Evaluating the effects of mefenoxam on taxonomic and functional dynamics of nontarget fungal communities during carrot cultivation

www.nature.com/scientificreports OPEN Evaluating the effects of mefenoxam on taxonomic and functional dynamics of nontarget fungal communities during carrot cultivation Setu Bazie Tagele  & Emma W. Gachomo * Ridomil Gold SL (45.3% a.i. mefenoxam) is a widely used chemical fungicide for the control of oomycetes. However, its impact on fungal communities remains unexplored. Therefore, the goal of this study was to examine the effects of mefenoxam on the temporal dynamics of fungal taxonomic and functional diversities during carrot cultivation under four treatment groups: mefenoxam application with and without Pythium inoculation, and untreated control groups with and without Pythium inoculation. Our in vitro sensitivity assay showed that the maximum recommended concentration of mefenoxam, 0.24 ppm, did not suppress the mycelial growth of P. irregulare. At 100 ppm, mycelial growth was only reduced by 11.4%, indicating that the isolate was resistant to mefenoxam. MiSeq sequencing data revealed transient taxonomic variations among treatments 2 weeks post-treatment. Mortierella dominated the fungal community in the mefenoxam-Pythium combination treatment, as confirmed through PCR using our newly designed Mortierella-specific primers. Conversely, mefenoxam-Pythium combination had adverse effects on Penicillium, Trichoderma, and Fusarium, and decrease the overall alpha diversity. However, these compositional changes gradually reverted to those observed in the control by the 12th week. The predicted ecological functions of fungal communities in all Pythium and mefenoxam treatments shifted, leading to a decrease in symbiotrophs and plant pathogen functional groups. Moreover, the community-level physiological profiling approach, utilizing 96-well Biolog FF microplates, showed discernible variations in the utilization of 95 diverse carbon sources among the treatments. Notably, arbutin, l-arabinose, Tween 80, and succinamic acid demonstrated a strong positive association with Mortierella. Our findings demonstrate that a single application of mefenoxam at its recommended rate triggers substantial taxonomic and functional shifts in the soil fungal community. Considering this impact, the conventional agricultural practice of repeated mefenoxam application is likely to exert considerable shifts on the soil ecosystem that may affect agricultural sustainability. Abbreviations CSS Carrot cavity spot CKNP Neither Pythium inoculation nor mefenoxam application CKP Pythium inoculation without mefenoxam application RNP Mefenoxam application without Pythium inoculation RP Both Pythium inoculation and mefenoxam application FLO Fungal-like organisms AWCD Average well color development USDA-NASS USDA National Agricultural Statistics Service Plant pathogenic fungi and fungal-like organisms (FLO), such as oomycetes are the major causes of preharvest and postharvest losses, accounting for a 20 to 40% reduction in crop yield1,2. Yield reductions due to infections Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92507, USA. * email: Scientific Reports | (2024) 14:9867 | https://doi.org/10.1038/s41598-024-59587-2 1 Vol.:(0123456789) www.nature.com/scientificreports/ by fungi and FLO result in a global food crisis and a massive economic loss estimated at over $100 billion2–4. Therefore, management of such plant diseases is necessary and fungicides have played a vital role in controlling the growth and survival of plant pathogenic fungi and FLO1,2,4,5. The global agricultural chemical pesticide market is anticipated to reach 122.1 billion in 2031 with an annual growth rate (CAGR) of 5.5%5. Over 7% of the global fungicide market targets single sites, making it easy for plant pathogens to develop resistance to t hem6. In addition, the frequent application of chemicals with a similar mode of action leads to a decline in their performance due to the development of resistance in the pathogen p opulation1,2. Moreover, chemical fungicides are harmful to nontarget organisms and only a small amount (0.1%) of the applied fungicides reach their intended target, not to mention their persistence and bioaccumulation in the e nvironment1. Ridomil Gold SL (45.3% a.i. mefenoxam) is a widely used fungicide in US agriculture7,8. Ridomil Gold SL (hereafter referred to as mefenoxam) was introduced due to metalaxyl resistance in several oomycete pathogens6,9,10. Mefenoxam is a superactive granular fungicide that can systemically control soilborne diseases caused by oomycetes and water mold, including Pythium-damping off, Pythium root rot, Pythium leak, and carrot cavity spot6,9–12. Mefenoxam is widely used in different crops such as tomatoes, onions, melons, soybeans, peas, carrots, apples, leafy vegetables and cotton, ornamentals, and turf and l awn12. In carrot production mefenoxam is used to control cavity spot caused by Pythium species13. In spite of resistance to mefenoxam being reported in several plant pathogens, including Phytophthora and Pythium spp.12,14–16, it is still widely used in the US17. The soil microbiome plays a crucial role in plant health and improves plant fitness and function under abiotic stress18–21. However, applications of chemical fungicides can lead to a long-term influence on soil microbes and soil ecosystem processes, such as nitrification and soil enzyme activities, which are essential for plant productivity22–24. Therefore, it is important to evaluate the impact of fungicides on nontarget organisms and the environment25. Previous studies suggested that the application of mefenoxam may have a deleterious effect on nontarget fungal p opulations26,27. However, details on its impact on the fungal community profile are l acking26,27. A study by Demanou et al.26 compared the number and position of the amplicon band, but failed to show the specific fungal taxa that were affected or enriched after mefenoxam application. Therefore, the objective of our study was to evaluate the effects of mefenoxam on the taxonomic and functional diversity of soil fungal communities in carrot cultivation. We hypothesized that the effects of mefenoxam on soil fungi would be minimal and temporal because it targets oomycetes and rapidly degrades in soil. In this study we applied the recommended dose of mefenoxam (0.24 ppm) to the soil in which carrots were grown. The experiment was performed both with and without the inoculation of Pythium, and the soil samples were collected after 2- and 12-weeks post mefenoxam application. The MiSeq raw sequence data were analyzed using QIIME2 and the predicted functional diversity was assessed using FUNGuild. Additionally, we examined the impact of mefenoxam on the metabolic activities of soil fungal communities using a Biolog FF MicroPlate. The results revealed that application of mefenoxam in the presence of Pythium led to significant, albeit temporary, alterations in fungal community assembly, ecological functions, (...truncated)