Microbial response to bensulfuron-methyl treatment in soil

Crystal structures of herbicide-detoxifying esterase reveal a lid loop affecting substrate binding and activity

SulE, an esterase, which detoxifies a variety of sulfonylurea herbicides through de-esterification, provides an attractive approach to remove environmental sulfonylurea herbicides and develop herbicide-tolerant crops. Here, we determined the crystal structures of SulE and an activity improved mutant P44R. Structural analysis revealed that SulE is a dimer with spacious binding pocket accommodating the large sulfonylureas substrate. Particularly, SulE contains a protruding β hairpin with a lid loop covering the active site of the other subunit of the dimer. The lid loop participates in substrate recognition and binding. P44R mutation altered the lid loop flexibility, resulting in the sulfonylurea heterocyclic ring repositioning to a relative stable conformation thus leading to dramatically increased activity. Our work provides important insights into the molecular mechanism of SulE, and establish a solid foundation for further improving the enzyme activity to various sulfonylurea herbicides through rational design.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Impact of Agrochemicals on Soil Microbiota and Management: A Review

The World Health Organization (WHO) states that in developing nations, there are three million cases of agrochemical poisoning. The prolonged intensive and indiscriminate use of agrochemicals adversely affected the soil biodiversity, agricultural sustainability, and food safety, bringing in long-term harmful effects on nutritional security, human and animal health. Most of the agrochemicals negatively affect soil microbial functions and biochemical processes. The alteration in diversity and composition of the beneficial microbial community can be unfavorable to plant growth and development either by reducing nutrient availability or by increasing disease incidence. Currently, there is a need for qualitative, innovative, and demand-driven research in soil science, especially in developing countries for facilitating of high-quality eco-friendly research by creating a conducive and trustworthy work atmosphere, thereby rewarding productivity and merits. Hence, we reviewed (1) the impact of various agrochemicals on the soil microbial diversity and environment; (2) the importance of smallholder farmers for sustainable crop protection and enhancement solutions, and (3) management strategies that serve the scientific community, policymakers, and land managers in integrating soil enhancement and sustainability practices in smallholder farming households. The current review provides an improved understanding of agricultural soil management for food and nutritional security.

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.

The mechanism of bensulfuron-methyl complexation with β-cyclodextrin and 2-hydroxypropyl-β-cyclodextrin and effect on soil adsorption and bio-activity

In this work, the inclusion complexes of hydrophobic herbicide bensulfuron-methyl (BSM) with β-cyclodextrin (β-CD) and (2-hydroxypropyl)-β-CD (2-HP-β-CD) were prepared and characterized. Phase solubility study showed that both β-CD and 2-HP-β-CD increased the solubility of BSM. Three-dimensional structures of the inclusion complexes were simulated by the molecular docking method. The docking results indicated that guest BSM could enter into the cavities of host CDs, folded, and centrally aligned inside the inclusion complexes. The benzene ring of the guest molecule was close to the wide rim of the host molecules; the pyrimidine ring and side chains of the guest molecule were oriented toward the narrow rim of the host molecule. The inclusion complexes were successfully prepared by the coprecipitation method. The physiochemical characterization data of 1H NMR, FT-IR, XRD, and DSC showed that the guest and host molecules were well included. BSM had lower soil adsorption and higher herbicidal activity in the complexation form with β-CD or 2-HP-β-CD than in the pure form. The present study provides an approach to develop a novel CDs-based formulation for hydrophobic herbicides.

Influence of Herbicide Triasulfuron on Soil Microbial Community in an Unamended Soil and a Soil Amended with Organic Residues

The effect of organic amendments and pesticides on a soil microbial community has garnered considerable interest due to the involvement of microorganisms in numerous soil conservation and maintenance reactions. The aim of this work was to assess the influence on a soil microbial community of the simultaneous application of the herbicide triasulfuron at three doses (2, 10, and 50 mg kg-1), with an organic amendment [sewage sludge (SS) or green compost (GC)]. Dissipation kinetics, soil microbial biomass, dehydrogenase activity (DHA) and respiration, and the profile of phospholipid fatty acids (PLFAs) extracted from the soil, were determined in unamended (S) soil and amended (S+SS and S+GC) ones. Triasulfuron dissipation followed the single first-order kinetics model. Half-life (DT50) values were higher in the amended soils than in the unamended one for the 10 and 50 mg kg-1 doses. The dissipation rates were lower in the S+GC soil for the three herbicide doses applied. In general, soil biomass, DHA and respiration values increased in SS- and GC-amended soils compared to the unamended one. DHA values decreased (S and S+SS) or increased (S+GC) with the incubation time of soil with herbicide at the different doses applied. Respiration values increased with the herbicide doses applied and decreased with the incubation time, although maximum values were obtained for soils treated with the highest dose after 70 days of incubation. PLFA analysis indicated different effects of triasulfuron on the soil microbial community structure depending on the organic amendments. While the increasing triasulfuron doses resulted in deeper alterations in the S soil, the time after triasulfuron application was the most important variation in the S+SS and S+GC soils. The overall results indicate that the soil amendment has an effect on herbicide dissipation rate and the soil microbial community. Initially, a high dose of triasulfuron had detrimental effects on the soil microbial community, which is important in the case of the long-term use of this compound.

Soil microbial community toxic response to atrazine and its residues under atrazine and lead contamination

Intensive use of atrazine and extensive dispersal of lead (Pb) have occurred in farmland with chemical agriculture development. However, the toxicological effect of their presence on soil microorganism remains unknown. The objective of this study was to investigate the impacts of atrazine or Pb on the soil microbiota, soil net nitrogen mineralization, and atrazine residues over a 28-day microcosm incubation. The Shannon-Wiener diversity index, typical microbe species, and a Neighbor-joining tree of typical species from sequencing denaturing gradient gel electrophoresis (DGGE) bands were determined across periodical sampling times. The results showed that the existence of atrazine or Pb (especially high concentration) in soils reduced microbial diversity (the lowest H value is 2.23) compared to the control (H = 2.59) after a 28-day incubation. The species richness reduced little (from 17~19 species to 16~17 species) over the research time. But soil microbial community was significantly affected by the incubation time after the exposure to atrazine or Pb. The combination of atrazine and Pb had a significant inhibition effect on soil net nitrogen nitrification. Atrazine and Pb significantly stimulated soil cumulative net nitrogen mineralization and nitrification. Pb (300 and 600 mg kg(-1)) accelerated the level of atrazine dissipation. The exposure might stimulate the significant growth of the autochthonous soil degraders which may use atrazine as C source and accelerate the dissipation of atrazine in soils.

The combined effects of atrazine and lead (Pb): relative microbial activities and herbicide dissipation

The experiment was conducted to investigate the effects of single and combined pollution from different concentrations of atrazine (field rate, FR, 2.0 mg kg(-1) and 5 times FR, 10 mg kg(-1)) and lead (Pb) (300 mg kg(-1) and 600 mg kg(-1)) on enzyme activity, basal soil respiration (BSR), and net nitrogen (N) mineralization (NNM) in soil after exposure for 0, 7, 14, 21, and 28 days. In addition, residual atrazine was measured in the samples of combined contamination. Results showed that the notable effects of either or both contaminants on the microbial activity and biological processes. Enzyme activity data demonstrated that the order of sensitivity to contamination was urease>invertase>catalase. BSR was strongly stimulated by atrazine/Pb at the early exposure (0-7 days for single contaminant and 7-14 days for combined contaminants). The stimulation effects on BSR were higher at low concentrations of the contamination (FR and Pb300). The combined treatments of 5FR+Pb600 inhibit BSR and NNM. Overall, the parameters associated with N cycling (urease and NNM) were more sensitive than others. Both Pb concentrations (300 and 600 mg/kg) had little influence on the dissipation of high concentrations of atrazine (5FR) during the 28-day-incubation. This study has provided useful information on potential ecotoxicology effects of combined contamination of atrazine and Pb on relative microbial biological process.

Growth inhibition of pathogenic bacteria by sulfonylurea herbicides

Emerging resistance to current antibiotics raises the need for new microbial drug targets. We show that targeting branched-chain amino acid (BCAA) biosynthesis using sulfonylurea herbicides, which inhibit the BCAA biosynthetic enzyme acetohydroxyacid synthase (AHAS), can exert bacteriostatic effects on several pathogenic bacteria, including Burkholderia pseudomallei, Pseudomonas aeruginosa, and Acinetobacter baumannii. Our results suggest that targeting biosynthetic enzymes like AHAS, which are lacking in humans, could represent a promising antimicrobial drug strategy.

Biodegradation of bensulfuron-methyl and its effect on bacterial community in paddy soils

Bensulfuron-methyl (BSM) is a new kind of sulfonylurea herbicide widely used to control broad-leaf weeds in rice paddies. The aim of this work was to study BSM biodegradation in paddy soils with BSM-degrading bacteria Bacillus megaterium L1 and Brevibacterium sp. BH and its effect on the structures of soil bacterial community. More than 90 % of BSM could be degraded in paddy soils with 0.0355 mg kg⁻¹ BSM concentration. Addition of BSM-degrading bacterial strains Bacillus megaterium L1 into BSM contaminated paddy soil could have the half-life time of BSM compared to treatment without Bacillus megaterium L1 inoculation. Denaturing gradient gel electrophoresis and principle component analysis indicated that the diversity of the soil microbial community structure changed along with the addition of BSM, which recovered at the end of the experiment (5 weeks). Addition of BSM-degrading bacteria Bacillus megaterium L1 enriched the diversity of soil microbial community structure in paddy soils. This study provides information on the biodegradation of BSM and BSM's influences on the soil bacteria microbial community structures.

Sorption behavior of bensulfuron-methyl on andisols and ultisols volcanic ash-derived soils: contribution of humic fractions and mineral-organic complexes

Bensulfuron-methyl sorption was studied in Andisol and Ultisol soils in view of their characteristic physical and chemical properties, presenting acidic pH and variable charge. Humic and fulvic acids (HA and FA) and humin (HUM) contributions were established. Sorption was studied by using two synthetic sorbents, an aluminum-silicate with iron oxide coverage and the same sorbent coated with humic acid. Freundlich model described Bensulfuron-methyl behavior in all sorbents (R(2) 0.969-0.998). K(f) for soils (8.3-20.7 microg(1-1/n) mL(1/n) g(-1)) were higher than those reported in the literature. Organic matter, halloysite or kaolinite, and specific surface area contributed to the global process. The highest K(f) for HA, FA and HUM were 539.5, 82.9, and 98.7 microg(1-1/n) mL(1/n) g(-1). Model sorbents described the participation of variable charge materials with high adsorption capacity. The constant capacitance model was used to assess effects of Bensulfuron-methyl adsorption on the distribution of SOH, SOH(2)(+) and SO(-) sites of sorbents.

Co-metabolic degradation of bensulfuron-methyl in laboratory conditions

The present study deals with the degradation of bensulfuron-methyl by microorganisms cultured with different sources of carbon, nitrogen and phosphorus. Addition of carbon source accelerated the degradation of bensulfuron-methyl under co-metabolism process. Sodium lactate was the best carbon source for the degradation of bensulfuron-methyl, compared to other carbon sources studied, and the degradation ratio of bensulfuron-methyl reached 79.5%, whereas only 34.6 and 29.7% were removed in the presence of glucose and sucrose, respectively. Supplement of nitrogen source also enhanced degradation of bensulfuron-methyl. However, no significant differences were observed in the loss of bensulfuron-methyl between organic nitrogen and inorganic source. Phosphate buffer was supplemented into the media to maintain neutral conditions for the advantage of the strain growth since increase in pH value was observed. An orthogonal array design was applied to arrange main factors singled out for investigating the influence of factor and interaction between them on the degradation of bensulfuron-methyl. Statistical analysis showed that the concentration of sodium lactate, bensulfuron-methyl and inoculum size were the main effects, and the interaction of sodium lactate and bensulfuron-methyl was of statistical significance.

Analysis of culturable and unculturable microbial community in bensulfuron-methyl contaminated paddy soils

To investigate the influence of bensulfuron-methyl (BSM) on culturable microbial quantities and unculturable microbial community structures, conventional and molecular biological methods were employed in five BSM treated soils with three replications, respectively. The results obtained with traditional culture-dependent methods showed that a low-level of BSM had slight and transient effects on culturable microorganisms; nevertheless, high concentration of BSM resulted in a dramatic decrease in bacterial colony forming units (cfus). The result obtained using denaturing gradient gel electrophoresis (DGGE) revealed that more than 17 bands were observed in low BSM contaminated soil samples and only 10 bands were detected in samples with high BSM contamination. In other words, the diversity of soil community structure is related to the concentration of BSM. Cluster analysis showed that the community structure under low level of contamination was more similar to that of the control, while heavy contaminated amendments were far away from the above group. In a sense, the cooperation of the traditional method and the molecular biological method is more powerful to study the soil microbial information in contaminated ecosystem.

Generalized models for prediction of pentachlorophenol dissipation dynamics in soils

Dissipation of pentachlorophenol (PCP) in soil was investigated and the chemical relationships with soil properties were addressed. The results indicate that the dissipation of extractable PCP residues can be described using first-order kinetics equations, with a half-dissipation time (T(1/2)) ranging from 6.5 to 173.3d. The sharply different patterns of PCP dissipation in different soils were closely related to soil properties. Correlations of stepwise regression equations obtained were significant at 0.01 probability level between soil parameters and extractable PCP residues (R(2)=0.974**) as well as T(1/2) values (R(2)=0.882**). Using pH together with organic carbon content (OC) and soil particle size distribution, the dissipation dynamics of PCP in soil could be accurately predicted.

The microbial degradation of azimsulfuron and its effect on the soil bacterial community

AIMS

Azimsulfuron is a recently introduced sulfonylurea herbicide useful in controlling weeds in paddy fields. To date very little information is available on the biodegradation of this pesticide and on its effect on the soil microbial community. The aim of this work was to study its biodegradation both in slurry soil microcosms and in batch tests with mixed and pure cultures.

METHODS AND RESULTS

Azimsulfuron was applied to forest bulk soil in order to study its effect on the structure of the bacterial soil community, as detectable by denaturant gradient gel electrophoresis (DGGE) analyses. Biodegradation and abiotic processes were investigated by HPLC analyses. In addition, a microbial consortium was selected, that was able to use azimsulfuron as the sole energy and carbon source. One of the metabolites produced by the consortium was isolated and identified through LC-MS analyses. Cultivable bacteria of the consortium were isolated and identified by 16S rDNA sequencing (1400 bp).

CONCLUSIONS

Azimsulfuron treatment seems to have the ability to cause changes in the bacterial community structure that are detectable by DGGE analyses. It is easily biodegraded both in microcosms and in batch tests, with the formation of an intermediate that was identified as 2-methyl-4-(2-methyl-2H-tetrazol-5-yl)-2H-pyrazole-3-sulfonamide.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study increases the knowledge on the biodegradation of azimsulfuron and its effects on the soil microbiota.

Accelerated degradation of N, N? (DBU) upon repeated application

In a recent study on the degradation of N,N'-dibutylurea (DBU), a breakdown product of benomyl [methyl 1-(butylcarbamoyl)-2-benzimidazole carbamate], the active ingredient in Benlate fungicides, degradation half-lives of 1.4-46.5 days were observed across several soils incubated at various combinations of soil moisture potential (-0.03 and -0.1 MPa) and temperature (23, 33, and 44 degrees C) for a single DBU application of 0.08 and 0.8 microg g(-1) (Lee et al. 2004). However, Benlate can be applied as often as every 7 days resulting in the repeated application of DBU likely to be present in the Benlate over a growing season. In this study, the effect of seven repeated DBU applications on mineralization rate was investigated in two soils, which encompass the range in rates previously observed. For the slower degrading soil, repeated DBU application increased mineralization from 0.029 to 0.99 day(-1) at the 0.08 microg g(-1) rate, and 0.037 to 0.89 day(-1) at the 0.8 microg g(-1) rate. For the faster degrading soil, effects on mineralization of repeated DBU applications were small to negligible. For the latter soil, the effect on mineralization of applied DBU concentrations from 0.0008 to 80 microg g(-1) was also investigated. Mineralization rates decreased from 0.43 to 0.019 day(-1) with increasing DBU concentrations. However, the amount of DBU mineralized by day 70 was similar across concentrations and averaged 83% of applied. Microbial respiration was not affected by increasing DBU concentrations. These findings support the supposition that DBU is readily degraded by soil microorganisms, thus unlikely to accumulate in agricultural soils.