Fungal Evolution in Anthropogenic Environments: Botrytis cinerea Populations Infecting Small Fruit Hosts in the Pacific Northwest Rapidly Adapt to Human-Induced Selection Pressures

Abstract

Many fungal pathogens have short generation times, large population sizes, and mixed reproductive systems, providing high potential to adapt to heterogeneous environments of agroecosystems. Such adaptation complicates disease management and threatens food production. A better understanding of pathogen population biology in such environments is important to reveal key aspects of adaptive divergence processes to allow improved disease management. Here, we studied how evolutionary forces shape population structure of Botrytis cinerea, the causal agent of gray mold, in the Pacific Northwest agroecosystems. Populations of B. cinerea from adjacent fields of small fruit hosts were characterized by combining neutral markers (microsatellites) with markers that directly respond to human-induced selection pressures (fungicide resistance). Populations were diverse, without evidence for recombination and association of pathogen genotype with host. Populations were highly localized with limited migration even among adjacent fields within a farm. A fungicide resistance marker revealed strong selection on population structure due to fungicide use. We found no association of resistance allele with genetic background, suggesting de novo development of fungicide resistance and frequent extinction/recolonization events by different genotypes rather than the spread of resistance alleles among fields via migration of a dominant genotype. Overall our results showed that in agroecosystems, B. cinerea populations respond strongly to selection by fungicide use with greater effect on population structure compared to adaptation to host plant species. This knowledge will be used to improve disease management by developing strategies that limit pathogen local adaptation to fungicides and other human-induced selection pressures present in Pacific Northwest agroecosystems and elsewhere. IMPORTANCE Agroecosystems represent an efficient model for studying fungal adaptation and evolution in anthropogenic environments. In this work, we studied what evolutionary forces shape populations of one of the most important fungal plant pathogens, B. cinerea, in small fruit agroecosystems of the Pacific Northwest. We hypothesized that host, geographic, and anthropogenic factors of agroecosystems structure B. cinerea populations. By combining neutral markers with markers that directly respond to human-induced selection pressures, we show that pathogen populations are highly localized and that selection pressure caused by fungicide use can have a greater effect on population structure than adaptation to host. Our results give a better understanding of population biology and evolution of this important plant pathogen in heterogeneous environments but also provide a practical framework for the development of efficient management strategies by limiting pathogen adaptation to fungicides and other human-induced selection pressures present in agroecosystems of the Pacific Northwest and elsewhere.

Population Genetic Analyses of Botrytis cinerea Isolates From Michigan Vineyards Using a High-Throughput Marker System Approach

“…Resistance to multiple fungicides and iprodione each explained approximately 7% of the variability observed, but boscalid resistance explained the majority of the differentiation (10% with SNPs and 14% with microsatellites). This is similar to other studies showing that fungicide resistance may be a driving factor in Botrytis population structure in agricultural systems (Kozhar et al, 2020). In summary, microsatellites and SNP markers were both effective at identifying population structure associated with major factors (e.g., fungicide resistance) in Botrytis.…”

“…This variability could be, in part, caused by regional differences in Botrytis population composition. Fungicide spray programs and the resulting resistance have repeatedly been shown to play a large role in Botrytis field population composition, but smaller differences caused by host, season, or marker resolution may also play a role (Wessels et al, 2016;Kozhar et al, 2020;Testempasis et al, 2020).…”

“…An increasing number of isolates with resistance to not only a single fungicide but also to multiple fungicides of different chemical classes have been reported (Leroch et al, 2013;Fernández-Ortuño et al, 2015;Saito et al, 2019;Alzohairy et al, 2020;Delong et al, 2020). Fungicide resistance frequencies have been shown to differ between years, crop hosts, and locations (Fernández-Ortuño et al, 2015;Delong et al, 2020;Kozhar et al, 2020).…”

The bud rot pathogens infecting cannabis (Cannabis sativa L., marijuana) inflorescences: symptomology, species identification, pathogenicity and biological control

“…The genus Botrytis contains up to 38 recognized species which differ in biology, morphology and host range and can be distinguished using a range of molecular approaches (Staats et al 2005;Garfinkel et al 2019;Garfinkel 2021). Botrytis cinerea is the most widespread generalist species, causing grey mould on over 1400 plant species (Garfinkel et al 2019;Kozhar et al 2020;Garfinkel 2021) and it is commonly found in both agricultural and nonagricultural environments (Bardin et al 2018) and is prevalent in greenhouses (Hausbeck and Pennypacker 1991;Carisse and van der Heyden 2015). Pathogen populations tend to be genetically diverse with little evidence for host specialization (Kozhar et al 2020).…”

Colonization of red raspberry flowers and fruit by Botrytis cinerea under commercial production conditions in northwestern Washington, USA

“…France (Fournier and Giraud, 2008), strawberry, blackberry, dandelion, and primrose in the UK (Rajaguru and Shaw, 2010), and strawberry, grapevine, tomato, and faba beans in Tunisia (Karchani-Balma et al, 2008). A recent population genetics study of B. cinerea infecting small fruit hosts in the Pacific Northwest, USA, showed high genotypic diversity of pathogen populations on a farm scale (Kozhar et al, 2020). Also, colonization of single tissues by multiple pathogen genotypes has been observed previously in strawberry (Hu et al, 2018) and other pathosystems (Milgroom and Peever, 2003;Sexton et al, 2006;Lopez-Villavicencio et al, 2007).…”