Monitoring bioremediation of atrazine in soil microcosms using molecular tools

Bioremediation of contaminated soil and groundwater by in situ biostimulation

Bioremediation by in situ biostimulation is an attractive alternative to excavation of contaminated soil. Many in situ remediation methods have been tested with some success; however, due to highly variable results in realistic field conditions, they have not been implemented as widely as they might deserve. To ensure success, methods should be validated under site-analogous conditions before full scale use, which requires expertise and local knowledge by the implementers. The focus here is on indigenous microbial degraders and evaluation of their performance. Identifying and removing biodegradation bottlenecks for degradation of organic pollutants is essential. Limiting factors commonly include: lack of oxygen or alternative electron acceptors, low temperature, and lack of essential nutrients. Additional factors: the bioavailability of the contaminating compound, pH, distribution of the contaminant, and soil structure and moisture, and in some cases, lack of degradation potential which may be amended with bioaugmentation. Methods to remove these bottlenecks are discussed. Implementers should also be prepared to combine methods or use them in sequence. Chemical/physical means may be used to enhance biostimulation. The review also suggests tools for assessing sustainability, life cycle assessment, and risk assessment. To help entrepreneurs, decision makers, and methods developers in the future, we suggest founding a database for otherwise seldom reported unsuccessful interventions, as well as the potential for artificial intelligence (AI) to assist in site evaluation and decision-making.

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

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

Probe-based qPCR assay enables the rapid and specific detection of bacterial degrading genes for the pesticide metaldehyde in soil

Metaldehyde, a molluscicide pesticide, has been identified as a pollutant of concern due to its repeated detection in drinking water, thereby generating numerous compliance failures for water utilities. Biological degradation potential for metaldehyde is widespread in soils, occurring at different rates, but to date, no molecular methods for its assessment have been reported. Here, three genes belonging to a shared metaldehyde-degrading gene cluster present in bacteria were used as candidates for development of a quantitative PCR (qPCR) assay for assessing the metaldehyde-degrading potential in soil. Screening of gene targets, primer pairs and optimization of reaction conditions led to the development of a sensitive and specific probe-based qPCR method for quantifying the mahY metaldehyde-degrading gene from soil. The technique was tested across 8 soils with different compositions and origins. The degrading pathway was detected in 4/8 soils, in which a higher number of gene copies correlated with periods of greater metaldehyde removal. Additionally, swift elimination of the pesticide was observed in soils with an elevated initial number of mahY gene copies. The gene cluster was not detected in other soils, even though metaldehyde removal occurred, indicating that other biological degrading pathways are also important in nature. The method described here is the first one available to estimate the microbial metaldehyde degradation potential and activity in soils, and can also be used to detect degrading microorganisms in systems such as sand filters for water purification or to monitor degrading strains in engineered processes.

Characterization, genome functional analysis, and detoxification of atrazine by Arthrobacter sp. C2

Residual injury of atrazine to the succeeding crops has been frequently reported. It is necessary to find a solution for the detoxification of atrazine contaminated soil. A high-efficient bacterial strain Arthrobacter sp. C2 for atrazine degradation was isolated in this study. The genomic information of the isolate C2, and its degradation characteristics and potential application in detoxification of atrazine contaminated soil were investigated. The results indicated that the isolate C2 genome contained 4,305,216 bp nucleotides, three plasmids, and 4705 coding genes. The degradation rates of atrazine at levels of 1, 10, 100 mg/L by the isolate C2 were 0.34, 1.94, 18.64 mg/L/d, respectively. The optimum temperature and pH for the isolate C2 to degrade atrazine were 30 °C and 7.0-9.0. Based on the metabolites detected by UPLC-TOF-MS/MS and genome annotation of the isolate C2, a common metabolic pathway of atrazine was proposed as that atrazine is firstly dechlorinated into hydroxyatrazine, and subsequently to N-isopropylammelide via dealkylation, and ultimately deaminated to cyanuric acid. Introduction of the isolate C2 into soil can enhance degradation of atrazine and thus eliminate the toxic effect of this herbicide on wheat growth. Our results indicate that the strain C2 could be a potential bioresource for bioremediation of atrazine contaminated soil.

Pollution adaptive responses of root-associated microbiomes induced the promoted but different attenuation of soil residual lindane: Differences between maize and soybean

Microorganisms colonize plant-associated environments and constitute complex communities aided in key functions for nutrient acquisition, disease suppression and abiotic stress resistance. In this study, we evaluated the variation of root-associated microbiomes of two typical farmland crops, maize (Zea mays L.) and soybean (Glycine max L. Merr.) respond to organochlorine pesticide stress, taking lindane as an example. Results showed that there were promoted but different attenuation rates of residual lindane in rhizosphere soils during maize and soybean growth, and the differential is due to the comprehensive effects of plant characters and microbial activities. Organochlorine pollution did not have significant impact on the microbial diversity and populations in all rhizo-compartments, but mostly stimulated the microbial connectivity. The multistep and decreasing processes for root-associated microbiomes of both maize and soybean were spatially different and mainly dependent on the shaping roles of host plants. These results expand our understandings of the organochlorine influence on the underground ecological system in crop-dependent soils.

Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation

Atrazine is an herbicide and a pollutant of great environmental concern that is naturally biodegraded by microbial communities. Paenarthrobacter aurescens TC1 is one of the most studied degraders of this herbicide. Here, we developed a genome scale metabolic model for P. aurescens TC1, iRZ1179, to study the atrazine degradation process at organism level. Constraint based flux balance analysis and time dependent simulations were used to explore the organism’s phenotypic landscape. Simulations aimed at designing media optimized for supporting growth and enhancing degradation, by passing the need in strain design via genetic modifications. Growth and degradation simulations were carried with more than 100 compounds consumed by P. aurescens TC1. In vitro validation confirmed the predicted classification of different compounds as efficient, moderate or poor stimulators of growth. Simulations successfully captured previous reports on the use of glucose and phosphate as bio-stimulators of atrazine degradation, supported by in vitro validation. Model predictions can go beyond supplementing the medium with a single compound and can predict the growth outcomes for higher complexity combinations. Hence, the analysis demonstrates that the exhaustive power of the genome scale metabolic reconstruction allows capturing complexities that are beyond common biochemical expertise and knowledge and further support the importance of computational platforms for the educated design of complex media. The model presented here can potentially serve as a predictive tool towards achieving optimal biodegradation efficiencies and for the development of ecologically friendly solutions for pollutant degradation.

Effects of the long-term application of atrazine on soil enzyme activity and bacterial community structure in farmlands in China

Atrazine has been used on Chinese farmlands for a long time and over a wide range. The concentration of atrazine (1.86-1100 mg kg^-1) has exceeded the allowable limit in the soil (1.0 mg kg^-1), and concern is increasing about the potential harm to farmland soil. Four treatments (AT₀, AT₆, AT₁₀, AT₁₆) were established to reveal the effects of the long-term application of atrazine on soil health. The results showed a nonlinear regulation of the atrazine residue concentrations in the four treatments. The highest concentration of atrazine residue was in AT₆, at 167 mg kg^-1, and the lowest concentration of atrazine residue was in AT₁₆, at 102 mg kg^-1, but there was no significant difference between AT₁₀ and AT₁₆. The soil urease activity decreased significantly with the increase in the years of atrazine application, the saccharase and cellulase activities in the AT₆ were significantly higher than those observed in the other three treatments, the catalase activity gradually decreased with the increase in atrazine application years, and the activity in AT₆ was significantly higher than that in AT₁₆. A total of 238 genera were identified by Illumina MiSeq sequencing, and 28 dominant genera were screened. Atrazine significantly increased the relative abundance of Actinobacteria and contributed to the relative abundance of Rubrobacter, Blastococcus, Promicromonospora, Jiangella, Psychroglaciecola and Acetobacteraceae_uncultured, which exhibited significantly higher abundance in AT₁₆ than in AT₀. Although there were atrazine-degrading bacteria in the soil, and the atrazine residue decreased with the increase in application years, the concentration of the atrazine residue was still nearly 100 times higher than the allowable limit in the soil, which is a great threat to the soil health.

Atrazine Bioremediation and Its Influence on Soil Microbial Diversity by Metagenomics Analysis

Pesticide accumulation in agricultural soils is an environmental concern, often addressed through distinct bioremediation strategies. This study has tried to analyze various soil bioremediation options viz., biostimulation, bioaugmentation, and natural attenuation in terms of efficiency and the response of autochthonous microbial flora by using atrazine as a model contaminant. Soil mesocosms were established with 100 kg of soil simulating the field conditions. The soil previously exposed to the herbicide was used for the bioaugmentation strategy undertaken in this study. We have tried to analyze how the microbial community responds to a foreign compound, both in terms of taxonomic and functional capacities? To answer this, we have analyzed metagenome of the mesocosms at a time point when 90% atrazine was degraded. Bioaugmentation for bioremediation proved to be efficient with a DT90 value of 15.48 ± 0.79 days, in comparison to the natural attenuation where the DT90 value was observed to be 41.20 ± 1.95 days. Metagenomic analysis revealed the abundance of orders Erysipelotrichales, Selemonadales, Clostridiales, and Thermoanaerobacterales exclusively in SBS mesocosm. Besides Pseudomonas, bacterial genera such as Achromobacter, Xanthomonas, Stenotrophomonas, and Cupriavidus have emerged as the dominant members in various bioremediation strategies tested in this study. Inclusive results suggest that inherent microbial flora adjust their community and metabolic machinery upon exposure to the pollutant. The site under pollutant stress showed efficient microbial communities to bio-remediate the newly polluted terrestrial ecologies in relatively less time and by economic means.

Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application

The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.

Fate of atrazine and its relationship with environmental factors in distinctly different lake sediments associated with hydrophytes

Atrazine contamination is of great concern due to its widespread occurrence in shallow lakes. Here, the distribution and degradation of atrazine in acidic and alkaline lake systems were investigated. Meanwhile, the bacterial communities in different sediments and the effects of environmental factors on atrazine-degrading bacteria were evaluated. In the lake systems without plants, atrazine levels in sediment interstitial water reached peak concentrations on the 4th d. More than 90% of atrazine was then degraded in all sediment interstitial water by day 30. Meanwhile, the degradation rate of atrazine in alkaline sediments was faster than that in acidic sediments. Values of hydroxylated metabolites in the acidic lake sediments tended to be greater. Moreover, the amounts of Proteobacteria, Actinobacteria, Firmicute, Nitrospinae, Aminicenantes, Ignavibacteriae and Saccharibacteria in acidic Tangxunhu Lake sediments were significantly different from alkaline Honghu Lake sediments, while the amounts of Cyanobacteria and Saccharibacteria in sediments treated with atrazine were significantly greater than those in sediments without atrazine (P < 0.05). Notably, pH was the most relevant environmental factor in the quantitative variation of atrazine-degrading bacteria, including in Clostridium-sensu-stricto, Pseudomonas, Comamonas and Rhodobacter. The Mantel test results indicated that the degradation of atrazine in different sediments was mainly affected by the sediment physicochemical properties rather than by the addition of atrazine and the cultivation of hydrophytes.

Impact of Atrazine Exposure on the Microbial Community Structure in a Brazilian Tropical Latosol Soil

Atrazine is a triazine herbicide that is widely used to control broadleaf weeds. Its widespread use over the last 50 years has led to the potential contamination of soils, groundwater, rivers, and lakes. Its main route of complete degradation is via biological means, which is carried out by soil microbiota using a 6-step pathway. The aim of the present study was to investigate whether application of atrazine to soil changes the soil bacterial community. We used 16S rRNA gene sequencing and qPCR to elucidate the microbial community structure and assess the abundance of the atrazine degradation genes atzA, atzD, and trzN in a Brazilian soil. The results obtained showed that the relative abundance of atzA and trzN, encoding triazine-initiating metabolism in Gram-negative and -positive bacteria, respectively, increased in soil during the first weeks following the application of atrazine. In contrast, the abundance of atzD, encoding cyanuric acid amidohydrolase-the fourth step in the pathway-was not related to the atrazine treatment. Moreover, the overall soil bacterial community showed no significant changes after the application of atrazine. Despite this, we observed increases in the relative abundance of bacterial families in the 4th and 8th weeks following the atrazine treatment, which may have been related to higher copy numbers of atzA and trzN, in part due to the release of nitrogen from the herbicide. The present results revealed that while the application of atrazine may temporarily increase the quantities of the atzA and trzN genes in a Brazilian Red Latosol soil, it does not lead to significant and long-term changes in the bacterial community structure.

A Storable Mediatorless Electrochemical Biosensor for Herbicide Detection

A novel mediatorless photo-bioelectrochemical sensor operated with a biofilm of the cyanobacterium Synechocystis PCC6803 wt. for herbicide detection with long term stability (>20 days) was successfully developed and tested. Photoanodic current generation was obtained in the absence of artificial mediators. The inhibitory effect on photocurrent of three commonly used herbicides (i.e., atrazine, diuron, and paraquat) was used as a means of measuring their concentrations in aqueous solution. The injection of atrazine and diuron into the algal medium caused an immediate photocurrent drop due to the inhibition of photosynthetic electron transport. The detected concentrations were suitable for environmental analysis, as revealed by a comparison with the freshwater quality benchmarks set by the Environmental Protection Agency of the United States (US EPA). In contrast, paraquat caused an initial increase (~2 h) of the photocurrent effect of about 200%, as this compound can act as a redox mediator between the cells and the anode. A relatively long-term stability of the biosensor was demonstrated, by keeping anodes colonized with cyanobacterial biofilm in the dark at 4 °C. After 22 days of storage, the performance in terms of the photocurrent was comparable with the freshly prepared biosensor. This result was confirmed by the measurement of chlorophyll content, which demonstrated preservation of the cyanobacterial biofilm. The capacity of this biosensor to recover after a cold season or other prolonged environmental stresses could be a key advantage in field applications, such as in water bodies and agriculture. This study is a step forward in the biotechnological development and implementation of storable mediatorless electrochemical biosensors for herbicide detection.

Assembly of root-associated microbiomes of typical rice cultivars in response to lindane pollution

Organochlorine pesticides have been extensively used for many years to prevent insect diseases of rice (Oryza sativa L.), but little is known about their residual impacts on the underground micro-ecology in anaerobic environment. In this glasshouse study, we characterized the lindane effects on the assembly of root-associated microbiomes of commonly used indica, japonica and hybrid rice cultivars, and their feedback in turn, in modifying lindane anaerobic dissipation during 60 days' rice production. The results showed that rice growth inhibited the anaerobic dissipation of lindane, but was not affected apparently by lindane at initial spiked concentration of 4.62 and 18.54 mg kg^-1 soil. Suppressed removal of lindane in rice planted treatments as compared with that in unplanted control was likely due to inhibited reductive dechlorination induced by a comprehensive effect of radial O₂ secretion of rice root and co-occurring Fe(III) reduction that consumed electron competitively in rice rhizosphere. However, the hybrid cultivar exhibited a less suppression than the conventional cultivars in high polluted soils. Bacteria was more sensitively responded to lindane pollution than fungal taxa, and Actinobacteria, Chloroflexi, Verrucomicrobia and Proteobacteria were the main different phyla between hybrid and conventional cultivars, with a more stable community structure exhibited in the hybrid rice under lindane stress. Our study highlights the assembly and variation of root-associated microbiomes in responses of lindane pollution, and suggests that hybrid rice cultivar might be most competent for cultivation in paddy fields polluted by lindane and other organochlorine pesticides, especially in the area with high residual levels.

Nitrogen-dependent induction of atrazine degradation pathway in Pseudomonas sp. strain AKN5

Soil isolate Pseudomonas sp. strain AKN5 degrades atrazine as the sole source of nitrogen. The strain showed expeditious growth on medium containing citrate as the carbon source and ammonium chloride as the nitrogen source as compared to citrate plus atrazine or cyanuric acid. Biochemical and nitrogen-source-dependent enzyme induction studies revealed that atrazine is metabolized through hydrolytic pathway and has two segments: the upper segment converts atrazine into cyanuric acid while the lower segment metabolizes cyanuric acid to CO2 and ammonia. Bioinformatics and co-transcriptional analyses suggest that atzA, atzB and atzC were transcribed as three independent transcripts while atzDEF were found to be transcribed as a single polycistronic mRNA indicating operonic arrangement. Transcriptional analysis showed inducible expression of atzA/B/C/DEF from atrazine grown cells while cyanuric acid grown cells showed significantly higher expression of atzDEF. Interestingly, growth profiles and enzyme activity measurements suggests that strain utilizes a simple nitrogen source (ammonium chloride) over the complex (atrazine or cyanuric acid) when grown on dual nitrogen source. These results suggest that atrazine degradation genes were up-regulated in the presence of atrazine but repressed in the presence of simple nitrogen source like ammonium chloride.

Microcosm study of atrazine bioremediation by indigenous microorganisms and cytotoxicity of biodegraded metabolites

Intensive use of atrazine in agriculture to increase crop productivity has resulted in pollution and consequently deteriorated the environment. Three isolated bacteria, Rhodococcus sp. BCH2 (RB), Bacillus sp. PDK1 (BP1) and Bacillus sp. PDK2 (BP2) possessing capability to degrade atrazine were used in different combinations (RB + BP1, RB + BP2, BP1 + BP2, RB + BP1 + BP2) to prepare a highly effective bacterial consortium which can significantly reduce the toxicity of atrazine. Cytotoxicity tests evaluated by MTT assay on HepG2 indicated significant decrease in the toxicity of atrazine by the consortium RB + BP1 + BP2 due to its effective degradation and formation of simpler and less/nontoxic metabolites compared to other combinations of consortia. A microcosm study was conducted to check the survivability of this consortium (RB + BP1 + BP2) in the presence of atrazine and indigenous soil microflora for four weeks. LC-Q-TOF/MS analysis revealed that RB + BP1 + BP2 could degrade atrazine to various simple metabolites in the microcosm. The cluster analysis of the DGGE patterns of the microcosm of control-soil, soil exposed to atrazine and soil augmented with consortium in the presence of atrazine (1000 mg kg^-1) revealed a shift in microbial community of soil. The microbial dynamics studies suggested that the augmented bacteria were well-thrived with natural microflora during four weeks of exposure to atrazine.

Changes in atrazine speciation and the degradation pathway in red soil during the vermiremediation process

Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is a triazine herbicide intensively used in agricultural production and is often detected in different environmental matrices at concentrations above the permitted limit. This study investigated the influence of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) on atrazine speciation and the degradation pathway. Our results revealed that both earthworms significantly accelerated atrazine degradation in a 28-day vermiremediation, and the residual atrazine declined from 4.23 ± 0.21 mg/kg in bulk soils to 0.51 ± 0.29 mg/kg (E. foetida) and 0.43 ± 0.19 mg/kg (A. robustus). By consuming organic matter (from 40.37 ± 1.14 to 36.31 ± 1.55 and 34.59 ± 1.13 g/kg for E. foetida and A. robustus) and neutralizing the soil pH (from 5.37 ± 0.27 to 6.36 ± 0.11 and 6.61 ± 0.30 for E. foetida and A. robustus), both earthworms reduced humus-fixed atrazine and increased the available atrazine. The percentage of available atrazine increased from 8.80 ± 0.21% in bulk soil to 10.30 ± 0.29% and 16.42 ± 0.18% in the vermiremediation treatments. Both earthworms promoted the hydroxyatrazine pathway by consuming soil organic matter and encouraged the deethylatrazine/deisopropylatrazine pathway by neutralizing the soil pH. Our findings unravel a new mechanism of vermiremediation by improving the soil physical-chemical properties and altering the atrazine degradation pathway, providing new insights into the influential factors on atrazine bioremediation in red soil.

Multiple spectroscopic analyses reveal the fate and metabolism of sulfamide herbicide triafamone in agricultural environments

Triafamone, a sulfamide herbicide, has been extensively utilized for weed control in rice paddies in Asia. However, its fate and transformation in the environment have not been established. Through a rice paddy microcosm-based simulation trial combined with multiple spectroscopic analyses, we isolated and identified three novel metabolites of triafamone, including hydroxyl triafamone (HTA), hydroxyl triafamone glycoside (HTAG), and oxazolidinedione triafamone (OTA). When triafamone was applied to rice paddies at a concentration of 34.2 g active ingredient/ha, this was predominantly distributed in the paddy soil and water, and then rapidly dissipated in accordance with the first-order rate model, with half-lives of 4.3-11.0 days. As the main transformation pathway, triafamone was assimilated by the rice plants and was detoxified into HTAG, whereas the rest was reduced into HTA with subsequent formation of OTA. At the senescence stage, brown rice had incurred triafamone at a concentration of 0.0016 mg/kg, but the hazard quotient was <1, suggesting that long-term consumption of the triafamone-containing brown rice is relatively safe. The findings of the present study indicate that triafamone is actively metabolized in the agricultural environment, and elucidation of the link between environmental exposure to these triazine or oxazolidinedione moieties that contain metabolites and their potential impacts is warranted.

Dissipation, occurrence and risk assessment of a phenylurea herbicide tebuthiuron in sugarcane and aquatic ecosystems in South China

In this study, a modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) method coupled with UPLC-QqQ-MS/MS analysis was developed to detect tebuthiuron in sugarcane fields and the surrounding aquatic ecosystems. Methodological validation showed the method developed was of favorable sensitivity, reproducibility and accuracy. For assessment of its dietary and ecological risks, dissipation and occurrence of tebuthiuron in situ were further investigated through a supervised field trial and an aquatic environment monitoring carried out in six dominant sugarcane production regions in South China. After application at the range of recommended dose, tebuthiuron dominantly distributed in soil, and then dissipated in accordance with the first-order rate model with the half-lives of 12.2-21.5 d. At pre-harvest intervals (PHI), occurrence of tebuthiuron was found to be 0.718-1.366 mg/kg and 0.016-0.034 mg/kg, in sugarcane and soil, respectively. The supervised trials median residue (STMR) of tebuthiuron in sugarcane was thus 0.024 mg/kg and the dietary Risk Quotient (RQ_d) was accordingly calculated as 2.34 × 10^-4, indicating safety on long-term consumption of sugarcane with tebuthiuron residues. Yet high risks of tebuthiuron towards soil ecosystems was noticed as it possessed maximum ecological Risk Quotient (RQ_e) at 1.97 to earthworms. In sugarcane field-surrounding aquatic environment, distribution of tebuthiuron was found to range from 0.007 mg/L to 0.022 mg/L, leading to high risk towards the aquatic ecosystem due to the maximum RQ_e at 440 to algae, irrespective of its low risks to invertebrate and fish. Taken together, our approach serve as an effective tool for monitoring residual tebuthiuron environmentally and also advance in-depth understanding of dietary and ecological risks posed by the phenylurea herbicide.

Bioaugmentation as a strategy for the remediation of pesticide-polluted soil: A review

Bioaugmentation, a green technology, is defined as the improvement of the degradative capacity of contaminated areas by introducing specific microorganisms, has emerged as the most advantageous method for cleaning-up soil contaminated with pesticides. The present review discusses the selection of pesticide-utilising microorganisms from various sources, their potential for the degradation of pesticides from different chemical classes in liquid media as well as soil-related case studies in a laboratory, a greenhouse and field conditions. The paper is focused on the microbial degradation of the most common pesticides that have been used for many years such as organochlorinated and organophosphorus pesticides, triazines, pyrethroids, carbamate, chloroacetamide, benzimidazole and derivatives of phenoxyacetic acid. Special attention is paid to bacterial strains from the genera Alcaligenes, Arthrobacter, Bacillus, Brucella, Burkholderia, Catellibacterium, Pichia, Pseudomonas, Rhodococcus, Serratia, Sphingomonas, Stenotrophomonas, Streptomyces and Verticillum, which have potential applications in the bioremediation of pesticide-contaminated soils using bioaugmentation technology. Since many factors strongly influence the success of bioaugmentation, selected abiotic and biotic factors such as pH, temperature, type of soil, pesticide concentration, content of water and organic matter, additional carbon and nitrogen sources, inoculum size, interactions between the introduced strains and autochthonous microorganisms as well as the survival of inoculants were presented.

Microbial changes linked to the accelerated degradation of the herbicide atrazine in a range of temperate soils

Accelerated degradation is the increased breakdown of a pesticide upon its repeated application, which has consequences for the environmental fate of pesticides. The herbicide atrazine was repeatedly applied to soils previously untreated with s-triazines for >5 years. A single application of atrazine, at an agriculturally relevant concentration, was sufficient to induce its rapid dissipation. Soils, with a range of physico-chemical properties and agricultural histories, showed similar degradation kinetics, with the half-life of atrazine decreasing from an average of 25 days after the first application to <2 days after the second. A mathematical model was developed to fit the atrazine-degrading kinetics, which incorporated the exponential growth of atrazine-degrading organisms. Despite the similar rates of degradation, the repertoire of atrazine-degrading genes varied between soils. Only a small portion of the bacterial community had the capacity for atrazine degradation. Overall, the microbial community was not significantly affected by atrazine treatment. One soil, characterised by low pH, did not exhibit accelerated degradation, and atrazine-degrading genes were not detected. Neutralisation of this soil restored accelerated degradation and the atrazine-degrading genes became detectable. This illustrates the potential for accelerated degradation to manifest when conditions become favourable. Additionally, the occurrence of accelerated degradation under agriculturally relevant concentrations supports the consideration of the phenomena in environmental risk assessments.

Effect of pesticides and metabolites on groundwater bacterial community

We assessed the effect of pesticides, especially commonly detected herbicides, on bacterial communities in groundwater. To this end, we used a combined approach with i) triazine-spiked experiments at environmentally relevant concentrations (1 and 10μg/L) in waters with contrasting contamination histories, and ii) in situ monitoring in a rural aquifer, where many additional biotic and abiotic parameters also affect the community. Microbial community was characterized by fingerprinting techniques (CE-SSCP), gene presence (atzA/B/C/D/E/F and amoA genes) and abundance (16S RNA, napA and narG genes). During triazine-spiked experiments, the bacterial community structure in reference water was modified following an exposure to atrazine (ATZ) and/or its metabolite desethylatrazine (DEA) at 1μg/L; in historically-contaminated water, the bacterial community structure was modified following an exposure to 10μg/L ATZ/DEA. Similarly, biodiversity indices and biomass in the reference water appeared affected at lower triazine concentrations than in the historically-contaminated water, though these end-points are less sensitive than the community structure. Our results thus suggest that the history of contamination induced a community tolerance to the tested triazines. ATZ and DEA were not degraded during the experiment and this was consistent with the absence of atz genes involved in their degradation in none of the tested conditions. In field monitoring, triazines that represent a historical and diffuse contamination of groundwater, participate in the microbial community structure, confirming the triazine effect observed under laboratory conditions. Other herbicides, such as chloroacetanilides that are applied today, did not appear to affect the whole community structure; they however induced a slight, but significant, increase in the abundance of nitrate-reducing bacteria. To our best knowledge, this is the first study on the microbial ecotoxicology of pesticides and their metabolites at environmentally relevant concentrations in groundwater.

Diverse Metabolic Capacities of Fungi for Bioremediation

Bioremediation refers to cost-effective and environment-friendly method for converting the toxic, recalcitrant pollutants into environmentally benign products through the action of various biological treatments. Fungi play a major role in bioremediation owing to their robust morphology and diverse metabolic capacity. The review focuses on different fungal groups from a variety of habitats with their role in bioremediation of different toxic and recalcitrant compounds; persistent organic pollutants, textile dyes, effluents from textile, bleached kraft pulp, leather tanning industries, petroleum, polyaromatic hydrocarbons, pharmaceuticals and personal care products, and pesticides. Bioremediation of toxic organics by fungi is the most sustainable and green route for cleanup of contaminated sites and we discuss the multiple modes employed by fungi for detoxification of different toxic and recalcitrant compounds including prominent fungal enzymes viz., catalases, laccases, peroxidases and cyrochrome P450 monooxygeneses. We have also discussed the recent advances in enzyme engineering and genomics and research being carried out to trace the less understood bioremediation pathways.

Draft Genome of the Arthrobacter sp. Strain Edens01

We report the draft genome sequence of Arthrobacter sp. strain Edens01, isolated from a leaf surface of a Rosa hybrid plant as part of the Howard Hughes Medical Institute-funded Student Initiated Microbial Discovery (SIMD) project. The genome has a total size of 3,639,179 bp and contig N₅₀ of 454,897 bp.

s-triazine degrading bacterial isolate Arthrobacter sp. AK-YN10, a candidate for bioaugmentation of atrazine contaminated soil

The Arthrobacter sp. strain AK-YN10 is an s-triazine pesticide degrading bacterium isolated from a sugarcane field in Central India with history of repeated atrazine use. AK-YN10 was shown to degrade 99 % of atrazine in 30 h from media supplemented with 1000 mg L(-1) of the herbicide. Draft genome sequencing revealed similarity to pAO1, TC1, and TC2 catabolic plasmids of the Arthrobacter taxon. Plasmid profiling analyses revealed the presence of four catabolic plasmids. The trzN, atzB, and atzC atrazine-degrading genes were located on a plasmid of approximately 113 kb.The flagellar operon found in the AK-YN10 draft genome suggests motility, an interesting trait for a bioremediation agent, and was homologous to that of Arthrobacter chlorophenolicus. The multiple s-triazines degradation property of this isolate makes it a good candidate for bioremediation of soils contaminated by s-triazine pesticides.

Soil mesocosm studies on atrazine bioremediation

Accumulation of pesticides in the environment causes serious issues of contamination and toxicity. Bioremediation is an ecologically sound method to manage soil pollution, but the bottleneck here, is the successful scale-up of lab-scale experiments to field applications. This study demonstrates pilot-scale bioremediation in tropical soil using atrazine as model pollutant. Mimicking field conditions, three different bioremediation strategies for atrazine degradation were explored. 100 kg soil mesocosms were set-up, with or without atrazine application history. Natural attenuation and enhanced bioremediation were tested, where augmentation with an atrazine degrading consortium demonstrated best pollutant removal. 90% atrazine degradation was observed in six days in soil previously exposed to atrazine, while soil without history of atrazine use, needed 15 days to remove the same amount of amended atrazine. The bacterial consortium comprised of 3 novel bacterial strains with different genetic atrazine degrading potential. The progress of bioremediation was monitored by measuring the levels of atrazine and its intermediate, cyanuric acid. Genes from the atrazine degradation pathway, namely, atzA, atzB, atzD, trzN and trzD were quantified in all mesocosms for 60 days. The highest abundance of all target genes was observed on the 6th day of treatment. trzD was observed in the bioaugmented mesocosms only. The bacterial community profile in all mesocosms was monitored by LH-PCR over a period of two months. Results indicate that the communities changed rapidly after inoculation, but there was no drastic change in microbial community profile after 1 month. Results indicated that efficient bioremediation of atrazine using a microbial consortium could be successfully up-scaled to pilot scale.

Influence of microbial and synthetic surfactant on the biodegradation of atrazine

The present study reports the effect of surfactants (rhamnolipids and triton X-100) on biodegradation of atrazine herbicide by strain A6, belonging to the genus Acinetobacter. The strain A6 was able to degrade nearly 80 % of the 250-ppm atrazine after 6 days of growth. The bacterium degraded atrazine by de-alkylation process. Bacterial cell surface hydrophobicity as well as atrazine solubility increased in the presence of surfactant. However, addition of surfactant to the mineral salt media reduced the rate and extent of atrazine degradation by decreasing the bioavailability of herbicide. On the contrary, addition of surfactant to atrazine-contaminated soil increased the rate and extent of biodegradation by increasing the bioavailability of herbicide. As compared to triton X-100, rhamnolipids were more efficient in enhancing microbial degradation of atrazine as a significant amount of atrazine was removed from the soil by rhamnolipids. Surfactants added for the purpose of hastening microbial degradation may have an unintended inhibitory effect on herbicide degradation depending upon contiguous condition, thus highlighting the fact that surfactant must be judiciously used in bioremediation of herbicides.

Draft genome sequence of atrazine-utilizing bacteria isolated from Indian agricultural soil

We report the draft genome sequences of two tropical bacterial isolates capable of degrading the herbicide atrazine. Alcaligenes sp. strain EGD-AK7 and Arthrobacter sp. strain AK-YN10 were isolated from Indian agricultural soil in which sugarcane is grown, with a reported history of atrazine use. EGD-AK7 has the atzABCDEF genes and AK-YN10 has the trzN and atzBC genes for atrazine degradation.

Genome Sequence of Alcaligenes sp. Strain HPC1271

We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicrobial activity against multidrug-resistant bacteria. Antibiotic production by Alcaligenes has not been frequently reported, and hence, the availability of the genome sequence should enable us to explore new antibiotic-producing gene clusters.