Functional and structural responses of soil N-cycling microbial communities to the herbicide mesotrione: a dose-effect microcosm approach

Herbicide application impacted soil microbial community composition and biochemical properties in a flooded rice field

Herbicide application is a common practice in intensive agriculture. However, accumulating herbicide residues in the ecosystem affects important soil attributes. The effect of two herbicides, pendimethalin and pretilachlor, on soil biochemical properties and microbial community composition was studied in a transplanted paddy field. Results reveal a gradual decline in herbicide residue up to 60 days after application. Changes in soil microbiological and biochemical properties (microbial biomass, enzymes, respiration, etc.) showed an inconsistent pattern across the treatments. Quantitative polymerase chain reaction analysis showed the archaeal, bacterial and fungal populations to be of higher order in control soil compared to the treated one. Amplicon sequencing (16S rRNA and ITS genes) exhibited that besides the unclassified genera, ammonia-oxidizing Crenarchaeota and the group represented by Candidatus Nitrososphaera were dominant in both the control and treated samples. Other archaeal genera viz. Methanosarcina and Bathyarchaeia showed a slight decrease in relative abundance of control (0.5 %) compared to the treated soil (0.7 %). Irrespective of treatments, the majority of bacterial genera comprised unclassified and uncultured species, accounting for >64-75 % in the control group and over 78.29 % in the treated samples. Members of Vicinamibacteraceae, Bacillus and Bryobacter were dominant in control samples. Dominant fungal genera belonging to unclassified groups comprised Curvularia, Aspergillus, and Emericellopsis in the control group, whereas Paraphysoderma and Emericellopsis in the herbicide-treated groups. Inconsistent response of soil properties and microbial community composition is evident from the present study, suggesting that the recommended dose of herbicides might not result in any significant change in microbial community composition. The findings of this investigation will help in the formulation of a framework for risk assessment and maintaining sustainable rice cultivation in herbicide- amended soils.

"Structural responses of non-targeted bacterial and hppd communities to the herbicide tembotrione in soil"

Tembotrione (TBT) is a β-triketone herbicide targeting the 4-Hydroxyphenylpyruvate dioxygenase enzyme (4-HPPD) of weeds. This molecule can also affect soil microorganisms, either through both direct and indirect toxic effects for microorganisms expressing 4-HPPD, or by promoting tolerant and/or degrading microbial populations. Our study aimed to characterize the impacts of TBT on the diversity of total- and hppd (coding for 4-HPPD) -soil bacterial communities. Soil microcosms were treated with the active ingredient TBT at the recommended field dose (100 g a.i/ha; D1) or the tenfold dose (D10). Soil samples were collected from 0 to 55 days post-treatment to study: (i) total- and hppd-bacterial diversities using 16SrRNA and hppd amplicons sequencing, respectively; (ii) TBT dissipation in soil. Both total- and hppd-bacterial community composition was not affected by TBT treatments (D1 and D10). However, D10 treatment slightly increased richness and phylogenetic diversity of the total bacterial community while decreasing hppd richness. Overall, the highest dose of TBT seemed to promote TBT-tolerant or TBT-degrading bacterial populations and to deplete TBT-sensitive ones. These effects were transient as TBT was rapidly dissipated with a DT50 of 7 days and 15 days for D1 and D10, respectively. Differential abundance analysis with a Generalized Linear Model allowed the identification of Sphingomonas, Steroidobacter and Lysobacter as genus that were influenced by TBT, and which could be used as a new class of exposure biomarkers.

Bacterial adaptation to rhizosphere soil is independent of the selective pressure exerted by the herbicide saflufenacil, through the modulation of catalase and glutathione S-transferase

Herbicides cause oxidative stress in nontarget microorganisms, which may exhibit adaptive responses to substances they have not previously encountered. Nevertheless, it is unclear whether these characteristics occur in bacteria isolated from agricultural soil. Two possible adaptation strategies of Stenotrophomonas sp. CMA26 was evaluated in agricultural soil in Brazil, which is considered stressful due to the intense use of pesticides. The study focused on degradation and antioxidant enzymes in response to the herbicide Heat, which was absent at the isolation site. The results indicated that higher concentrations of herbicide led to more intense stress conditions during the initial periods of growth. This was evidenced by elevated levels of malondialdehyde and peroxide, as well as a significant reduction in growth. Our data show that herbicide degradation is a selection-dependent process, as none of the 35 isolates from the same environment in our collection were able to degrade the herbicide. The stress was controlled by changes in the enzymatic modulation of catalase activity in response to peroxide and glutathione S-transferase activity in response to malondialdehyde, especially at higher herbicide concentrations. This modulation pattern is related to the bacterial growth phases and herbicide concentration, with a specific recovery response observed during the mid phase for higher herbicide concentrations. The metabolic systems that contributed to tolerance did not depend on the specific prior selection of saflufenacil. Instead, they were related to general stress responses, regardless of the stress-generating substance. This system may have evolved in response to reactive oxygen species, regardless of the substance that caused oxidative stress, by modulating of the activities of various antioxidant enzymes. Bacterial communities possessing these plastic tolerance mechanisms can survive without necessarily degrading herbicides. However, their presence can lead to changes in biodiversity, compromise the functionality of agricultural soils, and contribute to environmental contamination through drift.

Impact of ozonated water disinfestation on soil fungal community composition in continuous ginger field

This study aimed to explore the impact of ozonated water (OW) disinfestation on soil fungal community composition in continuous ginger field. All soil samples were collected in continuous ginger field. There were two groups and 5 time points (0, 1, 3, 5, 9 day) in our study, including OW disinfestation treatment group (O3 group) and control group (CK group). Via internal transcribed spacer (ITS) sequencing and further analysis, the changes of fungal community composition were determined. As a result, at 0 and 9 days after aeration, the operational taxonomic units (OTUs) in O3 group were significantly higher than that in CK group. Compared with the CK group, in O3 group: the ACE and Chao1 index significantly increased on day 1, and the Shannon index significantly decreased while Simpson index significantly increased on day 0 after aeration. In O3 group, there were dynamic changes of top 10 abundance fungi from the genus-level and the growth of Trichoderma and Rhodotorula had been promoted while Hannaella was inhibited. In conclusion, OW disinfestation had complicated impacts on fungal communities in continuous ginger fields. The growth of Trichoderma and Rhodotorula has been promoted during disinfestation, which provided more reference information for soil OW disinfestation research.

Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition

The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS). We extracted DNA extracted from collected samples and performed high-throughput sequencing of PCR amplicons from both the fungal ITS and prokaryotic 16S rRNA gene regions. Sequences were then grouped into amplicon sequence variants (ASVs) and subjected to network analysis. Based on both ITS and 16S rRNA gene data, a greater network size and edges were observed for all sample types from H-sites compared to L-sites at both SGS. Network analysis suggested that the number of potential microbial interactions/associations were greater in samples from H-sites compared to L-sites. Diversity analyses indicated that site-type was not a main driver of alpha and beta diversity in soybean-associated microbial communities. L-sites contained a greater percentage of fungal phytopathogens (ex: Fusarium, Macrophomina, Septoria), while H-sites contained a greater percentage of mycoparasitic (ex: Trichoderma) and entomopathogenic (ex: Metarhizium) fungal genera. Furthermore, roots from H-sites possessed a greater percentage of Bradyrhizobium and genera known to contain plant growth promoting bacteria (ex: Flavobacterium, Duganella). Overall, our results revealed that there were differences in microbial composition in soil and roots from H- and L-sites across a variety of soybean farms. Based on our findings, we hypothesize that differences in microbial composition could have a causative relationship with observed within-farm variability in soybean yield.

Ecotoxicological risk assessment of wastewater irrigation on soil microorganisms: Fate and impact of wastewater-borne micropollutants in lettuce-soil system

The implementation of the new Water Reuse regulation in the European Union brings to the forefront the need to evaluate the risks of using wastewater for crop irrigation. Here, a two-tier ecotoxicological risk assessment was performed to evaluate the fate of wastewater-borne micropollutants in soil and their ecotoxicological impact on plants and soil microorganisms. To this end, two successive cultivation campaigns of lettuces were irrigated with wastewater (at agronomical dose (not spiked) and spiked with a mixture of 14 pharmaceuticals at 10 and 100 µg/L each) in a controlled greenhouse experiment. Over the two cultivation campaigns, an accumulation of PPCPs was observed in soil microcosms irrigated with wastewater spiked with 100 μg/L of PPCPs with the highest concentrations detected for clarithromycin, hydrochlorothiazide, citalopram, climbazole and carbamazepine. The abundance of bacterial and fungal communities remained stable over the two cultivation campaigns and was not affected by any of the irrigation regimes applied. Similarly, no changes were observed in the abundance of ammonium oxidizing archaea (AOA) and bacteria (AOB), nor in clade A of commamox no matter the cultivation campaign or the irrigation regime considered. Only a slight increase was detected in clade B of commamox bacteria after the second cultivation campaign. Sulfamethoxazole-resistant and -degrading bacteria were not impacted either. The irrigation regimes had only a limited effect on the bacterial evenness. However, in response to wastewater irrigation the structure of soil bacterial community significantly changed the relative abundance of Acidobacteria, Chloroflexi, Verrucomicrobia, Beta-, Gamma- and Deltaprotebacteria. Twenty-eight operational taxonomic units (OTUs) were identified as responsible for the changes observed within the bacterial communities of soils irrigated with wastewater or with water. Interestingly, the relative abundance of these OTUs was similar in soils irrigated with either spiked or non-spiked irrigation solutions. This indicates that under both agronomical and worst-case scenario the mixture of fourteen PPCPs had no effect on soil bacterial community.

Side Effects of Pesticides and Metabolites in Groundwater: Impact on Denitrification

The impact of two pesticides (S-metolachlor and propiconazole) and their respective main metabolites (ESA-metolachlor and 1,2,4-triazole) on bacterial denitrification in groundwater was studied. For this, the denitrification activity and the bacterial diversity of a microbial community sampled from a nitrate-contaminated groundwater were monitored during 20 days in lab experiments in the presence or absence of pesticides or metabolites at 2 or 10 μg/L. The kinetics of nitrate reduction along with nitrite and N₂O production all suggested that S-metolachlor had no or only little impact, whereas its metabolite ESA-metolachlor inhibited denitrification by 65% at 10 μg/L. Propiconazole and 1,2,4-triazole also inhibited denitrification at both concentrations, but to a lesser extent (29–38%) than ESA-metolachlor. When inhibition occurred, pesticides affected the reduction of nitrate into nitrite step. However, no significant differences were detected on the abundance of nitrate reductase narG and napA genes, suggesting an impact of pesticides/metabolites at the protein level rather than on denitrifying bacteria abundance. 16S rRNA gene Illumina sequencing indicated no major modification of bacterial diversity in the presence or absence of pesticides/metabolites, except for ESA-metolachlor and propiconazole at 10 μg/L that tended to increase or decrease Shannon and InvSimpson indices, respectively. General growth parameters suggested no impact of pesticides, except for propiconazole at 10 μg/L that partially inhibited acetate uptake and induced a decrease in microbial biomass. In conclusion, pesticides and metabolites can have side effects at environmental concentrations on microbial denitrification in groundwater and may thus affect ecosystem services based on microbial activities.

Assessing the Effects of β-Triketone Herbicides on the Soil Bacterial and hppd Communities: A Lab-to-Field Experiment

Maize cultivators often use β-triketone herbicides to prevent the growth of weeds in their fields. These herbicides target the 4-HPPD enzyme of dicotyledons. This enzyme, encoded by the hppd gene, is widespread among all living organisms including soil bacteria, which are considered as “non-target organisms” by the legislation. Within the framework of the pesticide registration process, the ecotoxicological impact of herbicides on soil microorganisms is solely based on carbon and nitrogen mineralization tests. In this study, we used more extensive approaches to assess with a lab-to-field experiment the risk of β-triketone on the abundance and the diversity of both total and hppd soil bacterial communities. Soil microcosms were exposed, under lab conditions, to 1× or 10× the recommended dose of sulcotrione or its commercial product, Decano^®. Whatever the treatment applied, sulcotrione was fully dissipated from soil after 42 days post-treatment. The abundance and the diversity of both the total and the hppd bacterial communities were not affected by the herbicide treatments all along the experiment. Same measurements were led in real agronomical conditions, on three different fields located in the same area cropped with maize: one not exposed to any plant protection products, another one exposed to a series of plant protection products (PPPs) comprising mesotrione, and a last one exposed to different PPPs including mesotrione and tembotrione, two β-triketones. In this latter, the abundance of the hppd community varied over time. The diversity of the total and the hppd communities evolved over time independently from the treatment received. Only slight but significant transient effects on the abundance of the hppd community in one of the tested soil were observed. Our results showed that tested β-triketones have no visible impact toward both total and hppd soil bacteria communities.

Metabolic profiles in the course of the shikimic acid pathway of Raphanus sativus var. longipinnatus exposed to mesotrione and its degradation products

The influence of pesticides on the metabolism of edible plants has not been fully investigated. Moreover, once introduced into the environment, pesticides are degraded to many compounds with undefined bioactivity. In presented work, under experimental conditions, model edible plant (Raphanus sativus var. longipinnatus) was exposed to herbicide stress by application of a herbicide (mesotrione, 2-(4-methanesulfonyl-2-nitrobenzoyl)cyclohexane-1,3-dione, MES) or its degradation products (amino-4-(methylsulfonyl)benzoic acid, AMBA; 4-(methylsulfonyl)-2-nitrobenzoic acid MNBA; cyclohexane-1,3-dione, CHD). Metabolic profiles of plants were employed to estimate the plant's defence response to MES and its metabolites. The intensity of herbicide stress was determined by measuring the changes in chlorophyll and catecholamines concentration formed in the shikimic acid pathway. Non-target analysis was conducted by LC-MS/MS, determination of catecholamines by LC-FL, chlorophyll by spectrophotometry. The highest phytotoxicity is characterized by MES (2000%-fold increase in the content of herbicide stress marker (normetanephrine) compared to a blank), followed by CHD (500%) combined with 15% increase in chlorophyll concentration. AMBA and MNBA as stress factors caused the increase in the content of catecholamines in the plant (86-160%). Simultaneously, an increase in chlorophyll content was observed (26-50%). Such diversity of the organism's defence response, also visible on metabolic profiles, can be associated with the chemical structure of compounds that are stress factors. MES and CHD, in contrast to AMBA and MNBA, have cyclohexano-1,3-moiety in their structure, which seems to be responsible for herbicidal properties.

Comparative analysis of the effects of five soil fumigants on the abundance of denitrifying microbes and changes in bacterial community composition

Soil fumigation is currently the most effective method for controlling soil-borne pests and diseases in high-value crops. To better understand the effect of chloropicrin (CP), dazomet (DZ), dimethyl disulfide (DMDS), allyl isothiocyanate (AITC) and 1,3-dichloropropene (1,3-D) fumigants on soil microorganisms, this study monitored changes in the diversity and community composition of soil bacteria involved in denitrification using real-time PCR and high-throughput gene sequencing techniques. These five fumigants significantly decreased the bacterial population size in some phyla including Proteobacteria, Chloroflexi and Acidobacteria, and increased the bacterial population size in other phyla such as Firmicutes, Gemmatimonadetes, Actinobacteria, Verrucomicrobia, Saccharibacteria and Parcubacteria. Although bacterial diversity declined after CP fumigation, it was briefly stimulated by the other four fumigants. Meanwhile, all five fumigants temporarily decreased populations of denitrifying bacteria containing the napA, narG, nirS or nirK enzyme-encoding genes. Denitrifiers bearing the cnorB, qnorB or nosZ genes were relatively stable following DZ and DMDS fumigation. However, cnorB and nosZ decreased initially following CP, AITC and 1,3-D fumigation. Simultaneously, the abundance of qnorB significantly increased in AITC and 1,3-D fumigated soils. These results showed that soil fumigation significantly shifted the abundance and community structure of denitrifying bacteria. This study will help to predict the response of different phyla of denitrifying bacteria to soil fumigation.

Effects of herbicide on non-target microorganisms: Towards a new class of biomarkers?

Conventional agriculture still relies on the general use of agrochemicals (herbicides, fungicides and insecticides) to control various pests (weeds, fungal pathogens and insects), to ensure the yield of crop and to feed a constantly growing population. The generalized use of pesticides in agriculture leads to the contamination of soil and other connected environmental resources. The persistence of pesticide residues in soil is identified as a major threat for in-soil living organisms that are supporting an important number of ecosystem services. Although authorities released pesticides on the market only after their careful and thorough evaluation, the risk assessment for in-soil living organisms is unsatisfactory, particularly for microorganisms for which pesticide toxicity is solely considered by one global test measuring N mineralization. Recently, European Food Safety Authority (EFSA) underlined the lack of standardized methods to assess pesticide ecotoxicological effects on soil microorganisms. Within this context, there is an obvious need to develop innovative microbial markers sensitive to pesticide exposure. Biomarkers that reveal direct effects of pesticides on microorganisms are often viewed as the panacea. Such biomarkers can only be developed for pesticides having a mode of action inhibiting a specific enzyme not only found in the targeted organisms but also in microorganisms which are considered as "non-target organisms" by current regulations. This review explores possible ways of innovation to develop such biomarkers for herbicides. We scanned the herbicide classification by considering the mode of action, the targeted enzyme and the ecotoxicological effects of each class of active substance in order to identify those that can be tracked using sensitive microbial markers.

Nitrate addition promotes the nitrogen cycling processes under the co-contaminated tetrabromobisphenol A and copper condition in river sediment

Tetrabromobisphenol A (TBBPA) and copper (Cu) are the main pollutants at e-waste recycling sites and the effects of their biotoxicity on microorganisms have drawn extensive attention. Nitrate-based bioremediation has been applied to organic pollutant-contaminated sediments since nitrate is a favorable electron acceptor for microbes. However, the effects of TBBPA and Cu on nitrogen (N)-cycling microorganisms and bioremediation in co-contaminated sediments remain unclear. Thus, our study examined the effects of TBBPA and Cu with/without nitrate addition on the TBBPA biodegradation efficiencies, microbial activities, and N functional genes. It was found the biodegradation efficiencies of TBBPA were improved by the nitrate addition from 34.7% to 59.3% and from 22.6% to 42.8% in the TBBPA and TBBPA-Cu contaminated groups, respectively. The inhibitions of the catalase activity increased with the nitrate addition because of the anaerobic respiration of the microorganisms. In addition, the potential denitrification rate exhibited an increasing trend from 6.46 to 8.23 mg-N kg^-1 dry sediment day^-1 during the period of 15-90 days after adding nitrate to the co-contaminated group, whereas the potential nitrification rate exhibited an opposite trend and decreased from 4.47 to 3.19 mg-N kg^-1 dry sediment day^-1. The denitrification gene abundances of the N-cycling genes were 10⁷-10⁸ orders of magnitude higher and significantly increased in the nitrate addition groups. The amoA gene abundances were lower than the denitrification gene abundances and were 10⁵-10⁶ orders of magnitude in the same groups. Moreover, the interaction types of the pollutants on the gene abundances were changed from synergistic to antagonistic as nitrate addition. Our study emphasized the gap of knowledge on nitrate addition affecting N-cycling microbes in the combined pollutants exposure sediments, and will be helpful for further bioremediation in different contaminated scenarios.

Earthworms Mitigate Pesticide Effects on Soil Microbial Activities

Earthworms act synergistically with microorganisms in soils. They are ecosystem engineers involved in soil organic matter degradation and nutrient cycling, leading to the modulation of resource availability for all soil organisms. Using a soil microcosm approach, we aimed to assess the influence of the earthworm Aporrectodea caliginosa on the response of soil microbial activities against two fungicides, i.e., Cuprafor Micro® (copper oxychloride, a metal) and Swing® Gold (epoxiconazole and dimoxystrobin, synthetic organic compounds). The potential nitrification activity (PNA) and soil enzyme activities (glucosidase, phosphatase, arylamidase, and urease) involved in biogeochemical cycling were measured at the end of the incubation period, together with earthworm biomass. Two common indices of the soil biochemistry were used to aggregate the response of the soil microbial functioning: the geometric mean (Gmean) and the Soil Quality Index (SQI). At the end of the experiment, the earthworm biomass was not impacted by the fungicide treatments. Overall, in the earthworm-free soil microcosms, the two fungicides significantly increased several soil enzyme and nitrification activities, leading to a higher GMean index as compared to the non-treated control soils. The microbial activity responses depended on the type of activity (nitrification was the most sensitive one), on the fungicide (Swing® Gold or Cuprafor Micro®), and on the doses. The SQI indices revealed higher effects of both fungicides on the soil microbial activity in the absence of earthworms. The presence of earthworms enhanced all soil microbial activities in both the control and fungicide-contaminated soils. Moreover, the magnitude of the fungicide impact, integrated through the SQI index, was mitigated by the presence of earthworms, conferring a higher stability of microbial functional diversity. Our results highlight the importance of biotic interactions in the response of indicators of soil functioning (i.e., microbial activity) to pesticides.

Potential application of Pistia stratiotes for the phytoremediation of mesotrione and its degradation products from water

The aim of the present work is to estimate remediation potential of Pistia stratiotes, its ability to uptake mesotrione (MES) - one of the most frequently used herbicides, and its main degradation products: 2-amino-4-methylsulfonyl benzoic acid (AMBA) and 4-methylsulfonyl-2-nitrobenzoic acid (MNBA). This research focuses on model experiments performed under laboratory conditions. The results show that Pistia stratiotes can uptake up to 75% of degradation products from 1 L of surface water samples polluted with 0.4 µg/L of each analyte during 7 days without significant phytotoxic effect. Under the same experimental conditions, the effectiveness of mesotrione sorption is in the range of 42-58%. The phytotoxicity of this compound is higher in comparison to its degradation products (decrease of chlorophyll concentration in plant tissues exposed to MES 27-32% vs 4-13% in case of exposition to AMBA and MNBA). The adequate nutrition of the plants is crucial to their well-being and thus the sorption of pollutants.

Changes in the abundance and community composition of different nitrogen cycling groups in response to fumigation with 1,3-dichloropropene

The fumigant 1,3-dichloropropene (1,3-D) is widely-used to control pathogenic bacteria, fungi, nematodes and insects in soil before a crop is planted. Although fumigants in general have been reported to have a 'fertilizer effect' in the soil by increasing nitrogen availability, little is known of how a specific fumigant such as 1,3-D affects available nitrogen. This study used real-time quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing techniques to investigate the effects of 1,3-D on microorganisms involved in nitrogen cycling that were present in 2 soils: Jiangxi lateritic red soil and Beijing fluvo-aquic soil. The fumigant 1,3-D temporarily decreased the abundance of 11 functional genes involved in nitrogen-fixing, nitrification and denitrification in both soil types. Different nitrogen cycling groups recovered to the unfumigated level in various incubation phases. Microorganisms containing nifH, nxrB, napA and qnorB genes were most vulnerable to 1,3-D fumigation. However, a stronger and longer inhibition effect of 1,3-D on these 11 functional genes was observed in Jiangxi soil than in Beijing soil. At the same time, the abundance of nifH, AOBamoA, nirS, qnorB and cnorB genes was significantly increased 59 days after 1,3-D fumigation. Fumigation with 1,3-D significantly reduced the nitrogen-fixing bacteria Azospirillum and Paenibacillus; the nitrifiers Nitrosomonas and Nitrospira; and the denitrifiers Pseudomonas, Paracoccus and Sphingomonas. Conversely, fumigation with 1,3-D increased the nitrogen-fixing bacteria Bradyrhizobium and Rhizobium; the nitrification bacteria Nitrosospira and Nitrolancea; and the denitrification bacteria Sphingobium, Alcanivorax, Bacillus, Streptomyces and Aeromonas. Fumigation with 1,3-D therefore caused significant shifts in the species composition and number of microbes directly involved in nitrogen cycling in the short-term. These results contribute toward a better understanding of the impact of 1,3-D fumigation on various types of soil nitrogen-cycling groups.

Effects of the herbicide mesotrione on soil enzyme activity and microbial communities

Mesotrione (2-[4-(methylsulfonyl)-2-nithobenzoyl]-1, 3-cyclohexanedione) is a selective triketone herbicide that has been widely used in corn production for the past 15 years. However, its potential for risk to soil ecosystems is poorly documented. The present study investigated the soil enzyme activity and soil microbial community responses to a 20 days' mesotrione exposure at doses of 0.1, 1.0 and 5.0 mg/kg. On days 2, 5, 10 and 20, activities of soil β-glucosidase, urease and acid phosphatase, soil microbe abundances, soil microbial community structure and abundance of the AOA-amoA and AOB-amoA genes were measured. Results showed that activities of urease and acid phosphatase were relatively stable, with no difference found between the mesotrione-treated group and control at the end of exposure. But β-glucosidase activity was reduced in the 5.0 mg/kg mesotrione treatment. In the 1.0 and 5.0 mg/kg mesotrione-treated soil, abundance of bacteria, fungi and actinomycetes all were reduced. In the 0.1 mg/kg mesotrione-treated soil, only fungi abundance was reduced by the end of the exposure. The analysis of terminal restriction fragment length polymorphism (T-RFLP) revealed soil microbial community structure could be affected by mesotrione at all experimental doses, and microbial diversity declined slightly after mesotrione exposure. Abundance of AOA-amoA and AOB-amoA genes were reduced markedly in 1.0 and 5.0 mg/kg mesotrione-treated soil. The present study suggests that mesotrione at higher doses might induce negative impacts on soil microbes, a finding which merits additional research and which should be accounted for when application of this herbicide is considered.

Responses of Nitrogen-Cycling Microorganisms to Dazomet Fumigation

The influence of soil fumigation on microorganisms involved in transforming nitrogen remains little understood, despite the use of fumigants for many decades to control soil-borne pathogens and plant-parasitic nematodes. We used real-time PCR (quantitative polymerase chain reaction) and 16S rRNA gene amplicon sequencing techniques to monitor changes in the diversity and community structure of microorganisms associated with nitrogen transfer after the soil was fumigated with dazomet (DZ). We also examined nitrous oxide (N₂O) emissions from these microorganisms present in fumigated fluvo-aquic soil and lateritic red soil. Fumigation with DZ significantly reduced the abundance of 16S rRNA and nitrogen cycling functional genes (nifH, AOA amoA, AOB amoA, nxrB, narG, napA, nirK, nirS, cnorB, qnorB, and nosZ). At the same time, N₂O production rates increased between 9.9 and 30 times after fumigation. N₂O emissions were significantly correlated with NH 4 + , dissolved amino acids and microbial biomass nitrogen, but uncorrelated with functional gene abundance. Diversity indices showed that DZ temporarily stimulated bacterial diversity as well as caused a significant change in bacterial community composition. For example, DZ significantly decreased populations of N₂-fixing bacteria Mesorhizobium and Paenibacillus, nitrifiers Nitrosomonas, and the denitrifiers Bacillus, Pseudomonas, and Paracoccus. The soil microbial community had the ability to recover to similar population levels recorded in unfumigated soils when the inhibitory effects of DZ fumigation were no longer evident. The microbial recovery rate, however, depended on the physicochemical properties of the soil. These results provided useful information for environmental safety assessments of DZ in China, for improving our understanding of the N-cycling pathways in fumigated soils, and for determining the potential responses of different N-cycling groups after fumigation.

Toward Integrative Bacterial Monitoring of Metolachlor Toxicity in Groundwater

Common herbicides such as metolachlor (MET), and their transformation products, are frequently detected in groundwater worldwide. Little is known about the response of groundwater bacterial communities to herbicide exposure, and its potential use for ecotoxicological assessment. The response of bacterial communities exposed to different levels of MET from the Ariège alluvial aquifer (Southwest of France) was investigated in situ and in laboratory experiments. Variations in both chemistry and bacterial communities were observed in groundwater, but T-RFLP analysis did not allow to uncover a pesticide-specific effect on endogenous bacterial communities. To circumvent issues of hydrogeochemical and seasonal variations in situ, groundwater samples from two monitoring wells of the Ariège aquifer with contrasting records of pesticide contamination were exposed to different levels of MET in laboratory experiments. The standard Microtox® acute toxicity assay did not indicate toxic effects of MET, even at 5 mg L-1 (i.e., 1000-fold higher than in contaminated groundwater). Analysis of MET transformation products and compound-specific isotope analysis (CSIA) in laboratory experiments demonstrated MET biodegradation but did not correlate with MET exposure. High-throughput sequencing analysis (Illumina MiSeq) of bacterial communities based on amplicons of the 16S rRNA gene revealed that bacterial community differed mainly by groundwater origin rather than by its response to MET exposure. OTUs correlating with MET addition ranged between 0.4 to 3.6% of the total. Predictive analysis of bacterial functions impacted by pesticides using PICRUSt suggested only minor changes in bacterial functions with increasing MET exposure. Taken together, results highlight MET biodegradation in groundwater, and the potential use of bacterial communities as sensitive indicators of herbicide contamination in aquifers. Although detected effects of MET on groundwater bacterial communities were modest, this study illustrates the potential of integrating DNA- and isotopic analysis-based approaches to improve ecotoxicological assessment of pesticide-contaminated aquifers. GRAPHICAL ABSTRACTAn integrative approach was develop to investigate in situ and in laboratory experiments the response of bacterial communities exposed to different levels of MET from the Ariége alluvial aquifer (Southwest of France).

Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments

Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg^-1) and copper (Cu, 50-500 mg kg^-1) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg^-1 BDE 209 with a 100 mg kg^-1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments.

Effects of hexaconazole application on soil microbes community and nitrogen transformations in paddy soils

The ecological risks of widely used hexaconazole on soil microbes remain obscure. Thus, a 3-month-long experiment using two typical paddy soils in China (red soil and black soil) was conducted to assess the effects of hexaconazole (0.6 (T1) and 6 (T10) mgkg^-1 soil) on the overall microbial biomass, respiratory activity, bacterial abundance and community structure, and nitrogen transformations. Soil was sampled after 7, 15, 30, 60, and 90days of incubation. The half-lives of the two doses of hexaconazole varied from 122 to 135d in the black soil and from 270 to 845d in the red soil. Both dosages of hexaconazole did not affect NH⁺₄-N content, N₂-fixing bacterial populations, total bacterial diversity, and community structure, but transitorily decreased the populations of total bacteria in both soil types. In the black soil, T10 negatively affected microbial biomass carbon (MBC) and soil basal respiration (R_B), but transitorily increased NO^-₃-N concentration and ammonia-oxidizing bacteria populations, while T1 had almost no effect on most of the indicators. As for red soil, both concentrations of fungicide significantly, but transitorily, inhibited MBC and R_B, while only T10 had a relatively long stimulatory effect on NO^-₃-N concentration and ammonia-oxidizing archaea populations. This study showed that over application of hexaconazole is indeed harmful to soil microorganisms and may reduce soil quality and increase the risk of nitrogen loss in paddy soils.

Non-target effects on soil microbial parameters of the synthetic pesticide carbendazim with the biopesticides cantharidin and norcantharidin

Considering the fact that biopesticides are increasingly used to replace synthetic pesticides in pest control, it is necessary to assess their ecotoxicity and especially their non-target effects on soil microorganisms, which is largely unknown. In this study, the effects of the synthetic pesticide carbendazim and the biopesticides (cantharidin and norcantharidin) on soil microbial parameters in a silt loam soil were evaluated. By using commercial formulations at the recommended and higher rates, both cantharidin and norcantharidin induced adverse effects on soil invertase, phosphatase activities and fungal gene structure, but these changes were transient. After about two weeks, the harmful effects owing to the application of pesticides phased out and eventually became comparable with non-treated samples. The degradation of cantharidin and norcantharidin was rapid and can be completed within a few days in the soil. None of the three pesticides caused significant shifts in urease activity. This study provides a comprehensive assessment of the soil microbial toxicity of these biopesticides for reasonable and efficient usage.

Fate and ecotoxicological impact of new generation herbicides from the triketone family: An overview to assess the environmental risks

Triketones, derived chemically from a natural phytotoxin (leptospermone), are a good example of allelochemicals as lead molecules for the development of new herbicides. Targeting a new and key enzyme involved in carotenoid biosynthesis, these latest-generation herbicides (sulcotrione, mesotrione and tembotrione) were designed to be eco-friendly and commercialized fifteen-twenty years ago. The mechanisms controlling their fate in different ecological niches as well as their toxicity and impact on different organisms or ecosystems are still under investigation. This review combines an overview of the results published in the literature on β-triketones and more specifically, on the commercially-available herbicides and includes new results obtained in our interdisciplinary study aiming to understand all the processes involved (i) in their transfer from the soil to the connected aquatic compartments, (ii) in their transformation by photochemical and biological mechanisms but also to evaluate (iii) the impacts of the parent molecules and their transformation products on various target and non-target organisms (aquatic microorganisms, plants, soil microbial communities). Analysis of all the data on the fate and impact of these molecules, used pure, as formulation or in cocktails, give an overall guide for the assessment of their environmental risks.