Isolation and characterization of an atrazine-degradingRhodococcussp. strain MB-P1 from contaminated soil

Insights into the functional role of Actinomycetia in promoting plant growth and biocontrol in tea (Camellia sinensis) plants

Tea, a highly aromatic and globally consumed beverage, is derived from the aqueous infusion of dried leaves of Camellia sinensis (L.) O. Kuntze. Northeast India, encompassing an expansive geographical area between 24° and 27° N latitude and 88° and 95° E longitude, is a significant tea-producing region covering approximately 312,210 hectares. Despite its prominence, this region faces persistent challenges owing to a conducive climate that harbors the prevalence of pests, fungal pathogens, and weeds, necessitating agrochemicals. Helopeltis theivora, Oligonychus coffeae, and Biston suppressaria are prominent among the tea pests in this region. Concurrently, tea plants encounter fungal infections such as blister blight, brown root rot, and Fusarium dieback. The growing demand for safer tea production and the need to reduce pesticide and fertilizer usage has spurred interest in exploring biological control methods. This review focuses on Actinomycetia, which potentially safeguards plants from diseases and pest infestations by producing many bioactive substances. Actinomycetia, which resides in the tea rhizosphere and internal plant tissues, can produce antagonistic secondary metabolites and extracellular enzymes while promoting plant growth. Harnessing the biocontrol potential of Actinomycetia offers a promising solution to enhance tea production, while minimizing reliance on harmful agrochemicals, contributing to a more environmentally conscious and economically viable tea cultivation system.

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.

Inhibition of Biofilm and Virulence Properties of Pathogenic Bacteria by Silver and Gold Nanoparticles Synthesized from Lactiplantibacillus sp. Strain C1

The emergence of antibiotic resistance in microbial pathogens necessitates the development of alternative ways to combat the infections that arise. The current study used nanotechnology as an alternate technique to control virulence characteristics and biofilm development in Pseudomonas aeruginosa and Staphylococcus aureus. Furthermore, based on the acceptance and biocompatibility of the probiotic bacteria, we chose a lactic acid bacteria (LAB) for synthesizing two types of metallic nanoparticles (NPs) in this study. Using molecular techniques, the LAB strain C1 was isolated from Kimchi food samples and identified as Lactiplantibacillus sp. strain C1. The prepared supernatant from strain C1 was used to produce gold nanoparticles (AuNPs) and silver nanoparticles (AgNPs). C1-AuNPs and C1-AgNPs were characterized physiochemically using a variety of instruments. C1-AuNPs and C1-AgNPs had spherical shapes and sizes of 100.54 ± 14.07 nm (AuNPs) and 129.51 ± 12.31 nm (AgNPs), respectively. C1-AuNPs and C1-AgNPs were discovered to have high zeta potentials of -23.29 ± 1.17 and -30.57 ± 0.29 mV, respectively. These nanoparticles have antibacterial properties against several bacterial pathogens. C1-AuNPs and C1-AgNPs significantly inhibited the initial stage biofilm formation and effectively eradicated established mature biofilms of P. aeruginosa and S. aureus. Furthermore, when P. aeruginosa was treated with sub-MIC levels of C1-AuNPs and C1-AgNPs, their different virulence features were significantly reduced. Both NPs greatly inhibited the hemolytic activity of S. aureus. The inhibition of P. aeruginosa and S. aureus biofilms and virulence features by C1-AuNPs and C1-AgNPs can be regarded as viable therapeutic strategies for preventing infections caused by these bacteria.

Development of Efficient Genome-Reduction Tool Based on Cre/loxP System in Rhodococcus erythropolis

Rhodococcus has been extensively studied for its excellent ability to degrade artificial chemicals and its capability to synthesize biosurfactants and antibiotics. In recent years, studies have attempted to use Rhodococcus as a gene expression host. Various genetic tools, such as plasmid vectors, transposon mutagenesis, and gene disruption methods have been developed for use in Rhodococcus; however, no effective method has been reported for performing large-size genome reduction. Therefore, the present study developed an effective plasmid-curing method using the levansucrase-encoding sacB gene and a simple two-step genome-reduction method using a modified Cre/loxP system. For the results, R. erythropolis JCM 2895 was used as the model; a mutant strain that cured all four plasmids and deleted seven chromosomal regions was successfully obtained in this study. The total DNA deletion size was >600 kb, which corresponds mostly to 10% of the genome size. Using this method, a genome-structure-stabilized and unfavorable gene/function-lacking host strain can be created in Rhodococcus. This genetic tool will help develop and improve Rhodococcus strains for various industrial and environmental applications.

Antibiofilm and Antivirulence Activities of Gold and Zinc Oxide Nanoparticles Synthesized from Kimchi-Isolated Leuconostoc sp. Strain C2

The rapid emergence of antimicrobial resistance (AMR) among bacterial pathogens results in antimicrobial treatment failure and the high mortality rate associated with AMR. The application of nanoparticles synthesized from probiotics will be widely accepted due to their efficacy and biocompatibility in treating microbial infections in humans. The current work sought to isolate and identify lactic acid bacteria (LAB) from Kimchi. Based on 16S rRNA gene sequencing, the LAB isolate C2 was identified as a member of the genus Leuconostoc. The obtained supernatant from Leuconostoc sp. strain C2 was employed for the green synthesis of metal (AuNPs) and metal oxide (ZnONPs) nanoparticles. UV–vis absorption spectra, FTIR analysis, XRD, DLS, FE-TEM, and EDS mapping were used to fully characterize these C2-AuNPs and C2-ZnONPs. The C2-AuNPs were found to be spherical in shape, with a size of 47.77 ± 5.7 nm and zeta potential of −19.35 ± 0.67 mV. The C2-ZnONPs were observed to be rod-shaped and 173.77 ± 14.53 nm in size. The C2-ZnONPs zeta potential was determined to be 26.62 ± 0.35 mV. The C2-AuNPs and C2-ZnONPs were shown to have antimicrobial activity against different pathogens. Furthermore, these nanoparticles inhibited the growth of Candida albicans. The antibiofilm and antivirulence properties of these NPs against Pseudomonas aeruginosa and Staphylococcus aureus were thoroughly investigated. C2-AuNPs were reported to be antibiofilm and antivirulence against P. aeruginosa, whereas C2-ZnONPs were antibiofilm and antivirulence against both P. aeruginosa and S. aureus. Furthermore, these nanoparticles disrupted the preformed mature biofilm of P. aeruginosa and S. aureus. The inhibitory impact was discovered to be concentration-dependent. The current research demonstrated that C2-AuNPs and C2-ZnONPs exhibited potential inhibitory effects on the biofilm and virulence features of bacterial pathogens. Further studies are needed to unravel the molecular mechanism behind biofilm inhibition and virulence attenuation.

Impact of Paenarthrobacter ureafaciens ZF1 on the soil enzyme activity and microbial community during the bioremediation of atrazine-contaminated soils

Bioremediation of atrazine-contaminated soil is considered a safe and effective approach in removing contaminates from the soil. However, the effects of adding foreign organisms to assist bioremediation on soil environmental quality and ecosystem are unclear. Here, the ecological remediation potential of strain Paenarthrobacter ureafaciens ZF1 on atrazine-contaminated soil was investigated through miniature experiments using variations in soil enzymes and bacterial communities as indicators. The results showed that strain ZF1 accelerated atrazine degradation, which could completely degrade atrazine at concentrations of 100 mg·L^− 1 atrazine within 2 h in liquid medium and could remove up to 99.3% of atrazine (100 mg·kg^− 1 in soil) within 6 days. During soil bioremediation, atrazine promoted the activities of urease and cellulase, and inhibited the activities of sucrase and catalase, while the strain ZF1 significantly promoted the activities of these four enzymes. High-throughput sequencing of 16S rRNA genes showed that ZF1 affected the relative abundance and bacterial community structure, and promoted bacterial diversity and evenness. Furthermore, redundancy analysis revealed a certain correlation among the strain ZF1, atrazine residue, soil enzyme activity, and soil bacterial community. The strain ZF1 in this work demonstrated remarkable potential for ecological restoration, and can be an effective and environmentally friendly alternative in remediating atrazine-contaminated soil.

Actinobacteria: An eco-friendly and promising technology for the bioaugmentation of contaminants

Over the past two decades, various eco-friendly approaches utilizing microbial species to clean up contaminated environments have surfaced. In this aspect, actinobacteria have demonstrated their potential in contaminant degradation. The members of actinobacteria phylum exhibits a cosmopolitan distribution, which means that they can be found widely in both aquatic and terrestrial ecosystems. Actinobacteria play important ecological roles in the environment, such as degrading complex polymers, recycling compounds, and producing bioactive molecules. Hence, using actinobacteria to clean up contaminants is an attractive method in the field of biotechnology. This can be achieved through the green technology of bioaugmentation, whereby the degradative capacity of contaminated areas can be greatly improved through the introduction of specific microorganisms. This review describes actinobacteria as an eco-friendly and a promising technology for the bioaugmentation of contaminants, with focus on pesticides and heavy metals.

Soil bacterial community dynamics following bioaugmentation with Paenarthrobacter sp. W11 in atrazine-contaminated soil

Atrazine is one of the most widely used herbicides, however it and its metabolites cause widespread contamination in soil and ground water. Bioaugmentation is an effective method for remediation of environmental organic pollutants. High-throughput sequencing provides an important tool for understanding the changes of microbial community and function in response to pollutants degradation based on bioaugmentation. In this study, the effect of biodegradation with Paenarthrobacter sp. W11 and the change of microbial community during atrazine degradation were investigated. The results showed that bioaugmentation significantly accelerated the degradation rate of atrazine in soil and reduced the toxic effect of atrazine residues on wheat growth. The extra available NH₄⁺ through atrazine mineralization could serve as a nitrogen source to increase microbial numbers. High-throughput sequencing further revealed that the microbial community restored a new balance. The function of microbial community predicted by PICRUSt2 suggested that the biodegradation process of atrazine affected not only the atrazine degradation pathway, but also the nitrogen metabolism pathway. Methylobacillus and Pseudomonas were considered as the most important indigenous atrazine-degrading microorganisms, because their relative abundances were positively correlated with the relative abundance of Paenarthrobacter and atrazine degradation pathway. This study provides insight into the cooperation between indigenous microorganisms and external inoculums on atrazine degradation process.

Phloroglucinol-Gold and -Zinc Oxide Nanoparticles: Antibiofilm and Antivirulence Activities towards Pseudomonasaeruginosa PAO1

With the advancement of nanotechnology, several nanoparticles have been synthesized as antimicrobial agents by utilizing biologically derived materials. In most cases, the materials used for the synthesis of nanoparticles from natural sources are extracts. Natural extracts contain a wide range of bioactive components, making it difficult to pinpoint the exact component responsible for nanoparticle synthesis. Furthermore, the bioactive component present in the extract changes according to numerous environmental factors. As a result, the current work intended to synthesize gold (AuNPs) and zinc oxide (ZnONPs) nanoparticles using pure phloroglucinol (PG). The synthesized PG-AuNPs and PG-ZnONPs were characterized using a UV-Vis absorption spectrophotometer, FTIR, DLS, FE-TEM, zeta potential, EDS, and energy-dispersive X-ray diffraction. The characterized PG-AuNPs and PG-ZnONPs have been employed to combat the pathogenesis of Pseudomonas aeruginosa. P. aeruginosa is recognized as one of the most prevalent pathogens responsible for the common cause of nosocomial infection in humans. Antimicrobial resistance in P. aeruginosa has been linked to the development of recalcitrant phenotypic characteristics, such as biofilm, which has been identified as one of the major obstacles to antimicrobial therapy. Furthermore, P. aeruginosa generates various virulence factors that are a major cause of chronic infection. These PG-AuNPs and PG-ZnONPs significantly inhibit early stage biofilm and eradicate mature biofilm. Furthermore, these NPs reduce P. aeruginosa virulence factors such as pyoverdine, pyocyanin, protease, rhamnolipid, and hemolytic capabilities. In addition, these NPs significantly reduce P. aeruginosa swarming, swimming, and twitching motility. PG-AuNPs and PG-ZnONPs can be used as control agents for infections caused by the biofilm-forming human pathogenic bacterium P. aeruginosa.

Exogenous Zn2+ enhance the biodegradation of atrazine by regulating the chlorohydrolase gene trzN transcription and membrane permeability of the degrader Arthrobacter sp. DNS10

Enhancing the biodegradation efficiency of atrazine, a kind of commonly applied herbicide, has been attracted much more concern. Here, Zn²⁺ which has long been considered essential in adjusting cell physiological status was selected to investigate its role on the biodegradation of atrazine by Arthrobacter sp. DNS10 as well as the transmembrane transport of atrazine during the biodegradation period. The results of gas chromatography showed that the atrazine removal percentages (initial concentration was 100 mg L^-1) in 0.05 mM Zn²⁺ and 1.0 mM Zn²⁺ treatments were 94.42% and 86.02% respectively at 48 h, while there was also 66.43% of atrazine left in the treatment without exogenous Zn²⁺ existence. The expression of atrazine chlorohydrolase gene trzN in the strain DNS10 cultured with 0.05 mM and 1.0 mM Zn²⁺ was 7.30- and 4.67- times respectively compared with that of the non-zinc treatment. In addition, the flow cytometry test suggests that 0.05 mM of Zn²⁺ could better adjust the membrane permeability of strain DNS10, meanwhile, the amount of atrazine accumulation in the strain DNS10 co-cultured with this level Zn²⁺ was 2.21 times of that of the strain without Zn²⁺. This study may facilitate a better understanding of the mechanisms that exogenous Zn²⁺ enhances the biodegradation of atrazine by Arthrobacter sp. DNS10.

Bioaugmentation of atrazine removal in constructed wetland: Performance, microbial dynamics, and environmental impacts

Constructed wetland (CW) is an efficient technology to treat urban storm water runoff. However, the CW has limited capacity to degrade atrazine, a frequently detected herbicide in runoff. Bioaugmentation provides a feasible enhanced alternative; nevertheless, incorporating bioaugmentation into CW is likely to perpetuate the environmental consequences and incur complex trade-offs between environmental improvement and burdens. Since few efforts were made to improve above situation, the present work proposed the application of bioaugmentation, and tested the feasibility from both efficiency and sustainability dimensions. Results showed that bioaugmentation markedly enhanced atrazine degradation from 5 mg/L to below the threshold value within 43 day by increasing functional atrazine-degrading bacteria. Pseudomonas and Arthrobacter significantly proliferated among atrazine-degrading bacterial genera, indicating high adaptability and atrazine-degrading contribution. With life cycle assessment, enhancing 1 kg of atrazine degradation could decrease environmental burdens with 27.60 kg 1,4-DCB-Eq of freshwater-ecotoxicity reduction, and achieve shorter payback period compared to non-bioaugmented CW.

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

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

Deltamethrin impact in a cabbage planted soil: Degradation and effect on microbial community structure

Synthetic pyrethroids (SPs) are one of the most common pesticides used worldwide. Their use has greatly increased in the last decades and its' continuous application lead to added pesticides concentration in soil. Consequently, SPs may enter the food chain, affecting the environment and human health. The degradation over time of the pyrethroid pesticide deltamethrin applied to cabbages was monitored. The evolution was followed both on cabbages and the surrounding soils, and the soil microbial community characterized by next-generation sequencing of the 16S rRNA gene. The main shift in the microbial community structure was observed during the first 30 days after pesticides' application. The modification in the microbial community composition, where an increased abundance of Nocardioides sp. and Sphingomonas sp. were observed, was correlated respectively with the conversions of deltamethrin and its metabolite, 3-phenoxybenzoic acid (3-PBA). Although deltamethrin was not found in any of the tested samples (soil and cabbage) after 180 days, it caused an environmental impact much further than the 7 days security interval. These findings suggest that deltamethrin application can disturb soil microbial community and that natural biodegradation can have an important part in pesticides soil decontamination.

Study on the Isolation of Two Atrazine-Degrading Bacteria and the Development of a Microbial Agent

Two bacteria capable of efficiently degrading atrazine were isolated from soil, and named ATLJ-5 and ATLJ-11. ATLJ-5 and ATLJ-11 were identified as Bacillus licheniformis and Bacillus megaterium, respectively. The degradation efficiency of atrazine (50 mg/L) by strain ATLJ-5 can reach about 98.6% after 7 days, and strain ATLJ-11 can reach 99.6% under the same conditions. The degradation of atrazine is faster when two strains are used in combination. Adding the proper amount of fresh soil during the degradation of atrazine by these two strains can also increase the degradation efficiency. The strains ATLJ-5 and ATLJ-11 have high tolerance to atrazine, and can tolerate at least 1000 mg/L of atrazine. In addition, the strains ATLJ-5 and ATLJ-11 have been successfully made into a microbial agent that can be used to treat atrazine residues in soil. The degradation efficiency of atrazine (50 mg/kg) could reach 99.0% by this microbial agent after 7 days. These results suggest that the strains ATLJ-5 and ATLJ-11 can be used for the treatment of atrazine pollution.

Responses of atrazine degradation and native bacterial community in soil to Arthrobacter sp. strain HB-5

The bioremediation of soil contaminated with organic pesticides is a safe and effective approach to remove pollutants from the soil. However, whether the invasion of foreign aid organisms affects the local organisms has received increasing attention in recent years. Therefore, the purpose of this study was to examine the degradation ability of atrazine by the strain HB-5 and evaluate its effects on natural bacterial communities in a miniature pot experiment. Results showed that HB-5 accelerated the degradation of atrazine and the degradation half-life of atrazine was 3.3 times less than the natural soil. Additionally, HB-5 increased the quantities of indigenous bacteria, the microbial biomass carbon and the Shannon, Simpson and McIntosh diversity indices of soil microbes in its early stage of use, But these parameters in soil treated with HB-5 decreased to values as low as those found in the control at the later stage of incubation. These suggested that the bacteria vanished as atrazine was completely removed. These results demonstrated that Arthrobacter sp. strain HB-5 had great potential and would be an effective and environmental friendly technique to remove atrazine from the contaminated soil.

Characterisation of an efficient atrazine-degrading bacterium, Arthrobacter sp. ZXY-2: an attempt to lay the foundation for potential bioaugmentation applications

BACKGROUND

The isolation of atrazine-degrading microorganisms with specific characteristics is fundamental for bioaugmenting the treatment of wastewater containing atrazine. However, studies describing the specific features of such microorganisms are limited, and further investigation is needed to improve our understanding of bioaugmentation.

RESULTS AND CONCLUSIONS

In this study, strain Arthrobacter sp. ZXY-2, which displayed a strong capacity to degrade atrazine, was isolated and shown to be a potential candidate for bioaugmentation. The factors associated with the biodegrading capacity of strain ZXY-2 were investigated, and how these factors likely govern the metabolic characteristics that control bioaugmentation functionality was determined. The growth pattern of Arthrobacter sp. ZXY-2 followed the Haldane-Andrews model with an inhibition constant (K_i) of 52.76 mg L^-1, indicating the possible augmentation of wastewater treatment with relatively high atrazine concentrations (> 50 ppm). Real-time quantitative PCR (RT-qPCR) results showed a positive correlation between the atrazine degradation rate and the expression levels of three functional genes (trzN, atzB, and atzC), which helped elucidate the role of strain ZXY-2 in bioaugmentation. In addition, multiple copies of the atzB gene were putatively identified, explaining the higher expression levels of this gene than those of the other functional genes. Multiple copies of the atzB gene may represent a compensatory mechanism that ensures the biodegradation of atrazine, a feature that should be exploited in future bioaugmentation applications.

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.

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.

Complete genome sequence of Arthrobacter sp. ZXY-2 associated with effective atrazine degradation and salt adaptation

An atrazine-degrading strain Arthrobacter sp. ZXY-2 was originally isolated from Jilin Pesticide Plant (China). Strain ZXY-2 demonstrated excellent atrazine degradation performance and saline tolerance. Here we report the complete genome sequence of strain ZXY-2 contained a circular chromosome and five circular plasmids encoding for the mechanism of salt adaptation and pollutant degradation.

Optimization of culturing conditions for isolated Arthrobacter sp. ZXY-2, an effective atrazine-degrading and salt-adaptive bacterium

The isolated strainArthrobactersp. ZXY-2 could biodegrade atrazine effectively with high salinity resistance.

Actinobacteria: Current research and perspectives for bioremediation of pesticides and heavy metals

Actinobacteria exhibit cosmopolitan distribution since their members are widely distributed in aquatic and terrestrial ecosystems. In the environment they play relevant ecological roles including recycling of substances, degradation of complex polymers, and production of bioactive molecules. Biotechnological potential of actinobacteria in the environment was demonstrated by their ability to remove organic and inorganic pollutants. This ability is the reason why actinobacteria have received special attention as candidates for bioremediation, which has gained importance because of the widespread release of contaminants into the environment. Among organic contaminants, pesticides are widely used for pest control, although the negative impact of these chemicals in the environmental balance is increasingly becoming apparent. Similarly, the extensive application of heavy metals in industrial processes lead to highly contaminated areas worldwide. Several studies focused in the use of actinobacteria for cleaning up the environment were performed in the last 15 years. Strategies such as bioaugmentation, biostimulation, cell immobilization, production of biosurfactants, design of defined mixed cultures and the use of plant-microbe systems were developed to enhance the capabilities of actinobacteria in bioremediation. In this review, we compiled and discussed works focused in the study of different bioremediation strategies using actinobacteria and how they contributed to the improvement of the already existing strategies. In addition, we discuss the importance of omic studies to elucidate mechanisms and regulations that bacteria use to cope with pollutant toxicity, since they are still little known in actinobacteria. A brief account of sources and harmful effects of pesticides and heavy metals is also given.

Photocatalytic degradation of atrazine herbicide with Illuminated Fe+3-TiO2 Nanoparticles

BACKGROUND

Atrazine is a herbicide that is widely used to control broadleaf and grassy weeds for growing many crops especially in maize production. It is a frequently detected herbicide in many groundwater resources. This study aimed to assess the feasibility of using ultraviolet radiation UV and fortified nanoparticles of titanium dioxide (TiO₂) doped with trivalent iron to remove atrazine from aqueous phase and determin the removal efficiency under the optimal conditions.

RESULTS

The results of this study demonstrated that the maximum atrazine removal rate was at pH = 11 in the presence of Fe^{+ 3}-TiO₂ catalyst =25 mg/L and the initial concentration of atrazine equal to 10 mg/L. As the reaction time increased, the removal rate of herbicide increased as well. Atrazine removal rate was enhanced by the effect of UV radiation on catalyst activation in Fe⁺³-TiO₂/UV process. It was also revealed that pH has no significant effect on atrazine removal efficiency (p > 0.05).

CONCLUSION

Based on the data obtained in this study, atrazine removal efficiency was increased by increasing pH, initial atrazine concentration, catalyst, and contact time. The results also showed Fe⁺³-TiO₂/UV process was an appropriate method to reduce atrazine in contaminated water resources. In conclusion, Fe⁺³-TiO₂/UV process may enhance the rate of atrazine reduction in highly polluted water resources (more than 99%).

Draft Genome Sequence of a Versatile Hydrocarbon-Degrading Bacterium, Rhodococcus pyridinivorans Strain KG-16, Collected from Oil Fields in India

We describe here a 5.8-Mb draft genome sequence of Rhodococcus pyridinivorans strain KG-16, which was obtained from the soil samples collected from the oilfields of Krishna-Godavari basin in India. This genomic resource can provide insights into the pathways and mechanisms of hydrocarbon degradation and potentially aid in bioremediation applications.

Isolation of Indole Utilizing Bacteria Arthrobacter sp. and Alcaligenes sp. From Livestock Waste

Indole is an interspecies and interkingdom signaling molecule widespread in different environmental compartment. Although multifaceted roles of indole in different biological systems have been established, little information is available on the microbial utilization of indole in the context of combating odor emissions from different types of waste. The present study was aimed at identifying novel bacteria capable of utilizing indole as the sole carbon and energy source. From the selective enrichment of swine waste and cattle feces, we identified Gram-positive and Gram-negative bacteria belonging to the genera Arthrobacter and Alcaligenes. Bacteria belonging to the genus Alcaligenes showed higher rates of indole utilization than Arthrobacter. Indole at 1.0 mM for growth was completely utilized by Alcaligenes sp. in 16 h. Both strains produced two intermediates, anthranilic acid and isatin, during aerobic indole metabolism. These isolates were also able to grow on several indole derivatives. Interestingly, an adaptive response in terms of a decrease in cell size was observed in both strains in the presence of indole. The present study will help to explain the degradation of indole by different bacteria and also the pathways through which it is catabolized. Furthermore, these novel bacterial isolates could be potentially useful for the in situ attenuation of odorant indole and its derivatives emitted from different types of livestock waste.

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.

Microbial degradation of herbicides

Herbicides remain the most effective, efficient and economical way to control weeds; and its market continues to grow even with the plethora of generic products. With the development of herbicide-tolerant crops, use of herbicides is increasing around the world that has resulted in severe contamination of the environment. The strategies are now being developed to clean these substances in an economical and eco-friendly manner. In this review, an attempt has been made to pool all the available literature on the biodegradation of key herbicides, clodinafop propargyl, 2,4-dichlorophenoxyacetic acid, atrazine, metolachlor, diuron, glyphosate, imazapyr, pendimethalin and paraquat under the following objectives: (1) to highlight the general characteristic and mode of action, (2) to enlist toxicity in animals, (3) to pool microorganisms capable of degrading herbicides, (4) to discuss the assessment of herbicides degradation by efficient microbes, (5) to highlight biodegradation pathways, (6) to discuss the molecular basis of degradation, (7) to enlist the products of herbicides under degradation process, (8) to highlight the factors effecting biodegradation of herbicides and (9) to discuss the future aspects of herbicides degradation. This review may be useful in developing safer and economic microbiological methods for cleanup of soil and water contaminated with such compounds.

Biodegradation of atrazine by Rhodococcus sp. BCH2 to N-isopropylammelide with subsequent assessment of toxicity of biodegraded metabolites

Atrazine is a persistent organic pollutant in the environment which affects not only terrestrial and aquatic biota but also human health. Since its removal from the environment is needed, atrazine biodegradation is achieved in the present study using the bacterium Rhodococcus sp. BCH2 isolated from soil, long-term treated with atrazine. The bacterium was capable of degrading about 75 % atrazine in liquid medium having pH 7 under aerobic and dark condition within 7 days. The degradation ability of the bacterium at various temperatures (20-60 °C), pH (range 3-11), carbon (glucose, fructose, sucrose, starch, lactose, and maltose), and nitrogen (ammonium molybdate, sodium nitrate, potassium nitrate, and urea) sources were studied for triumph optimum atrazine degradation. The results indicate that atrazine degradation at higher concentrations (100 ppm) was pH and temperature dependent. However, glucose and potassium nitrate were optimum carbon and nitrogen source, respectively. Atrazine biodegradation analysis was carried out by using high-performance thin-layer chromatography (HPTLC), Fourier transform infrared spectroscopy (FTIR), and liquid chromatography quadrupole time-of-flight (LC/Q-TOF-MS) techniques. LC/Q-TOF-MS analysis revealed formation of various intermediate metabolites including hydroxyatrazine, N-isopropylammelide, deisopropylhydroxyatrazine, deethylatrazine, deisopropylatrazine, and deisopropyldeethylatrazine which was helpful to propose biochemical degradation pathway of atrazine. Furthermore, the toxicological studies of atrazine and its biodegraded metabolites were executed on earthworm Eisenia foetida as a model organism with respect to enzymatic (SOD and Catalase) antioxidant defense mechanism and lipid peroxidation studies. These results suggest innocuous degradation of atrazine by Rhodococcus sp. BCH2 in nontoxic form. Therefore the Rhodococcus sp.BCH2 could prove a valuable source for the eco-friendly biodegradation of atrazine pesticide.

Influence of microbial and synthetic surfactant on the biodegradation of atrazine

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

Degradation of 2,4-dinitroanisole (DNAN) by metabolic cooperative activity of Pseudomonas sp. strain FK357and Rhodococcus imtechensis strain RKJ300

2,4-Dinitroanisole (DNAN) is an insensitive explosive ingredient used by many defense agencies as a replacement for 2,4,6-trinitrotoluene. Although the biotransformation of DNAN under anaerobic condition has been reported, aerobic microbial degradation pathway has not been elucidated. An n-methyl-4-nitroaniline degrading bacterium Pseudomonas sp. strain FK357 transformed DNAN into 2,4-dinitrophenol (2,4-DNP) as an end product. Interestingly, when strain FK357 was co-cultured with a 2,4-DNP degrading Rhodococcus imtechensis strain RKJ300, complete and high rate of DNAN degradation was observed with no accumulation of intermediates. Enzyme assay using cell extracts of strain FK357 demonstrated that O-demethylation reaction is the first step of DNAN degradation with formation of 2,4-DNP and formaldehyde as intermediates. Subsequently, 2,4-DNP was degraded by strain RKJ300 via the formation of hydride-Meisenheimer complex. The present study clearly demonstrates that complete degradation of DNAN occurs as a result of the metabolic cooperative activity of two members within a bacterial consortium.

Aerobic degradation of N-methyl-4-nitroaniline (MNA) by Pseudomonas sp. strain FK357 isolated from soil

N-Methyl-4-nitroaniline (MNA) is used as an additive to lower the melting temperature of energetic materials in the synthesis of insensitive explosives. Although the biotransformation of MNA under anaerobic condition has been reported, its aerobic microbial degradation has not been documented yet. A soil microcosms study showed the efficient aerobic degradation of MNA by the inhabitant soil microorganisms. An aerobic bacterium, Pseudomonas sp. strain FK357, able to utilize MNA as the sole carbon, nitrogen, and energy source, was isolated from soil microcosms. HPLC and GC-MS analysis of the samples obtained from growth and resting cell studies showed the formation of 4-nitroaniline (4-NA), 4-aminophenol (4-AP), and 1, 2, 4-benzenetriol (BT) as major metabolic intermediates in the MNA degradation pathway. Enzymatic assay carried out on cell-free lysates of MNA grown cells confirmed N-demethylation reaction is the first step of MNA degradation with the formation of 4-NA and formaldehyde products. Flavin-dependent transformation of 4-NA to 4-AP in cell extracts demonstrated that the second step of MNA degradation is a monooxygenation. Furthermore, conversion of 4-AP to BT by MNA grown cells indicates the involvement of oxidative deamination (release of NH2 substituent) reaction in third step of MNA degradation. Subsequent degradation of BT occurs by the action of benzenetriol 1, 2-dioxygenase as reported for the degradation of 4-nitrophenol. This is the first report on aerobic degradation of MNA by a single bacterium along with elucidation of metabolic pathway.

Biodegradation of the allelopathic chemical m-tyrosine by Bacillus aquimaris SSC5 involves the homogentisate central pathway

m-Tyrosine is an amino acid analogue, exuded from the roots of fescue grasses, which acts as a potent allelopathic and a broad spectrum herbicidal chemical. Although the production and toxic effects of m-tyrosine are known, its microbial degradation has not been documented yet. A soil microcosm study showed efficient degradation of m-tyrosine by the inhabitant microorganisms. A bacterial strain designated SSC5, that was able to utilize m-tyrosine as the sole source of carbon, nitrogen, and energy, was isolated from the soil microcosm and was characterized as Bacillus aquimaris. Analytical methods such as HPLC, GC-MS, and ¹H-NMR performed on the resting cell samples identified the formation of 3-hydroxyphenylpyruvate (3-OH-PPA), 3-hydroxyphenylacetate (3-OH-PhAc), and homogentisate (HMG) as major intermediates in the m-tyrosine degradation pathway. Enzymatic assays carried out on cell-free lysates of m-tyrosine-induced cells confirmed transamination reaction as the first step of m-tyrosine degradation. The intermediate 3-OH-PhAc thus obtained was further funneled into the HMG central pathway as revealed by a hydroxylase enzyme assay. Subsequent degradation of HMG occurred by ring cleavage catalyzed by the enzyme homogentisate 1, 2-dioxygenase. This study has significant implications in terms of understanding the environmental fate of m-tyrosine as well as regulation of its phytotoxic effect by soil microorganisms.

Metabolism of 2-chloro-4-nitroaniline via novel aerobic degradation pathway by Rhodococcus sp. strain MB-P1

2-chloro-4-nitroaniline (2-C-4-NA) is used as an intermediate in the manufacture of dyes, pharmaceuticals, corrosion inhibitor and also used in the synthesis of niclosamide, a molluscicide. It is marked as a black-listed substance due to its poor biodegradability. We report biodegradation of 2-C-4-NA and its pathway characterization by Rhodococcus sp. strain MB-P1 under aerobic conditions. The strain MB-P1 utilizes 2-C-4-NA as the sole carbon, nitrogen, and energy source. In the growth medium, the degradation of 2-C-4-NA occurs with the release of nitrite ions, chloride ions, and ammonia. During the resting cell studies, the 2-C-4-NA-induced cells of strain MB-P1 transformed 2-C-4-NA stoichiometrically to 4-amino-3-chlorophenol (4-A-3-CP), which subsequently gets transformed to 6-chlorohydroxyquinol (6-CHQ) metabolite. Enzyme assays by cell-free lysates prepared from 2-C-4-NA-induced MB-P1 cells, demonstrated that the first enzyme in the 2-C-4-NA degradation pathway is a flavin-dependent monooxygenase that catalyzes the stoichiometric removal of nitro group and production of 4-A-3-CP. Oxygen uptake studies on 4-A-3-CP and related anilines by 2-C-4-NA-induced MB-P1 cells demonstrated the involvement of aniline dioxygenase in the second step of 2-C-4-NA degradation. This is the first report showing 2-C-4-NA degradation and elucidation of corresponding metabolic pathway by an aerobic bacterium.

Development of an HPLC method for determination of pentachloronitrobenzene, hexachlorobenzene and their possible metabolites

Background

Pentachloronitrobenzene (PCNB) and hexachlorobenzene (HCB) are highly toxic and widespread in every environmental compartment. Some of metabolic products such as amino/nitro containing chlorinated aromatic compounds can be determined by gas chromatography coupled with electron capture detector (GC-ECD). However, it is difficult to identify some of chlorophenolic and chloroquinolic intermediates produced from PCNB and HCB by the above mentioned technique. Therefore, for analysis of these compounds and their metabolites, we have developed a high performance liquid chromatography (HPLC) based method.

Results

The extraction of PCNB and HCB from soil and minimal salt medium was carried out with ethyl acetate and hexane respectively with good recoveries (98% for PCNB and 97% for HCB). The validation of the proposed extraction and HPLC method was done by analysis of PCNB and HCB biodegradation and their metabolites identification from anaerobic enriched soil samples.

Conclusion

A rapid, sensitive and simple HPLC based analytical method was developed for the analysis of PCNB, HCB and their possible intermediates.