Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control

Abstract

Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B1 is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployment of biological control agents that comprise two nonaflatoxigenic A. flavus strains, either Afla-Guard (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations of A. flavus in cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815 A. flavus isolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinct A. flavus evolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies.

Genomic and metabolomic diversity within a familial population of Aspergillus flavus

“…The finding that six of the F1s (O1-O6) were genomically similar to non-aflatoxigenic parent 1587G was unexpected and could be the result of conidia or hyphal fragments from 1587G that survived preparation of the ascospore suspension. An alternative explanation to this unexpected finding could relate to proposed introgression of the biocontrol genome into offspring as observed in a field population (Molo et al, 2022). Perhaps the 1587G genome dominated during meiosis and failed to facilitate shuffling of genetic material in some of the F1s.…”

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

“…Similarly, the application of single AF- A. flavus isolates of the aflatoxin biocontrol products, Afla-Guard ® and AF36, resulted in persistence overtime. In addition, the most extensive carry-over studies, involving thousands of isolates, were carried out in the U.S. with AF36 [ 23 , 60 , 61 ]. A similar carry-over was observed on African small holder farms with Aflasafe, a biocontrol product containing four AF- strains as its active ingredients [ 24 ].…”

Aflatoxin biocontrol in practice requires a multidisciplinary, long-term approach

“…For products aiming to exploit the population genetics approach, extensive sensitization and research efforts will be needed to demonstrate that (i) the active ingredient isolates mate in nature and decrease the average aflatoxin production potentials of the resulting communities (Molo et al, 2022) compared to the potentials prior to treatment, (ii) that the progenies will not pose a risk to future cropping systems, the environment, and organisms interacting in areas surrounding fields receiving treatment (environmental impact assessment); (iii) logistic feasibility for both field sampling and conduct the molecular assays for matingtype profile determination, and (iv) plans for manufacturing and distributing multiple products when farmers need them. For the fungus-free strategy (e.g., production, and concentration and packaging of inhibitory compounds for field/storage application), the regulatory process could be similar as for chemical pesticides and will require extensive toxicological and ecotoxicological studies.…”

“…Products containing atoxigenic fungi that could recombine in nature with field resident fungi have been proposed (Molo et al, 2019;Carbone, 2021) although field recombination has been detected either when fastidious laboratory conditions are used and in limited number of isolates (Horn et al, 2014) or in on-station field trials (Molo et al, 2022). Traditionally, the possibility of field recombination between biocontrol isolates and field populations was seen as a serious drawback because of concerns on emergence of highly toxigenic, competitive strains (Ehrlich, 2014;Ehrlich et al, 2015) or strains with novel toxin profiles (Olarte et al, 2015).…”

“…That strategy, called a population genetics approach (Carbone, 2021), hypothesizes that reduced application regimes would be needed compared to other formulations (Andrews et al, 2020). Although carry-over effects have been detected in large-scale farmer fields (Cotty, 2000(Cotty, , 2006Jaime et al, 2017), smallholder farmer fields (Atehnkeng et al, 2022), and on-station trials managed by researchers (Weaver and Abbas, 2019;Molo et al, 2022), atoxigenic isolates applied during a cropping season are not expected to remain for a long term in a treated field. A large portion of the applied fungi and resulting progeny, if or when produced, would move from the treated field, and would be replaced by genotypes arriving from other locations due to climatic events and/or agronomic practices.…”