Impacts of fludioxonil resistance on global gene expression in the necrotrophic fungal plant pathogen Sclerotinia sclerotiorum

A new point mutation (D1158N) in histidine kinase Bos1 confers high-level resistance to fludioxonil in field gray mold disease

Gray mold, caused by the fungus Botrytis cinerea, is one of the most important plant diseases worldwide that is prone to developing resistance to fungicides. Currently, the phenylpyrrole fungicide fludioxonil exhibits excellent efficacy in the control of gray mold in China. In this study, we detected the fludioxonil resistance of gray mold disease in Shouguang City of Shandong Province, where we first found fludioxonil-resistant isolates of B. cinerea in 2014. A total of 87 single spore isolates of B. cinerea were obtained from cucumbers in greenhouse, and 3 of which could grow on PDA plates amended with 50 μg/mL fludioxonil that was defined as high-level resistance, with a resistance frequency of 3.4%. Furthermore, the 3 fludioxonil-resistant isolates also showed high-level resistance to the dicarboximide fungicides iprodione and procymidone. Sequencing comparison revealed that all the 3 fludioxonil-resistant isolates had a point mutation at codon 1158, GAC (Asp) → AAC (Asn) in the histidine kinase Bos1, which was proved to be the reason for fludioxonil resistance. In addition, the fludioxonil-resistant isolates possessed an impaired biological fitness compared to the sensitive isolates based on the results of mycelial growth, conidiation, virulence, and osmotic stress tolerance determination. Taken together, our results indicate that the high-level resistance to fludioxonil caused by the Bos1 point mutation (D1158N) has emerged in the field gray mold disease, and the resistance risk is relatively high, and fludioxonil should be used sparingly.

Overexpression of FgPtp3 Is Involved in Fludioxonil Resistance in Fusarium graminearum by Inhibiting the Phosphorylation of FgHog1

Fusarium graminearum is the main causal agent of Fusarium head blight (FHB), a destructive disease in cereal crops worldwide. Resistance to fludioxonil has been reported in F. graminearum in the field, but its underlying mechanisms remain elusive. In this study, 152 fludioxonil-resistant (FR) mutants of F. graminearum were obtained by selection in vitro. The FR strains exhibited dramatically impaired fitness, but only 7 of the 13 analyzed strains possessed mutations in genes previously reported to underlie fludioxonil resistance. Comparison between the FR-132 strain and its parental strain PH-1 using whole genome sequencing revealed no mutations between them, but transcriptome analysis, after the strains were treated with 0.5 μg/mL fludioxonil, revealed 2778 differently expressed genes (DEGs) mapped to 96 KEGG pathways. Investigation of DEGs in the MAPK pathway showed that overexpression of the tyrosine protein phosphatase FgPtp3, but not FgPtp2, enhanced fludioxonil resistance. Further analysis found that FgPtp3 interacted directly with FgHog1 to regulate the phosphorylation of Hog1, and overexpressed FgPtp3 in PH-1 could significantly suppress the phosphorylation of FgHog1 and hinder signal transmission of the HOG-MAPK pathway. Overall, FgPtp3 plays a significant role in regulating fludioxonil resistance in F. graminearum.

Interaction effect of fungicide and chitosan on non-target lichenized fungi

Excessive use of plant growth stimulants and pesticides is currently a considerable problem, especially in agriculture, horticulture, and arboriculture. Understanding the impacts of these compounds and their combinations on non-target organisms is crucial to minimize unintended consequences, while maintaining their use in plant protection. The aim of this study was to test how long-term spraying with different solutions of natural biostimulator chitosan, synthetic fungicide Switch 62.5 WG, and their combinations affects the physiology of epiphytic lichen Xanthoria parietina naturally occurring in fruit orchards and farmlands. We showed that fungicides composed of fludioxionil and cypronidil, as well as the combined use of such fungicides together with chitosan, can cause the considerable impairment of lichen physiology, and these disturbances relate to both algal and fungal partners of the symbiotic association. This negative effect was especially visible in the loss of cell membrane integrity, the high level of membrane lipid peroxidation, and changes in chlorophyll fluorescence parameters on the last day of the experiment. The combined use of these agents also leads to clear disturbances in the functioning of the mitochondrial respiratory chain, which was manifested by increased NADH dehydrogenase activity, while the use of these compounds separately led to a decrease in the activity of this enzyme. We concluded that the regular use of these agents in fruit tree cultivation may cause serious ecological consequences for epiphytic lichen communities as a result of the death of lichen thalli. This study suggests that the impact of some plant protection agents, both individually and in combinations, merits further attention in terms of their impact on non-target fungi.

Transcriptomic Analysis of Resistant and Wild-Type Botrytis cinerea Isolates Revealed Fludioxonil-Resistance Mechanisms

Botrytis cinerea, the causal agent of gray mold, is one of the most destructive pathogens of cherry tomatoes, causing fruit decay and economic loss. Fludioxonil is an effective fungicide widely used for crop protection and is effective against tomato gray mold. The emergence of fungicide-resistant strains has made the control of B. cinerea more difficult. While the genome of B. cinerea is available, there are few reports regarding the large-scale functional annotation of the genome using expressed genes derived from transcriptomes, and the mechanism(s) underlying such fludioxonil resistance remain unclear. The present study prepared RNA-sequencing (RNA-seq) libraries for three B. cinerea strains (two highly resistant (LR and FR) versus one highly sensitive (S) to fludioxonil), with and without fludioxonil treatment, to identify fludioxonil responsive genes that associated to fungicide resistance. Functional enrichment analysis identified nine resistance related DEGs in the fludioxonil-induced LR and FR transcriptome that were simultaneously up-regulated, and seven resistance related DEGs down-regulated. These included adenosine triphosphate (ATP)-binding cassette (ABC) transporter-encoding genes, major facilitator superfamily (MFS) transporter-encoding genes, and the high-osmolarity glycerol (HOG) pathway homologues or related genes. The expression patterns of twelve out of the sixteen fludioxonil-responsive genes, obtained from the RNA-sequence data sets, were validated using quantitative real-time PCR (qRT-PCR). Based on RNA-sequence analysis, it was found that hybrid histidine kinase, fungal HHKs, such as BOS1, BcHHK2, and BcHHK17, probably involved in the fludioxonil resistance of B. cinerea, in addition, a number of ABC and MFS transporter genes that were not reported before, such as BcATRO, BMR1, BMR3, BcNMT1, BcAMF1, BcTOP1, BcVBA2, and BcYHK8, were differentially expressed in the fludioxonil-resistant strains, indicating that overexpression of these efflux transporters located in the plasma membranes may associate with the fludioxonil resistance mechanism of B. cinerea. All together, these lines of evidence allowed us to draw a general portrait of the anti-fludioxonil mechanisms for B. cinerea, and the assembled and annotated transcriptome data provide valuable genomic resources for further study of the molecular mechanisms of B. cinerea resistance to fludioxonil.

Exploring Potential Mechanisms of Fludioxonil Resistance in Fusarium oxysporum f. sp. melonis

Melon Fusarium wilt (MFW), which is caused by Fusarium oxysporum f. sp. melonis (FOM), is a soil-borne disease that commonly impacts melon cultivation worldwide. In the absence of any disease-resistant melon cultivars, the control of MFW relies heavily on the application of chemical fungicides. Fludioxonil, a phenylpyrrole fungicide, has been shown to have broad-spectrum activity against many crop pathogens. Sensitivity analysis experiments suggest that fludioxonil has a strong inhibitory effect on the mycelial growth of FOM isolates. Five fludioxonil-resistant FOM mutants were successfully generated by repeated exposure to fludioxonil under laboratory conditions. Although the mutants exhibited significantly reduced mycelial growth in the presence of the fungicide, there initially appeared to be little fitness cost, with no significant difference (p < 0.05) in the growth rates of the mutants and wild-type isolates. However, further investigation revealed that the sporulation of the fludioxonil-resistant mutants was affected, and mutants exhibited significantly (p < 0.05) reduced growth rates in response to KCl, NaCl, glucose, and mannitol. Meanwhile, molecular analysis of the mutants strongly suggested that the observed fludioxonil resistance was related to changes in the sequence and expression of the FoOs1 gene. In addition, the current study found no evidence of cross-resistance between fludioxonil and any of the other fungicides tested. These results indicate that fludioxonil has great potential as an alternative method of control for FOM in melon crops.

Sensitivity of Colletotrichum fructicola and Colletotrichum siamense of Peach in China to Multiple Classes of Fungicides and Characterization of Pyraclostrobin-Resistant Isolates

Anthracnose, mainly caused by Colletotrichum gloeosporioides species complex including Colletotrichum fructicola and Colletotrichum siamense, is a devastating disease of peach. Chemical control has been widely used for years, but management failures have increased with the commonly used fungicides. Therefore, screening of sensitivity of Colletotrichum spp. to fungicides with different modes of action is needed to make proper management strategies for peach anthracnose. In this study, the sensitivity of 80 isolates of C. fructicola and C. siamense was screened for pyraclostrobin, procymidone, prochloraz, and fludioxonil based on mycelial growth inhibition at discriminatory doses. Results showed that C. fructicola and C. siamense isolates were highly resistant to procymidone and fludioxonil with 100% resistance frequencies to both fungicides, but sensitive to prochloraz, i.e., no resistant isolates were found. For pyraclostrobin, 74% of C. fructicola isolates showed high resistance, 26% showed low resistance, and all of the C. siamense isolates showed low resistance. No positive cross-resistance was observed between pyraclostrobin and azoxystrobin even when they are members of the same quinone outside inhibitor (QoI) fungicide group or between pyraclostrobin and non-QoIs. Resistant isolates to QoI fungicides were evaluated for the fitness penalty. Results showed that no significant differences except for the mycelial growth rates that were detected between high- and low-resistance isolates of C. fructicola. Molecular characterization of the Cyt b gene revealed that the G143A point mutation was the determinant of the high resistance in C. fructicola. This study demonstrated the resistance status of C. fructicola and C. siamense to different fungicides and briefly discussed implications of that resistance. Demethylation inhibitor fungicides were found to be the best option among the different chemicals studied here, to control peach anthracnose in China.