Impact of fomesafen on the soil microbial communities in soybean fields in Northeastern China

Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation

Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. The persistence, phytotoxicity, and negative impact on crop rotation associated with this herbicide have led to an increasing concern about the buildup of fomesafen residues in agricultural soils. The exigent matter of treatment and remediation of soils contaminated with fomesafen has surfaced. Nevertheless, the degradation pathway of fomesafen in soil remains nebulous. In this study, Bacillus sp. Za was utilized to degrade fomesafen residues in black and yellow brown soils. Fomesafen's degradation rate by strain Za in black soil reached 74.4%, and in yellow brown soil was 69.2% within 30 days. Twelve intermediate metabolites of fomesafen were identified in different soils, with nine metabolites present in black soil and eight found in yellow brown soil. Subsequently, the degradation pathway of fomesafen within these two soils was inferred. The dynamic change process of soil bacterial community structure in the degradation of fomesafen by strain Za was analyzed. The results showed that strain Za potentially facilitate the restoration of bacterial community diversity and richness in soil samples treated with fomesafen, and there were significant differences in species composition at phylum and genus levels between these two soils. However, both soils shared a dominant phylum and genus, Actinobacteriota, Proteoobacteria, Firmicutes and Chloroflexi dominated in two soils, with a high relative abundance of Sphingomonas and Bacillus. Moreover, an intermediate metabolite acetaminophen degrading bacterium, designated as Pseudomonas sp. YXA-1, was isolated from yellow brown soil. When strain YXA-1 was employed in tandem with strain Za to remediate fomesafen contaminated soil, the degradation rate of fomesafen markedly increased. Overall, this study furnishes crucial insights into the degradation pathway of fomesafen in soil, and presents bacterial strain resources potentially beneficial for soil remediation in circumstances of fomesafen contamination.

Coupling multifactor dominated the biochemical response and the alterations of intestinal microflora of earthworm Pheretima guillelmi due to typical herbicides

The excessive application of herbicides on farmlands can substantially reduce labor costs and increase crop yields, but can also have undesirable effects on terrestrial ecosystems. To evaluate the ecological toxicity of herbicides, metolachlor and fomesafen, two typical herbicides that are extensively used worldwide were chosen as target pollutants, and the endogeic earthworm Pheretima guillelmi, which is widely distributed in China, was selected as the test organism. A laboratory-scale microcosmic experiment was set, and energy resources, enzymes, and the composition and connections of intestinal microorganisms in earthworms were determined. Both herbicides depleted the energy resources of the earthworms, especially glycogen contents; increased the levels of antioxidant enzymes; and inhibited acetylcholinesterase. Moreover, the richness and diversity of the intestinal bacterial community of the earthworms were suppressed. Additionally, the bacterial composition at the genus level changed greatly and the connections between dominant bacteria increased dramatically. Most interactions among the bacterial genera belonging to the same and different phyla showed mutualism and competition, respectively. Importantly, metolachlor with higher toxicity had a transitory effect on these indicators in earthworms, whereas fomesafen, with lower toxicity but stronger bioaccumulation potential, exerted a sustaining impact on earthworms. Collectively, these results indicate that the toxic effects of herbicides on terrestrial organisms should be comprehensively considered in combination with biological toxicity, persistence, bioaccumulation potential, and other factors.

A nitroreductase DnrA catalyzes the biotransformation of several diphenyl ether herbicides in Bacillus sp. Za

Diphenyl ether herbicides, typical globally used herbicides, threaten the agricultural environment and the sensitive crops. The microbial degradation pathways of diphenyl ether herbicides are well studied, but the nitroreduction of diphenyl ether herbicides by purified enzymes is still unclear. Here, the gene dnrA, encoding a nitroreductase DnrA responsible for the reduction of nitro to amino groups, was identified from the strain Bacillus sp. Za. DnrA had a broad substrate spectrum, and the K_m values of DnrA for different diphenyl ether herbicides were 20.67 μM (fomesafen), 23.64 μM (bifenox), 26.19 μM (fluoroglycofen), 28.24 μM (acifluorfen), and 36.32 μM (lactofen). DnrA also mitigated the growth inhibition effect on cucumber and sorghum through nitroreduction. Molecular docking revealed the mechanisms of the compounds fomesafen, bifenox, fluoroglycofen, lactofen, and acifluorfen with DnrA. Fomesafen showed higher affinities and lower binding energy values for DnrA, and residue Arg244 affected the affinity between diphenyl ether herbicides and DnrA. This research provides new genetic resources and insights into the microbial remediation of diphenyl ether herbicide-contaminated environments. KEY POINTS: • Nitroreductase DnrA transforms the nitro group of diphenyl ether herbicides. • Nitroreductase DnrA reduces the toxicity of diphenyl ether herbicides. • The distance between Arg244 and the herbicides is related to catalytic efficiency.

Influence of the casing layer on the specific volatile compounds and microorganisms by Agaricus bisporus

One of the major variables affecting yield of the mushroom Agaricus bisporus is the casing layer, which directly affects the productivity and mass. Here, volatile organic compounds were extracted by headspace solid-phase microextraction and high-throughput sequencing was used to analyze the microbial community diversity. The relationship between mushroom yield at different cropping stages and the contents of volatile organic compounds and microorganisms in three different casing layers: peat, peat + soil and soil were systematically evaluated. The result shows that Benzaldehyde and (E)-2-octenal which stimulate yield, obviously increased as mushrooms grew, while 3-octanone, which inhibits yield, decreased over time in all three casing layers. However, there was not a strong correlation between the concentration of volatile compounds and yield. In addition, more than 3,000 bacterial operational taxonomic units (OTUs) by performing high throughput sequencing of the microbes were obtained in the three casing layers. Interestingly, the microbial community compositions were very similar between the three casing layers at a later cropping stage, but the community richness varied significantly in different casing layers and at different cropping stages. At the phylum level, the communities had similar structures but were quantitively very different, and this was even more obvious at the genus level. Principal component analysis revealed significant alterations in microbial community structure in different casing layers. Sphingomonas, Dongia and Achromobacter were the dominant genera at cropping stage 1, and the stage 3 were abundant in Saccharibacteria_norank, Pseudomonas, Flavobacterium and Brevundimonas, which was positively correlated with yield, while the abundance of Pseudomonas at stage 1 and Lactococcus and Bacillus at stage 3 was negatively correlated with yield. These results provide a guide for the development and agricultural application of microbial agents for yield improvement in the production of A. bisporus.

Target gene mutation and enhanced metabolism confer fomesafen resistance in an Amaranthus retroflexus L. population from China

Amaranthus retroflexus L., a troublesome annual dicotyledonous weed species, is highly competitive with soybean (Glycine max L.). A single-dose herbicide-resistance screening assay identified an A. retroflexus population with suspected resistance to fomesafen. Whole-plant dose-response assays demonstrated that the resistant population (2492) was resistant to protoporphyrinogen oxidase (PPO)-inhibiting herbicides (50.6-fold fomesafen resistance and > 8.1-fold lactofen resistance) compared to a susceptible (S) population. PPX2 gene sequence analysis showed an Arg₁₂₈Gly amino acid substitution in the 2492 population. Moreover, pretreatment of malathion and the fomesafen metabolic assays through HPLC-MS demonstrated enhanced fomesafen metabolism in the 2492 population. Additionally, the 2492 population was 10.4-fold more resistant to the ALS-inhibiting herbicide imazethapyr and 16.8-fold more resistant to thifensulfuron-methyl than the S population. ALS gene sequence analysis showed an Ala₂₀₅Val amino acid substitution in the 2492 population. This population of A. retroflexus has coexisting target-site resistance and non-target-site mechanisms for resistance to fomesafen. Multiple herbicide resistance may mean it is necessary to adjust weed management strategies to better control the resistant population.

Biochar alleviated the toxicity of atrazine to soybeans, as revealed by soil microbial community and the assembly process

Atrazine has a detrimental effect on soybean growth in corn-soybean rotation systems. A knowledge gap exists regarding how rhizosphere microbial interactions respond to atrazine stress, and specifically, whether they may alleviate the detriment of atrazine on soybeans, this serving as a target to alleviate the adverse impact. Biochar are widely used for remediation in herbicide contamination soil, however, little is known about how biochar fuels the microbiomes in rhizosphere to improve soybean performance. We investigated the response of the microbial community to atrazine stress with and without biochar application to soybean cultivation in a greenhouse experiment. Atrazine had detrimental effects on soybeans and nodules, reshaping the microbial community in both the bulk and rhizosphere soil. Biochar application was able to ameliorate atrazine effects on soybean and nodule activity, with an increase in competition among microbes in the soybean rhizosphere soils. Biochar favored the probiotics such as the bacteria Lysobacter, Paenarthrobacter, and Sediminibacterium in the rhizosphere soils. The relative abundance of Lysobacter exhibited strong-negative correlations with potential pathogens. Elastic net regression with bioindicators and environmental factors accurately predicted the residual content of atrazine in soil. Collectively, our results provide a practical strategy of using biochar to improve soil quality for corn-soybean rotation that is contaminated with residual atrazine. Overall, beneficial plant microbes and changes in microbial interactions and assembly processes in the soybean rhizosphere are capable of alleviating atrazine stress on soybean growth.

Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators

The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, "Candidatus Nitrosopumilus", and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.

Integrated microbiology and metabolomics analysis reveal plastic mulch film residue affects soil microorganisms and their metabolic functions

Research on microplastic pollution of terrestrial soils is catching up with the aquatic environment, especially agricultural soil systems. Plastic residues have caused various environmental problems in mulch film extensively used agricultural areas. However, studies focusing specifically on the potential influence of mulch film residues on the metabolic cycle of soil systems have yet to be conducted. Here, high-throughput sequencing combined with metabolomics were first used to study the effects of residual mulch on soil microbial communities and related metabolic functions. Plastic film treatment did not significantly affect soil physicochemical properties including pH, organic matter and nitrogen, etc in short term. However, it did significantly changed overall community structure of soil bacteria, and interfered with complexity of soil bacterial symbiosis networks; exposure time and concentration of residues were particularly important factors affecting community structure. Furthermore, metabolomics analysis showed that film residue significantly changed soil metabolite spectrum, and interfered with basic carbon and lipid metabolism, and also affected basic cellular processes such as membrane transport and, in particular, interfered with the biosynthesis of secondary metabolites, as well as, biodegradation and metabolism of xenobiotics. Additionally, through linear discriminant and collinear analysis, some new potential microplastic degrading bacteria including Nitrospira, Nocardioidaceae and Pseudonocardiaceae have been excavated.

Residues and dietary intake risk assessments of clomazone, fomesafen, haloxyfop-methyl and its metabolite haloxyfop in spring soybean field ecosystem

Soybean is an important oilseed crop, but weed can have a significant effect on soybean yield. Clomazone, fomesafen, and haloxyfop-methyl are high-efficacy herbicides, and the combination of these herbicides shows an ideal effect on weed control. However, the residues of these herbicides and their impacts on human health are still largely unknown. In the current study, a rapid, sensitive, and selective method using modified QuECHERS procedure combined with HPLC-MS/MS was established to detect these herbicides in soybean matrices. The limits of quantification were 0.01, 0.01 and 0.025 mg/kg for haloxyfop-methyl, haloxyfop and fomesafen, and 0.005, 0.005 and 0.0125 mg/kg for clomazone in green soybean, soybean grain, and straw, with the average recoveries ranging from 80% to 107%. The terminal residues of the target compounds were all below the corresponding limits of quantification. The dietary risk assessment showed that the risk quotient values were far below the acceptable human consumption levels.

Effects of cloransulam-methyl and diclosulam on soil nitrogen and carbon cycle-related microorganisms

Cloransulam-methyl and diclosulam are applied to soybean fields to control broad-leaved weeds. These herbicides have become a focus of attention because of their low application dose and high-efficiency advantages. However, the effects of these two herbicides on soil microorganisms are unknown. The present study investigated the effects of 0.05, 0.5, and 2.5 mg kg^-1 of cloransulam-methyl or diclosulam on soil microbes after 7, 14, 28, 42, and 56 days of exposure. The results showed that the two herbicides increased the abundances of functional bacteria related to pesticide degradation. Based on the genetic expression results, we speculated that 0.05 mg kg^-1 of these two herbicides inhibited the nitrification reaction but promoted the denitrification reaction. Diclosulam at a concentration of 0.5 mg kg^-1 may enhance the ability of microbes to fix carbon. β-glucosidase activity was activated by the two herbicides at a concentration of 2.5 mg kg^-1. Diclosulam had a positive effect on urease, but cloransulam-methyl activated urease activity only at concentrations of 0.05 and 0.5 mg kg^-1. The results of the integrated biomarker response showed that the toxicity of diclosulam was greater than that of cloransulam-methyl. Our research provides data for evaluating the environmental risks of cloransulam-methyl and diclosulam.

Effects of sulfoxaflor on greenhouse vegetable soil N2O emissions and its microbial driving mechanism

The wide application of pesticides ensures the safety of food production, but it also has a serious impact on soil ecosystem. Although sulfoxaflor as a pesticide has great potential for application due to its excellent insecticidal activity and low crossresistance, little is known about its soil environmental safety risks. In this study, the effects of sulfoxaflor on N₂O emissions and microorganisms in greenhouse vegetable soils were studied by indoor simulation culture experiments. Dynamic changes of soil main inorganic N and N₂O emission rate were tested, and the abundance and community of total bacteria and microorganisms related to N cycle were analyzed. The results indicated that soil microorganisms rapidly degraded sulfoxaflor, and the N₂O emissions rate and ammonium nitrogen (NH₄⁺-N) content significantly increased, while nitrate nitrogen (NO₃^--N) content was significantly decreased. Sulfoxaflor significantly changed the abundance and community of total bacteria, nitrite reducing and nitrous oxide reducing bacteria, but had no significant effect on ammoxidation microorganisms. The N₂O emission rate was positively correlated with gene abundance of denitrifying microorganisms. Under 65% soil maximum water holding capacity, sulfoxaflor may broke the dynamic balance of N₂O production and consumption in the denitrification process, which caused a significant increase in N₂O emission. Therefore, the application of sulfoxaflor had a certain effect on N cycling and utilization in greenhouse vegetable soil.

Effect of fomesafen on the embryonic development of zebrafish

Fomesafen is widely used in agriculture and can be detected in the environment and agricultural products. Research on the developmental toxicity of fomesafen in animals is currently very limited. Here, we used zebrafish as an animal model to evaluate the toxicity of fomesafen in developing aquatic vertebrates and higher animals. From 6h to 72h following fertilization, exposure of zebrafish embryos to 5, 10 and 20 mg/L of fomesafen resulted in pericardial edema, a reduction in heart rate, shortening of body length, and yolk sac edema. Fomesafen reduced the number of immune cells such as neutrophils and macrophages, increased the expression of a number of inflammatory factors, induced the up-regulation of the oxidative stress response and apoptosis, and disrupted the activity of enzymes related to nerve development, which affected the motility of the embryos. In conclusion, the results provide new evidence for the comprehensive assessment of fomesafen toxicity in aquatic vertebrates.

Simultaneous Analysis and Dietary Exposure Risk Assessment of Fomesafen, Clomazone, Clethodim and Its Two Metabolites in Soybean Ecosystem

A commercial formulation, 37% dispersible oil suspension (DOS) (fomesafen, clomazone, and clethodim), is being registered in China to control annual or perennial weeds in soybean fields. In this paper, a liquid chromatography tandem mass spectrometry method with QuEChERS (quick, easy, cheap, effective, rugged, and safe) sample preparation was developed for the simultaneous determination of fomesafen, clomazone, clethodim, and its two metabolites (CSO and CSO2) in soybean, green soybean, and soybean straw samples. The mean recoveries of our developed method for the five analytes in three matrices were ranged from 71% to 116% with relative standard deviations (RSDs) less than 12.6%. The limits of quantification (LOQs) were 0.01 mg/kg in soybean, 0.01 mg/kg in green soybean, and 0.02 mg/kg in soybean straw while the limits of detection (LODs) ranged from 0.018 to 0.125 μg/kg for these five analytes. The highest final residual amount of CSO2 in green soybean samples (0.015 mg/kg) appeared in Anhui, and the highest in soybean straw samples was 0.029 mg/kg in Guangxi, whilst the terminal residues of fomesafen, clomazone, clethodim and CSO were lower than LOQs (0.01 mg/kg) in all samples. Furthermore, these terminal residues were all lower than the maximum residue limits (MRLs) set by China (0.1 mg/kg for fomesafen and clethodim, 0.05 mg/kg for clomazone) at harvest. Additional chronic dietary risk was evaluated using a risk quotients (RQs) method based on Chinese dietary habits. The chronic dietary exposure risk quotients were 4.3 for fomesafen, 0.12 for clomazone, and 19.3 for clethodim, respectively, which were significantly lower than 100. These results demonstrated that the dietary exposure risk of fomesafen, clomazone, and clethodim used in soybean according to good agricultural practices (GAP) was acceptable and would not pose an unacceptable health risk to Chinese consumers. These results not only offer insight with respect to the analytes, but also contribute to environmental protection and food safety.

Fomesafen impacts bacterial communities and enzyme activities in the rhizosphere

Fomesafen, a long-lived protoporphyrinogen-oxidase inhibitor, specially developed for post-emergence control of broad-leaf weeds, is used widely in soybean fields in northern China (Dayan and Duke, 2010). The impact of fomesafen on microbial communities in rhizosphere soils, however, is unknown. In this study we examined fomesafen degradation as well as its effects in the rhizosphere of soybean plants grown in a greenhouse. Fomesafen had shorter half-life in rhizosphere soil than previously reported for bulk soil from the same location (87 vs 120 days). The enzyme activity of soil extracts and the microbial community composition of 16S rRNA genes (16S) amplified from soil DNA were also investigated. Although not immediately apparent, both the high (37.5 mg kg-1) and low (18.75 mg kg-1) doses of fomesafen significantly decreased urease and invertase activities in the rhizosphere soil from days 30 and 45 respectively until the end of the experiment (90 days). Analysis of 16S amplicons demonstrated that fomesafen had a dose dependent effect, decreasing alpha diversity and altering beta diversity. Significant phylum level decreases were observed in five of the ten phyla that were most abundant in the control. Proteobacteria was the only phylum whose relative abundance increased in the presence of fomesafen, driven by increases in the genera Methylophilacaea, Dyella, and Sphingomonas. The functional implications of changes in 16S abundance as predicted using PICRUSt suggested that fomesafen enriched for enzymes involved in xenobiotic metabolism and detoxification (cytochrome P450s and glutathione metabolism). Our data suggest that, despite being degraded more rapidly in the rhizosphere than in bulk soil, fomesafen had long-lasting functional impacts on the soil microbial community.

Soil-applied biochar increases microbial diversity and wheat plant performance under herbicide fomesafen stress

The herbicide "fomesafen" causes phytotoxicity to the rotational wheat crop and may reduce its yield. Considering that biochar may improve remediation and biophysical conditions of the contaminated soil environments to benefit plant growth. Here, we investigated the impacts of three levels of the wheat straw-derived biochar (1%, 2%, and 4% (w/w)) on growth, physiological properties, and rhizosphere microbial communities of the wheat (Triticum aestivum) seedlings under the fomesafen stress using high-throughput sequencing. The results showed that biochar amended into soil significantly reduced the uptake of wheat to fomesafen and thereby eliminate its toxicity to wheat seedlings. Moreover, biochar increased the abundance and diversity of plant beneficial bacterial and fungal taxa in the rhizosphere of wheat seedlings. Compared with the three addition amounts, amendment with 2% of biochar has the best effects to reduce the toxicity of fomesafen on wheat seedlings and maintain the balance of soil microbial community structure in soil contaminated with fomesafen (1.0 mg kg^-1). Overall, our results suggest that the level of biochar application influences the structure and diversity of soil microbiome (and mycobiome) and plant performance under abiotic stress conditions.