensuring important time and cost savings. The outputs of this study will serve to design better aflatoxin management strategies for pistachio and other crops.

Biocontrol of Aflatoxins Using Non-Aflatoxigenic Aspergillus flavus: A Literature Review

Aflatoxins (AFs) are mycotoxins, predominantly produced by Aspergillus flavus, A. parasiticus, A. nomius, and A. pseudotamarii. AFs are carcinogenic compounds causing liver cancer in humans and animals. Physical and biological factors significantly affect AF production during the pre-and post-harvest time. Several methodologies have been developed to control AF contamination, yet; they are usually expensive and unfriendly to the environment. Consequently, interest in using biocontrol agents has increased, as they are convenient, advanced, and friendly to the environment. Using non-aflatoxigenic strains of A. flavus (AF⁻) as biocontrol agents is the most promising method to control AFs’ contamination in cereal crops. AF⁻ strains cannot produce AFs due to the absence of polyketide synthase genes or genetic mutation. AF⁻ strains competitively exclude the AF⁺ strains in the field, giving an extra advantage to the stored grains. Several microbiological, molecular, and field-based approaches have been used to select a suitable biocontrol agent. The effectiveness of biocontrol agents in controlling AF contamination could reach up to 99.3%. Optimal inoculum rate and a perfect time of application are critical factors influencing the efficacy of biocontrol agents.

Monitoring Aspergillus flavus Genotypes in a Multi-Genotype Aflatoxin Biocontrol Product With Quantitative Pyrosequencing

Aflatoxins pose significant food security and public health risks, decrease productivity and profitability of animal industries, and hamper trade. To minimize aflatoxin contamination in several crops, a biocontrol technology based on atoxigenic strains of Aspergillus flavus is commercially used in the United States and some African countries. Significant efforts are underway to popularize the use of biocontrol in Africa by various means including incentives. The purpose of this study was to develop quantitative pyrosequencing assays for rapid, simultaneous quantification of proportions of four A. flavus biocontrol genotypes within complex populations of A. flavus associated with maize crops in Nigeria to facilitate payment of farmer incentives for Aflasafe (a biocontrol product) use. Protocols were developed to confirm use of Aflasafe by small scale farmers in Nigeria. Nested PCR amplifications followed by sequence by synthesis pyrosequencing assays were required to quantify frequencies of the active ingredients and, in so doing, confirm successful use of biocontrol by participating farmers. The entire verification process could be completed in 3-4 days proving a savings over other monitoring methods in both time and costs and providing data in a time frame that could work with the commercial agriculture scheme. Quantitative pyrosequencing assays represent a reliable tool for rapid detection, quantification, and monitoring of multiple A. flavus genotypes within complex fungal communities, satisfying the requirements of the regulatory community and crop end-users that wish to determine which purchased crops were treated with the biocontrol product. Techniques developed in the current study can be modified for monitoring other crop-associated fungi.

A Polyphasic Approach Aids Early Detection of Potentially Toxigenic Aspergilli in Soil

Key chili and maize growing areas of Pakistan were selected for a focused baseline study of the levels of Aspergillus spp. Investigations were undertaken using a combination of molecular and culture-based techniques. Samples investigated included soil samples, one-year-old corn cobs, and fresh chili from selected locations. Aspergillus strains obtained from corn cobs were screened using coconut milk agar, resulting in one strain that was positive for aflatoxin production. Whole genome sequencing (WGS) with low coverage techniques were employed to screen the isolates for differences in the ribosomal RNA gene cluster and mitochondrial genome, with the aflatoxigenic strain proving to have a distinctive profile. Finally, strains were subjected to matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry (MALDI-ToF-MS) in order to obtain a proteomic ‘fingerprint’ which was used to distinguish the aflatoxigenic strain from the other isolates. The next generation sequencing (NGS) study was broadened to incorporate metabarcoding with ITS rRNA for determining the microbial biodiversity of the soil samples and presumptive screening for the presence of aflatoxigenic strains. Using information gleaned from the WGS results, a putative aflatoxigenic operational taxonomic unit (OTU) was observed in four of the 15 soil samples screened by metabarcoding. This method may have beneficial applications in early detection and surveillance programs in agricultural soils and commodities.

Frequent Shifts in Aspergillus flavus Populations Associated with Maize Production in Sonora, Mexico

Aspergillus flavus frequently contaminates maize, a critical staple for billions of people, with aflatoxins. Diversity among A. flavus L morphotype populations associated with maize in Sonora, Mexico was assessed and, in total, 869 isolates from 83 fields were placed into 136 vegetative compatibility groups (VCGs) using nitrate-nonutilizing mutants. VCG diversity indices did not differ in four agroecosystems (AES) but diversity significantly differed among years. Frequencies of certain VCGs changed manyfold over single years in both multiple fields and multiple AES. Certain VCGs were highly frequent (>1%) in 2006 but frequencies declined repeatedly in each of the two subsequent years. Other VCGs that had low frequencies in 2006 increased in 2007 and subsequently declined. None of the VCGs were consistently associated with any AES. Fourteen VCGs were considered dominant in at least a single year. However, frequencies often varied significantly among years. Only 9% of VCGs were detected all 3 years whereas 66% were detected in only 1 year. Results suggest that the most realistic measurements of both genetic diversity and the frequency of A. flavus VCGs are obtained by sampling multiple locations in multiple years. Single-season sampling in many locations should not be substituted for sampling over multiple years.

Distribution and incidence of atoxigenic Aspergillus flavus VCG in tree crop orchards in California: A strategy for identifying potential antagonists, the example of almonds

To identify predominant isolates for potential use as biocontrol agents, Aspergillus flavus isolates collected from soils of almond, pistachio and fig orchard in the Central Valley of California were tested for their membership to 16 atoxigenic vegetative compatibility groups (VCGs), including YV36, the VCG to which AF36, an atoxigenic isolate commercialized in the United States as biopesticide, belongs. A surprisingly large proportion of isolates belonged to YV36 (13.3%, 7.2% and 6.6% of the total almond, pistachio and fig populations, respectively), while the percentage of isolates belonging to the other 15 VCGs ranged from 0% to 2.3%. In order to gain a better insight into the structure and diversity of atoxigenic A. flavus populations and to further identify predominant isolates, seventeen SSR markers were then used to genetically characterize AF36, the 15 type-isolates of the VCGs and 342 atoxigenic isolates of the almond population. There was considerable genetic diversity among isolates with a lack of differentiation among micro-geographical regions or years. Since isolates sharing identical SSR profiles from distinct orchards were rare, we separated them into groups of at least 3 closely-related isolates from distinct orchards that shared identical alleles for at least 15 out of the 17 loci. This led to the identification of 15 groups comprising up to 24 closely-related isolates. The group which contained the largest number of isolates were members of YV36 while five groups were also found to be members of our studied atoxigenic VCGs. These results suggest that these 15 groups, and AF36 in particular, are well adapted to various environmental conditions in California and to tree crops and, as such, are good candidates for use as biocontrol agents.

Aflatoxin-free transgenic maize using host-induced gene silencing

Aflatoxins, toxic secondary metabolites produced by some Aspergillus species, are a universal agricultural economic problem and a critical health issue. Despite decades of control efforts, aflatoxin contamination is responsible for a global loss of millions of tons of crops each year. We show that host-induced gene silencing is an effective method for eliminating this toxin in transgenic maize. We transformed maize plants with a kernel-specific RNA interference (RNAi) gene cassette targeting the aflC gene, which encodes an enzyme in the Aspergillus aflatoxin biosynthetic pathway. After pathogen infection, aflatoxin could not be detected in kernels from these RNAi transgenic maize plants, while toxin loads reached thousands of parts per billion in nontransgenic control kernels. A comparison of transcripts in developing aflatoxin-free transgenic kernels with those from nontransgenic kernels showed no significant differences between these two groups. These results demonstrate that small interfering RNA molecules can be used to silence aflatoxin biosynthesis in maize, providing an attractive and precise engineering strategy that could also be extended to other crops to improve food security.

Degeneration of aflatoxin gene clusters in Aspergillus flavus from Africa and North America

Aspergillus flavus is the most common causal agent of aflatoxin contamination of food and feed. However, aflatoxin-producing potential varies widely among A. flavus genotypes with many producing no aflatoxins. Some non-aflatoxigenic genotypes are used as biocontrol agents to prevent contamination. Aflatoxin biosynthesis genes are tightly clustered in a highly conserved order. Gene deletions and presence of single nucleotide polymorphisms (SNPs) in aflatoxin biosynthesis genes are often associated with A. flavus inability to produce aflatoxins. In order to identify mechanisms of non-aflatoxigenicity in non-aflatoxigenic genotypes of value in aflatoxin biocontrol, complete cluster sequences of 35 A. flavus genotypes from Africa and North America were analyzed. Inability of some genotypes to produce aflatoxin resulted from deletion of biosynthesis genes. In other genotypes, non-aflatoxigenicity originated from SNP formation. The process of degeneration differed across the gene cluster; genes involved in early biosynthesis stages were more likely to be deleted while genes involved in later stages displayed high frequencies of SNPs. Comparative analyses of aflatoxin gene clusters provides insight into the diversity of mechanisms of non-aflatoxigenicity in A. flavus genotypes used as biological control agents. The sequences provide resources for both diagnosis of non-aflatoxigenicity and monitoring of biocontrol genotypes during biopesticide manufacture and in the environment.

Genetic Analysis of the Aspergillus flavus Vegetative Compatibility Group to Which a Biological Control Agent That Limits Aflatoxin Contamination in U.S. Crops Belongs

Some filamentous fungi in Aspergillus section Flavi produce carcinogenic secondary compounds called aflatoxins. Aflatoxin contamination is routinely managed in commercial agriculture with strains of Aspergillus flavus that do not produce aflatoxins. These non-aflatoxin-producing strains competitively exclude aflatoxin producers and reshape fungal communities so that strains with the aflatoxin-producing phenotype are less frequent. This study evaluated the genetic variation within naturally occurring atoxigenic A. flavus strains from the endemic vegetative compatibility group (VCG) YV36. AF36 is a strain of VCG YV36 and was the first fungus used in agriculture for aflatoxin management. Genetic analyses based on mating-type loci, 21 microsatellite loci, and a single nucleotide polymorphism (SNP) in the aflC gene were applied to a set of 237 YV36 isolates collected from 1990 through 2005 from desert legumes and untreated fields and from fields previously treated with AF36 across the southern United States. One haplotype dominated across time and space. No recombination with strains belonging to VCGs other than YV36 was detected. All YV36 isolates carried the SNP in aflC that prevents aflatoxin biosynthesis and the mat1-2 idiomorph at the mating-type locus. These results suggest that VCG YV36 has a clonal population structure maintained across both time and space. These results demonstrate the genetic stability of atoxigenic strains belonging to a broadly distributed endemic VCG in both untreated populations and populations where the short-term frequency of VCG YV36 has increased due to applications of a strain used to competitively exclude aflatoxin producers. This work supports the hypothesis that strains of this VCG are not involved in routine genetic exchange with aflatoxin-producing strains.

Genetic variability of Aspergillus flavus isolates from a Mississippi corn field

A nontoxigenic Aspergillus flavus strain, K49, is currently being tested as a biological control agent in corn fields in the Mississippi Delta. However, little is known about the overall genetic diversity of A. flavus from year to year in corn fields and specifically in Mississippi. Our objective was to assess the genetic variability of A. flavus isolates from different seasons, inoculum sources, and years, from a no-till corn field. Of the 175 A. flavus isolates examined, 74 and 97 had the typical norB-cypA type I (1.5 kb) and type II (1.0 kb) deletion patterns, respectively. Variability in the sequence of the omtA gene of the majority of the field isolates (n = 118) was compared to strain K49. High levels of haplotypic diversity (24 omtA haplotypes; Hd = 0.61 ± 0.04) were found. Among the 24 haplotypes, two were predominant, H1 (n = 71), which consists of mostly toxigenic isolates, and H49 (n = 18), which consists of mostly atoxigenic isolates including K49. Toxigenic isolates were prevalent (60%) in this natural population. Nonetheless, about 15% of the population likely shared the same ancestral origin with K49. This study provides valuable information on the diversity of A. flavus. This knowledge can be further used to develop additional biological control strains.

Evaluation of the Atoxigenic Aspergillus flavus Strain AF36 in Pistachio Orchards

The atoxigenic strain Aspergillus flavus AF36, which has been extensively used as a biocontrol agent in commercial corn and cotton fields to reduce aflatoxin contamination, was applied in research pistachio orchards from 2002 to 2005 and in commercial pistachio orchards from 2008 to 2011. AF36 was applied as hyphae-colonized steam-sterilized wheat seed (the same product and same application rate as used in cotton fields). In all orchards, applying the wheat-AF36 product substantially increased the proportion of vegetative compatibility group (VCG) YV36, the VCG to which AF36 belongs, within A. flavus soil communities. Application of the AF36 product in additional years further increased YV36 in the soil until it composed 93% of the A. flavus isolates in treated commercial orchards. Nonetheless, application of the AF36 product did not result in increased incidence of kernel decay of the nuts. For nuts harvested from commercial orchards, reductions in percentages of samples contaminated with aflatoxin from treated orchards (relative to that for untreated orchards) ranged from 20 to 45%, depending on the year. Because of the high value of pistachio nuts and the costs associated with rejection of shipments due to aflatoxin contamination, these reductions are significant and valuable to the pistachio industry.

Mycotoxins that affect the North American agri-food sector: state of the art and directions for the future

This paper summarises workshop discussions at the 5th international MYCORED meeting in Ottawa, Canada (June 2012) with over 200 participants representing academics, government and industry scientists, government officials and farming organisations (present in roughly equal proportions) from 27 countries. Workshops centred on how mycotoxins in food and feed affect value chains and trade in the region covered by the North American Free Trade Agreement. Crops are contaminated by one or more of five important mycotoxins in parts of Canada and the United States every year, and when contaminated food and feed are consumed in amounts above tolerable limits, human and animal health are at risk. Economic loss from such contamination includes reduced crop yield, grain quality, animal productivity and loss of domestic and export markets. A systematic effort by grain producers, primary, transfer, and terminal elevators, millers and food and feed processers is required to manage these contaminants along the value chain. Workshops discussed lessons learned from investments in plant genetics, fungal genomics, toxicology, analytical and sampling science, management strategies along the food and feed value chains and methods to ameliorate the effects of toxins in grain on animal production and on reducing the impact of mycotoxins on population health in developing countries. These discussions were used to develop a set of priorities and recommendations.

Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi

Before the recent revolution in molecular biology, field studies on fungal communities were mostly confined to fruit bodies, whereas mycelial interactions were studied in the laboratory. Here we combine high-throughput sequencing with a fruit body inventory to study simultaneously mycelial and fruit body occurrences in a community of fungi inhabiting dead wood of Norway spruce. We studied mycelial occurrence by extracting DNA from wood samples followed by 454-sequencing of the ITS1 and ITS2 regions and an automated procedure for species identification. In total, we detected 198 species as mycelia and 137 species as fruit bodies. The correlation between mycelial and fruit body occurrences was high for the majority of the species, suggesting that high-throughput sequencing can successfully characterize the dominating fungal communities, despite possible biases related to sampling, PCR, sequencing and molecular identification. We used the fruit body and molecular data to test hypothesized links between life history and population dynamic parameters. We show that the species that have on average a high mycelial abundance also have a high fruiting rate and produce large fruit bodies, leading to a positive feedback loop in their population dynamics. Earlier studies have shown that species with specialized resource requirements are rarely seen fruiting, for which reason they are often classified as red-listed. We show with the help of high-throughput sequencing that some of these species are more abundant as mycelium in wood than what could be expected from their occurrence as fruit bodies.

Nutrient environments influence competition among Aspergillus flavus genotypes

The population dynamics of Aspergillus flavus, shaped in part by intraspecific competition, influence the likelihood and severity of crop aflatoxin contamination. Competition for nutrients may be one factor modulating intraspecific interactions, but the influences of specific types and concentrations of nutrients on competition between genotypes of A. flavus have not been investigated. Competition between paired A. flavus isolates on agar media was affected by varying concentrations of carbon (sucrose or asparagine) and nitrogen (nitrate or asparagine). Cocultivated isolate percentages from conidia and agar-embedded mycelia were quantified by measurements of isolate-specific single-nucleotide polymorphisms with quantitative pyrosequencing. Compositions and concentrations of nutrients influenced conidiation resulting from cocultivation, but the percentages of total conidia from each competing isolate were not predicted by sporulation of isolates grown individually. Success during sporulation did not reflect the outcomes of competition during mycelial growth, and the extents to which isolate percentages from conidia and mycelia differed varied among both isolate pairs and media. Whether varying concentrations of sucrose, nitrate, or asparagine increased, decreased, or had no influence on competitive ability was isolate dependent. Different responses of A. flavus isolates to nutrient variability suggest genotypes are adapted to different nutrient environments that have the potential to influence A. flavus population structure and the epidemiology of aflatoxin contamination.

Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus and evidence for cryptic heterokaryosis

Aspergillus flavus is the major producer of carcinogenic aflatoxins (AFs) in crops worldwide. Natural populations of A. flavus show tremendous variation in AF production, some of which can be attributed to environmental conditions, differential regulation of the AF biosynthetic pathway and deletions or loss-of-function mutations in the AF gene cluster. Understanding the evolutionary processes that generate genetic diversity in A. flavus may also explain quantitative differences in aflatoxigenicity. Several population studies using multilocus genealogical approaches provide indirect evidence of recombination in the genome and specifically in the AF gene cluster. More recently, A. flavus has been shown to be functionally heterothallic and capable of sexual reproduction in laboratory crosses. In the present study, we characterize the progeny from nine A. flavus crosses using toxin phenotype assays, DNA sequence-based markers and array comparative genome hybridization. We show high AF heritability linked to genetic variation in the AF gene cluster, as well as recombination through the independent assortment of chromosomes and through crossing over within the AF cluster that coincides with inferred recombination blocks and hotspots in natural populations. Moreover, the vertical transmission of cryptic alleles indicates that while an A. flavus deletion strain is predominantly homokaryotic, it may harbour AF cluster genes at a low copy number. Results from experimental matings indicate that sexual recombination is driving genetic and functional hyperdiversity in A. flavus. The results of this study have significant implications for managing AF contamination of crops and for improving biocontrol strategies using nonaflatoxigenic strains of A. flavus.

Influence of the host contact sequence on the outcome of competition among aspergillus flavus isolates during host tissue invasion

Biological control of aflatoxin contamination by Aspergillus flavus is achieved through competitive exclusion of aflatoxin producers by atoxigenic strains. Factors dictating the extent to which competitive displacement occurs during host infection are unknown. The role of initial host contact in competition between pairs of A. flavus isolates coinfecting maize kernels was examined. Isolate success during tissue invasion and reproduction was assessed by quantification of isolate-specific single nucleotide polymorphisms using pyrosequencing. Isolates were inoculated either simultaneously or 1 h apart. Increased success during competition was conferred to the first isolate to contact the host independent of that isolate's innate competitive ability. The first-isolate advantage decreased with the conidial concentration, suggesting capture of limited resources on kernel surfaces contributes to competitive exclusion. Attempts to modify access to putative attachment sites by either coating kernels with dead conidia or washing kernels with solvents did not influence the success of the first isolate, suggesting competition for limited attachment sites on kernel surfaces does not mediate first-isolate advantage. The current study is the first to demonstrate an immediate competitive advantage conferred to A. flavus isolates upon host contact and prior to either germ tube emergence or host colonization. This suggests the timing of host contact is as important to competition during disease cycles as innate competitive ability. Early dispersal to susceptible crop components may allow maintenance within A. flavus populations of genetic types with low competitive ability during host tissue invasion.

Variation in competitive ability among isolates of Aspergillus flavus from different vegetative compatibility groups during maize infection

ABSTRACT Aspergillus flavus, the primary causal agent of aflatoxin contamination, includes many genetically diverse vegetative compatibility groups (VCGs). Competitive ability during infection of living maize kernels was quantified for isolates from 38 VCGs. Kernels were inoculated with both a common VCG, CG136, and another VCG; after 7 days (31 degrees C), conidia were washed from kernels, and aflatoxins and DNA were extracted from kernels and conidia separately. CG136-specific single-nucleotide polymorphisms were quantified by pyrosequencing; VCGs co-inoculated with CG136 produced 46 to 85 and 51 to 84% of A. flavus DNA from kernels and conidia, respectively. Co-inoculation with atoxigenic isolates reduced aflatoxin up to 90% and, in some cases, more than predicted by competitive exclusion alone. Conidia contained up to 42 ppm aflatoxin B(1), indicating airborne conidia as potentially important sources of environmental exposure. Aflatoxin-producing potential and sporulation were negatively correlated. For some VCGs, sporulation during co-infection was greater than that predicted by kernel infection, suggesting that some VCGs increase dispersal while sacrificing competitive ability during host tissue colonization. The results indicate both life strategy and adaptive differences among A. flavus isolates and provide a basis for selection of biocontrol strains with improved competitive ability, sporulation, and aflatoxin reduction on target hosts.

Molecular characterization of toxigenic and atoxigenic Aspergillus flavus isolates, collected from peanut fields in China

AIMS

The objectives of this study were to assess the genetic relationships between toxigenic and atoxigenic isolates of Aspergillus flavus collected from peanut fields in China, and to analyse deletions within the aflatoxin biosynthetic gene cluster for the atoxigenic isolates.

METHODS AND RESULTS

Analysis of random-amplified polymorphic DNA and microsatellite-primed PCR data showed that the toxigenic and atoxigenic isolates of A. flavus were not clustered based on their regions and their ability of aflatoxin and sclerotial production. These results were further supported by DNA sequence of ITS, pksA and omtA genes. PCR assays showed that 24 of 35 isolates containing no detectable aflatoxins had the entire aflatoxin gene cluster. Eleven atoxigenic isolates had five different deletion patterns in the cluster.

CONCLUSIONS

Toxigenic and atoxigenic isolates of A. flavus are genetically similar, but some atoxigenic isolates having deletions within the aflatoxin gene cluster can be identified readily by PCR assays.

SIGNIFICANCE AND IMPACT OF THE STUDY

Because the extensive deletions within the aflatoxin gene cluster are not rare in the atoxigenic isolates, analysis of deletion within the cluster would be an effective method for the rapid screening of atoxigenic isolates for developing biocontrol agents.

Quantification of conidial density of Aspergillus flavus and A. parasiticus in soil from almond orchards using real-time PCR

AIMS

To design the Aspergillus flavus and Aspergillus parasiticus-specific primers and a real-time PCR assay for quantification of the conidial density in soil.

METHODS AND RESULTS

Aspergillus flavus and A. parasiticus-specific DNA primers were designed based on internal transcribed spacer sequences to distinguish these two species and from other Aspergillus and other fungal species. A method of pathogen DNA extraction directly from soil samples was developed. Using the designed primers, a real-time PCR assay was developed to quantitatively determine the conidial density of each A. flavus and A. parasiticus in soil, after generating corresponding standard curves. Known conidial densities of each A. flavus or A. parasiticus in soil significantly correlated with those tested with the real-time PCR.

CONCLUSIONS

This study demonstrated the applicability of the real-time PCR assay in studies of quantifying A. flavus and A. parasiticus in soil as inoculum sources.

SIGNIFICANCE AND IMPACT OF THE STUDY

The A. flacus and A. parasitic-specific primers can be widely used in aflatoxin research. The real-time PCR assay developed in this study provides a potential approach to quantify the plant pathogen density from not only soil but also other sources in relation to aflatoxin contamination from environment, food and feed commodities.