Inoculation of an atrazine-degrading strain, Chelatobacter heintzii Cit1, in four different soils: effects of different inoculum densities

Tracking atrazine degradation in soil combining 14C-mineralisation assays and compound-specific isotope analysis

The quantification of pesticide dissipation in agricultural soil is challenging. In this study, we investigated atrazine biodegradation in both liquid and soil experiments bioaugmented with distinct atrazine-degrading bacterial isolates. This was achieved by combining 14C-mineralisation assays and compound-specific isotope analysis of atrazine. In liquid experiments, the three bacterial isolates mineralised over 40% of atrazine, demonstrating their potential for extensive degradation. However, the kinetics of mineralisation and degradation varied among the isolates. Carbon stable isotope fractionation was similar for Pseudomonas isolates ADPT34 and ADP2T0, but slightly higher for Chelatobacter SR27. In soil experiments, atrazine primarily degraded into atrazine-desethyl, while atrazine-hydroxy was mainly observed in experiments with SR27. Atrazine mineralisation in soil by ADPT34 and SR27 exceeded 40%, whereas ADP2T0 exhibited a mineralisation rate of 10%. In experiments with ADPT34 and SR27, atrazine 14C-residues were predominantly found in the non-extractable fraction, whereas they accumulated in the extractable fraction in the experiment with ADP2T0. Compound-specific isotope analysis (CSIA) relies on changes of stable isotope ratios and holds potential to evaluate herbicide transformation in soil. CSIA of atrazine indicated atrazine biodegradation in water and solvent extractable soil fractions and varied between 29% and 52%, depending on the bacterial isolate. Despite atrazine degradation in both soil fractions, a significant portion of atrazine residues persisted, depending on the bacterial degrader, initial cell concentration, and mineralisation and degradation rates. Overall, our approach can aid in quantifying atrazine persistence and degradation in soil, and in optimizing bioaugmentation strategies for remediating soils contaminated with persistent herbicides.

DGT method for the in situ measurement of triazines and the desorption kinetics of atrazine in soil

Triazines are frequently detected in nature water and agricultural soils worldwide. They are considered harmful to plants, animals, and the human health. In this study, diffusive gradients in thin films (DGT) method was developed for the assessment of several triazines. DGT device was used for the in situ measurement of atrazine in a pesticide factory and obtained reliable data. The atrazine concentrations measured by DGT, and solvent extraction method was in a constant ratio. The DIFS model was coupled with DGT technique to study the desorption kinetics of atrazine in four kinds of different soils. The yellow-brown soil was more inclined to adsorb atrazine than other three soils. 2_D DIFS model was used to obtain the partition coefficient for labile atrazine (K_dl), the values of the response time (T_c), and desorption/adsorption rates (k₁ and k_-1). The yellow-brown soil has a larger labile pool size, and a faster resupply speed of atrazine. The 1_D DIFS model was used to simulate the profiles of atrazine concentrations in soil solution and solid phase. The results show that the desorption of atrazine in soil was limited by kinetic limitation at short time, and was limited by the solid phase reservoir at long time.

Triazine Herbicides Risk Management Strategies on Environmental and Human Health Aspects Using In-Silico Methods

As an effective herbicide, 1, 3, 5-Triazine herbicides (S-THs) are used widely in the pesticide market. However, due to their chemical properties, S-THs severely threaten the environment and human health (e.g., human lung cytotoxicity). In this study, molecular docking, Analytic Hierarchy Process—Technique for Order Preference by Similarity to the Ideal Solution (AHP-TOPSIS), and a three-dimensional quantitative structure-active relationship (3D-QSAR) model were used to design S-TH substitutes with high herbicidal functionality, high microbial degradability, and low human lung cytotoxicity. We discovered a substitute, Derivative-5, with excellent overall performance. Furthermore, Taguchi orthogonal experiments, full factorial design of experiments, and the molecular dynamics method were used to identify three chemicals (namely, the coexistence of aspartic acid, alanine, and glycine) that could promote the degradation of S-THs in maize cropping fields. Finally, density functional theory (DFT), Estimation Programs Interface (EPI), pharmacokinetic, and toxicokinetic methods were used to further verify the high microbial degradability, favorable aquatic environment, and human health friendliness of Derivative 5. This study provided a new direction for further optimizations of novel pesticide chemicals.

Rapid biodegradation of atrazine by a novel Paenarthrobacter ureafaciens ZY and its effects on soil native microbial community dynamic

An atrazine-utilizing bacterium, designated as ZY, was isolated from agricultural soil and identified as Paenarthrobacter ureafaciens. The P. ureafaciens ZY demonstrated a significant degradation capacity of atrazine, with the degradation efficiency of 12.5 mg L^-1 h^-1 in liquid media (at pH 7, 30°C, and the atrazine level of 100 mg L^-1). The P. ureafaciens ZY contained three atrazine-degrading genes (i.e., trzN, atzB, and atzC) could metabolize atrazine to form cyanuric acid, which showed lower biotoxicity than the parent atrazine as predicted by Ecological Structure Activity Relationships model. A laboratory-scale pot experiment was performed to examine the degradation of atrazine by P. ureafaciens ZY inoculation and investigate its effects on the native microbial communities. The results exhibited that the P. ureafaciens ZY was conductive to the degradation of atrazine, increased the total soil phospholipid fatty acids at the atrazine level of 50, 70, and 100 mg kg^-1. By using high-throughput sequencing analysis, Frateuria, Dyella, Burkholderia-Caballeronia-Paraburkholderia were considered as the most important indigenous atrazine-degrading microorganisms due to their relative abundances were positively correlated with the atrazine degradation rate. In addition, P. ureafaciens ZY also increased the abundance of atrazine-degrading genus Streptomyces and Bacillus, indicating that there may be a synergic relationship between them in the process of atrazine degradation. Our work provides a new insight between inoculums and native microorganisms on the degradation of atrazine.

The efficient persistence and migration of Cupriavidus gilardii T1 contribute to the removal of MCPA in laboratory and field soils

The application of exogenous biodegradation strains in pesticide-polluted soils encounters the challenges of migration and persistence of inoculants. In this study, the degradation characteristics, vertical migration capacity, and microbial ecological risk assessment of an enhanced green fluorescent protein (EGFP)-tagged 2-Methyl-4-chlorophenoxyacetic acid (MCPA)-degrading strain Cupriavidus gilardii T1 (EGFP) were investigated in the laboratory and field soils. The optimum remediation conditions for T1 (EGFP) was characterized in soils. Meanwhile, leaching experiments showed that T1 (EGFP) migrated vertically downwards in soil and contribute to the degradation of MCPA at different depths. After inoculation with T1 (EGFP), a high expression levels of EGFP gene was observed at 28 d in the laboratory soil and at 45 d in the field soil. The degradation rates of MCPA were ≥ 60% in the laboratory soil and ≥ 48% in the field soil, indicating that T1 (EGFP) can efficiently and continuously remove MCPA in both laboratory and field conditions. In addition, the inoculation of T1 (EGFP) not only showed no significant impact on the soil microbial community structure but also can alleviate the negative effects induced by MCPA to some extent. Overall, our findings suggested that T1 (EGFP) strain is an ecologically safe resource for the in situ bioremediation of MCPA-contaminated soils.

A synergistic bacterial pool decomposes tebuthiuron in soil

This study aimed to propose an eco-compatible strategy to mitigate the possible environmental contamination caused by tebuthiuron. Therefore, we screened potential tebuthiuron-degrading microorganisms from conventional (CS) and no-till (NTS) systems producing sugarcane. Then, they were bioprospected for their ability of decomposing the target-molecule at 2.48 mmol g-1 and 4.96 mmol g-1 into CO2 via respirometry. Integrating microbiota from CS and NTS into an advantageously synergistic bacterial pool produced the highest specific-growth rate of CO2 of 89.60 mg day-1, so outstripped the other inoculum. The bacterial CN-NTS framework notably stabilized the sigmoidal Gompertz curve on microbial degradation earliest and enabled the seeds of Lactuca sativa to germinate healthiest throughout ecotoxicological bioassay for cross-validation. Our study is preliminary, but timely to provide knowledge of particular relevance to progress in the field's prominence in remediating terrestrial ecosystems where residual tebuthiuron can persist and contaminate. The analytical insights will act as an opening of solutions to develop high-throughput biotechnological strategies for environmental decontamination.

Biodegradation of chlorpyrifos by a Weissella confusa strain and evaluation of some probiotic traits

Pesticides play an important role in agriculture; however, their excessive use causes several problems such as pollution of ecosystems and risks to human health. The presence of microorganisms able to degrade these pollutants can reduce their negative effect. The objective of this study was to test the capacity of Weissella confusa Lb.Con to tolerate or to degrade the chlorpyrifos pesticide. The results showed the capacity of the strain to tolerate a concentration of 200 μg/ml of chlorpyrifos. The strain Lb.Con has a remarkable capacity to grow in glucose-free MRS medium which contains different concentrations of chlorpyrifos. HPLC analysis showed that this strain was able to remove about 25% of chlorpyrifos. The evaluation of some probiotic properties showed that the strain Lb.Con had a remarkable resistance to the gastrointestinal conditions and a good antibacterial activity towards the pathogenic bacteria. The probiotic potential was evaluated to verify the possible use of W. confusa Lb.Con to detoxify harmful chlorpyrifos contained in food.

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.

Augmentation of Atrazine biodegradation by two Bacilli immobilized on α-Fe2O3 magnetic nanoparticles

In this study, a novel immobilizing carrier with α-Fe₂O₃ magnetic nanoparticles was developed and used for immobilization of atrazine-degrading bacterial isolates of Bacillus spp. Since the free cells of microorganisms generally not succeed to degrade pollutants; thus, extra treatments are alluring to make strides biodegradation. Scanning electron microscope (SEM) images appeared that after immobilization the bacterial cells were totally retained and entirely distributed on the surface of α-Fe₂O₃ magnetic nanoparticles_. The performance of α-Fe₂O₃ immobilized cells in atrazine (ATZ) degradation was compared with the free cells, which was about 90.56% in 20 days. Experimental results exhibited that ATZ could be degraded at a broad range of physicochemical parameters viz. pH (4.0 to 9.0), temperature (20 to 45 °C), ATZ concentration (50 to 300 mg L⁻¹) and agitation speed (50 to 300 rpm), which underlines that α-Fe₂O₃ immobilized cells could tolerate a higher range of ATZ concentration as compared to free cells. This research demonstrated that α-Fe₂O₃ could be applied as a potential carrier in cell immobilization and biodegradation of ATZ herbicide with greater efficiency.

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.

Impact of dry-wet and freeze-thaw events on pesticide mineralizing populations and their activity in wetland ecosystems: A microcosm study

Riparian wetlands are proposed to mitigate diffuse pollution of surface water by pesticides in agricultural landscapes. Wetland ecosystems though are highly dynamic environments and seasonal disturbances such as freezing and drying can affect microbial population sizes in the sediment and their functionality including pesticide biodegradation, which has hardly been studied. This study examined the effect of artificially induced dry-wet or freeze-thaw events on the mineralization of the pesticides isoproturon (IPU) and 2-methoxy-4-chlorophenoxy acetic acid (MCPA) in wetland microcosms, either without or with prior enrichment of IPU/MCPA degrading populations. Without prior enrichment, mineralization of IPU and MCPA was significantly reduced after exposure to especially freeze-thaw events, as evidenced by lower mineralization rates and longer lag times compared to non-exposed microcosms. However, herbicide mineralization kinetics correlated poorly with cell numbers of herbicide mineralizers as estimated by a most probable number (MPN) approach and the number of IPU and MCPA mineralizers was unexpectedly higher in freeze-thaw and dry-wet cycle exposed setups compared to the control setups. This suggested that the observed effects of season-bound disturbances were due to other mechanisms than decay of pesticide mineralizers. In addition, in systems in which the growth of pesticide mineralizing bacteria was stimulated by amendment of IPU and MCPA, exposure to a freeze-thaw or dry-wet event only marginally affected the herbicide mineralization kinetics. Our results show that season bound environmental disturbances can affect pesticide mineralization kinetics in wetlands but that this effect can depend on the history of pesticide applications.

The potential for bioaugmentation of sand filter materials from waterworks using bacterial cultures degrading 4-chloro-2-methylphenoxyacetic acid

BACKGROUND

The herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) is found frequently in Danish groundwater in concentrations exceeding the EU threshold limit of 0.1 µg L(-1) . Groundwater is used for drinking water, and one potential remediation strategy is bioaugmentation using inoculation of sand filters at affected waterworks with degrader bacteria. Numerous bacteria degrading phenoxyacetic acid herbicide have previously been isolated, and they may be candidates for bioaugmentation processes. Designing the optimum inoculum, however, requires knowledge of the capacity for degrading realistically low herbicide concentrations and the robustness of the bacteria when inoculated into sand filter materials.

RESULTS

Testing a range of different MCPA-mineralising bacterial combinations, using a high-throughput microplate radiorespirometric mineralisation assay, highlighted three efficient cocultures for mineralising low MCPA concentrations. Cocultures demonstrating a shorter time delay before initiation of (14) C-ring-labelled MCPA mineralisation to (14) CO2 , and a more extensive mineralisation of MCPA, compared with those of single strains, were found. When inoculated into different sand filter materials, the coculture effect was diminished, but several single strains enhanced MCPA mineralisation significantly at low MCPA concentrations.

CONCLUSION

This study shows that an increase in the potential for mineralisation of low herbicide concentrations in sand filter materials can be achieved by inoculating with bacterial degrader cultures. © 2014 Society of Chemical Industry.

Optimization of parameters for anaerobic co-metabolic degradation of TBBPA

The addition of different carbon and nitrogen sources can promote tetrabromobisphenol A degradation to varying degrees under co-metabolism process. A kinetic model was developed to evaluate the degradation efficiency using different carbon and nitrogen sources. Sodium formate was found to be the best carbon source for tetrabromobisphenol A degradation. The degradation rate reached 96.2% with a half-life of 4.1d. Nitrogen supplementation can also accelerate tetrabromobisphenol A degradation. Organic nitrogen is generally better than inorganic nitrogen. A response surface methodology based on the central composite design was applied to determine the optimum conditions. It showed that concentration of sodium formate, yeast extraction, tetrabromobisphenol A, and inoculum size of microorganism were important factors, and the interaction between either of two variables played different roles. Under the optimum conditions (sodium formate 11.5mg/L, yeast extraction 2.5mg/L, TBBPA 1.1mg/L and inoculum size 3.4%), TBBPA degradation rate reached the maximum.

The gompertz function can coherently describe microbial mineralization of growth-sustaining pesticides

Mineralization of (14)C-labeled tracers is a common way of studying the environmental fate of xenobiotics, but it can be difficult to extract relevant kinetic parameters from such experiments since complex kinetic functions or several kinetic functions may be needed to adequately describe large data sets. In this study, we suggest using a two-parameter, sigmoid Gompertz function for parametrizing mineralization curves. The function was applied to a data set of 252 normalized mineralization curves that represented the potential for degradation of the herbicide MCPA in three horizons of an agricultural soil. The Gompertz function fitted most of the normalized curves, and trends in the data set could be visualized by a scatter plot of the two Gompertz parameters (rate constant and time delay). For agricultural topsoil, we also tested the effect of the MCPA concentration on the mineralization kinetics. Reduced initial concentrations lead to shortened lag-phases, probably due to reduced need for bacterial growth. The effect of substrate concentration could be predicted by simply changing the time delay of the Gompertz curves. This delay could to some extent also simulate concentration effects for 2,4-D mineralization in agricultural soil and aquifer sediment and 2,6-dichlorobenzamide mineralization in single-species, mineral medium.

Biodegradation of cypermethrin by a novel Catellibacterium sp. strain CC-5 isolated from contaminated soil

The bacterial strain CC-5, isolated from contaminated soil and identified as Catellibacterium sp. based on morphology and partial 16S rDNA gene sequence analysis, utilized cypermethrin as its sole carbon source and degraded 97% of 100 mg·L(-1) cypermethrin within 7 days. The optimal degradation conditions were determined to be 30 °C and pH 7.0. Degradation was found to follow a first-order model at initial cypermethrin concentrations below 400 mg·L(-1). Strain CC-5 suffered substrate inhibition at high cypermethrin concentrations, and the biodegradation kinetics were successfully described by the Haldane model, with a maximal specific degradation rate of 1.36 day(-1), an inhibition constant of 164.61 mg·L(-1), and a half-saturation constant of 101.12 mg·L(-1). Inoculating cypermethrin-treated soil samples with strain CC-5 resulted in a higher rate of cypermethrin removal than that in noninoculated soil, regardless of whether the soil had previously been sterilized. These results reveal that the bacterial strain may possess potential to be used in bioremediation of pyrethroid-contaminated environment.

Minimal pesticide-primed soil inoculum density to secure maximum pesticide degradation efficiency in on-farm biopurification systems

Addition of pesticide-primed soil containing adapted pesticide degrading bacteria to the biofilter matrix of on farm biopurification systems (BPS) which treat pesticide contaminated wastewater, has been recommended, in order to ensure rapid establishment of a pesticide degrading microbial community in BPS. However, uncertainties exist about the minimal soil inoculum density needed for successful bioaugmentation of BPS. Therefore, in this study, BPS microcosm experiments were initiated with different linuron primed soil inoculum densities ranging from 0.5 to 50 vol.% and the evolution of the linuron mineralization capacity in the microcosms was monitored during feeding with linuron. Successful establishment of a linuron mineralization community in the BPS microcosms was achieved with all inoculum densities including the 0.5 vol.% density with only minor differences in the time needed to acquire maximum degradation capacity. Moreover, once established, the robustness of the linuron degrading microbial community towards expected stress situations proved to be independent of the initial inoculum density. This study shows that pesticide-primed soil inoculum densities as low as 0.5 vol.% can be used for bioaugmentation of a BPS matrix and further supports the use of BPS for treatment of pesticide-contaminated wastewater at farmyards.

Influence of microorganisms and leaching on simazine attenuation in an agricultural soil

Simazine is an s-triazine herbicide world widely used for the control of broadleaf weeds. The influence of leaching and microorganisms on simazine attenuation in an agricultural soil long-term treated with this herbicide was studied. To elucidate the leaching potential of simazine in this soil, undisturbed soil columns amended with simazine were placed in a specially designed system and an artificial precipitation was simulated. To evaluate the simazine removal by soil microorganisms, three soil microcosm sets were established: i) control soil; ii) soil subjected to gamma irradiation (γ-soil) and iii) γ-soil inoculated with the simazine-degrading bacterium Pseudomonas sp. strain MHP41. The simazine-degrading microorganisms in soil were estimated using an indicator for respiration combined with MPN enumeration. The simazine removal in soil was monitored by GC-ECD and HPLC. In this agricultural soil the leaching of the applied simazine was negligible. The gamma irradiation decreased in more than one order of magnitude the cultivable heterotrophic bacteria and reduced the simazine-degrading microorganisms. Simazine was almost completely depleted (97%) in control soil by natural attenuation after 23 d, whereas in γ-soil only 70% of simazine was removed. The addition of the simazine-degrading strain MHP41 to γ-soil restored and upheld high stable simazine catabolic microorganisms as well as increased the simazine removal (87%). The results indicated that simazine is subjected to microbial degradation with negligible leaching in this agricultural soil and pointed out the crucial role of native microbiota in the herbicide removal.

Studies revealing bioremediation potential of the strain Burkholderia sp. GB-01 for abamectin contaminated soils

Burkholderia sp. GB-01 strain was used to study different factors affecting its growth for inoculum production and then evaluated for abamectin degradation in soil for optimization under various conditions. The efficiency of abamectin degradation in soil by strain GB-01 was seen to be dependent on soil pH, temperature, initial abamectin concentration, and inoculum size along with inoculation frequency. Induction studies showed that abamectin depletion was faster when degrading cells were induced by pre-exposure to abamectin. Experiments performed with varying concentrations (2-160 mg Kg(-1)) of abamectin-spiked soils showed that strain GB-01 could effectively degrade abamectin over the range of 2-40 mg Kg(-1). The doses used were higher than the recommended dose for an agricultural application of abamectin, taking in account the over-use or spill situations. A cell density of approximately 10(8) viable cells g(-1) dry weight of soil was found to be suitable for bioremediation over a temperature range of 30-35°C and soil pH 7.5-8.5. This is the first report on bacterial degradation of abamectin in soil by a Burkholderia species, and our results indicated that this bacterium may be useful for efficient removal of abamectin from contaminated soils.

Biodegradation kinetics of 2,4-D by bacterial strains isolated from soil

The aim of the study was to characterize the 2,4-dichlorophenoxyacetic acid (2,4-D) degradative potential of three bacterial strains identified by MIDI-FAME profiling as Burkholderia cepacia (DS-1), Pseudomonas sp. (DS-2) and Sphingomonas paucimobilis (DS-3) isolated from soil with herbicide treatment history. All strains were capable of using herbicide as the only source of carbon and energy when grown in mineral salt medium (MSM) containing 2,4-D (50 mg/l). Over a 10 day incubation period, 69%, 73% and 54% of the initial dose of 2,4-D were degraded by strains DS-1, DS-2 and DS-3, respectively. Analysis of 2,4-dichlorophenol (2,4-DCP) concentration, the main metabolite of 2,4-D degradation, revealed that strains DS-1 and DS-2 may also have the potential to metabolize this compound. The percentage of 2,4-DCP removal was 67% and 77% in relation to maximum values of 9.5 and 9.2 mg/l determined after 4 and 2 days for MSM+DS-1 and MSM+DS-2, respectively. The degradation kinetics of 2,4-D (50 mg/kg) in sterile soil (SS) showed different potential of tested strains to degrade 2,4-D. The times within which the initial 2,4-D concentration was reduced by 50% (DT50) were 6.3, 5.0 and 9.4 days for SS+DS-1, SS+DS-2 and SS+DS-3, respectively.

Biodegradation of beta-cypermethrin and 3-phenoxybenzoic acid by a novel Ochrobactrum lupini DG-S-01

A newly isolated bacterium DG-S-01 from activated sludge utilized beta-cypermethrin (beta-CP) and its major metabolite 3-phenoxybenzoic acid (3-PBA) as sole carbon and energy source for growth in mineral salt medium (MSM). Based on the morphology, physio-biochemical characteristics, and 16S rDNA sequence analysis, DG-S-01 was identified as Ochrobactrum lupini. DG-S-01 effectively degraded beta-CP with total inocula biomass A(590 nm) = 0.1-0.8, at 20-40 °C, pH 5-9, initial beta-CP 50-400 mg L(-1) and metabolized to yield 3-PBA leading to complete degradation. Andrews equation was used to describe the special degradation rate at different initial concentrations. Degradation rate parameters q(max), K(s) and K(i) were determined to be 1.14 d(-1), 52.06 mg L(-1) and 142.80 mg L(-1), respectively. Maximum degradation was observed at 30 °C and pH 7.0. Degradation of beta-CP was accelerated when MSM was supplemented with glucose, beef extract and yeast extract. Studies on biodegradation in liquid medium showed that over 90% of the initial dose of beta-CP (50 mg L(-1)) was degraded under the optimal conditions within 5d. Moreover, the strain also degraded beta-cyfluthrin, fenpropathrin, cyhalothrin and deltamethrin. These results reveal that DG-S-01 may possess potential to be used in bioremediation of pyrethroid-contaminated environment.

Transgenic tobacco plants expressing atzA exhibit resistance and strong ability to degrade atrazine

Atrazine chlorohydrolase (AtzA) catalyzes hydrolytic dechlorination and can be used in detoxification of atrazine, a herbicide widely employed in the control of broadleaf weeds. In this study, to investigate the potential use of transgenic tobacco plants for phytoremediation of atrazine, atzA genes from Pseudomonas sp. strain ADP and Arthrobacter strain AD1 were transferred into tobacco. Three and four transgenic lines, expressing atzA-ADP and atzA-AD1, respectively, were produced by Agrobacterium-mediated transformation. Molecular characterization including PCR, RT-PCR and Southern blot revealed that atzA was inserted into the tobacco genome and stably inherited by and expressed in the progenies. Seeds of the T(1) transgenic lines had a higher germination percentage and longer roots than the untransformed plants in the presence of 40-150 mg/l atrazine. The T(2) transgenic lines grew taller, gained more dry biomass, and had higher total chlorophyll content than the untransformed plants after growing in soil containing 1 or 2 mg/kg atrazine for 90 days. No atrazine residue remained in the soil in which the T(2) transgenic lines were grown (except 401), while, in the case of the untransformed plants, 0.91 mg (81.3%) and 1.66 mg (74.1%) of the atrazine still remained in the soil containing 1 and 2 mg/kg of atrazine, respectively, indicating that the transgenic lines could degrade atrazine effectively. The transgenic tobacco lines developed could be useful for phytoremediation of atrazine-contaminated soil and water.

Biodegradation kinetics of the benzimidazole fungicide thiophanate-methyl by bacteria isolated from loamy sand soil

Degradation of the fungicide thiophanate-methyl (TM) by Enterobacter sp. TDS-1 and Bacillus sp. TDS-2 isolated from sandy soil previously treated with TM was studied in mineral salt medium (MSM) and soil. Both strains were able to grow in MSM supplemented with TM (50 mg l(-1)) as the sole carbon source. Over a 16 days incubation period, 60 and 77% of the initial dose of TM were degraded by strains TDS-1 and TDS-2, respectively, and disappearance of TM was described by first-order kinetics. Medium supplementation with glucose markedly stimulated bacterial growth; while the final rate of TM degradation was reduced by 21 and 27% for strains TDS-1 and TDS-2, respectively as compared to medium with TM only. Moreover, this additional carbon source changed the TM degradation kinetics, which proceeded according to a zero-order model. This effect was linked to substrate competition and/or a strong decrease of medium pH. Isolates degraded TM (100 mg kg(-1)) in soil with rate constants of 0.186 and 0.210 day(-1), following first-order rate kinetics, and the time in which the initial TM concentration was reduced by 50% (DT50) in soils inoculated with strains TDS-1 and TDS-2 were 6.3 and 5.1 days, respectively. Analysis of TM degradation products in soil showed that the tested strains may have the potential to transform carbendazim (MBC) to 2-aminobenzimidazole (2-AB), and may be useful for a bioremediation of MBC-polluted soils.

Hydrocarbon degradation and plant colonization by selected bacterial strains isolated from Italian ryegrass and birdsfoot trefoil

AIMS

To assess the degradation potential and plant colonization capacity of four alkane-degrading strains (ITSI10, ITRI15, ITRH76 and BTRH79) in combination with birdsfoot trefoil and Italian ryegrass and to evaluate the diversity of indigenous alkane-degrading soil bacteria in the rhizo- and endosphere.

METHODS AND RESULTS

Contaminated soil was prepared by spiking agricultural soil with 10 g diesel fuel per kg soil. Italian ryegrass (Lolium multiflorum var. Taurus) and birdsfoot trefoil (Lotus corniculatus var. Leo) were inoculated with four alkane-degrading strains. Hydrocarbon degradation (up to 57%) was observed in all inoculated treatments of vegetated and unvegetated samples. Italian ryegrass in combination with compost and BTRH79 showed highest degradation, while birdsfoot trefoil performed best with compost and strain ITSI10. Cultivation-based as well as cultivation-independent analysis showed that both strains were competitive colonizers.

CONCLUSIONS

The combination between vegetation, inoculation with well-performing degrading bacteria and compost amendment was an efficient approach to reduce hydrocarbon contamination. Two Pantoea sp. strains, ITSI10 and BTRH79, established well in the plant environment despite the presence of a variety of other, indigenous alkane-degrading bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study suggests that the application of degrading bacterial strains, which are able to compete with the native microflora and to tightly associate with plants, are promising candidates to be used for phytoremediation applications.

Rhizosphere remediation of chlorpyrifos in mycorrhizospheric soil using ryegrass

The potential of ryegrass for rhizosphere bioremediation of chlorpyrifos in mycorrhizal soil was investigated by the green house pot culture experiments. The pot cultured soil amended at initial chlorpyrifos concentration of 10mg/kg was observed to be degraded completely within 7 days where the rest amended concentrations (25-100mg/kg) decreased rapidly under the influence of ryegrass mycorrhizosphere as the incubation progressed till 28 days. This bioremediation of chlorpyrifos in soil is attributed to the microorganisms associated with the roots in the ryegrass rhizosphere, therefore the microorganisms surviving in the rhizospheric soil spiked at highest concentration (100mg/kg) was assessed and used for isolation of chlorpyrifos degrading microorganisms. The potential degrader identified by 16s rDNA analysis using BLAST technique was Pseudomonas nitroreducens PS-2. Further, bioaugmentation for the enhanced chlorpyrifos biodegradation was performed using PS-2 as an inoculum in the experimental set up similar to the earlier. The heterotrophic bacteria and fungi were also enumerated from the inoculated and non-inoculated rhizospheric soils. In bioaugmentation experiments, the percentage dissipation of chlorpyrifos was 100% in the inoculated rhizospheric soil as compared to 76.24, 90.36 and 90.80% in the non-inoculated soil for initial concentrations of 25, 50 and 100mg/kg at the 14th, 21st and 28th day intervals respectively.

A feasibility study of immobilized and free mixed culture bioaugmentation for treating atrazine in infiltrate

A feasibility study of phosphorylated-polyvinyl alcohol immobilized and free mixed bacterial culture bioaugmentation for removing atrazine in agricultural infiltrate was conducted utilizing a sand column setup. The effects of bacterial cell loading and infiltration rate on atrazine degradation were investigated by short-term tests in which the amount of synthetic infiltrate fed through was five times of the void volume (five pore volumes) of the sand column. In addition, the loss of the inoculated atrazine-degrading cultures and the change of bacterial community were determined. Selected tests were continued for monitoring a long-term performance of the system (50 pore volumes of the sand column). The results indicated that the inoculated cells removed 42-80% of the atrazine. The infiltration rate and cell loading significantly affected the atrazine removal. In the short-term tests, the immobilized and free cells provided similar atrazine removal; however, leaching of the free cells was much greater than that of the immobilized cells. For the long-term performance, only the immobilized cells provided consistent atrazine removal efficiency throughout the test. Both immobilized and free cell systems exhibited a significant change in bacterial community structure during the atrazine degradation experiments. The infiltration rate was a significant factor for the change.

Biodegradation of the organophosphorus insecticide diazinon by Serratia sp. and Pseudomonas sp. and their use in bioremediation of contaminated soil

An enrichment culture technique was used for the isolation of bacteria responsible for biodegradation of diazinon in soil. Three bacterial strains were screened and identified by MIDI-FAME profiling as Serratia liquefaciens, Serratia marcescens and Pseudomonas sp. All isolates were able to grow in mineral salt medium (MSM) supplemented with diazinon (50 mgL(-1)) as a sole carbon source, and within 14d 80-92% of the initial dose of insecticide was degraded by the isolates and their consortium. Degradation of diazinon was accelerated when MSM was supplemented with glucose. However, this process was linked with the decrease of pH values, after glucose utilization. Studies on biodegradation in sterilized soil showed that isolates and their consortium exhibited efficient degradation of insecticide (100mg kg(-1) soil) with a rate constant of 0.032-0.085d(-1), and DT(50) for diazinon was ranged from 11.5d to 24.5d. In contrast, degradation of insecticide in non-sterilized soil, non-supplemented earlier with diazinon, was characterized by a rate constant of 0.014d(-1) and the 7-d lag phase, during which only 2% of applied dose was degraded. The results suggested a strong correlation between microbial activity and chemical processes during diazinon degradation. Moreover, isolated bacterial strains may have potential for use in bioremediation of diazinon-contaminated soils.

Atrazine degradation by stable mixed cultures enriched from agricultural soil and their characterization

AIMS

The aim of this work was to enrich stable mixed cultures from atrazine-contaminated soil. The cultures were examined for their atrazine biodegradation efficiencies in comparison with J14a, a known atrazine-degrading strain of Agrobacterium radiobacter. The cultures were also characterized to identify community structure and bacterial species present.

METHODS AND RESULTS

The cultures were enriched and then stabilized in bacterial media. The stable mixed cultures and J14a were tested in a medium containing 100 microg l(-1) of atrazine. For all cultures, atrazine was removed 33-51% within 7 days and the cell optical density increased from 0.05 to between 0.50 and 0.70. Four isolates designated ND1, ND2, ND3 and ND4 were purified from the mixed cultures and identified based on sequence analysis of the 16 S rRNA gene as Alcaligenes faecalis, Klebsiella ornithinolytica, Bacillus megaterium and Agrobacterium tumefaciens, respectively. An atrazine-degrading gene, atzA, was present in ND2 and ND4.

CONCLUSIONS

The stable mixed cultures obtained could degrade atrazine. Klebsiella ornithinolytica ND2 and Ag. tumefaciens ND4 are atrazine degraders.

SIGNIFICANCE AND IMPACT OF THE STUDY

The novel stable mixed cultures could be used for bioremediating crop fields contaminated with atrazine. This is the first report of the atzA gene in Kl. ornithinolytica.

Method for measuring substrate preferences by individual members of microbial consortia proposed for bioaugmentation

In this study we used the assimilation of isotope labeled CO(2) to measure the substrate preferences by two different bioaugmentation mixtures proposed for bioremediation of diesel oil contamination. All active microorganisms assimilate CO(2) in various carboxylation processes involved in growth. The CO(2) assimilation by the two mixtures was measured upon addition of glucose, diesel oil or specific compounds present in diesel oil (naphthalene, toluene, hexadecane, and octane). It was shown that within short term incubations with diesel oil (<5 h), one bioaugmentation mixture was superior to the other regarding the assimilation of CO(2). This observation was confirmed in a labor-intensive long term microcosm study (60 days). The applied method open various possibilities for fast pre-testing of substrate-preferences by microbial-bioaugmentation mixtures without microcosm experiments, on-site tests, and complicated chemical analysis. This study also demonstrates the possibility to obtain further information on the substrate preferences at a single cell level of phylogenetically defined microbial subgroups in bioaugmentation mixtures, based on combined analyses of microautoradiography and fluorescence in situ hybridization.

Isolation and identification of atrazine-degrading bacteria from corn field soil in Fars province of Iran

In this study several agricultural fields with a long history of atrazine application in Fars province of Iran have been explored for their potential of atrazine biodegradation. After several subculturing for a period of 300 days acclimation, leads to an enhancement of atrazine biodegradation rate. A successful enrichment culture with a high capability for atrazine degradation was obtained (88%). A combination of enrichment culture technique, in a basal salt medium containing atrazine and carbon sources under nitrogen limitation and plating on indicator atrazine agar, have permitted the isolation of bacterial consortium with high capability of using atrazine as a nitrogen source. Seven gram-negative and one gram-positive bacterial strain, which were able to use this herbicide as a sole source of nitrogen, were isolated from Darehasalouie Kavar corn field soil. Based on physiological, biochemical and nutritional characteristics, the isolated bacteria were identified as Pseudomonas alcaligenes, Acidovorax sp., Pseudomonas putida, Ralstonia eutrophus, Pseudomonas syiringe, Erwinia tracheiphila, Entrobacter agglomerans and Micrococcus varians. Therefore, the bacterial consortium in liquid culture containing carbon sources and atrazine as a sole source of nitrogen, degrade added atrazine more than 80%.

Enhancing cell survival of atrazine degrading Rhodococcus erythropolis NI86/21 cells encapsulated in alginate beads

AIMS

To develop a method to produce beads with encapsulated Rhodococcus erythropolis NI86/21 with high cell density, extended shelf life, ease of handling and good atrazine degradation capabilities in both liquid and in agricultural soil.

METHODS AND RESULTS

Our findings show that the supplementary recovery step in nutrient broth media shortly after cell encapsulation facilitates cell survival in both wet and dry beads upon extended storage at 4 degrees C. Air drying has little or no impact on encapsulated R. erythropolis cell's ability to degrade atrazine in liquid or soil. Bead storage for periods extending up to 12 months at 4 degrees C did not affect the capacity of R. erythropolis encapsulated cells to degrade atrazine in either BMN or nonsterile soil extracts. Bentonite-amended beads formulated with 1% skim milk and exposed to the supplementary growth step, outperformed all other bead formats. These beads provided adequate numbers of vigorous R. erythropolis cells in either liquid or soil media to degrade atrazine.

CONCLUSIONS

Supplementary growth in nutrient broth media immediately following cell encapsulation greatly enhances R. erythropolis cells survival in both wet and dry beads upon extended storage at 4 degrees C. Wet and dried beads have similar capacity for atrazine degradation, and their usefulness and appeal in agronomic practise will only be known after bioassay evaluation and successful demonstration at field scale using incurred residues.

SIGNIFICANCE AND IMPACT OF THE STUDY

R. erythropolis NI86/21 encapsulated cells have the potential to reduce residual atrazine in soil, thereby minimizing the likelihood of off-site transport to ground or river water and reduce the loss of crops because of phytotoxicity of residual herbicide. Owing to their ease of handling, storage and possible compatibilities with pre-existing mechanical equipment, dried bead formats are ideally suited for agricultural and remediational applications.

The Impact of Bioaugmentation on Metal Cyanide Degradation and Soil Bacteria Community Structure

Metal cyanides are significant contaminants of many soils found at the site of former industrial activity. In this study we isolated bacteria capable of degrading ferric ferrocyanide and K2Ni(CN)4. One of these bacteria a Rhodococcus spp. was subsequently used to bioaugment a minimal medium broth, spiked with K2Ni(CN)4, containing 1 g of either an uncontaminated topsoil or a former coke works site soil. Degradation of the K2Ni(CN)4 was observed in both soils, however, bioaugmentation did not significantly impact the rate or degree of K2Ni(CN)4 removal. Statistical analysis of denaturing gradient gel electrophoresis profiles showed that the topsoil bacterial community had a higher biodiversity, and its structure was not significantly affected by either K2Ni(CN)4 or bioaugmentation. In contrast, profiles from the coke works site indicated significant changes in the bacterial community in response to these additions. Moreover, in both soils although bioaugmentation did not affect rates of biodegradation the Rhodococcus spp. did become established in the communities in broths containing both top and coke works soil. We conclude that bacterial communities from contaminated soils with low biodiversity are much more readily perturbed through interventions such as contamination events or bioaugmentation treatments and discuss the implications of these findings for bioremediation studies.

Degradation of simazine by microorganisms isolated from soils of Spanish olive fields

The capability of the microbial flora isolated from an olive field soil from Andalusia to mineralize simazine has been analyzed. From this soil, a group of bacteria capable of degrading 60 mg simazine litre(-1) in less than a week has been isolated. These microorganisms showed a low capacity for degrading this herbicide to carbon dioxide. When total DNA was isolated from this group of bacteria, we were able to detect by PCR the presence of only the atzC and the trzN genes. Some components of this bacterial population have been identified by sequencing of specific fragments from bacterial 16S rDNA, including Variovorax sp, Pseudoxanthomonas mexicana Thierry et al, Acidovorax sp and Methylopila capsulata Doronina et al. These data suggest that this consortium of bacteria performs an incomplete degradation of the simazine

A microcosm study on bioremediation of p-nitrophenol-contaminated soil using Arthrobacter protophormiae RKJ100

p-Nitrophenol (PNP), a toxic nitroaromatic compound, can build up in soils due to extensive usage of nitrophenolic pesticides and hence needs to be removed. Arthrobacter protophormiae RKJ100, a PNP-degrading organism, was used in this work to study factors affecting its growth, and then evaluated for its capacity to degrade PNP in soil microcosms. Molasses (10%) treated with 0.1% potassium hexacyanoferrate was found to be a suitable and cheap carbon source for inoculum preparation. Induction studies showed that PNP depletion was quicker when cells were induced by pre-exposure to PNP. The efficiency of PNP degradation in soil by strain RKJ100 was seen to be dependent on pH, temperature, initial PNP concentration and inoculum size. Microcosm studies performed with varying concentrations (1.4-210 ppm) of PNP-spiked soils showed that strain RKJ100 could effectively degrade PNP over the range 1.4-140 ppm. A cell density of 2x10(8) colony forming units/g soil was found to be suitable for PNP degradation over a temperature range of 20-40 degrees C and at a slightly alkaline pH (7.5). Our results indicate that strain RKJ100 has potential for use in in situ bioremediation of PNP-contaminated sites. This is a model study that could be used for decontamination of sites contaminated also with other compounds.

Characterization of Arthrobacter nicotinovorans HIM, an atrazine-degrading bacterium, from agricultural soil New Zealand

Arthrobacter nicotinovorans HIM was isolated directly from an agricultural sandy dune soil 6 months after a single application of atrazine. It grew in minimal medium with atrazine as sole nitrogen source but was unable to mineralize 14C-ring-labelled atrazine. Atrazine was degraded to cyanuric acid. In addition to atrazine the bacterium degraded simazine, terbuthylazine, propazine, cyanazine and prometryn but was unable to grow on terbumeton. When added to soil, A. nicotinovorans HIM did enhance mineralization of 14C-ring-labelled atrazine and simazine, in combination with naturally occurring cyanuric acid degrading microbes resident in the soil. Using PCR, the atrazine-degradation genes atzABC were identified in A. nicotinovorans HIM. Cloning of the atzABC genes revealed significant homology (>99%) with the atrazine degradation genes of Pseudomonas sp. strain ADP. The atrazine degradation genes were held on a 96 kbp plasmid.