Degradation of atrazine in soil by Streptomyces

Characterization and novel pathway of atrazine catabolism by Agrobacterium rhizogenes AT13 and its potential for environmental bioremediation

Agrobacterium rhizogenes AT13, a novel bacterial strain that was isolated from contaminated soil, could utilize atrazine as the sole nitrogen, thereby degrading it. Optimization of the degradation reaction using a Box-Behnken design resulted in 99.94% atrazine degradation at pH 8.57, with an inoculum size of 3.10 × 10⁹ CFU/mL and a concentration of 50 mg/L atrazine. Ultra-high performance liquid chromatography-electrospray ionization-high resolution mass spectrometry (UPLC-ESI-HRMS), liquid chromatography tandem mass spectrometry (LC-MS/MS) and high performance liquid chromatography (HPLC) analyses identified and quantified six reported metabolites and a novel metabolite (2-hydroxypropazine) from atrazine degradation by AT13. On the basis of these metabolites, we propose an atrazine degradation pathway that includes dichlorination, hydroxylation, deamination, dealkylation and methylation reactions. The toxicity of the degradation products was evaluated by Toxicity Estimation Software Tool (T.E.S.T). Bioaugmentation of atrazine-polluted soils/water with strain AT13 significantly improved the atrazine removal rate. Thus, AT13 has potential applications in bioremediation.

Bioaugmentation of Atrazine-Contaminated Soil With Paenarthrobacter sp. Strain AT-5 and Its Effect on the Soil Microbiome

Atrazine, a triazine herbicide, is widely used around the world. The residue of atrazine due to its application in the fore-rotating crop maize has caused phytotoxicity to the following crop sweet potato in China. Bioaugmentation of atrazine-contaminated soil with atrazine-degrading strains is considered as the most potential method to remove atrazine from soil. Nevertheless, the feasibility of bioaugmentation and its effect on soil microbiome still need investigation. In this study, Paenarthrobacter sp. AT-5, an atrazine-degrading strain, was inoculated into agricultural soils contaminated with atrazine to investigate the bioaugmentation process and the reassembly of the soil microbiome. It was found that 95.9% of 5 mg kg⁻¹ atrazine was removed from the soils when inoculated with strain AT-5 with 7 days, and the phytotoxicity of sweet potato caused by atrazine was significantly alleviated. qRT-PCR analysis revealed that the inoculated strain AT-5 survived well in the soils and maintained a relatively high abundance. The inoculation of strain AT-5 significantly affected the community structure of the soil microbiome, and the abundances of bacteria associated with atrazine degradation were improved.

Biodegradation of herbicide (atrazine) in contaminated soil using various bioprocessed materials

The concept of biostimulation i.e. enhancing the intrinsic degradation potential of a polluted matrix via the addition of amendments, nutrients, or other limiting factors has been used for a wide variety of xenobiotics. The objective of this research work was to study the degradation of atrazine (25 ppm) in soil amended with biogas slurry, mushroom spent compost, farmyard manure and sodium citrate as one of the chemical amendment. In the lab scale experiments carried out up to 21 days, atrazine in soil was extracted by column method and analyzed by HPLC. The atrazine dissipation was observed to be highest (34%) with biogas slurry. The study on synergistic effect of sodium citrate with farmyard manure showed a negative effect in initial phase, but dissipation gradually increased after 1st week (i.e. 32% degradation after 21 days). Although addition of organic manures has been an integral part of sustainable agriculture practices; the present findings give a new dimension of it's utilization for removal of persistent pesticides.

The 1.92-A structure of Streptomyces coelicolor A3(2) CYP154C1. A new monooxygenase that functionalizes macrolide ring systems

Evolutionary links between cytochrome P450 monooxygenases, a superfamily of extraordinarily divergent heme-thiolate proteins catalyzing a wide array of NADPH/NADH- and O(2)-dependent reactions, are becoming better understood because of availability of an increasing number of fully sequenced genomes. Among other reactions, P450s catalyze the site-specific oxidation of the precursors to macrolide antibiotics in the genus Streptomyces introducing regiochemical diversity into the macrolide ring system, thereby significantly increasing antibiotic activity. Developing effective uses for Streptomyces enzymes in biosynthetic processes and bioremediation requires identification and engineering of additional monooxygenases with activities toward a diverse array of small molecules. To elucidate the molecular basis for substrate specificity of oxidative enzymes toward macrolide antibiotics, the x-ray structure of CYP154C1 from Streptomyces coelicolor A3(2) was determined (Protein Data Bank code ). Relocation of certain common P450 secondary structure elements, along with a novel structural feature involving an additional beta-strand transforming the five-stranded beta-sheet into a six-stranded variant, creates an open cleft-shaped substrate-binding site between the two P450 domains. High sequence similarity to macrolide monooxygenases from other microbial species translates into catalytic activity of CYP154C1 toward both 12- and 14-membered ring macrolactones in vitro.

Influence of rhamnolipids and triton X-100 on the biodegradation of three pesticides in aqueous phase and soil slurries

The effect of surfactants on the biodegradation of trifluralin and atrazine (by Streptomyces PS1/5) and coumaphos (by degrading consortia from a contaminated cattle dip) in liquid cultures and soil slurries was tested at different concentrations of a rhamnolipid mixture (Rh-mix) and Triton X-100 (TX-100). The extent of trifluralin biodegradation in liquid culture was improved at high concentrations of both surfactants. The extent of atrazine degradation dropped in the presence of either surfactant. Coumaphos biodegradation improved slightly at Rh-mix dosages >3000 microM; however, it was readily inhibited by TX-100 at amounts above the critical micelle concentration. In soil slurries, the extent of both trifluralin and atrazine biodegradation was higher in Hagerstown A (HTA) soil than in Hagerstown B (HTB) soil and was not significantly affected by the presence of either surfactant. The onset of trifluralin biodegradation was retarded at higher concentrations of surfactants. In the absence of surfactant, up to 98% of coumaphos in both soil slurries was transformed. At increasing dosages of Rh-mix, the onset of coumaphos biodegradation was retarded, but the removal efficiency of the pesticide increased. Rh-mix and TX-100 depletion was observed during Streptomyces PS1/5 growth in liquid cultures. Rh-mix concentration also decreased during coumaphos biodegradation, whereas TX-100 concentration was not affected. These results suggest that surfactants, added for the purpose of increasing the apparent water solubility of hydrophobic organic compounds, may have unintended effects on both the rate and extent of biodegradation of the target compounds if the surfactants can also be degraded by the microorganisms in the system.

Isolation and characterisation of new Gram-negative and Gram-positive atrazine degrading bacteria from different French soils

The capacity of 12 soils to degrade atrazine was studied in laboratory incubations using radiolabelled atrazine. Eight soils showed enhanced degradation of this compound. Twenty-five bacterial strains able to degrade atrazine were isolated by an enrichment method from 10 of these soils. These soils were chosen for their wide range of physico-chemical characteristics. Their history of treatment with atrazine was also variable. The genetic diversity of atrazine degraders was determined by amplified ribosomal restriction analysis (ARDRA) of the 16S rDNA gene with three restriction endonucleases. The 25 bacterial strains were grouped into five ARDRA types. By sequencing and aligning the 16S rDNA genes, the isolates were shown to belong to the Gram-negative species Chelatobacter heintzii, Aminobacter aminovorans, Stenotrophomonas maltophilia and to the Gram-positive genus Arthrobacter crystallopoietes. These species were not described previously as being capable of atrazine degradation. Most Gram-negative bacteria could mineralise (14)C ring labelled atrazine and carried the atzA, atzB, atzC and trzD genes. Gram-positive strains could convert atrazine to cyanuric acid and carried only the atzB and atzC genes. In this study, we describe the atrazine degradation capacities and corresponding genes in bacterial species that were not known as atrazine degraders. We report for the first time the occurrence of the trzD gene in these atrazine-mineralising bacteria and we demonstrate the potential use of colony hybridisation to isolate bacteria involved in atrazine degradation.

Degradation of atrazine, metolachlor, and pendimethalin in pesticide-contaminated soils: effects of aged residues on soil respiration and plant survival

This study was conducted to determine the effects of pesticide mixtures on degradation patterns of parent compounds as well as effects on soil microbial respiration. Bioavailability of residues to sensitive plant species was also determined. Soil for this study was obtained from a pesticide-contaminated area within an agrochemical dealer site. Degradation patterns were not affected by the presence or absence of other herbicides in this study. Atrazine concentrations were significantly lower at 21 through 160 days aging time compared to day 0 concentrations. Metolachlor and pendimethalin concentrations were not significantly different over time and remained high throughout the study. Microbial respiration was suppressed in treated soils from day 21 to day 160. Soybean and canola were the most successful plant species in the germination and survival tests. Generally, with increased aging of pesticides in soil, germination time decreased. Survival time of plants increased over time for some treatments indicating possible decreased bioavailability of pesticide residues. In some cases, survival time decreased at the longer 160-day aging period, possibly indicating a change in bioavailability, perhaps as the result of formation of more bioavailable and phytotoxic metabolites. No interactive effects were noted for mixtures of pesticides compared to individually applied pesticides in terms of degradation of the parent compound or on seed germination, plant survival, or microbial respiration.

Field-scale remediation of atrazine-contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase

We performed the first field-scale atrazine remediation study in the United States using chemically killed, recombinant organisms. This field study compared biostimulation methods for enhancing atrazine degradation with a novel bioaugmentation protocol using a killed and stabilized whole-cell suspension of recombinant Escherichia coli engineered to overproduce atrazine chlorohyrolase, AtzA. AtzA dechlorinates atrazine, producing non-toxic and non-phytotoxic hydroxyatrazine. Soil contaminated by an accidental spill of atrazine (up to 29,000 p.p.m.) supported significant populations of indigenous microorganisms capable of atrazine catabolism. Laboratory experiments indicated that supplementing soil with carbon inhibited atrazine biodegradation, but inorganic phosphate stimulated atrazine biodegradation. A subsequent field-scale study consisting of nine (0.75m3) treatment plots was designed to test four treatment protocols in triplicate. Control plots contained moistened soil; biostimulation plots received 300p.p.m. phosphate; bioaugmentation plots received 0.5% (w/w) killed, recombinant E. coli cells encapsulating AtzA; and combination plots received phosphate plus the enzyme-containing cells. After 8 weeks, atrazine levels declined 52% in plots containing killed recombinant E. coli cells, and 77% in combination plots. In contrast, atrazine levels in control and biostimulation plots did not decline significantly. These data indicate that genetically engineered bacteria overexpressing catabolic genes significantly increased degradation in this soil heavily contaminated with atrazine.