Isolation and characterization of an atrazine-degrading bacterium from industrial wastewater in China

Mitigating risks from atrazine drift to soybeans through foliar pre-spraying with a degrading bacterium

Herbicides play a crucial role in managing weeds in agriculture, ensuring the productivity and quality of crops. However, herbicide drift poses a significant threat to sensitive plants, necessitating the consideration of ecosystem-based solutions to address this issue. In this study, foliar pre-spraying of atrazine-degrading Paenarthrobacter sp. AT5 was proposed as a new approach to mitigate the risks associated with atrazine drift on soybeans. Exposure to atrazine reduced chlorophyll levels and disturbed the antioxidant system and metabolic processes in soybean leaves, ultimately causing leaves to turn yellow. However, by pre-spraying, strain AT5 successfully colonized the surface of soybean leaves and mitigated the harmful effects of atrazine. This was achieved by slowing down atrazine absorption, expediting its reduction (half-life decreased from 2.22 d to 0.86 d), altering its degradation pathway (enhancing hydroxylation while weakening alkylation), and enhancing the interaction within phyllosphere bacteria communities. This study introduces a new approach that is both eco-friendly and user-friendly for reducing the risks of herbicide drift to sensitive crops, hence promoting the development of mixed cropping.

Physiological and transcriptomic changes drive robust responses in Paenarthrobacter sp. AT5 to co-exposure of sulfamethoxazole and atrazine

Agricultural waterways are often contaminated with herbicide and antibiotic residues due to the widespread use of these chemicals in modern agriculture. The search for resistant bacterial strains that can adapt to and degrade these mixed contaminants is essential for effective in situ bioremediation. Herein, by integrating chemical and transcriptomic analyses, we shed light on mechanisms through which Paenarthrobacter sp. AT5, a well-known atrazine-degrading bacterial strain, can adapt to sulfamethoxazole (SMX) while degrading atrazine. When exposed to SMX and/or atrazine, strain AT5 increased the production of extracellular polymeric substances and reactive oxygen species, as well as the rate of activity of antioxidant enzymes. Atrazine and SMX, either alone or combined, increased the expression of genes involved in antioxidant responses, multidrug resistance, DNA repair, and membrane transport of lipopolysaccharides. Unlike atrazine alone, co-exposure with SMX reduced the expression of genes encoding enzymes involved in the lower part of the atrazine degradation pathway. Overall, these findings emphasize the complexity of bacterial adaptation to mixed herbicide and antibiotic residues and highlight the potential of strain AT5 in bioremediation efforts.

Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia

Biodegradation holds promise as an effective and sustainable process for the removal of synthetic chemical pollutants. Nevertheless, rational engineering of biodegradation for pollutant remediation remains an unfulfilled goal, while chemical pollution of waters and soils continues to advance. Efforts to (i) identify functional bacteria from aquatic and soil microbiomes, (ii) assemble them into biodegrading consortia, and (iii) identify maintenance and performance determinants, are challenged by large number of pollutants and the complexity in the enzymology and ecology of pollutant biodegradation. To overcome these challenges, approaches that leverage knowledge from environmental bio-chem-informatics and metabolic engineering are crucial. Here, we propose a novel high-throughput bio-chem-informatics pipeline, to link chemicals and their predicted biotransformation pathways with potential enzymes and bacterial strains. Our framework systematically selects the most promising candidates for the degradation of chemicals with unknown biotransformation pathways and associated enzymes from the vast array of aquatic and soil bacteria. We substantiated our perspective by validating the pipeline for two chemicals with known or predicted pathways and show that our predicted strains are consistent with strains known to biotransform those chemicals. Such pipelines can be integrated with metabolic network analysis built upon genome-scale models and ecological principles to rationally design fit-for-purpose bacterial communities for augmenting deficient biotransformation functions and study operational and design parameters that influence their structure and function. We believe that research in this direction can pave the way for achieving our long-term goal of enhancing pollutant biodegradation.

The Chironomid Microbiome Plays a Role in Protecting Its Host From Toxicants

Organisms are assemblages of the host and their endogenous bacteria, which are defined as microbiomes. The host and its microbiome undergo a mutual evolutionary process to adapt to changes in the environment. Chironomids (Diptera; Chironomidae), are aquatic insects that grow and survive in polluted environments; however, the mechanisms that protect them under these conditions are not fully understood. Here we present evidence that the chironomids’ microbiome enables them to survival in polluted environments. It has been demonstrated that about 40% of the microbiota that inhabit Chironomus transvaalensis egg masses and larvae has the potential to detoxify different toxicants. Metagenomic analysis of Chironomus ramosus larvae demonstrated the presence of genes in the insects’ microbiome that can help the insects to survive in hostile environments. A set of experiments demonstrated that short exposure of C. transvaalensis larvae to metals significantly changed their microbiota composition in comparison to unexposed larvae. Another experiment, that followed Koch’s postulates, demonstrated that disinfected C. transvaalensis larvae can survive toxic lead and chromium exposure when they are recolonized with bacteria that can detoxify these toxic metals. This accumulating research, points to the conclusion that the chironomid microbiome plays a role in protecting its host from toxicants.

Chironomus ramosus Larval Microbiome Composition Provides Evidence for the Presence of Detoxifying Enzymes

Chironomids (Diptera; Chironomidae) are aquatic insects that are abundant in freshwater. We aimed to study the endogenous microbiota composition of Chironomus ramosus larvae that were sampled from the Mutha River and a laboratory culture in India. Furthermore, we performed a metagenomic analysis of the larval microbiome, sampled from the Mutha River. Significant differences were found between the bacterial community composition of C. ramosus larvae that were sampled from the Mutha River and the laboratory culture. A total of 54.7% of the amplicon sequence variants (ASVs) that were identified in the larvae from the Mutha River were unique, compared to only 12.9% of unique ASVs that were identified from the laboratory-reared larvae. The four most abundant phyla across all samples were: Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes, while the nine most abundant genera were: Aeromonas, Alkanindiges, Breznakia, Cetobacterium, Chryseobacterium, Desulfovibrio, Dysgonomonas, Thiothrix, and Vibrio. Moreover, in the metagenomic analysis, we detected bacterial genes and bacterial pathways that demonstrated the ability to degrade different toxic compounds, detoxify metal, and confer resistance to antibiotics and UV radiation, amongst other functions. The results illuminate the fact that there are detoxifying enzymes in the C. ramosus larval microbiome that possibly play a role in protecting the insect in polluted environments.

Atrazine detoxification by intracellular crude enzyme extracts derived from epiphytic root bacteria associated with emergent hydrophytes

The present study demonstrated atrazine detoxification by intracellular crude enzyme extracts of Pseudomonas spp. strains ACB and TLB. Indigenous bacterial protein-based remediation techniques could be an alternative to bioaugmentation which pose multiple challenges when applied to the field. Intracellular enzymes were extracted from strains ACB and TLB and their degradation potential of 10 mg L^-1 was determined using Gas Chromatography; further, enzyme extracts were subjected to protein profiling studies. In span of 6 h, enzyme extracts of strain ACB showed maximum degradation at 30 °C and 40 °C (71%) and enzyme extracts of strain TLB showed maximum degradation at 40 °C (48%). Atrazine degradation by enzyme extracts of strain ACB showed maximum degradation at pH 7 (71%) and pH 6 (69%) in 6 h. Similarly, enzyme extracts of strain TLB showed maximal degradation at pH 6 (46%) in 6 h. The present study demonstrated, for the first time, efficient atrazine remediation by intracellular crude enzyme extracts from epiphytic root bacteria at a range of temperature and pH conditions. Protein profiling studies indicated that atrazine induced expression of CoA ester lyase and alkyl hydroperoxide reductase in the strains ACB and TLB respectively. Expressions of these proteins have never been associated with atrazine exposure.

Optimization studies on biodegradation of atrazine by Bacillus badius ABP6 strain using response surface methodology

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Atrazine is widely used herbicide that causes harmful effects to living organisms.

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A bacterial isolate Bacillus badius ABP6 strain was used in the study.

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Optimization parameters showed better influence on the Biodegradation process of atrazine.

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Response surface methodology is a promising approach for Biodegradation enhancement by optimizing process parameters.

In this study, the optimization of distinctive environmental factors such as pH, temperature, agitation-speed and atrazine-concentration on atrazine degradation by utilizing Bacillus badius ABP6 strain, has been done through response-surface-methodology (RSM). The optimum-conditions after analysis for the maximum atrazine degradation were: pH 7.05, temperature 30.4 °C, agitation-speed 145.7 rpm, and atrazine-concentration 200.9 ppm. The prescribed model was approved for high F-value (95.92), very low P-value (<0.01) and non- significant lack of fit (0.1627). It was observed that under the optimized-conditions, the R² value of regression models for all the response variables was 0.9897 and the maximum atrazine degradation i.e. 89.7 % was found. Finally for graphical representation, the validated optimum-conditions of variables and responses were simulated using three dimensional plots (3D). The confirmation of the model is successful to suggest the optimization parameters of atrazine degradation under in-situ condition by bacterial isolate employing response-surface-methodology optimization tool of Design expert software (new version 10.0.1).

Biodiversity, isolation and genome analysis of sulfamethazine-degrading bacteria using high-throughput analysis

Sulfamethazine (SM2) is one of the sulfonamide antibiotics that is frequently detected in aquatic environment. Given the complex structure of SM2 and its potential threat to the environment, it is necessary to determine the degradation behavior of high-concentration SM2. The mechanisms of community structure and diversity of activated sludge were analyzed. A novel SM2-degrading strain YL1 was isolated which can degrade SM2 with high concentration of 100 mg L^-1. Strain YL1 was identified as Paenarthrobacter ureafaciens and there was also a significant increase in the genus during acclimation. Additional SM2 metabolic mechanisms and genomic information of YL1 were analyzed for further research. The succession of the community structure also investigated the effect of SM2 on the activated sludge. This result not only advances the current understanding of microbial ecology in activated sludge, but also has practical implications for the design and operation of the environmental bioprocesses for treatment of antimicrobial-bearing waste streams.

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.

Dynamic characteristics of AHLs-secreting strain Aeromonas sp. A-L2 and its bioaugmentation during quinoline biodegradation

AIMS

In order to probe a more environmentally friendly method of pollutant treatment based on microbial bioaugmentation and quorum sensing (QS) effects.

METHODS AND RESULTS

The dynamic characteristics and QS effects of the acylated homoserine lactones (AHLs)-secreting strain Aeromonas sp. A-L2 (A-L2), which was isolated from the activated sludge system, was discussed. According to the liquid chromatography-mass spectrometry results, N-butyryl-homoserine lactone (C4-HSL) and N-hexanoyl-homoserine lactone (C6-HSL) were the major AHLs secreted by strain A-L2, and the swarming of strain Ochrobactrum sp. LC-1 (LC-1) was induced by these compounds. The extracellular polymeric substance secretion of the strain LC-1 was mainly led by C6-HSL, and the biofilm formation ability was mainly influenced by C6-HSL or C4-HSL (60 μg l^-1 ). The optimal AHLs secretion conditions of strain A-L2 were also studied. Drawing support from the AHLs-secreting strain A-L2 during quinoline degradation by strain LC-1, the degradation time was greatly shortened.

CONCLUSIONS

Hence, AHLs-secreting strain A-L2 can be useful as an AHLs continuous supplier during bioaugmentation and pollutant biodegradation.

SIGNIFICANCE AND IMPACT OF THE STUDY

The bioaugmentation process of strain A-L2 on quinoline biodegradation based on QS effects would lay a certain theoretical and practical significance for large-scale applications.

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.

Biodegradation of persistent environmental pollutants by Arthrobacter sp

Persistent environmental pollutants are a growing problem around the world. The effective control of the pollutants is of great significance for human health. Some microbes, especially Arthrobacter, can degrade pollutants into nontoxic substances in various ways. Here, we review the biological properties of Arthrobacter adapting to a variety of environmental stresses, including starvation, hypertonic and hypotonic condition, oxidative stress, heavy metal stress, and low-temperature stress. Furthermore, we categorized the Arthrobacter species that can degrade triazines, organophosphorus, alkaloids, benzene, and its derivatives. Metabolic pathways behind the various biodegradation processes are further discussed. This review will be a helpful reference for comprehensive utilization of Arthrobacter species to tackle environmental pollutants.

Development of graphene oxide/chitosan composite membrane on ceramic support for atrazine remediation by MBR process

Graphene oxide (GO)-based composite ultrafiltration (UF) membranes were prepared on macroporous ceramic support tubes following a new way. Chitosan was used as an intermediate matrix between the substrate and GO coating. It has hydroxyl and amine groups, which enhances its film forming capacity with hydrophilic GO. This led us to use them as precursors for membrane development. Process efficiency of the prepared UF membrane was assessed in terms of the removal of toxic pesticide atrazine in side-stream membrane bioreactor (MBR) processes. Response surface methodology (RSM) was used to optimize the atrazine biodegradation efficiency. Enhanced atrazine removal of > 95% was obtained in the MBR treatment at the optimized conditions. Hermia's model equations were applied to analyze the mechanism of membrane fouling in the UF-MBR system. The influencing parameters were studied in details and pneumatic backpulsing was applied to minimize fouling in the UF-MBR system by statistical analysis. Mixed liquor suspended solids (MLSS) was found to affect both atrazine biodegradation and membrane fouling; hence, its effect was thoroughly analyzed. The developed process hence proved to be highly proficient in terms of such organic pesticides removal for long-term operations.

Enhanced atrazine removal by hydrophyte-bacterium associations and in vitro screening of the isolates for their plant growth-promoting potential

Emergent hydrophytes Acorus calamus, Typha latifolia, and Phragmites karka and epiphytic root bacteria isolated from their rhizoplanes were exposed to atrazine (5 and 10 mg l^-1) individually and in plant-bacterium combination for 15 days hydroponically. It was observed that A. calamus-Pseudomonas sp. strain, the ACB combination, was best in decontamination, showing 91% and 87% removal of 5 and 10 mg l^-1 atrazine. Plant-bacterium association led to significant increase in atrazine decontamination as compared to decontamination by either plant or bacterium alone, indicating a synergistic action of the hydrophytes and isolates which led to enhanced atrazine removal. To the best of our knowledge this is the first report on the potential of plant-bacterium combinations for atrazine decontamination. The isolates showed augmented growth in the presence of plants and were able to alleviate atrazine stress in them. These isolates exhibited plant growth-promoting traits such as auxin, siderophore, Poly(3-hydroxybutyric acid)/succinogycan, ammonia, catalase production and solubilization of inorganic phosphate in vitro. The use of plant-bacterium mutualistic symbiosis for atrazine mitigation is a relatively simple, inexpensive, and clean technique and this phytoremediation-rhizoremediation combination is suggested to be tried on field to establish their potential for clean-up of contaminated sites.

Biodegradation of atrazine by the novel Citricoccus sp. strain TT3

A previously undescribed atrazine-degrading bacterial strain TT3 capable of growing with atrazine as its sole nitrogen source was isolated from soil at the wastewater outfall of a pesticide factory in China. Phenotypic characterization and 16S rRNA gene sequencing indicated that the isolate belonged to the genus Citricoccus. Polymerase chain reaction (PCR) analysis revealed that TT3 contained the atrazine-degrading genes trzN, atzB, and atzC. The range for growth and atrazine degradation of TT3 was found to be pH 6.0-11.0, with a preference for alkaline conditions. At 30°C and pH 7.0, the strain removed 50mg/L atrazine in 66h with 1% inoculum. These results demonstrate that Citricoccus sp. TT3 has great potential for bioremediation of atrazine-contaminated sites, particularly in alkaline environments. To the best of our knowledge, there are no previous reports of Citricoccus strains that degrade atrazine, and therefore this work provides a novel candidate for atrazine bioremediation.

Assessment of bacterial biodetoxification of herbicide atrazine using Aliivibrio fischeri cytotoxicity assay with prolonged contact time

In our study, we determined and compared the atrazine-biodetoxification ability of 41 bacterial strains and 21 consortia created of those with over 50% degradation rate in pure cultures. Biodegradation capacity was measured with GC-MS. Detoxification was assessed based on the cytotoxic effect of end-products to Aliivibrio fischeri in chronic bioluminescence inhibition assay with 25 h contact time. Chronic A. fischeri assay adapted to a microplate, which is suitable for examine numerous residues simultaneously, also appeared to be significantly more sensitive to atrazine compared to the standard acute (30 min) test. Due to its sensitivity, the chronic assay could be a valuable tool to provide a more comprehensive view of the ecological risks of atrazine and other chemicals. Thirteen strains were able to degrade more than 50% of 50 ppm atrazine. Four of these belong to Rhodococcus aetherivorans, R. qingshengii, Serratia fonticola and Olivibacter oleidegradans which species' atrazine degrading ability has never been reported before. Four consortia degrading ability was more effective than that of the creating individual strains; moreover, their residues did not show cytotoxic effects to A. fischeri. However, in several cases, the degradation products of sole strains and consortia resulted in significant bioluminescence inhibition. Thus high biodegradation (>90%) does not certainly mean the reduction or cessation of toxicity highlighting the importance of the evaluation of biological effects of degradation residues to improve the efficiency and abate the ecological risks of bioremediation techniques.

Strengthen effects of dominant strains on aerobic digestion and stabilization of the residual sludge

In order to strengthen the aerobic digestion of residual sludge, shorten the time of sludge stabilization and further reduce operating costs, 3 dominant strains identified as Pseudomonas sp. L3, Acinetobacter sp. L16 and Bacillus sp. L19 were isolated from long-term aerobic digestion sludge. Results showed that the sludge stabilization time were reduced by 3-4days compared with the control when the dominant strains were added to the process of sludge aerobic digestion. The addition of dominant strains accelerated the accumulation of TOC, nitrate nitrogen and ammonia nitrogen in the digestive solution at different levels, and it was beneficial to the dissolution of phosphorus. Controlling DO 3-5mg/L, pH 6.5, the strains of Pseudomonas sp. L3 and Bacillus sp. L19 were combined dosing with the dosage of 2% in the process of sludge aerobic digestion, compared with the control, digestion rates of TOC and MLSS were increased about 19% and 16%, respectively.

Pseudomonas sp. ZXY-1, a newly isolated and highly efficient atrazine-degrading bacterium, and optimization of biodegradation using response surface methodology

Atrazine, a widely used herbicide, is increasing the agricultural production effectively, while also causing great environmental concern. Efficient atrazine-degrading bacterium is necessary to removal atrazine rapidly to keep a safe environment. In the present study, a new atrazine-degrading strain ZXY-1, identified as Pseudomonas, was isolated. This new isolated strain has a strong ability to biodegrade atrazine with a high efficiency of 9.09mg/L/hr. Temperature, pH, inoculum size and initial atrazine concentration were examined to further optimize the degradation of atrazine, and the synthetic effect of these factors were investigated by the response surface methodology. With a high quadratic polynomial mathematical model (R²=0.9821) being obtained, the highest biodegradation efficiency of 19.03mg/L/hr was reached compared to previous reports under the optimal conditions (30.71°C, pH7.14, 4.23% (V/V) inoculum size and 157.1mg/L initial atrazine concentration). Overall, this study provided an efficient bacterium and approach that could be potentially useful for the bioremediation of wastewater containing atrazine.

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.

Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China

Background

Soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. In the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation.

Methods

Atrazine-degrading bacteria were isolated by direct plating on a specially developed SM agar. The atrazine degradation genes trzN and atzABC were detected by multiplex PCR. The diversity of atrazine degraders was characterized by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) genotyping followed by 16S rRNA gene phylogenetic analysis. The occurrence of atrazine-degrading bacteria was also assessed by conventional PCR targeting trzN and atzABC in soil DNA.

Results

A total of 116 atrazine-degrading isolates were recovered from bulk and rhizosphere soils sampled near an atrazine factory and from geographically distant maize fields. Fifteen genotypes were distinguished among 56 industrial isolates, with 13 of them representing eight phylogenetic groups of the genus Arthrobacter. The remaining two were closely related to Pseudomonas alcaliphila and Gulosibacter molinativorax and constituted major components of the atrazine-degrading community in the most heavily contaminated industrial plantless soil. All isolates from the adjacent sites inhabited by cogon grass or common reed were various Arthrobacter spp. with a strong prevalence of A. aurescens group. Only three genotypes were distinguished among 60 agricultural strains. Genetically similar Arthrobacter ureafaciens bacteria which occurred as minor inhabitants of cogon grass roots in the industrial soil were ubiquitous and predominant atrazine degraders in the maize rhizosphere. The other two genotypes represented two distant Nocardioides spp. that were specific to their geographic origins.

Conclusions

Direct plating on SM agar enabled rapid isolation of atrazine-degrading bacteria and analysis of their natural diversity in soil. The results obtained provided evidence that contaminated soils harbored communities of genetically distinct bacteria capable of individually degrading and utilizing atrazine. The community structures of culturable atrazine degraders were habitat-specific. Bacteria belonging to the genus Arthrobacter were the predominant degraders of atrazine in the plant rhizosphere.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0868-3) contains supplementary material, which is available to authorized users.

Catalytic improvement and structural analysis of atrazine chlorohydrolase by site-saturation mutagenesis

To improve the catalytic activity of atrazine chlorohydrolase (AtzA), amino acid residues involved in substrate binding (Gln71) and catalytic efficiency (Val12, Ile393, and Leu395) were targeted to generate site-saturation mutagenesis libraries. Seventeen variants were obtained through Haematococcus pluvialis-based screening, and their specific activities were 1.2–5.2-fold higher than that of the wild type. For these variants, Gln71 tended to be substituted by hydrophobic amino acids, Ile393 and Leu395 by polar ones, especially arginine, and Val12 by alanine, respectively. Q71R and Q71M significantly decreased the Km by enlarging the substrate-entry channel and affecting N-ethyl binding. Mutations at sites 393 and 395 significantly increased the kcat/Km, probably by improving the stability of the dual β-sheet domain and the whole enzyme, owing to hydrogen bond formation. In addition, the contradictory relationship between the substrate affinity improvement by Gln71 mutation and the catalytic efficiency improvement by the dual β-sheet domain modification was discussed.

Ancient Evolution and Recent Evolution Converge for the Biodegradation of Cyanuric Acid and Related Triazines

Cyanuric acid was likely present on prebiotic Earth, may have been a component of early genetic materials, and is synthesized industrially today on a scale of more than one hundred million pounds per year in the United States. In light of this, it is not surprising that some bacteria and fungi have a metabolic pathway that sequentially hydrolyzes cyanuric acid and its metabolites to release the nitrogen atoms as ammonia to support growth. The initial reaction that opens the s-triazine ring is catalyzed by the unusual enzyme cyanuric acid hydrolase. This enzyme is in a rare protein family that consists of only cyanuric acid hydrolase (CAH) and barbiturase, with barbiturase participating in pyrimidine catabolism by some actinobacterial species. The X-ray structures of two cyanuric acid hydrolase proteins show that this family has a unique protein fold. Phylogenetic, bioinformatic, enzymological, and genetic studies are consistent with the idea that CAH has an ancient protein fold that was rare in microbial populations but is currently becoming more widespread in microbial populations in the wake of anthropogenic synthesis of cyanuric acid and other s-triazine compounds that are metabolized via a cyanuric acid intermediate. The need for the removal of cyanuric acid from swimming pools and spas, where it is used as a disinfectant stabilizer, can potentially be met using an enzyme filtration system. A stable thermophilic cyanuric acid hydrolase from Moorella thermoacetica is being tested for this purpose.

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.

Enhancement the Enzymatic Activity of Phenol-Degrading Microbes Immobilized on Agricultural Residues during the Biodegradation of Phenol in Petrochemical Wastewater

In this study, we illustrated enhanced biodegradation enzyme activity and the strains growth using the plants residues as carriers during the biodegradation of phenol in petrochemical wastewater. The three phenol-degrading strains named as A1, A2 and A3 were selected for an immobilized microorganism technique. A1, A2 and A3 were identified asPenicilliumoxalicum,Aspergillussp. andSphingobacteriumsp. using detailed morphological, biochemical and molecular characterization. The growth and degradation rate of phenol in wastewater by strains A1, A2 and A3 pre-grown in the agricultural residues (peanut shell) were higher than the free strains. Compared with the free strains,the enzyme activity of strains A1,A2 and A3, using the residues for pre-grown, increased 29.01 U/L, 30.30 U/L and 38.07 U/L, respectively. Hence, the immobilized microorganism technique is conducive to the phenol degradation.

Kinetics of aerobic and anaerobic biomineralization of atrazine in surface and subsurface agricultural soils in Ohio

The purpose of this study was to assess atrazine mineralization in surface and subsurface samples retrieved from vertical cores of agricultural soils from two farm sites in Ohio. The Defiance site (NW-Ohio) was on soybean-corn rotation and Piketon (S-Ohio) was on continuous corn cultivation. Both sites had a history of atrazine application for at least a couple of decades. The clay fraction increased at the Defiance site and the organic matter and total N content decreased with depth at both sites. Mineralization of atrazine was assessed by measurement of (14)CO2 during incubation of soil samples with [U-ring-(14)C]-atrazine. Abiotic mineralization was negligible in all soil samples. Aerobic mineralization rate constants declined and the corresponding half-lives increased with depth at the Defiance site. Anaerobic mineralization (supplemented with nitrate) was mostly below the detection at the Defiance site. In Piketon samples, the kinetic parameters of aerobic and anaerobic biomineralization of atrazine displayed considerable scatter among replicate cores and duplicate biometers. In general, this study concludes that data especially for anaerobic biomineralization of atrazine can be more variable as compared to aerobic conditions and cannot be extrapolated from one agricultural site to another.

Privileged s-triazines: structure and pharmacological applications

This review summarizes recent reports on s-triazine and its respective analogs from the medicinal chemistry angle. Due to its high reactivity and binding characteristic towards various enzymes, s-triazine has attracted attention. This is combined with facile synthesis and interesting pharmacology. The triazine class demonstrates wide biological applications - including antimicrobial, antituberculosis, anticancer, antiviral and antimalarial. In this article the library of s-triazine-based molecular designs has been collated with respective bioactivity. Compounds are further compared with other heterocyclic/nontriazine moieties to correlate the efficiency of privileged s-triazine. We hope this article may assist chemists in their drug design and discovery efforts.

Evaluation of the agronomic performance of atrazine-tolerant transgenic japonica rice parental lines for utilization in hybrid seed production

Currently, the purity of hybrid seed is a crucial limiting factor when developing hybrid japonica rice (Oryza sativa L.). To chemically control hybrid seed purity, we transferred an improved atrazine chlorohydrolase gene (atzA) from Pseudomonas ADP into hybrid japonica parental lines (two maintainers, one restorer), and Nipponbare, by using Agrobacterium-mediated transformation. We subsequently selected several transgenic lines from each genotype by using PCR, RT-PCR, and germination analysis. In the presence of the investigated atrazine concentrations, particularly 150 µM atrazine, almost all of the transgenic lines produced significantly larger seedlings, with similar or higher germination percentages, than did the respective controls. Although the seedlings of transgenic lines were taller and gained more root biomass compared to the respective control plants, their growth was nevertheless inhibited by atrazine treatment compared to that without treatment. When grown in soil containing 2 mg/kg or 5 mg/kg atrazine, the transgenic lines were taller, and had higher total chlorophyll contents than did the respective controls; moreover, three of the strongest transgenic lines completely recovered after 45 days of growth. After treatment with 2 mg/kg or 5 mg/kg of atrazine, the atrazine residue remaining in the soil was 2.9–7.0% or 0.8–8.7% respectively, for transgenic lines, and 44.0–59.2% or 28.1–30.8%, respectively, for control plants. Spraying plants at the vegetative growth stage with 0.15% atrazine effectively killed control plants, but not transgenic lines. Our results indicate that transgenic atzA rice plants show tolerance to atrazine, and may be used as parental lines in future hybrid seed production.

Isolation and characterization of atrazine mineralizing Bacillus subtilis strain HB-6

Atrazine is a widely used herbicide with great environmental concern due to its high potential to contaminate soil and waters. An atrazine-degrading bacterial strain HB-6 was isolated from industrial wastewater and the 16S rRNA gene sequencing identified HB-6 as a Bacillus subtilis. PCR assays indicated that HB-6 contained atrazine-degrading genes trzN, atzB and atzC. The strain HB-6 was capable of utilizing atrazine and cyanuric acid as a sole nitrogen source for growth and even cleaved the s-triazine ring and mineralized atrazine. The strain demonstrated a very high efficiency of atrazine biodegradation with a broad optimum pH and temperature ranges and could be enhanced by cooperating with other bacteria, suggesting its huge potential for remediation of atrazine-contaminated sites. To our knowledge, there are few Bacillus subtilis strains reported that can mineralize atrazine, therefore, the present work might provide some new insights on atrazine remediation.

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.

Nitrogen impacts on atrazine-degrading Arthrobacter strain and bacterial community structure in soil microcosms

The objective of this study was to investigate the impacts of exogenous nitrogen on a microbial community inoculated with the atrazine-degrading Arthrobacter sp. in soil amended with a high concentration of atrazine. Inoculated and uninoculated microcosms for biodegradation tests were constructed. Atrazine degradation capacity of the strain DAT1 and the strain's atrazine-metabolic potential and survival were assessed. The relative abundance of the strain DAT1 and the bacterial community structure in soils were characterized using quantitative PCR in combination with terminal restriction fragment length polymorphism. Atrazine degradation by the strain DAT1 and the strain's atrazine-metabolic potential and survival were not affected by addition of a medium level of nitrate, but these processes were inhibited by addition of a high level of nitrate. Microbial community structure changed in both inoculated and uninoculated microcosms, dependent on the level of added nitrate. Bioaugmentation with the strain DAT1 could be a very efficient biotechnology for bioremediation of soils with high concentrations of atrazine.

Monitoring bioremediation of atrazine in soil microcosms using molecular tools

Molecular tools in microbial community analysis give access to information on catabolic potential and diversity of microbes. Applied in bioremediation, they could provide a new dimension to improve pollution control. This concept has been demonstrated in the study using atrazine as model pollutant. Bioremediation of the herbicide, atrazine, was analyzed in microcosm studies by bioaugmentation, biostimulation and natural attenuation. Genes from the atrazine degrading pathway atzA/B/C/D/E/F, trzN, and trzD were monitored during the course of treatment and results demonstrated variation in atzC, trzD and trzN genes with time. Change in copy number of trzN gene under different treatment processes was demonstrated by real-time PCR. The amplified trzN gene was cloned and sequence data showed homology to genes reported in Arthrobacter and Nocardioides. Results demonstrate that specific target genes can be monitored, quantified and correlated to degradation analysis which would help in predicting the outcome of any bioremediation strategy.

Isolation and characterization of an Arthrobacter sp. strain HB-5 that transforms atrazine

A bacterial strain (HB-5) capable of utilizing atrazine as sole carbon and nitrogen source for growth was isolated from an industrial wastewater sample by enrichment culture. The isolate was identified as Arthrobacter sp. according to its phenotypic features, physiologic and biochemical characteristics, and phylogenetic analysis. The strain exhibited faster atrazine degradation rates in atrazine-containing mineral media than the well-characterized atrazine-degrading bacteria Pseudomonas sp. ADP. The broad optimum pH and temperature ranges observed for strain HB-5 indicate that it has potential for remediation of atrazine-contaminated sites. Strain HB-5 first metabolizes atrazine to yield hydroxyatrazine. Then, the bacterium metabolizes hydroxyatrazine to cyanuric acid, but could not mineralize atrazine.

Atrazine is not readily mineralised in 24 temperate soils regardless of pre-exposure to triazine herbicides

Mineralisation of atrazine in soil has been shown to depend on previous exposure of the herbicide. In this study, 24 Danish soils were collected and screened for potential to mineralise atrazine. Six soils were chosen, because they had never been exposed to atrazine, whereas 18 soils were chosen because of their history of application of atrazine or the related compound terbuthylazine. None of the 24 soils revealed a mineralisation potential of more than 4% of the added atrazine within a 60 day timeframe. In an atrazine adapted French soil, we found 60% mineralisation of atrazine in 30 days. Cattle manure was applied in order to boost the microbial activity, and a 2-3% increase in the atrazine mineralisation was found in some of the temperate soils, while in the highly adapted French soil it caused a 5% reduction.

Prevalence of the gene trzN and biogeographic patterns among atrazine-degrading bacteria isolated from 13 Colombian agricultural soils

The following study evaluated the diversity and biogeography of 83 new atrazine-degrading bacteria and the composition of their atrazine degradation genes. These strains were isolated from 13 agricultural soils and grouped according to rep-PCR genomic fingerprinting into 11 major clusters, which showed biogeographic patterns. Three clusters (54 strains) belonged to the genus Arthrobacter, seven clusters (28 strains) were similar to the genus Nocardioides and only one strain was a gram-negative from the genus Ancylobacter. PCR assays for the detection of the genes atzA, B, C, D, E, F and trzN conducted with each of the 83 strains revealed that 82 strains (all gram positive) possessed trzN, 74 of them possessed the combination of trzN, atzB and atzC, while only the gram-negative strain had atzA. A similar PCR assay for the two analogous genes, atzA and trzN, responsible for the first step of atrazine degradation, was performed with DNA extracted directly from the enrichment cultures and microcosms spiked with atrazine. In these assays, the gene trzN was detected in each culture, while atzA was detected in only six out of 13 soils. These results raise an interesting hypothesis on the evolutionary ecology of the two atrazine chlorohydrolase genes (i.e. atzA and trzN) and about the biogeography of atrazine-degrading bacteria.

Agronomic and environmental implications of enhanced s-triazine degradation

Novel catabolic pathways enabling rapid detoxification of s-triazine herbicides have been elucidated and detected at a growing number of locations. The genes responsible for s-triazine mineralization, i.e. atzABCDEF and trzNDF, occur in at least four bacterial phyla and are implicated in the development of enhanced degradation in agricultural soils from all continents except Antarctica. Enhanced degradation occurs in at least nine crops and six crop rotation systems that rely on s-triazine herbicides for weed control, and, with the exception of acidic soil conditions and s-triazine application frequency, adaptation of the microbial population is independent of soil physiochemical properties and cultural management practices. From an agronomic perspective, residual weed control could be reduced tenfold in s-triazine-adapted relative to non-adapted soils. From an environmental standpoint, the off-site loss of total s-triazine residues could be overestimated 13-fold in adapted soils if altered persistence estimates and metabolic pathways are not reflected in fate and transport models. Empirical models requiring soil pH and s-triazine use history as input parameters predict atrazine persistence more accurately than historical estimates, thereby allowing practitioners to adjust weed control strategies and model input values when warranted.

Taxonomic and functional diversity of atrazine-degrading bacterial communities enriched from agrochemical factory soil

AIMS

To characterize atrazine-degrading potential of bacterial communities enriched from agrochemical factory soil by analysing diversity and organization of catabolic genes.

METHODS AND RESULTS

The bacterial communities enriched from three different sites of varying atrazine contamination mineralized 65-80% of (14) C ring-labelled atrazine. The presence of trzN-atzBC-trzD, trzN-atzABC-trzD and trzN-atzABCDEF-trzD gene combinations was determined by PCR. In all enriched communities, trzN-atzBC genes were located on a 165-kb plasmid, while atzBC or atzC genes were located on separated plasmids. Quantitative PCR revealed that catabolic genes were present in up to 4% of the community. Restriction analysis of 16S rDNA clone libraries of the three enrichments revealed marked differences in microbial community structure and diversity. Sequencing of selected clones identified members belonging to Proteobacteria (α-, β- and γ-subclasses), the Actinobacteria, Bacteroidetes and TM7 division. Several 16S rRNA gene sequences were closely related to atrazine-degrading community members previously isolated from the same contaminated site.

CONCLUSIONS

The enriched communities represent a complex and diverse bacterial associations displaying heterogeneity of catabolic genes and their functional redundancies at the first steps of the upper and lower atrazine-catabolic pathway. The presence of catabolic genes in small proportion suggests that only a subset of the community has the capacity to catabolize atrazine.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides insights into the genetic specificity and the repertoire of catabolic genes within bacterial communities originating from soils exposed to long-term contamination by s-triazine compounds.

Genetic potential, diversity and activity of an atrazine-degrading community enriched from a herbicide factory effluent

AIMS

To characterize an atrazine-degrading bacterial community enriched from the wastewater of a herbicide factory.

METHODS AND RESULTS

The community mineralized 81.4 +/- 1.9% of [(14)C-ring]atrazine and 31.0 +/- 1.8% of [(14)C-ethyl]atrazine within 6 days of batch cultivation in mineral salts medium containing atrazine as the sole nitrogen source. Degradation activity of the community towards different chloro- and methylthio-substituted s-triazine compounds was also demonstrated. Restriction analysis of amplified 16S rDNA revealed high diversity of bacterial populations forming the community, with Pseudomonas species dominating in the clone library. Atrazine-degrading genetic potential of the community determined by PCR revealed the presence of trzN, atzB, atzC and trzD genes. The trzN, atzB and atzC genes were shown to be located on a plasmid of 322 kb. Quantitative PCR showed that relative abundances of atzB, atzC and trzD genes were approx. 100-fold lower than 16S rDNA.

CONCLUSIONS

The enriched community represents a complex bacterial association expressing substantial atrazine-mineralizing activity and a broad specificity towards a range of s-triazine compounds.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study is beginning to yield insights into the richness, genetic potential and density of functional atrazine-mineralizing community that could be a potential bioaugmentation agent for improving biotransformation processes in wastewaters bearing different s-triazine compounds.