Exposure to fungicide difenoconazole reduces the soil bacterial community diversity and the co-occurrence network complexity

Fabrication of self-defense enzymic biocatalyst for harmless degradation of difenoconazole through post-synthesis infiltration and modification

Difenoconazole (DIF) non-point source pollution presents significant eco-environmental challenges. In the present study, an efficient self-defensive biocatalytic system (D4/enzyme-PDA-MOFs@Sponge) was constructed for the first time through post-synthesis infiltration and cold-plasma discharge modification. The system exhibits strong antibacterial capabilities, achieving 93.39 % and 99.02 % inhibition against Escherichia coli and Staphylococcus aureus, respectively, demonstrating its outstanding self-defense ability against external organism invasion. For DIF degradation, immobilized extracellular and intracellular enzymes achieve 73.2 % and 66.9 % removal rates within 48 h, with total organic carbon removal of 81.3 % and 86.3 %, respectively, indicating efficient mineralization. The "birdcage trapping-enzymatic" mechanism enables rapid substrate adsorption and in-situ catalysis, generating low-toxicity transformation products. Notably, the biocatalyst maintains over 45.7 % degradation efficiency after five reuse cycles, showcasing robust reusability. This work provides a promising, environmentally friendly approach for mitigating DIF pollution through efficient, harmless degradation.

Investigation of the mechanisms involved in the biocontrol activities of natural products from a marine soil bacterium against rice blast

BACKGROUND

Rice blast, caused by Pyricularia oryzae, is a devastating fungal disease threatening global rice production. Overreliance on chemical fungicides has raised environmental concerns and led to resistant strains, necessitating the development of sustainable alternatives. This study integrated marine microbiology and natural antifungal compounds to create eco-friendly alternatives to chemical fungicides for disease management.

RESULTS

We identified Pseudomonas aeruginosa R64 with broad-spectrum antimicrobial activity from mangrove soil in the Mai Po Nature Reserve. The R64 fermentation extract (RFE) exhibited multifaceted inhibition of P. oryzae, suppressing mycelial growth, conidiation, conidial germination and appressorial formation, while disturbing cell wall and membrane function. It also attenuated virulence by impairing appressorial penetration and invasive growth. Further chemical analysis identified phenazines and quinolines as the primary compounds in RFE, corroborated by PCR detection of corresponding phenazine biosynthetic gene clusters. Comparative bioassays with two main bioactive components of RFE, phenazine-1-carboxamide (PCN) and phenazine-1-carboxylic acid (PCA), against P. oryzae implicated PCN as the principal antifungal effector. RFE and PCN had higher efficacy than tricyclazole in P. oryzae growth inhibition, but were less effective than isoprothiolane. Furthermore, RFE and PCN displayed lower acute ecotoxicity to an environmental indicator organism than isoprothiolane, suggesting their potential as sustainable biopesticides for rice blast management.

CONCLUSION

Natural products from mangrove soil bacterium P. aeruginosa R64 inhibited key developmental and infection processes of P. oryzae, effectively reducing rice blast development. The promising disease inhibition and low ecotoxicity of mangrove-associated bacteria highlight their untapped potential for innovative, eco-friendly fungicide mining for sustainable agriculture. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Optimizing difenoconazole degradation via sequential photoelectrochemical oxidation and biodegradation treatments

The growing global demand for food has intensified the use of pesticides in conventional agriculture, raising concerns about their environmental contamination and persistence. This study proposes an integrated strategy for the degradation of difenoconazole (DFZ), combining photoelectrochemical oxidation (PECO) with biodegradation. A mixed metal oxide anode, Ti/(RuO2)0.8(Sb2O4)0.1(TiO2)0.1 was successfully synthesized via the ionic liquid method, and a mangrove-derived Bacillus sp. isolate was employed in a sequential treatment process. Individually, the Bacillus strain degraded 74.56 % of DFZ1 and 72.52 % of DFZ2, while PECO alone achieved a lower removal efficiency of 32 %. Notably, the sequential application of PECO followed by biodegradation enhanced the degradation rates to 77.81 % for DFZ1 and 74.45 % for DFZ2. Additionally, this combined approach significantly reduced chemical oxygen demand (70.6 %) and toxicity, as evidenced by improved lettuce seed germination indices. These findings underscore the potential of integrating PECO with biodegradation as a promising strategy for the remediation of difenoconazole (DFZ), offering new perspectives for the treatment of recalcitrant triazole compounds in contaminated environments.

Comprehensive Study of Difenoconazole in Soil: Kinetics, Dissipation, Metabolism, and Microbial Toxicity

Difenoconazole is a persistent and widely used fungicide, but comprehensive long-term studies on its dissipation/degradation in soil and its influence on the soil microbiota are still lacking. Here, on the one hand, a long-term study of its dissipation/degradation in soil, after the application of a commercial product, has been carried out under laboratory conditions (2 doses and 2 soils) and field conditions (greenhouse, 1 dose and 1 soil). The results have revealed that the difeconazole had half-life (DT50) values over 175 days under laboratory conditions and over 115 days in the field trial. In general, difenoconazole tends to be more persistent in clay soils and when applied at higher doses. A total of eight metabolites were tentatively identified during the degradation process; one of them had not been previously described in soils. The main metabolite was difenoconazole alcohol, which exhibited high persistence (detected for more than 100 days in soils), indicating the risk of exposure not only to the active substance. On the other hand, the effect of difenoconazole on soil microbiota was tested in the laboratory after 3 months of exposure at the recommended dose in two soils. Under these conditions, the microbial activity and functionality were not affected by the application of the fungicide. However, a slight increase in microbial activity was observed following the application of difenoconazole. This increase was not associated with a negative impact on microbial functionality but rather suggests a potential adaptive response to the fungicide. These results highlight the influence and interaction of biotic and abiotic factors in the soil with respect to disturbances in the ecosystem.

Impacts of sulfur application on microbial communities and functional attributes in rubber plantation soil

Elemental sulfur is widely used in fungicide applications to control crop diseases in agricultural systems, but its effects on soil microbial communities are largely unknown. In China, significant amounts of elemental sulfur are sprayed annually on rubber plantations to support crop performance. To investigate the effects of sulfur spraying on microbial diversity, composition, interactions, and functionalities in rubber plantation soil, soil samples from rubber plantations in Yunnan, South China, were collected, and bacterial and fungal communities were analyzed through high-throughput sequencing. Results showed that sulfur application did not alter the alpha diversity but the beta diversity of the soil bacterial community. Notably, sulfur disturbed the relative abundances of Chloroflexi and Planctomycetes. Certain bacteria (e.g., Bacillus and Sinomonas) thrived under sulfur treatment, influencing nutrient cycling. The ecological network analysis revealed enhanced bacterial and fungal interconnections. Sulfur application had a limited impact on microbial phenotypes and community functions, yet it inhibited sulfur compound respiration. These findings indicate that sulfur spraying can shift microbial community composition and influence nutrient cycling by favoring specific microbial groups. Despite its limited impact on microbial phenotypes, sulfur affects key metabolic processes, such as sulfur respiration, which are vital for soil health and microbial activity. The results highlight the need for sustainable sulfur management to optimize nutrient cycling and soil health on rubber plantations.

Effects of herbicide mixtures on the diversity and composition of microbial community and nitrogen cycling function on agricultural soil: A field experiment in Northeast China

Herbicide mixtures application is a widespread and effective practice in modern agriculture; however, a knowledge gap exists regarding the potential ecotoxicological effects of herbicide mixtures in agricultural systems. Here, the effects of various doses of herbicide mixtures (atrazine, nicosulfuron, and mesotrione) under different varieties of maize cultivation on the structure and function of microbial communities and soil chemical parameters were clarified through field experiments. The results showed that the application of herbicide mixtures increased the bacterial and fungal community alpha diversity at jointing and maturity, indicating a prolonged effect of the herbicide mixtures. Moreover, herbicide mixtures alter the composition of bacterial and fungal communities, with sensitive taxa suppressed and herbicide-tolerant taxa enriched. The herbicide mixtures significantly reduced the abundances of Bacillus even at lower doses, but Penicillum was enriched. FAPROTAX analysis and quantitative PCR (qPCR) results showed that herbicide mixtures inhibited the soil nitrogen-cycle process and related genes AOA-amoA, AOB-amoA, and nifH at maize seedling stage. Moreover, network analysis showed that low concentrations of the herbicide mixtures increased bacterial interactions while high concentrations inhibited them, which indicated that the network complexity may be herbicide concentration dependent. A synthetic community (SynCom) consisting of six bacterial strains was established for the biodegradation of the herbicide mixtures based on the analysis of the bacterial network, which resulted in an increase in the degradation efficiency of nicosulfuron by 15.90%. Moreover, potted maize experiment showed that the addition of the SynCom alleviated the toxic effects of herbicide mixtures on the plants. In summary, this study provides a comprehensive perspective for assessing the ecological risk at taxonomic and functional levels and the biodegradation approach of herbicide mixtures residue on agricultural soils in Northeastern China.

Emergence of Triazole-Resistant Cryptococcus neoformans after Exposure to Environmentally Relevant Concentrations of Difenoconazole in Liquid Medium and Soil

The rapid global emergence and spread of resistance to clinical triazoles in Cryptococcus neoformans have been associated with the use of agricultural triazole fungicides. However, there is no direct evidence currently linking the emergence of triazole-resistant C. neoformans (TRCN) strains to the application of triazole fungicides in soil. This study investigated whether triazole resistance in C. neoformans could be induced by difenoconazole, an agricultural triazole fungicide, in liquid medium and soil. Our findings reveal that environmentally relevant concentrations of difenoconazole can drive cross-resistance to clinical triazoles in C. neoformans through the upregulation of ERG11 and efflux pump genes (AFR1, AFR3, and MDR1). Notably, the prevalence of TRCN strains in soil correlates with residual difenoconazole levels, with significantly more TRCN isolates observed at two- and five-fold the recommended dose than at the standard dose. These results provide direct evidence linking agricultural triazole use to the emergence of TRCN and highlight the importance of applying difenoconazole at or below the recommended dosage to mitigate resistance development in soil environments. This study addresses a critical gap in the understanding of the environmental drivers of triazole resistance and underscores the need for responsible fungicide use to prevent the spread of resistant pathogens.

Fungicide seed treatments delay arbuscular mycorrhizal fungi colonization of winter wheat in the greenhouse, but the effect is attenuated in the field

Seed-applied fungicides support agricultural production by controlling seed- or soil-borne diseases. However, they can impact non-target soil organisms. In this study, we investigated the effect of eight seed treatments (including two authorized for organic farming) on root colonization of winter wheat (Triticum aestivum L.) by arbuscular mycorrhizal (AM) fungi. One experiment was conducted in greenhouse conditions, on a sterile substrate inoculated with the AM fungus Rhizophagus irregularis MUCL 41833 and one in field conditions, where winter wheat was colonized by native soil AM fungi. In greenhouse conditions, the six conventional seed treatments reduced root colonization five weeks after sowing. No difference with the control treatment was measured thereafter for a product containing triazole alone. In contrast, seed treatments containing fludioxonil (fungicide molecule alone or formulated with the triazole difenoconazole), and prochloraz formulated with the triazole triticonazole significantly reduced root colonization until 11 weeks after sowing. Notably, when formulated with sedaxane, the adverse effect of fludioxonil was reduced. The negative effect of seed treatments on AM fungal root colonization in field was smaller than in the greenhouse and generally not significant, with disparate results from one timestep to another. This may be related to the dilution or the degradation of the active ingredients in the soil during the winter period or AM fungal species/strain involved in symbiosis. Overall, our results outline that the direct effect of seed treatment is highly variable depending on the modes of action, half-lives and interactions between active ingredients. By contributing to highlight the undesired effects of pesticides on AM fungi (i.e., by delaying root colonization), this study pleads for a reduction of pesticide applications to encourage the rapid and efficient establishment of functional mycorrhizal symbioses.

Pyraclostrobin repeated treatment altered the degradation behavior in soil and negatively affected soil bacterial communities and functions

This study investigated the degradation dynamics of the fungicide pyraclostrobin in three apple orchard soils, along with the responses of soil bacterial community compositions, functions, co-occurrence patterns, and soil nitrogen cycling, under repeated treatment strategies in laboratory conditions. The degradation half-lives of pyraclostrobin varied across the soil types, ranging from 15.7 to 43.4 days, in the following order: Anyang soil > Qingdao soil > Yangling soil. Repeated pyraclostrobin treatment affected degradation behaviors across the different soils. Pyraclostrobin significantly inhibited soil microbial activity and reduced soil bacterial diversity, with more pronounced negative effects observed at high-concentration treatment. Pyraclostrobin clearly changed soil bacterial community structures, significantly enriching potentially degradative bacterial genera such as Methylibium and Nocardioides, which showed increases in the relative abundances of 3.0-181.8 % compared with control. Additionally, pyraclostrobin reduced the complexity of soil bacterial networks and modified the diversity of functional modules. Notably, repeated treatment severely disrupted soil nitrogen cycling, with the absolute abundances of amoA, amoB, nifH, nirK, and nirS in high-concentration treatment decreasing by up to 19.4-91.8 % compared with control. Collectively, pyraclostrobin repeated application altered the degradation behavior, inhibited soil microbial activities, modified soil bacterial community structures and co-occurrence patterns, and seriously disrupted soil nitrogen cycling.

Salicylic acid mitigates the physiological and biochemistry toxicity of fungicide difenoconazole and reduces its accumulation in wheat (Triticum aestivum L.)

Continuous misuse of difenoconazole (DFZ) results in farmland contamination, posing risks to crops and human health. Salicylic acid (SA) has been shown to enhance plant resistance and reduce pesticide phytotoxicity and accumulation. However, whether SA effectively reduces DFZ phytotoxicity and accumulation and its underlying mechanisms remain poorly understood. To address this, a short-term indoor experiment and a long-term outdoor pot experiment were conducted to evaluate the potential of SA to alleviate DFZ-induced phytotoxicity and its effects on DFZ uptake, translocation, metabolism, and accumulation. The underlying mechanisms were explored through physiological, biochemical, and gene expression analyses. The results showed that DFZ induced oxidative damage and reduced photosynthesis by 15.6% in wheat. SA upregulated the expression of genes encoding antioxidant enzymes (POD, CAT, SOD1, and SOD2) in the roots and leaves of DFZ-exposed plants, leading to a 7.5%-13.4% increase in antioxidant enzyme activities and a subsequent 9.7%-14.5% decrease in reactive oxygen species levels. Additionally, SA increased the total chlorophyll content by 16.3%, which was enhanced by regulating chlorophyll synthesis and degradation-related genes, thereby improving the net photosynthetic rate by 12.2%. Furthermore, SA upregulated the expression of lignin biosynthesis-related, CYP450, and GST genes, which reduced DFZ uptake and accelerated its degradation. Consequently, the wheat grain DFZ content decreased by 36.2%, thus reducing the health risk index. This study confirms the potential of SA to reduce DFZ phytotoxicity and accumulation. Based on these findings, we recommend using SA in DFZ-contaminated areas to mitigate phytotoxicity and the associated human dietary exposure risks.

Pathway Elucidation and Key Enzymatic Processes in the Biodegradation of Difenoconazole by Pseudomonas putida A-3

The extensive agricultural use of the fungicide difenoconazole (DIF) and its associated toxicity increasingly damage ecosystems and human health. Thus, an urgent need is to develop environmentally friendly technological approaches capable of effectively removing DIF residues. In this study, strain Pseudomonas putida A-3 was isolated for the first time which can degrade DIF efficiently. After optimization of the degradation conditions, the degradation rate reached 75.98%. Moreover, a new DIF degradation pathway, including hydroxylation, hydrolysis, dechlorination, and ether bond breaking. The acute and chronic toxicity of DIF degradation products assessed using ECOSAR software showed lower toxicity than the parent compound. Furthermore, strain A-3 remarkably accelerated the degradation of DIF in contaminated water-sediment systems. We successfully predicted six potential key enzymes for DIF degradation based on the results of whole genome sequencing, RT-qPCR, and molecular docking. Overall, the results revealed novel pathways for DIF biodegradation and provide a strong candidate for bioremediation of DIF residue-polluted environments.

Nanocarriers boost non-systemic fluazinam transportation in plants and microbial community enrichment in soil

Utilizing nanotechnology for pesticide delivery can enhance their uptake and distribution in plants, thereby boosting pesticide efficiency. Fluazinam, a highly effective broad-spectrum fungicide with unique mode of action, is hindered by its poor systemic conductivity, limiting its field control efficacy. In this study, fluazinam-loaded nanocapsules were developed, which exhibited significantly higher inhibitory activity against various Phytophthora species compared to the commercial suspension concentrate. Notably, the nanocapsules demonstrated pronounced effects on reducing ATP content in Phytophthora capsici and effectively controlled pepper blight and cucumber downy mildew. Tracking the distribution of fluorescein isothiocyanate (FITC) fluorescein-labeled fluazinam nanocapsules revealed their presence in roots seven days after treatment. High-performance liquid chromatography (HPLC) analysis confirmed the easy absorption and transport of fluazinam nanocapsules by pepper plants. Moreover, treatment with fluazinam nanocapsules significantly increased the expression of two exocytosis genes, FACP and RABF2a, in pepper tissues. Lastly, fluazinam nanocapsules were found to enhance the relative abundance of beneficial bacteria in the soil microbial community. This study presents a promising approach to enhance the upward transport capability of non-systemic pesticides, offering novel insights into their application and improved efficacy.

Increasing pesticide diversity impairs soil microbial functions

Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated the stochasticity of soil microbes and multitrophic networks through amplicon sequencing, assessed soil community functions related to carbon (C), N, phosphorus (P), and sulfur (S) cycling, and characterized the dominant bacterial life history strategies via metagenomics along a gradient of increasing pesticide diversity under two N addition levels. Our findings show that higher pesticide diversity enriches the abundance of bacterial specialists and opportunists capable of degrading or resisting pesticides, reducing the proportion of bacterial generalists in the absence of N addition. These shifts can complicate multitrophic microbial networks. Under increased pesticide diversity, selective pressure may drive bacteria to streamline their average genome size to conserve energy while enhancing C, N, P, and S metabolic capacities, thus accelerating soil nutrient loss. In comparison, N addition was found to reduce bacterial niche differentiation at higher pesticide diversity, mitigating the impacts of network complexity and functional traits associated with pesticide diversity, ultimately alleviating soil nutrient loss. Our results reveal the contrasting impacts of pesticide diversity on microbial functions under different N input scenarios and emphasize that strategic N fertilizer management can mitigate the ecological effects of pesticide use in agricultural systems.

Effect of fungicides on soil respiration, microbial community, and enzyme activity: A global meta-analysis (1975-2024)

Fungicides effectively prevent and control crop diseases caused by microorganisms; however, they also unintentionally affect soil microorganisms and enzyme activity. This study conducted a meta-analysis of 73 published studies to investigate the effects of fungicide application concentration and duration on soil respiration, microbial diversity, and enzyme activity. Increasing the concentration of fungicide application significantly reduced soil basal respiration and microbial carbon, with inhibitory effects reaching 1.45 % and 7.37 %, respectively, at 5 times the recommended application rate. The application of fungicides significantly reduced the activities of alkaline phosphatase, neutral phosphatase, acid phosphatase, dehydrogenase, and urease, with the activities of alkaline phosphatase and urease decreasing by 15.43 % and 7.76 %, respectively. Additionally, the application of fungicides significantly reduced fungi, actinomycetes, Shannon index, Simpson index, and McIntosh index while not affecting bacterial diversity. When the fungicide concentration is at 0-1 times, 1-5 times, and > 5 times, the number of fungi decreases by 14.53 %, 19.91 %, and 33.81 %, respectively. Temporally, soil basal respiration and microbial carbon significantly declined in the first 0-21d after fungicide application, but no such inhibitory effect was observed after 21d. Even 56 days after using the fungicide, it inhibited the activities of alkaline phosphatase and catalase by 13.14 % and 7.13 %, respectively. As time after the application of fungicides increases, the number of fungi decreases significantly, while the number of actinomycetes gradually recovers. Overall, fungicides inhibit the abundance, diversity, and enzyme activity of soil microorganisms; however, precise control of fungicide dosage is essential to minimize their toxic effects on soil.

Dynamic response of soil microbial communities and network to hymexazol exposure

Fungicides are an essential component of current agricultural practices, but their extensive use has raised concerns about their effects on non-target soil microorganisms, which carry out essential ecosystem functions. However, despite the complexity of microbial communities, many studies investigating their response to fungicides focus only on bacteria or fungi at one point in time. In this study, we used amplicon sequencing to assess the effect of the fungicide hymexazol on the diversity, composition, and co-occurrence network of soil bacteria, fungi, and protists at 7, 21, and 60 days after application. We found that hymexazol had very little effect on microbial alpha-diversity, but that microbial community composition and OTU differential abundance were altered over the duration of the experiment, even after hymexazol concentrations were undetectable. The co-occurrence patterns within and between microbial kingdoms were affected by hymexazol dose, suggesting that indirect effects may play a role in the microbial community response. Nitrogen cycling was also affected, with a transient hymexazol-associated increase in the abundance of ammonia-oxidizing microorganisms and soil nitrate concentration. These findings highlight that the effects of fungicides on soil microorganisms are dynamic and extensive, spanning several taxonomic kingdoms.

Key bacterial taxa with specific metabolisms and life history strategies sustain soil microbial network stability exposed to carbendazim and deoxynivalenol

Co-contamination of carbendazim (CBD) and deoxynivalenol (DON) is common in agricultural soils, yet their ecological impact on soil microbiome remains poorly assessed. Here, we investigated the influence of CBD and DON on the structure, function, and co-occurrence networks of soil microbiome. The combined treatment of CBD and DON significantly exacerbated the negative impacts on soil microbial diversity, functional diversity, and microbial network stability compared to individual treatments. Specifically, Lysobacter, Gemmatimonas, Nitrospira, Massilia, and Bacillus were identified as indicator species for CBD and DON. Simultaneously, the abundance of genes involved in key ecological functions, such as nitrification (amoA) and organic phosphorus mineralization (phoAD), was significantly reduced. Notably, key bacterial taxa Nitrospira and Gemmatimonas, with K-life history strategy and capabilities for nitrification and organic nitrogen mineralization, played crucial roles in promoting positive interactions in networks. Furthermore, variance partitioning analysis (VPA) and structural equation modeling (SEM) demonstrated that the abundance and niche breadth of key bacterial taxa were the primary drivers of microbial network stability. In conclusion, our study provides new insights into how soil microbiomes and networks respond to pesticides and mycotoxins, aiding in a more comprehensive assessment of exposure risks.

Thiophanate-methyl and its major metabolite carbendazim weaken rhizobacteria-mediated defense responses in cucumbers against Fusarium wilt

The effect of fungicides on the plant-rhizosphere microbiome is a subject of ongoing debate, but whether any alteration in the rhizosphere microbiome could affect plant health is an issue that has not been thoroughly investigated. To address this deficiency, we analyzed the rhizosphere microbiome of wilt disease-resistant and disease-susceptible cucumber cultivars to determine whether (and which) plant-associated microorganisms have a role in disease resistance. We further assessed whether the fungicides thiophanate-methyl and carbendazim affect the rhizosphere microbiome, which may contribute to the plant's immune response. Based on results acquired with both radicle-inoculation and soil-inoculation methods, cultivars Longyuanxiuchun (LYXC) and Shuyan2 (SY2) were identified as being disease resistant, whereas Zhongnong6 (ZN6) and Zhongnong38 (ZN38) were susceptible. The microbiome structure differed substantially between the resistant and susceptible plants, with LYXC and SY2 each having a significantly greater Shannon index than Zhongnong38. These results revealed that the disease-resistant cucumber cultivars recruited more beneficial bacteria, i.e., Bacillus, in their rhizosphere soil; as such, Bacillus was identified as a keystone genus in the microbial co-occurrence network. Thus, the presence of Bacillus may help cucumbers defend against fungal pathogens within the rhizosphere. Bacillus subtilis strain LD15, which was isolated from LYXC rhizosphere soil, could suppress pathogen growth, in vitro, and reduce disease severity in pot assays. Moreover, evidence also confirmed the accumulation of LD1 in the rhizosphere soil of resistant cucumber cultivars. For LYXC, application of thiophanate-methyl or carbendazim altered the microbiome structure, decreased bacterial diversity, and reduced the abundance of Bacillus species. Finally, pot assays verified that fungicide application decreased the proportion of LD15 in rhizosphere soil. From a microbial perspective, thiophanate-methyl and carbendazim may weaken the rhizobacteria-mediated defense response of cucumbers against cucumber Fusarium wilt disease. Our findings reveal a role for the rhizosphere microbiome in protecting plants from pathogens and constitute a reference for assessing the ecotoxicological risk of pesticides to non-target soil microorganisms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00181-5.

Difenoconazole Induced Damage of Bovine Mammary Epithelial Cells via ER Stress and Inflammatory Response

Difenoconazole (DIF) is a fungicide used to control various fungi. It is absorbed on the surface of different plants and contributes significantly to increased crop production. However, DIF is reported to exhibit toxicity to fungi and to aquatic plants, fish, and mammals, including humans, causing adverse effects. However, research on the impact of DIF on the mammary epithelial cells of herbivorous bovines is limited. DIF-induced damage and accumulation in the mammary glands can have direct and indirect effects on humans. Therefore, we investigated the effects and mechanisms of DIF toxicity in MAC-T cells. The current study revealed that DIF reduces cell viability and proliferation while triggering apoptotic cell death through the upregulation of pro-apoptotic proteins, including cleaved caspase 3 and Bcl-2-associated X protein (BAX), and the downregulation of leukemia type 2 (BCL-2). DIF also induced endoplasmic reticulum (ER) stress by increasing the expression of genes or proteins of Bip/GRP78, protein disulfide isomerase (PDI), activating transcription factor 4 (ATF4), C/EBP homologous protein (CHOP), and endoplasmic reticulum oxidoreductase 1 Alpha (ERO1-Lα). We demonstrated that DIF induces mitochondria-mediated apoptosis in MAC-T cells by activating ER stress pathways. This cellular damage resulted in a significant increase in the expression of inflammatory response genes and proteins, including cyclooxygenase 2 (COX2), transforming growth factor beta 3 (TGFB3), CCAAT enhancer binding protein delta (CEBPD), and iNOS, in DIF-treated groups. In addition, spheroid formation by MAC-T cells was suppressed by DIF treatment. Our findings suggest that DIF exposure in dairy cows may harm mammary gland function and health and may indirectly affect human consumption of milk.

Exploring the impact of plant genotype and fungicide treatment on endophytic communities in tomato stems

This study examines how plant genotype can influence the microbiome by comparing six tomato genotypes (Solanum lycopersicum) based on their traditional vs. commercial backgrounds. Using Illumina-based sequencing of the V6-V8 regions of 16S and ITS2 rRNA genes, we analyzed and compared the endophytic bacterial and fungal communities in stems to understand how microbiota can differ and be altered in plant genotypes and the relation to human manipulation. Our results reflect that traditional genotypes harbor significantly more exclusive microbial taxa and a broader phylogenetic background than the commercial ones. Traditional genotypes were significantly richer in Eurotiomycetes and Sordariomycetes fungi, while Lasiosphaeriaceae was more prevalent in commercial genotypes. TH-30 exhibited the highest bacterial abundance, significantly more than commercial genotypes, particularly in Actinomycetia, Bacteroidia, and Gammaproteobacteria. Additionally, traditional genotypes had higher bacterial diversity, notably in orders like Cytophagales, Xanthomonadales, and Burkholderiales. Moreover, we performed an evaluation of the impact of a systemic fungicide (tebuconazole-dichlofluanide) to simulate a common agronomic practice and determined that a single fungicide treatment altered the stem endophytic microbiota. Control plants had a higher prevalence of fungal orders Pleosporales, Helotiales, and Glomerellales, while treated plants were dominated by Sordariomycetes and Laboulbeniomycetes. Fungal community diversity significantly decreased, but no significant impact was observed on bacterial diversity. Our study provides evidence that the background of the tomato variety impacts the fungal and bacterial stem endophytes. Furthermore, these findings suggest the potential benefits of using of traditional genotypes as a source of novel beneficial microbiota that may prove highly valuable in unpredicted challenges and the advancement in sustainable agriculture.

Deciphering the role of nitric oxide in mitigation of systemic fungicide induced growth inhibition and oxidative damage in wheat

Consento (CON) poses a significant environmental hazard as a systemic fungicide, adversely affecting the health of non-target organisms. Nitric oxide (NO), a signaling molecule, is known to play a crucial role in plant physiology and abiotic stress tolerance. However, whether NO plays any role to enhance fungicide CON tolerance in wheat seedlings is yet unclear. Therefore, we conducted a hydroponic experiment i) to investigate the morpho-physio-biochemical changes of wheat seedlings to fungicide CON stress, and ii) to examine the effects of NO and fungicide CON treatments on oxidative damage, antioxidant system, secondary metabolism and detoxification of systemic fungicide in wheat seedlings. The results showed that CON fungicide at the highest (4X) concentration significantly decreased wheat seedlings fresh weight (46.89%), shoot length (40.26%), root length (56.11%) and total chlorophyll contents (67.44%) in a dose response relationship. Moreover, CON significantly increased hydrogen peroxide, malondialdehyde, catalase, ascorbate peroxidase, glutathione-S-transferase, and peroxidase activities while decreased reduced glutathione (GSH) content. This ultimately impaired the redox homeostasis of cells, leading to oxidative damage in cell membrane. Under fungicide treatment, the addition of NO reduced the fungicide phytotoxicity, with an increase of over 60% in seedling growth. The NO application mitigated CON phytotoxicity as reflected by significantly increased chlorophyll pigments (69.88%) and decreased oxidative damage in wheat leaves. Indeed, the NO alleviatory effect was able to increase the tolerance of seedlings to fungicide, which resulted increments in antioxidant and detoxification enzymes activity, with the enhanced GSH level (78.54%). Interestingly, NO alleviated CON phytotoxicity through the phenylpropanoid pathway by enhancing the activity of secondary metabolism enzymes such as phenylalanine ammonia-lyase (47.28%), polyphenol oxidase (9%), and associated metabolites such as phenolic acids (77.62%), flavonoids (34.33%) in wheat leaves. Our study has provided evidence that NO plays a key role in the metabolism and detoxification of systemic fungicide in wheat through enhanced activity of antioxidants, detoxifications and secondary metabolic enzymes.

Trichoderma based formulations control the wilt disease of chickpea (Cicer arietinum L.) caused by Fusarium oxysporum f. sp. ciceris, better when inoculated as consortia: findings from pot experiments under field conditions

Background

Commercial/chemical pesticides are available to control Fusarium wilt of chickpea, but these antifungals have numerous environmental and human health hazards. Amongst various organic alternatives, use of antagonistic fungi like Trichoderma, is the most promising option. Although, Trichoderma spp. are known to control Fusarium wilt in chickpea but there are no reports that indicate the biocontrol efficacy of indigenous Trichoderma spp. against the local pathogen, in relation to environmental conditions.

Methods

In the present study, biological control activity of Trichoderma species formulations viz., Trichoderma asperellum, Trichoderma harzianum (strain 1), and Trichoderma harzianum (strain 2), either singly or in the form of consortia, was investigated against Fusarium oxysporum f. sp. ciceris, the cause of Fusarium wilt in chickpea, in multiyear pot trials under open field conditions. The antagonistic effect of Trichoderma spp. was first evaluated in in vitro dual culture experiments. Then the effects of Trichoderma as well as F. oxysporum, were investigated on the morphological parameters, disease incidence (DI), and disease severity (DS) of chickpea plants grown in pots.

Results

In dual culture experiments, all the Trichoderma species effectively reduced the mycelial growth of F. oxysporum. T. asperellum, T. harzianum (strain 1), and T. harzianum(strain 2) declined the mycelial growth of F. oxysporumby 37.6%, 40%, and 42%. In open field pot trials, the infestation of F. oxysporum in chickpea plants significantly reduced the morphological growth of chickpea. However, the application of T. asperellum, T. harzianum (strain 1), and T. harzianum (strain 2), either singly or in the form of consortia, significantly overcome the deleterious effects of the pathogen, thereby resulted in lower DI (22.2% and 11.1%) and DS (86% and 92%), and ultimately improved the shoot length, shoot fresh weight and shoot dry weight by 69% and 72%, 67% and 73%, 68% and 75%, during the years 1 and 2, respectively, in comparison with infested control. The present study concludes the usefulness and efficacy of Trichoderma species in controlling wilt disease of chickpea plants under variable weather conditions.

Effects of biodegradable (PBAT/PLA) and conventional (LDPE) mulch film residues on bacterial communities and metabolic functions in different agricultural soils

Soil health is a crucial aspect of sustainable agriculture and food production, necessitating attention to the ecological risks associated with substantial amounts of mulch film residues. Biodegradable mulch films (BDMs) carry the same risk of mulch film residues formation as low-density polyethylene (LDPE) mulch films during actual use. More information is needed to elucidate the specific impacts of mulch film residues on the soil environment. Integrated 16S rRNA gene sequencing and non-targeted metabolomics, this study revealed the response patterns of bacterial communities, metabolites, and metabolic functions in the soil from three different agricultural regions to the presence of mulch film residues. LDPE mulch film residues negatively impacted the bacterial communities in the soils of Heilongjiang (HLJ) and Yunnan (YN) and had a lesser impact on the metabolic spectrum in the soils of HLJ, YN, and Xinjiang (XJ). BDM residues had a greater negative impact on all three soils in terms of both the bacterial communities and metabolites. The impact of BDM treatment on the soils of HLJ, YN, and XJ increased sequentially in that order. It is recommended that, when promoting the use of biodegradable mulch films, a fuller assessment should be made, accounting for local soil properties.

Contamination Status of Novel Organophosphate Esters Derived from Organophosphite Antioxidants in Soil and the Effects on Soil Bacterial Communities

The contamination status of novel organophosphate esters (NOPEs) and their precursors organophosphite antioxidants (OPAs) and hydroxylated/diester transformation products (OH-OPEs/di-OPEs) in soils across a large-scale area in China were investigated. The total concentrations of the three test NOPEs in soil were 82.4-716 ng g-1, which were considerably higher than those of traditional OPEs (4.50-430 ng g-1), OPAs (n.d.-30.8 ng g-1), OH-OPEs (n.d.-0.49 ng g-1), and di-OPEs (0.57-21.1 ng g-1). One NOPE compound, i.e., tris(2,4-di-tert-butylphenyl) phosphate (AO168 = O) contributed over 65% of the concentrations of the studied OPE-associated contaminants. A 30-day soil incubation experiment was performed to confirm the influence of AO168 = O on soil bacterial communities. Specific genera belonging to Proteobacteria, such as Lysobacter and Ensifer, were enriched in AO168 = O-contaminated soils. Moreover, the ecological function of methylotrophy was observed to be significantly enhanced (t-test, p < 0.01) in soil treated with AO168 = O, while nitrogen fixation was significantly inhibited (t-test, p < 0.01). These findings comprehensively revealed the contamination status of OPE-associated contaminants in the soil environment and provided the first evidence of the effects of NOPEs on soil microbial communities.

Tracing the dissipation of difenoconazole, its metabolites and co-formulants in tomato: A comprehensive analysis by chromatography coupled to high resolution mass spectrometry in laboratory and greenhouse trials

The study evaluated Ceremonia 25 EC®, a plant protection product (PPP) containing difenoconazole, in tomato crops, to identify potential risks associated with PPPs, and in addition to this compound, known metabolites from difenoconazole degradation and co-formulants present in the PPP were monitored. An ultra high performance liquid chromatography coupled to quadrupole-Orbitrap mass analyser (UHPLC-Q-Orbitrap-MS) method was validated with a working range of 2 μg/kg (limit of quantification, LOQ) to 200 μg/kg. Difenoconazole degradation followed a biphasic double first-order in parallel (DFOP) kinetic model in laboratory and greenhouse trials, with high accuracy (R2 > 0.9965). CGA-205374, difenoconazole-alcohol, and hydroxy-difenoconazole metabolites were tentatively identified and semi-quantified in laboratory trials by UHPLC-Q-Orbitrap-MS from day 2 to day 30. No metabolites were found in greenhouse trials. Additionally, 13 volatile co-formulants were tentatively identified by gas chromatography (GC) coupled to Q-Orbitrap-MS, detectable up to the 7th day after PPP application. This study provides a comprehensive understanding of difenoconazole dissipation in tomatoes, identification of metabolites, and detection of co-formulants associated with the applied PPP.

Soil microbial community fragmentation reveals indirect effects of fungicide exposure mediated by biotic interactions between microorganisms

Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.

Actinomycetota, a central constituent microbe during long-term exposure to diazinon, an organophosphorus insecticide

Microbial biodegradation is a primary pesticide remediation pathway. Despite diazinon is one of the most frequently used organophosphate insecticides worldwide, its effect on soil microbial community remains obscure. We hypothesize that diazinon exposure reshapes microbial community, among them increased microbes may play a crucial role in diazinon degradation. To investigate this, we collected soil from an organic farming environment, introduced diazinon, cultivated it in a greenhouse, and then assessed its effects on soil microbiomes at three distinct time points: 20, 40, and 270 days after treatment (DAT). Results from HPLC showed that the level of diazinon was gradually degraded by 98.8% at 270 DAT when compared with day zero, whereas 16S rRNA gene analysis exhibited a significant reduction in the bacterial diversity, especially at the early two time points, indicating that diazinon may exert selection pressure to the bacteria community. Here, the relative abundance of phylum Actinomycetota increased at 20 and 40 DATs. In addition, the bacterial functional gene profile employing PICRUSt2 prediction also revealed that diazinon exposure induced the genomic function related to xenobiotics biodegradation and metabolism in soil, such as CYB5B, hpaC, acrR, and ppkA. To validate if bacterial function is caused by increased relative abundance in diazinon enriched soil, further bacteria isolation resulted in obtaining 25 diazinon degradation strains out of 103 isolates. Notably, more than 70% (18 out of 25) isolates are identified as phylum Actinomycetota, which empirically confirms and correlates microbiome and PICRUSt2 results. In conclusion, this study provides comprehensive information from microbiome analysis to obtaining several bacteria isolates responsible for diazinon degradation, revealing that the phylum Actinomycetota is as a key taxon that facilitates microbial biodegradation in diazinon spoiled soil. This finding may assist in developing a strategy for microbial detoxification of diazinon, such as using an Actinomycetota rich synthetic community (SynCom).

Impact of repeated fumigant applications on soil properties, crop yield, and microbial communities in a plastic-mulched tomato production system

Pre-plant soil fumigation is widely applied to control nematodes, soil-borne fungal pathogens, and weeds in vegetable crops. However, most of the research evaluating the effect of fumigants on crop yield and soil microbial communities has been done on single compounds despite growers mainly applying fumigant combinations. We studied the effect of different fumigant combinations (chloropicrin, 1,3-dichloropropene, and metam potassium) on soil properties, crop yield, and the soil bacterial and fungal microbiome for two consecutive years in a plastic-mulched tomato production system in Florida (United States). While combinations of fumigants did not improve plant productivity more than the individual application of these products, application of fumigants with >60 % chloropicrin did significantly increase yield. Fumigant combinations had no significant effect on bacterial diversity, but fumigants with >35 % chloropicrin reduced soil fungal diversity and induced temporary changes in the soil bacterial and fungal community composition. These changes included short-term increases in the relative abundance of Firmicutes and Ascomycota, as well as decreases in other bacterial and fungal taxa. Repeated fumigation reduced network complexity and the relative abundance of several predicted bacterial functions and fungal guilds, particularly after fumigation and at end of harvest (3-months post fumigation). A structural equation model (SEM) showed fumigants not only directly impact crop yield, but they can also indirectly determine variations in plant productivity through effects on the soil microbiome. Overall, this study increases our understanding of the environmental and agricultural impacts of fumigants in a plastic-mulched tomato production system.

Endophytic biofungicide Bacillus subtilis (NBRI-W9) reshapes the metabolic homeostasis disrupted by the chemical fungicide, propiconazole in tomato plants to provide sustainable immunity against non-target bacterial pathogens

Chemical and microbial fungicides (Bio/fungicide) act differentially on plant systems. The present work assessed the metabolic profile of tomato plants vis-a-vis endophytic diversity after spraying of Propiconazole (PCZ) and endophytic biofungicide Bacillus subtilis (W9). Bio/fungicides were sprayed on tomato plants and evaluated for phenotypic, biochemical, and metabolic profiles after one week. In W9 treatment, a significant increase in relative abundance of several metabolites was observed including sugars, sugar alcohols, fatty-acids, organic-acids, and amino-acids. Polysaccharides and fatty acids showed a significant positive correlation with Rhizobiales, Burkholderiales, Bacillales, and Lactobacillales, respectively (p < 0.05). The PCZ and W9 treated plant's metabolic status significantly affected their resistance to non-target, bacterial pathogen P. syringae. Compared to PCZ and control, W9 treatment reduced the ROS deposition and expression of antioxidants gene GPx, PO (~0.1-1.7fold). It enhanced the genes related to the Phenylpropanoid pathway (∼1.6-5.2 fold), PR protein (~1.2-3.4 fold), and JA biosynthesis (~1.7-4.3 fold), resulting in reduced disease incidence. The results provide novel insights into the effects of endophytic biofungicide and chemical fungicides on the plant's metabolic status, its relation to the endophytes, and role in altering the plant's immune system.

Degradation of Triazole Fungicides by Plant Growth-Promoting Bacteria from Contaminated Agricultural Soil

The widespread application of triazole fungicides (TFs) in agricultural practices can result in the considerable accumulation of active compound residues in the soil and a subsequent negative impact on the soil microbiota and crop health. In this study, we isolated three TF-degrading bacterial strains from contaminated agricultural soils and identified them as Klebsiella sp., Pseudomonas sp., and Citrobacter sp. based on analysis of morphological characteristics and 16S rRNA gene sequences. The strains used three common TFs, namely hexaconazole, difenoconazole, and propiconazole, as their only sources of carbon and energy for growth in a liquid mineral salt medium, with high concentrations (~ 500 mg/l) of each TF. In addition to the ability to degrade fungicides, the isolates also exhibited plant growth-promoting characteristics, such as nitrogen fixation, indole acetic acid production, phosphate dissolution, and cellulose degradation. The synergistic combination of three bacterial isolates significantly improved plant growth and development with an increased survival rate (57%), and achieved TF degradation ranging from 85.83 to 96.59% at a concentration of approximately 50 mg/kg of each TF within 45 days in the soil-plant system. Based on these findings, the three strains and their microbial consortium show promise for application in biofertilizers, to improve soil health and facilitate optimal plant growth.

Disentangling the effects of terroir, season, and vintage on the grapevine fungal pathobiome

The composition, diversity and dynamics of microbial communities associated with grapevines may be influenced by various environmental factors, including terroir, vintage, and season. Among these factors, terroir stands out as a unique possible determinant of the pathobiome, the community of plant-associated pathogens. This study employed high-throughput molecular techniques, including metabarcoding and network analysis, to investigate the compositional dynamics of grapevine fungal pathobiome across three microhabitats (soil, woody tissue, and bark) using the Furmint cultivar. Samples were collected during late winter and late summer in 2020 and 2021, across three distinct terroirs in Hungary's Tokaj wine region. Of the 123 plant pathogenic genera found, Diplodia, Phaeomoniella, and Fusarium displayed the highest richness in bark, wood, and soil, respectively. Both richness and abundance exhibited significant disparities across microhabitats, with plant pathogenic fungi known to cause grapevine trunk diseases (GTDs) demonstrating highest richness and abundance in wood and bark samples, and non-GTD pathogens prevailed soil. Abundance and richness, however, followed distinct patterns Terroir accounted for a substantial portion of the variance in fungal community composition, ranging from 14.46 to 24.67%. Season and vintage also contributed to the variation, explaining 1.84 to 2.98% and 3.67 to 6.39% of the variance, respectively. Notably, significant compositional differences in fungi between healthy and diseased grapevines were only identified in wood and bark samples. Cooccurrence networks analysis, using both unweighted and weighted metrics, revealed intricate relationships among pathogenic fungal genera. This involved mostly positive associations, potentially suggesting synergism, and a few negative relationships, potentially suggesting antagonistic interactions. In essence, the observed differences among terroirs may stem from environmental filtering due to varied edaphic and mesoclimatic conditions. Temporal weather and vine management practices could explain seasonal and vintage fungal dynamics. This study provides insights into the compositional dynamics of grapevine fungal pathobiome across different microhabitats, terroirs, seasons, and health statuses. The findings emphasize the importance of considering network-based approaches in studying microbial communities and have implications for developing improved viticultural plant health strategies.

The rapid emergence of antifungal-resistant human-pathogenic fungi

During recent decades, the emergence of pathogenic fungi has posed an increasing public health threat, particularly given the limited number of antifungal drugs available to treat invasive infections. In this Review, we discuss the global emergence and spread of three emerging antifungal-resistant fungi: Candida auris, driven by global health-care transmission and possibly facilitated by climate change; azole-resistant Aspergillus fumigatus, driven by the selection facilitated by azole fungicide use in agricultural and other settings; and Trichophyton indotineae, driven by the under-regulated use of over-the-counter high-potency corticosteroid-containing antifungal creams. The diversity of the fungi themselves and the drivers of their emergence make it clear that we cannot predict what might emerge next. Therefore, vigilance is critical to monitoring fungal emergence, as well as the rise in overall antifungal resistance.

Exposure to three herbicide mixtures influenced maize root-associated microbial community structure, function and the network complexity

Herbicide mixtures are a new and effective agricultural strategy for managing suppress weed resistance and have been widely used in controlling weeding growth in maize fields. However, the potential ecotoxicological impact of these mixtures on the microbial community structure and function within various root-associated niches, remains inadequately understood. Here, the effects of nicosulfuron, mesotrione and atrazine on soil enzyme activity and microbial community structure and function were investigated when applied alone and in combination. The findings indicated that herbicide mixtures exhibit a prolonged half-life compared to single herbicides. Ecological niches are the major factor influencing the structure and functions of the microbial community, with the rhizosphere exhibiting a more intensive response to herbicide stress. Herbicides significantly inhibited the activities of soil functional enzymes, including dehydrogenase, urease and sucrose in the short-term. Single herbicide did not drastically influence the alpha or beta diversity of the soil bacterial community, but herbicide mixtures significantly increased the richness of the fungal community. Meanwhile, the key functional microbial populations, such as Pseudomonas and Enterobacteriaceae, were significantly altered by herbicide stress. Both individual and combined use of the three herbicides reduced the complexity and stability of the bacterial network but increased the interspecific cooperations of fungal community in the rhizosphere. Moreover, by quantification of residual herbicide concentrations in the soil, we showed that the degradation period of the herbicide mixture was longer than that of single herbicides. Herbicide mixtures increased the contents of NO3--N and NH4+-N in the soil in the short-term. Overall, our study provided a comprehensive insight into the response of maize root-associated microbial communities to herbicide mixtures and facilitated the assessment of the ecological risks posed by herbicide mixtures to the agricultural environment from an agricultural sustainability perspective.

Core bacteria carrying the genes associated with the degradation of atrazine in different soils

Atrazine residues can pose serious threats to soil ecology and human health. Currently, the underlying relationship between soil microbial communities and the degradation genes associated with atrazine degradation remains unclear. In this study, the degradation characteristics of atrazine was investigated in ten different soil types. Further, diversity and abundance of degradation genes and succession of the bacterial community were also studied. The degradation of 10 mg/kg atrazine in different soil types exhibited an initial rapid trend followed by a gradual slowdown, adhering to the first-order kinetic equation. Atrazine significantly increased the absolute abundance of atz degradation genes. The increase in the absolute abundance of atzC gene was the largest, whereas that of atzA gene was the smallest, and the trzD gene was only detected in the Binzhou loam soil. Co-occurrence network analysis showed that the number of potential bacterial hosts of atzC was the highest compared with the other atz genes. Atrazine also altered the structural composition of the soil microbial community. The relative abundances of Ochrobactrum, Nocardiopsis, Lactobacillus, and Brevibacterium was increased in the atrazine-treated soils, while those of Conexibate, Solirubacter, and Micromonospora was decreased significantly compared with the control. Additionally, four atrazine-degrading bacterial strains Rhizobium AT1, Stenotrophomonas AT2, Brevibacterium AT3, and Bacillus AT4 were isolated from the atrazine-treated soils. After 14 d for inoculation, their degradation rate for 10 mg/L atrazine ranged from 17.56 % to 30.55 %. Moreover, the relative abundances of the bacterial genera, including these four isolates, in the atrazine-treated soil were significantly higher than those in the control, indicating that they were involved in the synergistic degradation of atrazine in the soil. This study revealed the degradation characteristics of atrazine, distribution of degradation genes, and succession of microbial communities, and explored the internal relationship between microbial community structure and atrazine degradation mechanisms in different soil types.

Deciphering the degradation characteristics of the fungicides imazalil and penflufen and their effects on soil bacterial community composition, assembly, and functional profiles

The adsorption-desorption and degradation characteristics of two widely applied fungicides, imazalil and penflufen, and the responses of soil bacterial diversity, structure, function, and interaction after long-term exposure were systemically studied in eight different soils. The adsorption ability of imazalil in soil was significantly higher than that of penflufen. Both imazalil and penflufen degraded slowly in most soils following the order: imazalil > penflufen, with soil pH, silt, and clay content being the potential major influencing factors. Both imazalil and penflufen obviously inhibited the soil microbial functional diversity, altered the soil bacterial community and decreased its diversity. Although exposure to low and high concentrations of imazalil and penflufen strengthened the interactions among the soil bacterial communities, the functional diversity of the co-occurrence network tended to be simple at high concentrations, especially in penflufen treatment. Both imazalil and penflufen markedly disturbed soil nitrogen cycling, especially penflufen seriously inhibited most nitrogen cycling processes, such as nitrogen fixation and nitrification. Meanwhile, sixteen and ten potential degradative bacteria of imazalil and penflufen, respectively, were found in soils, including Kaistobacter and Lysobacter. Collectively, the long-term application of imazalil and penflufen could cause residual accumulation in soils and subsequently result in serious negative effects on soil ecology.

Heavy metal pollution triggers a shift from bacteria-based to fungi-based soil micro-food web: Evidence from an abandoned mining-smelting area

Heavy metals pose significant threats to soil biota, ultimately disrupting soil micro-food web. However, no studies have yet elucidated the impact of heavy metals on soil micro-food web. In this study, we explored the response of bacteria, fungi, nematodes, and soil micro-food web along a gradient of heavy metals in an abandoned smelting-mining area. We found that bacteria responded strongly to heavy metals, whereas fungi showed greater resistance and tolerance. Nematodes responses were less apparent. With the increasing levels of heavy metal pollution, the importance of heavy metal-tolerant organisms in micro-food webs increased significantly. For instance, the keystone bacteria in soil micro-food web shifted from copiotrophic to oligotrophic types, while the keystone nematodes shifted from to bacterial-feeding (e.g., Eucephalobus) to fungal-feeding species (e.g., Ditylenchus). Additionally, elevated heavy metal concentrations increased the proportion of fungi (e.g., Mortierellomycota), intensifying their interactions with bacteria and nematodes and causing a shift from bacteria-based to fungi-based soil micro-food web. Furthermore, heavy metal contamination induced a more complex and stable soil micro-food web. Overall, we highlight the changes in soil micro-food web as a mechanism for coping with heavy metal stress. Our study provides valuable insights into how heavy metal pollution can cause shifts in soil micro-food webs and has critical implications for enhancing our understanding of the ecological consequences of environmental pollution at the ecosystem level.

Significant roles of core prokaryotic microbiota across soil profiles in an organic contaminated site: Insight into microbial assemblage, co-occurrence patterns, and potentially key ecological functions

Extreme environmental disturbances induced by organic contaminated sites impose serious impacts on soil microbiomes. However, our understanding of the responses of the core microbiota and its ecological roles in organic contaminated sites is limited. In this study, we took a typical organic contaminated site as an example and investigated the composition and structure, assembly mechanisms of core taxa and their roles in key ecological functions across soil profiles. Results presented that core microbiota with a considerably lower number of species (7.93%) than occasional taxa presented comparatively high relative abundances (38.04%) yet, which was mainly comprised of phyla Proteobacteria (49.21%), Actinobacteria (12.36%), Chloroflexi (10.63%), and Firmicutes (8.21%). Furthermore, core microbiota was more influenced by geographical differentiation than environmental filtering, which possessed broader niche widths and stronger phylogenetic signals for ecological preferences than occasional taxa. Null modelling suggested that stochastic processes dominated the assembly of the core taxa and maintained a stable proportion along soil depths. Core microbiota had a greater impact on microbial community stability and possessed higher functional redundancy than occasional taxa. Additionally, the structural equation model illustrated that core taxa played pivotal roles in degrading organic contaminants and maintaining key biogeochemical cycles potentially. Overall, this study deepens our knowledge of the ecology of core microbiota under complicated environmental conditions in organic contaminated sites, and provides a fundamental basis for preserving and potentially utilizing core microbiota to maintain soil health.

The widespread presence of triazole fungicides in greenhouse soils in Shandong Province, China: A systematic study on human health and ecological risk assessments

Triazole fungicides (TFs) are extensively used on greenhouse vegetables and are ubiquitously detected in the environment. However, the human health and ecological risks associated with the presence of TFs in the soil are unclear. In this study, ten widely used TFs were measured in 283 soil samples from vegetable greenhouses across Shandong Province, China, and their potential human health and ecological risks were assessed. Among all soil samples, difenoconazole, myclobutanil, triadimenol, and tebuconazole were the top detected TFs, with detection rates of 85.2-100%; these TFs had higher residues, with average concentrations of 5.47-23.8 μg/kg. Although most of the detectable TFs were present in low amounts, 99.3% of the samples were contaminated with 2-10 TFs. Human health risk assessment based on hazard quotient (HQ) and hazard index (HI) values indicated that TFs posed negligible non-cancer risks for both adults and children (HQ range, 5.33 × 10-10 to 2.38 × 10-5; HI range, 1.95 × 10-9 to 3.05 × 10-5, <1). Ecological risk assessment based on the toxicity exposure ratio (TER) and risk quotient (RQ) values indicated that difenoconazole was a potential risk factor for soil organisms (TERmax = 1 for Eisenia foetida, <5; RQmean = 1.19 and RQmax = 9.04, >1). Moreover, 84 of the 283 sites showed a high risk (RQsite range, 1.09-9.08, >1), and difenoconazole was the primary contributor to the overall risk. Considering their ubiquity and potential hazards, TFs should be continuously assessed and prioritized for pesticide risk management.

Effect of Trichoderma viride on rhizosphere microbial communities and biocontrol of soybean root rot

Biological seed dressing is a cost-effective means to protect plant roots from pathogens. Trichoderma is generally considered as one of the most common biological seed dressings. However, there is still a dearth of information on the effects of Trichoderma on microbial community of rhizosphere soil. High-throughput sequencing was used to analyze the effects of Trichoderma viride and a chemical fungicide on microbial community of soybean rhizosphere soil. The results showed that both T. viride and chemical fungicide could significantly reduce the disease index of soybean (15.11% for Trichoderma and 17.33% for Chemical), while no significant difference was observed between them. Both T. viride and chemical fungicide could affect the structure of rhizosphere microbial community, they increased the β-diversity of microbial community and significantly reduce the relative abundance of Saprotroph-Symbiotroph. Chemical fungicide could reduce the complexity and stability of co-occurrence network. However, T. viride is beneficial for maintaining network stability and increasing network complexity. There were 31 bacterial genera and 21 fungal genera significantly correlated with the disease index. Furthermore, several potential plant pathogenic microorganisms were also positively correlated with disease index, such as Fusarium, Aspergillus, Conocybe, Naganishia, and Monocillium. From this work, T. viride may be used as a substitute for chemical fungicide to control soybean root rot and be more friendly to soil microecology.

Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome

Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.

A novel bidirectional regulation mechanism of mancozeb on the dissemination of antibiotic resistance

The high abundance of antibiotic resistance genes (ARGs) in the fungicide residual environment, posing a threat to the environment and human health, raises the question of whether and how fungicide promotes the prevalence and dissemination of antibiotic resistance. Here, we reported a novel mechanism underlying bidirectional regulation of a typical heavy-metal-containing fungicide mancozeb on the horizontal transfer of ARGs. Our findings revealed that mancozeb exposure significantly exerted oxidative and osmotic stress on the microbes and facilitated plasmid-mediated ARGs transfer, but its metallic portions (Mn and Zn) were potentially utilized as essential ions by microbes for metalating enzymes to deal with cellular stress and thus reduce the transfer. The results of transcriptome analysis with RT-qPCR confirmed that the expression levels of cellular stress responses and conjugation related genes were drastically altered. It can be concluded mancozeb bidirectionally regulated the ARGs dissemination which may be attributed to the diverse effects on the microbes by its different portions. This novel mechanism provides an updated understanding of neglected fungicide-triggered ARGs dissemination and crucial insight for comprehensive risk assessment of fungicides.

Uptake, Translocation, and Terminal Residue of Chlorantraniliprole and Difenoconazole in Rice: Effect of the Mixed-Application with Adjuvant

Plant oil adjuvants are widely used to improve the utilization rate of pesticides. In this study, the uptake, translocation, and terminal residue of chlorantraniliprole and difenoconazole spraying with plant oil adjuvant in rice (Oryza sativa L.) were evaluated. After being mixed with the tank-mixed plant oil adjuvant, the cuticular wax of rice leaf was destroyed, which decreased the hydrophobicity of the rice leaf and facilitated the wetting, spreading, and penetration of pesticides onto the rice leaf. Additionally, the adjuvant promoted the translocation of difenoconazole from leaves to stems, but had little effect on the translocation of difenoconazole from leaves to roots, while inhibiting chlorantraniliprole translocation. Although adjuvant increased the initial deposition of chlorantraniliprole and difenoconazole on rice, the terminal residue was not significantly affected. The findings can promote the safe use of chlorantraniliprole and difenoconazole in rice production, especially when used with plant oil adjuvants. In the future, studies on more rice cultivars will be necessary to determine the generality of the conclusions.

Changes in the gut microbiota of rats after exposure to the fungicide Mancozeb

Mancozeb is a fungicide commonly used in pest control programs, especially to protect vineyards. Its toxicity has already been evidenced in several studies. However, its influence on the composition and diversity of the gut microbiota remains unknown. In this work, the adverse impact of Mancozeb on the intestinal microbiota was investigated using a rodent model. Adult male Sprague Dawley rats were randomized into three groups: Control (standard diet), MZ1 (Mancozeb dose: 250 mg/kg bw/day), and MZ2 (Mancozeb dose: 500 mg/kg bw/day). After 12 weeks of experiment, animals were euthanized, and feces present in the intestine were collected. After fecal DNA extraction, the V4 region of the 16S rRNA gene was amplified followed by sequencing in an Ion S5™ System. Alpha and beta diversity analysis showed significant differences between Control and Mancozeb groups (MZ1 e MZ2), but no difference between MZ1 and MZ2 was observed. Seven genera significantly increased in abundance following Mancozeb exposure, while five genera decreased. Co-occurrence analyses revealed that the topological properties of the microbial networks, which can be used to infer co-occurrence interaction patterns among microorganisms, were significantly lower in both groups exposed to Mancozeb when compared to Control. In addition, 23 differentially abundant microbial metabolic pathways were identified in Mancozeb-treated groups mainly related to a change in energy metabolism, LPS biosynthesis, and nucleotide biosynthesis. In conclusion, the exposure to Mancozeb presented side effects by changing the composition of the microbiota in rats, increasing bacterial diversity regardless of the dose used, reducing the interaction patterns of the microbial communities, and changing microbial metabolic pathways.

Fungicide sensitivity of grapevine bacteria with plant growth-promoting traits and antagonistic activity as non-target microorganisms

This study evaluates the capacity of commercial formulations of synthetic fungicides to inhibit grapevine bacterial growth when sprayed on vineyards to control diseases, such as downy mildew, powdery mildew and secondary rots. Fungicide sensitivity plate assays were carried out on bacteria isolated from vineyards that were also identified and characterized for their plant growth-promoting (PGP) traits and antifungal activity. The high taxonomic variability of bacteria screened with different chemical classes of fungicides is one new finding of this study. Seven out of 11 fungicides were able to inhibit the growth of bacteria at a concentration corresponding to the maximum dose allowed by law in spray treatments of vineyards. Bacterial sensitivity to each fungicide varied greatly. Many sensitive isolates displayed PGP traits and/or antagonistic activity. This study shows the potential impact of fungicidal treatments on grapevine bacterial microbiota. The involvement of bacteria beneficial to the growth and health of plants underlines the importance of this investigation. Our data reveal that the control of a certain disease may be possible using fungicides that have no or low impact on natural non-target microbiota. Understanding the action mechanisms of the active ingredients in these products is a priority for the development of new eco-friendly pesticides.

The long-acting herbicide mesosulfuron-methyl inhibits soil microbial community assembly mediating nitrogen cycling

Mesosulfuron-methyl is a widely used herbicide in wheat fields. We previously reported that mesosulfuron-methyl alters the bacterial/fungal community structure in experimental indoor microcosms, ultimately affecting NO₃^--N and NH₄⁺-N contents in soil nitrogen (N) cycling. However, how mesosulfuron-methyl application alter soil N cycling by changing microbial community assembly is unknown. Here, we designed an outdoor experiment comprising 2-month periods to investigate changes in soil N-cycle functional genes and structural shifts in the microbial community assembly in response to mesosulfuron-methyl applied at 11.25 and 112.5 g a.i. hm^-2. Results showed that high mesosulfuron-methyl input significantly decreased AOA amoA and nirK abundances within the initial 15 days, but increased AOB amoA on day 60. The nifH abundance displayed a stimulation-inhibition trend. Moreover, high mesosulfuron-methyl input decreased the network's complexity, and newly formed multiple network modules exhibited strong negative associations with nifH, AOB amoA, nirK and nirS. Further structural equation model demonstrated that mesosulfuron-methyl did reveal strong direct inhibition of nirK, and it indirectly affected nirK by changing nifH abundance and Planomicrobium. Thus mesosulfuron-methyl perturbs N-cycling processes by reshaping bacterial community assembly. Taken together, our study provides theoretical support for determining the microbiological mechanism by which mesosulfuron-methyl affects soil N cycling.

"Fishcide" effect of the fungicide difenoconazole in freshwater fish (Labeo rohita): A multi-endpoint approach

Difenoconazole is widely used to protect crops, fruits, and vegetables. However, this fungicide can enter aquatic environments and cause harmful effects to non-target organisms and induce little-known biological disorders. Thus, aiming to expand our knowledge about the ecotoxicity of difenoconazole on freshwater ichthyofauna, we aimed to determine the median lethal concentration (LC₅₀) of difenoconazole and evaluate its possible impacts from different toxicity biomarkers, using freshwater fish Labeo rohita as a model system. Using the probit analysis method, the 96 h LC₅₀ value of difenoconazole in the fish was calculated as 4.5 mg L^-1. Posteriorly, fish were exposed to two sublethal concentrations (0.45 mg L^-1 1/10th and 0.9 mg L^-1 1/5th LC₅₀ value) for 21 days. A significant reduction of superoxide dismutase (SOD) and catalase (CAT) activity was noted in the gill, liver, and kidneys of fish compared to the control groups. The level of glutathione-S-transferase (GST) and lipid peroxidation (LPO) activity was higher in all vital tissues of difenoconazole-treated fish. Histological alterations in the gill include epithelial lifting, lamellar fusion, hypertrophy, and epithelial necrosis. At the same time, the liver showed pyknotic nucleus, vacuolation, cellular edema and tubular necrosis, shrinkage of glomeruli, vacuolation, and pyknotic nuclei in the kidney. DNA damage was increased significantly with tail formation based on the concentration and time-dependent manner. Therefore, our study confirms that the exposure of L. rohita to difenoconazole induces negative biological consequences and sheds light on the danger of this fungicide for freshwater fish species. We believe that studies like ours can support actions and strategies for the remediation/mitigation of aquatic pollution by difenoconazole and for the conservation of freshwater ichthyofauna.

Natural compounds derived from Brassicaceae plants as an alternative to synthetic fungicides and their influence on soil fungus diversity

BACKGROUND

The study aimed to develop a new formulation based on active substances of natural origin to protect plant seedlings against fungal pathogens, and to evaluate the effect of this formulation on fungal communities in arable soil.

RESULTS

Coating seeds of common crop plants with a p-coumaric acid (p-CA)-based preparation resulted in a significant reduction in the growth of most of the tested pathogens. When applied to soil, both the p-CA-based formulation and Porter 250 EC had a similar overall effect on soil fungal communities and significantly altered the structure of fungal communities at all of the times examined. Shifts in the fungal community composition concerned less than 2% of the total number of amplicon sequence variants (ASVs). The strongest impact of the formulations on soil microbiota was recorded at the fourth week of treatment. Two ASVs assigned to Botrytis and Chromelosporium, known as plant pathogens, and an unidentified ASV from Diversisporales encompassing the arbuscular mycorrhizal fungi (AMF), were significantly depleted in soil samples treated with p-CA in comparison with Porter 250 EC.

CONCLUSION

The p-CA-based preparation has the potential to be used as an alternative to synthetic fungicides. It shows a similar effect to Porter 250 EC on the organization of soil communities, determining changes in the character of the communities of fungi in general, at any given time. Moreover, p-CA caused a reduction in ASVs belonging to Botrytis and Chromelosporium (plant pathogens) and ASVs of Diversisporales (containing arbuscular mycorrhizal fungi) in comparison with the commercial compound that was analyzed. © 2022 Society of Chemical Industry.

Highly efficient in-situ cleaner degradation of difenoconazole by two novel dominant strains: Microflora diversity, monoclonal isolation, growth factor optimization, intermediates, and pathways

The non-point source pollution of difenoconazole (DIF) has become a serious environmental issue, increasingly causes indelible damages to eco-environment and human health due to its toxicity, persistence, and biomagnification. An eco-friendly, cost-effective, and efficient control technology is imperative towards a cleaner and sustainable agricultural production. Herein, a dominant microflora of efficiently degrading DIF was successfully screened, and its microbial diversity was investigated. Two novel degrading strains were isolated and identified as Phyllobacterium sp. (T-1) and Aeromonas sp. (T-2). The results of growth factor optimization indicated that the degradation rates of DIF (C₀ = 20 mg/L) by strain T-1 and T-2 were up to 96.32% and 97.86% within 14 d, respectively, under the optimal conditions. Moreover, there no obvious synergy between strain T-1 and strain T-2. From catalytic kinetics of enzymes, the intracellular enzyme of strain T-1 dominated the degradation of DIF (C₀ = 20 mg/L) entirely with the degradation rate of 82.4% (48 h), the extracellular enzyme showed little catalytic activity. However, the degrade rates of DIF (C₀ = 20 mg/L) by both intracellular and extracellular enzymes of strain T-2 were 77.99% and 26.73% within 48 h, respectively. Moreover, these enzymes remained an undiminished catalytic activity within 48 h. DIF was degraded by strain T-1 to three main transformation products (DIF-TPs 406, DIF-TPs 216, and DIF-TPs 198) undergoing hydroxyl substitution, hydrolysis, cleavage of ether bond between benzene rings, and rearrangement, while two additional products (DIF-TPs 281 and DIF-TPs 237) were generated with the biodegradation of strain T-2, excepting for DIF-TPs 406 and DIF-TPs 216, involving hydrolysis, hydroxylation, and ether bond cleavage between benzene rings. Moreover, QSAR simulation showed that the by-products were almost much lower toxicity or even non-toxic to three typical aquatic organisms (fish, daphnia, and green algae) than DIF. This study not only provides an in depth understanding of DIF bioelimination, but also be instrumental in cleaner management of DIF-contaminated soil. This study can promote the sustainable development of agriculture.

Effect of tank-mixed adjuvant on the behavior of chlorantraniliprole and difenoconazole in soil

In this study, both laboratory and field studies were performed to analyze the effect of the presence of tank-mixed methylated plant oil adjuvant on the adsorption and degradation of chlorantraniliprole (CAP) and difenoconazole (DIF) in soil. Adsorption kinetics and isotherms experiments were conducted according to the equilibrium oscillation method. Fourier transform infrared spectroscopy (FT-IR) analysis, soil contact angle, and zeta potential were used to research the interaction mechanism of adsorption. Fluorescence excitation emission matrix (FEEM) measurements were conducted to characterize soil dissolved organic matter. Field experiment was conducted to investigate the degradation of CAP and DIF combined with adjuvant. DIF exhibited a significantly higher Freundlich maximum adsorption capacity than CAP, which is consistent with the higher octanol-water partition coefficient of DIF. The sorption of CAP and DIF under laboratory conditions was significantly increased with the presence of adjuvant. Soils with high humic acids have strong adsorption capacity and contribute to significant adsorption of CAP and DIF. The half-lives of CAP and DIF tested in fluvo-aquic soil under field conditions were slightly reduced by the adjuvant. Adjuvant reduced the Groundwater Ubiquity Score (GUS) indices of CAP from 1.51 to 1.31, whereas that of DIF from 0.39 to 0.25. Combination between the pesticides and soil molecules can be enhanced, thereby promoting the adsorption and degradation of CAP and DIF in soil, and further reducing their potential to leach into groundwater when 0.1% methylated plant oil adjuvant was mixed and applied.

Effect of fumigants and non-fumigants on nematode and weed control, crop yield, and soil microbial diversity and predicted functionality in a strawberry production system

Fumigants are commonly used to control soil-borne pathogens of high-value crops, but they may also impact non-target soil microorganisms. Increasing interest in the use of sustainable management practices to control plant- and root-parasitic nematodes has resulted in the formulation of non-fumigant nematicides (chemicals or bionematicides) which are considered environmentally friendly alternatives to fumigants. However, the impact of these new products compared to standard fumigants on soil-borne pathogens, plant production, and the diversity and composition of non-target microbial communities in all crops remains unclear. To begin to address this knowledge gap, we examined the effect of fumigants commonly used in Florida (United States) strawberry production and newly formulated non-fumigant nematicides on nematode and weed control, plant growth, crop yield, and bacterial and fungal community diversity and predicted functionality. We found the standard fumigants increased crop yields and reduced weed pressure more than non-fumigants. Both fumigants and non-fumigants were an efficient management strategy to control sting nematodes. Treatments also impacted the abundance of specific beneficial and antagonistic taxa. Both fumigants and non-fumigants reduced soil bacterial and fungal diversity, an effect that remained for six months, thus suggesting a potential residual impact of these products on soil microorganisms. However, only fumigants altered soil microbial community composition and reduced network complexity, inducing a decrease or even a loss of some predicted bacterial and fungal functions, particularly during the first weeks after fumigation. Nevertheless, soil collected at the end of the season showed significant levels of root-knot nematode suppression in a growth chamber experiment, irrespective of the previous treatment. By linking the effect of fumigants and non-fumigants on soil-borne pests, plant and production, and the soil microbiome, this study increases our knowledge regarding the environmental impact of these products.

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

BACKGROUND

Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented.

RESULTS

We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil's previous fumigation exposure.

CONCLUSIONS

The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.