Degradation of acetochlor by consortium of two bacterial strains and cloning of a novel amidase gene involved in acetochlor-degrading pathway

Enhanced Dechlorination of the Herbicide Acetochlor by an Anaerobic Consortium via Sulfate Acclimation

Acetochlor residues can contaminate anoxic habitats where anaerobic microbial transformation dominates. Herein, a highly efficient anaerobic acetochlor-degrading consortium ACT6 was enriched using sulfate and acetochlor as selection pressures. The acclimated consortium ACT6 showed an 8.7-fold increase in its ability to degrade acetochlor compared with the initial consortium ACT1. Two degradation pathways of acetochlor were found: reductive dechlorination and thiol-substitution dechlorination in the chloroacetyl group, in which the latter dominated. Acclimation enhanced the abundances of Desulfovibrio, Proteiniclasticum, and Lacrimispora from 0.7 to 28.0% (40-fold), 4.7 to 18.1% (4-fold), and 2.3 to 12.3% (5-fold), respectively, which were positively correlated with sulfate concentrations and acetochlor degradation ability. Three acetochlor-degrading anaerobes were isolated from the acclimated consortium ACT6, namely Cupidesulfovibrio sp. SRB-5, Proteiniclasticum sp. BAD-10, and Lacrimispora sp. BAD-7. This study provides new insights into the anaerobic catabolism of acetochlor and the anaerobic treatment of acetochlor in wastewater.

Current insights into environmental acetochlor toxicity and remediation strategies

Acetochlor is a selective pre-emergent herbicide that is widely used to control annual grass and broadleaf weeds. However, due to its stable chemical structure, only a small portion of acetochlor exerts herbicidal activity in agricultural applications, while most of the excess remains on the surfaces of plants or enters ecosystems, such as soil and water bodies, causing harm to the environment and human health. In recent years, researchers have become increasingly focused on the repair of acetochlor residues. Compared with traditional physical and chemical remediation methods, microorganisms are the most effective way to remediate chemical pesticide pollution, such as acetochlor, because of their rich species, wide distribution, and diverse metabolic pathways. To date, researchers have isolated and identified many high-efficiency acetochlor-degrading strains, such as Pseudomonas oleovorans, Klebsiella variicola, Bacillus subtilus, Rhodococcus, and Methylobacillus, among others. The microbial degradation pathways of acetochlor include dechlorination, hydroxylation, N-dealkylation, C-dealkylation, and dehydrogenation. In addition, the microbial enzymes, including hydrolase (ChlH), debutoxylase (Dbo), and monooxygenase (MeaXY), responsible for acetochlor biodegradation are also being investigated. In this paper, we review the migration law of acetochlor in the environment, its toxicity to nontarget organisms, and the main metabolic methods. Moreover, we summarize the latest progress in the research on the microbial catabolism of acetochlor, including the efficient degradation of microbial resources, biodegradation metabolic pathways, and key enzymes for acetochlor degradation. At the end of the article, we highlight the existing problems in the current research on acetochlor biodegradation, provide new ideas for the remediation of acetochlor pollution in the environment, and propose future research directions.

Recombinant Amidases: Recent Insights and its Applications in the Production of Industrially Important Fine Chemicals

The current research for the synthesis of industrially important fine chemicals is more inclined towards developing enzyme-based processes. The biotransformation reactions wherein microbial cells/enzymes are used, have become essential in making the process efficient, green, and economical. Amongst industrially important enzymes, amidase is one of the most versatile tools in biocatalysis and biotransformation reactions. It shows broad substrate specificity and sturdy functional characteristics because of its promiscuous nature. Further, advancement in the area led to the development of amidase recombinant systems, which are developed using biotechnology and enzyme engineering tools. Additionally, recombinant amidases may be instrumental in commercializing the synthesis of fine chemicals such as hydroxamic acids that have a significant pharmaceutical market. Hence, the present review focuses on highlighting and assimilating the tools and techniques used in developing recombinant systems followed by their applications.

Combined application of up to ten pesticides decreases key soil processes

Natural systems are under increasing pressure by a range of anthropogenic global change factors. Pesticides represent a nearly ubiquitously occurring global change factor and have the potential to affect soil functions. Currently the use of synthetic pesticides is at an all-time high with over 400 active ingredients being utilized in the EU alone, with dozens of these pesticides occurring concurrently in soil. However, we presently do not understand the impacts of the potential interaction of multiple pesticides when applied simultaneously. Using soil collected from a local grassland, we utilize soil microcosms to examine the role of both rate of change and number of a selection of ten currently used pesticides on soil processes, including litter decomposition, water stable aggregates, aggregate size, soil pH, and EC. Additionally, we used null models to enrich our analyses to examine potential patterns caused by interactions between pesticide treatments. We find that both gradual and abrupt pesticide application have negative consequences for soil processes. Notably, pesticide number plays a significant role in affecting soil health. Null models also reveal potential synergistic behavior between pesticides which can further their consequences on soil processes. Our research highlights the complex impacts of pesticides, and the need for environmental policy to address the threats posed by pesticides.

Molecular design of environment-friendly amide herbicide substitutes with high efficacy, low phytotoxicity and medication safety

The primary goal of this investigation was to formulate an ecologically sustainable alternative to amide herbicides (AHs) characterized by robust herbicidal effectiveness, minimal corn phytotoxicity, and commendable pharmaceutical safety. We employed comparative molecular similarity index analysis (CoMSIA), a three-dimensional quantitative structure-activity relationship (3D-QSAR) model, which systematically outlined parameters such as herbicidal effectiveness, corn phytotoxicity, and AHs biodegradability. Subsequently, after thorough evaluation, we carefully selected a group of fourteen stable AH-substitute compounds known for their safety and environmental compatibility, considering aspects like pharmacokinetics, toxicokinetics, functional properties, and environmental friendliness. This resulted in a significant increase in herbicidal effectiveness, ranging from 21.64% to 34.07%, alongside a decrease in corn phytotoxicity within the range of 12.19-20.87%. Furthermore, we achieved an improvement in biodegradability, measured within the spectrum of 4.92-9.40%. Importantly, these changes also correlated with the reduction of hepatotoxicity, mutagenicity, and cutaneous health risks. Finally, we delved into the mechanisms underlying the improved herbicidal effectiveness, reduced corn phytotoxicity, and enhanced biodegradability of AHs substitutes through molecular docking and analysis of amino acid interactions. The investigation concluded that non-covalent forces governing the interaction between AHs substitutes and receptor proteins are crucial in determining herbicidal effectiveness, corn phytotoxicity, and biodegradability. Specifically, Van der Waals and electrostatic forces emerged as key factors governing the binding affinities of AH molecules with receptor proteins, both before and after modification. In summary, this study introduces innovative approaches in the field of agricultural chemical weeding technology and provides a theoretical framework for the environmentally responsible management of AHs herbicides.

Insights into the metabolic pathways and biodegradation mechanisms of chloroacetamide herbicides

Chloroacetamide herbicides are widely used around the world due to their high efficiency, resulting in increasing levels of their residues in the environment. Residual chloroacetamides and their metabolites have been frequently detected in soil, water and organisms and shown to have toxic effects on non-target organisms, posing a serious threat to the ecosystem. As such, rapid and efficient techniques that eliminate chloroacetamide residues from the ecosystem are urgently needed. Degradation of these herbicides in the environment mainly occurs through microbial metabolism. Microbial strains such as Acinetobacter baumannii DT, Bacillus altitudinis A16, Pseudomonas aeruginosa JD115, Sphingobium baderi DE-13, Catellibacterium caeni DCA-1, Stenotrophomonas acidaminiphila JS-1, Klebsiella variicola B2, and Paecilomyces marquandii can effectively degrade chloroacetamide herbicides. The degradation pathway of chloroacetamide herbicides in aerobic bacteria is mainly initiated by an N/C-dealkylation reaction, followed by aromatic ring hydroxylation and cleavage processes, whereas dechlorination is the initial reaction in anaerobic bacteria. The molecular mechanisms associated with bacterial degradation of chloroacetamide herbicides have been explored, with amidase, hydrolase, reductase, ferredoxin and cytochrome P450 oxygenase currently known to play a pivotal role in the catabolic pathways of chloroacetamides. The fungal pathway for the degradation of these herbicides is more complex with more diversified products, and the degradation enzymes and genes involved remain to be discovered. However, there are few reviews specifically summarizing the microbial degrading species and biochemical mechanisms of chloroacetamide herbicides. Here, we briefly summarize the latest progress resulting from research on microbial strain resources and enzymes involved in degradation of these herbicides and their corresponding genes. Furthermore, we explore the biochemical pathways and molecular mechanisms for biodegradation of chloroacetamide herbicides in depth, thereby providing a reference for further research on the bioremediation of such herbicides.

Wide substrate range for a candidate bioremediation enzyme isolated from Nocardioides sp. strain SG-4 G

Narrow substrate ranges can impact heavily on the range of applications and hence commercial viability of candidate bioremediation enzymes. Here we show that an ester hydrolase from Nocardioides strain SG-4 G has potential as a bioremediation agent against various pollutants that can be detoxified by hydrolytic cleavage of some carboxylester, carbamate, or amide linkages. Previously we showed that a radiation-killed, freeze-dried preparation (ZimA) of this strain can rapidly degrade the benzimidazole fungicide carbendazim due to the activity of a specific ester hydrolase, MheI. Here, we report that ZimA also has substantial hydrolytic activity against phthalate diesters (dimethyl, dibutyl, and dioctyl phthalate), anilide (propanil and monalide), and carbamate ester (chlorpropham) herbicides under laboratory conditions. The reaction products are substantially less toxic, or inactive as herbicides, than the parent compounds. Tests of strain SG-4 G and Escherichia coli expressing MheI found they were also able to hydrolyse dimethyl phthalate, propanil, and chlorpropham, indicating that MheI is principally responsible for the above activities.

Revealing the driving synergistic degradation mechanism of Rhodococcus sp. B2 on the bioremediation of pretilachlor-contaminated soil

The pretilachlor has been widely used worldwide and has contaminated the environment for many years. The environmental fate of pretilachlor and its residues removal from the contaminated environment have attracted great concern. Reportedly, pretilachlor could partly be transformed to HECDEPA by Rhodococcus sp. B2. However, the effects of pretilachlor on soil bacterial communities and its complete metabolic pathway remain unknown. Herein, we investigated the mechanism of driving synergistic degradation of pretilachlor by strain B2 in the soil. The results revealed that pretilachlor showed a negative effect on bacterial communities and caused significant variations in the community structure. Strain B2 showed the ability to remediate the pretilachlor-contaminated soils and network analysis revealed that it may drive the enrichment of potential pretilachlor-degrading bacteria from the soil. The soil pretilachlor degradation may be facilitated by the members of the keystone families Comamonadaceae, Caulobacteraceae, Rhodospirillaceae, Chitinophagaceae, and Sphingomonadaceae. Meanwhile, Sphingomonas sp. M6, a member of the Sphingomonadaceae family, has been isolated from the strain B2 inoculation sample soil. The co-culture, comprising strain M6 and B2, could synergistic degrade pretilachlor within 30 h, which is the highest degradation rate. Strain M6 could completely degrade the HECDEPA via CDEPA and DEA. In the soil, a comparable pretilachlor degradation pathway may exist. This study suggested that strain B2 had the potential to drive the remediation of pretilachlor-contaminated soils.

Sulfate-Dependent Anaerobic Degradation of Herbicide Acetochlor by a Sulfate-Reducing Bacterium Cupidesulfovibrio sp. SRB-5

Acetochlor, an important chloroacetamide herbicide (CAAH) widely used in agriculture, has resulted in environmental contamination, especially of anoxic habitats. In this study, a sulfate-reducing bacterium, designated as SRB-5, was isolated from anaerobic activated sludge and was identified as Cupidesulfovibrio sp. This bacterium possesses a novel anaerobic pathway capable of degrading acetochlor. In this pathway, sulfate is first reduced to sulfide, which attacks the C-Cl bond of acetochlor and abiotically forms acetochlor-thioalcohol and dis-S-acetochlor. These further undergo microbial degradation, producing the intermediates acetochlor ethanesulfonic acid, 2-methyl-6-ethylaniline, and 2-ethylaniline. The degradation half-times of acetochlor (100 μM) by strain SRB-5 were 2.4 and 4.2 days in industrial wastewater and paddy sludge, respectively. Strain SRB-5 could also degrade alachlor, propisochlor, butachlor, pretilachlor, and metolachlor, and the degradation kinetics fit the pseudo-first-order kinetics equation. This work highlights the potential application of strain SRB-5 for the remediation of CAAHs-contaminated sites.

Superabsorbent hydrogel as a formulation to promote mineralization and accelerate degradation of acetochlor in soils

The excessive use of herbicides had caused serious environmental pollution and ecological problems. Therefore, it is imperative to explore an effective method to reduce herbicide residues and pollution. In the present study, we used superabsorbent hydrogels coated ¹⁴C-acetochlor (SH-ACE) to investigate its behavior in different soils under oxic conditions. After 100 days, the mineralization by SH-ACE was increased by 2.3%, 2.5% and 3.3% in the red clay soils, fluvio-marine yellow loamy soils and coastal saline soils, respectively, compared to the control group. This result indicated that the SH-ACE treatment resulted in more complete degradation and detoxification of acetochlor. In addition, the dissipation rates of acetochlor were significantly faster in the SH-ACE treatment, which reduced the persistence of acetochlor. The probable degradation pathways of acetochlor involved dechlorination, hydroxylation, deethoxymethylation, and the formation of thioacetic acid derivatives in the two treatments, but the contents of transformation products were completely different. These findings suggest that the SH-ACE treatment has a significant effect to accelerate the degradation of acetochlor. When developing green pesticides, we emphasize that superabsorbent hydrogel coating treatment should be considered as a promising method for ecological safety in the environment.

Construction and comparison of synthetic microbial consortium system (SMCs) by non-living or living materials immobilization and application in acetochlor degradation

The microbial degradation of pesticides by pure or mixed microbial cultures has been thoroughly explored, however, they are still difficult to apply in real environmental remediation. Here, we constructed a synthetic microbial consortium system (SMCs) through the immobilization technology by non-living or living materials to improve the acetochlor degradation efficiency. Rhodococcus sp. T3-1, Delftia sp. T3-6 and Sphingobium sp. MEA3-1 were isolated for the SMCs construction. The free-floating consortium with the composition ratio of 1:2:2 (Rhodococcus sp. T3-1, Delftia sp. T3-6 and Sphingobium sp. MEA3-1) demonstrated 94.8% degradation of acetochlor, and the accumulation of intermediate metabolite 2-methyl-6-ethylaniline was decreased by 3 times. The immobilized consortium using composite materials showed synergistic effects on the acetochlor degradation with maximum degradation efficiency of 97.81%. In addition, a novel immobilization method with the biofilm of Myxococcus xanthus DK1622 as living materials was proposed. The maximum 96.62% degradation was obtained in non-trophic media. Furthermore, the immobilized SMCs showed significantly enhanced environmental robustness, reusability and stability. The results indicate the promising application of the immobilization methods using composite and living materials in pollutant-contaminated environments.

The Novel Amidase PcnH Initiates the Degradation of Phenazine-1-Carboxamide in Sphingomonas histidinilytica DS-9

Phenazines are an important class of secondary metabolites and are primarily named for their heterocyclic phenazine cores, including phenazine-1-carboxylic acid (PCA) and its derivatives, such as phenazine-1-carboxamide (PCN) and pyocyanin (PYO). Although several genes involved in the degradation of PCA and PYO have been reported so far, the genetic foundations of PCN degradation remain unknown. In this study, a PCN-degrading bacterial strain, Sphingomonas histidinilytica DS-9, was isolated. The gene pcnH, encoding a novel amidase responsible for the initial step of PCN degradation, was cloned by genome comparison and subsequent experimental validation. PcnH catalyzed the hydrolysis of the amide bond of PCN to produce PCA, which shared low identity (only 26 to 33%) with reported amidases. The K_m and k_cat values of PcnH for PCN were 33.22 ± 5.70 μM and 18.71 ± 0.52 s^-1, respectively. PcnH has an Asp-Lys-Cys motif, which is conserved among amidases of the isochorismate hydrolase-like (IHL) superfamily. The replacement of Asp37, Lys128, and Cys163 with alanine in PcnH led to the complete loss of enzymatic activity. Furthermore, the genes pcaA1A2A3A4 and pcnD were found to encode PCA 1,2-dioxygenase and 1,2-dihydroxyphenazine (2OHPC) dioxygenase, which were responsible for the subsequent degradation steps of PCN. The PCN-degradative genes were highly conserved in some bacteria of the genus Sphingomonas, with slight variations in the sequence identities. IMPORTANCE Phenazines have been widely acknowledged as a natural antibiotic for more than 150 years, but their degradation mechanisms are still not completely elucidated. Compared with the studies on the degradation mechanism of PCA and PYO, little is known regarding PCN degradation by far. Previous studies have speculated that its initial degradation step may be catalyzed by an amidase, but no further studies have been conducted. This study identified a novel amidase, PcnH, that catalyzed the hydrolysis of PCN to PCA. In addition, the PCA 1,2-dioxygenase PcaA1A2A3A4 and 2OHPC dioxygenase PcnD were also found to be involved in the subsequent degradation steps of PCN in S. histidinilytica DS-9. And the genes responsible for PCN catabolism are highly conserved in some strains of Sphingomonas. These results deepen our understanding of the PCN degradation mechanism.

Anaerobic biodegradation and detoxification of chloroacetamide herbicides by a novel Proteiniclasticum sediminis BAD-10T

Chloroacetamide herbicides (CAAHs) are important herbicides that were widely used to control agricultural weeds. However, their mass applications have seriously contaminated environment, and they are toxic to living beings. CAAHs are easy to enter anoxic environments such as subsoil, wetland sediment, and groundwater, where CAAHs are mainly degraded by anaerobic organisms. To date, there are no research on the anaerobic degradation of CAAHs by pure isolate and toxicity of anaerobic metabolites of CAAHs. In this study, the anaerobic degradation kinetics and metabolites of CAAHs by an anaerobic isolate BAD-10^T and the toxicity of anaerobic metabolites were studied. Isolate BAD-10^T could degrade alachlor, acetochlor, propisochlor, butachlor, pretilachlor and metolachlor with the degradation kinetics fitting the pseudo-first-order kinetics equation. The degradation rates of CAAHs were significantly affected by the length of N-alkoxyalkyl groups, the shorter the N-alkoxyalkyl groups, the higher the degradation rates. Four metabolites 2-ethyl-6-methyl-N-(ethoxymethyl)-acetanilide (EMEMA), N-(2-methyl-6-ethylphenyl)-acetamide (MEPA), N-2-ethylphenyl acetamide and 2-ethyl-N-carboxyl aniline were identified during acetochlor degradation, and an anaerobic catabolic pathway of acetochlor was proposed. The toxicity of EMEMA and EMPA for zebrafish, Arabidopsis and Chlorella ellipsoidea were obviously lower than that of acetochlor, indicating that the anaerobic degradation of acetochlor by isolate BAD-10^T is a detoxification process. The work reveals the anaerobic degradation kinetics and catabolic pathway of CAAHs and highlights a potential application of Proteiniclasticum sediminis BAD-10^T for bioremediation of CAAHs residue-contaminated environment.

Sinanaerobacter chloroacetimidivorans gen. nov., sp. nov., an obligate anaerobic bacterium isolated from anaerobic sludge

An obligate anaerobic bacterial strain (BAD-6^T) capable of degrading acetochlor and butachlor was isolated from an anaerobic acetochlor-degrading reactor. Cells were Gram-stain positive, straight to gently curved rods with flagella. The major fermentation products in peptone-yeast broth were acetate and butyrate. The optimum temperature and pH for growth was 30 °C and 7.2-7.5, respectively. The major cellular fatty acids (> 10%) were C_14:0 FAME, C_16:0 FAME and cyc-9,10-C_19:0 DMA. Genome sequencing revealed a genome size of 4.80 Mb, a G + C content of 43.6 mol% and 4741 protein-coding genes. The most closely related described species on the basis of 16S rRNA gene sequences was Anaerovorax odorimutans NorPut^T in the order Clostridiales of the class Clostridia with sequence similarity of 94.9%. The nucleotide identity (ANI) value and digital DNA-DNA hybridization (dDDH) between the genomes of strain BAD-6^T and Ana. odorimutans NorPut^T were 70.9% and 15.9%, respectively. Based on the distinct differences in phylogenetic and phenotypic characteristics between strain BAD-6^T and related species, Sinanaerobacter chloroacetimidivorans gen. nov., sp. nov. is proposed to accommodate the strain. Strain BAD-6^T is the type strain (= CCTCC AB 2021092^T = KCTC 25290^T).

Efficient removal of acetochlor pesticide from water using magnetic activated carbon: Adsorption performance, mechanism, and regeneration exploration

In this study, MnFe₂O₄ supported activated carbon magnetic adsorbent (MnFe₂O₄@AC) was successfully prepared by a simple one-pot solvothermal method and used for the adsorption and removal of acetochlor from aqueous media. Results showed that MnFe₂O₄@AC with a MnFe₂O₄/AC mass ratio of 1:2 was characterized by good magnetism and high acetochlor adsorption capacity over a wide ranging pH, ionic strength, and humic acid concentration in an aqueous solution. Acetochlor was adsorbed on MnFe₂O₄@AC mainly by hydrogen bonding, π-π interactions, and pore-filling via film, intraparticle, and pore diffusion steps. Adsorption reaction generally approached an equilibrium after 10 h, with the adsorption capacity being ca. 226 mg g^-1 for 0.2 g L^-1 adsorbent at 25 °C. Adsorbate (acetochlor) degradation and adsorbent regeneration were simultaneously achieved through heat-activated peroxymonosulfate (PMS) oxidation catalyzed by MnFe₂O₄ on the AC surface with >90% degradation efficiency at ≥9.6 mM PMS concentration at 70 °C within 12 h. However, the adsorption capacity of the regenerated adsorbent decreased by 50% of its original capacity. This needs to be addressed in future studies. MnFe₂O₄@AC adsorbent has the advantages of high adsorption capacity, good magnetism, and catalyzation, which are promising for adsorption, separation, and degradation for the effective removal and treatment of acetochlor as well as other organic contaminants in different types of waters.

Identification of novel catabolic genes involved in 17β-estradiol degradation by Novosphingobium sp. ES2-1

Novosphingobium sp. ES2-1 is an efficient 17β-estradiol (E2)-degrading bacterium, which can convert E2 to estrone (E1), then to 4-hydroxyestrone (4-OH-E1) for subsequent oxidative cracking. In this study, the molecular bases for this process were elucidated. Two novel monooxygenase systems EstP and EstO were shown to catalyse the oxygenation of E1 and 4-OH-E1, respectively. EstP was a three-component cytochrome P450 monooxygenase system consisting of EstP1 (P450 monooxygenase), EstP2 (ferredoxin) and EstP3 (ferredoxin reductase). Ultraperformance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) analysis revealed that EstP catalysed the 4-hydroxylation of E1 to produce 4-OH-E1. The resultant 4-OH-E1 was further oxidized by a two-component monooxygenase system EstO consisting of EstO1 (flavin-dependent monooxygenases) and EstO2 (flavin reductase). UPLC-HRMS combined with ¹ H-nuclear magnetic resonance analysis demonstrated that EstO catalysed the breakage of C9-C10 to yield a ring B-cleavage product. In addition, the oxygenase component genes estP1 and estO1 exhibited contrary inductive behaviours when exposed to different steroids, suggesting that EstP1-mediated 4-hydroxylation was E2-specific, whereas EstO1-mediated monooxygenation might be involved in the degradation of testosterone, androstenedione, progesterone and pregnenolone. This also implied that the mechanisms of the catabolism of different steroids by the same microorganism might be partially interlinked.

Carbamate C-N Hydrolase Gene ameH Responsible for the Detoxification Step of Methomyl Degradation in Aminobacter aminovorans Strain MDW-2

Methomyl {bis[1-methylthioacetaldehyde-O-(N-methylcarbamoyl)oximino]sulfide} is a highly toxic oxime carbamate insecticide. Several methomyl-degrading microorganisms have been reported so far, but the role of specific enzymes and genes in this process is still unexplored. In this study, a protein annotated as a carbamate C-N hydrolase was identified in the methomyl-degrading strain Aminobacter aminovorans MDW-2, and the encoding gene was termed ameH A comparative analysis between the mass fingerprints of AmeH and deduced proteins of the strain MDW-2 genome revealed AmeH to be a key enzyme of the detoxification step of methomyl degradation. The results also demonstrated that AmeH was a functional homodimer with a subunit molecular mass of approximately 34 kDa and shared the highest identity (27%) with the putative formamidase from Schizosaccharomyces pombe ATCC 24843. AmeH displayed maximal enzymatic activity at 50°C and pH 8.5. K_m and k _cat of AmeH for methomyl were 87.5 μM and 345.2 s^-1, respectively, and catalytic efficiency (k _cat/K_m ) was 3.9 μM^-1 s^-1 Phylogenetic analysis revealed AmeH to be a member of the FmdA_AmdA superfamily. Additionally, five key amino acid residues (162, 164, 191, 193, and 207) of AmeH were identified by amino acid variations.IMPORTANCE Based on the structural characteristic, carbamate insecticides can be classified into oxime carbamates (methomyl, aldicarb, oxamyl, etc.) and N-methyl carbamates (carbaryl, carbofuran, isoprocarb, etc.). So far, research on the degradation of carbamate pesticides has mainly focused on the detoxification step and hydrolysis of their carbamate bond. Several genes, such as cehA, mcbA, cahA, and mcd, and their encoding enzymes have also been reported to be involved in the detoxification step. However, none of these enzymes can hydrolyze methomyl. In this study, a carbamate C-N hydrolase gene, ameH, responsible for the detoxification step of methomyl in strain MDW-2 was cloned and the key amino acid sites of AmeH were investigated. These findings provide insight into the microbial degradation mechanism of methomyl.

Anaerobic biodegradation of acetochlor by acclimated sludge and its anaerobic catabolic pathway

Acetochlor is a chloroacetamide herbicide that has been widely used for weed control in recent decades. The contamination from its residue in the environment has raised major serious concerns. The aerobic degradation of acetochlor has been well studied; however, little is known regarding its anaerobic degradation. In the study, anaerobic sludge with high acetochlor degradation efficiency was obtained by pressure acclimation in a continuous flow anaerobic reactor. The acetochlor degradation dynamics followed a first-order kinetic reaction equation. The acclimated sludge could degrade six chloroacetamide herbicides with the degradation efficiencies observed as alachlor > acetochlor > propisochlor > butachlor > pretilachlor > metolachlor, and the N-alkoxyalkyl structure of these herbicides significantly affected their biodegradability. Five metabolites, 2-ethyl-6-methyl-N-(ethoxymethyl)-acetanilide, N-(2-methyl-6-ethylphenyl) acetamide, N-2-ethylphenyl acetamide, N-2-ethylphenyl formamide and 2-ethyl-N-carboxyl aniline were identified, and a putative anaerobic acetochlor degradation pathway, initiated by dechlorination, was subsequently proposed. During acclimation, the community diversity of both eubacteria and archaea in the anaerobic sludge decreased, while the abundance of microbes belonging to genera Sporomusa, Sporobacterium, Dechloromonas, Azotobacter and Methanobacterium were significantly increased and dominated the acclimated sludge, and showing a positive correlation with the acetochlor degradation capacity. These findings should be valuable to elucidate the mechanisms associated with the anaerobic catabolism of acetochlor and facilitate the engineering application of anaerobic treatment for removing acetochlor from wastewater.

Steel slag and biochar amendments decreased CO2 emissions by altering soil chemical properties and bacterial community structure over two-year in a subtropical paddy field

Waste amendments, such as steel slag and biochar, have been reported as a strategy for improving soil fertility, crop productivity, and carbon (C) sequestration in agricultural lands. However, information regarding the subsequent effects of steel slag and biochar on C cycling and the underlying microbial mechanisms in paddy soils remains limited. Hence, this study aimed to examine the effect of these waste amendments (applied in 2015-2017) on total soil CO₂ emissions, total and active soil organic C (SOC) contents, and microbial communities in the early and late seasons in a subtropical paddy field. The results showed that despite the exogenous C input from these waste amendments (steel slag, biochar and slag + biochar), they significantly (P < 0.05) decreased total CO₂ emissions (e.g., by 41.9-59.6% at the early season), compared to the control soil. These amendments also significantly (P < 0.001) increased soil salinity and pH. The increased soil pH had a negative effect (r = -0.37, P < 0.05) on microbial biomass C (MBC). The biochar and slag + biochar treatments (cf. control) significantly (P < 0.001) increased SOC contents in the both seasons. The amendments altered the soil microbial community structure that associated with soil C cycling: (1) all three amendments increased the relative abundance of Agromyces and Streptomyces, which was associated with higher soil pH (cf. control); and (2) biochar and slag + biochar treatments caused a higher relative abundance of Sphingomonas, which was supported by high SOC contents under those amendments. Overall, this study demonstrated that the steel slag and biochar amendments altered microbial community composition due to changes in key soil properties, such as salinity, pH and SOC contents, with implications for increasing soil C stocks while mitigating CO₂ emissions in the paddy field.

Characteristics and Diversity of Endophytic Bacteria in Endangered Chinese Herb Glehnia littoralis Based on Illumina Sequencing

Glehnia littoralis is an endangered medicinal plant growing in the coastal ecological environment and plays an important role in coastal ecosystems. The endophytes in the plant have a significant role in promoting plant growth and enhancing plant stress resistance. However, the endophytic bacterial structure associated with halophyte G. littoralis is still not revealed. In this project, the construction and diversity of endophytic bacterial consortium associated with different tissues of G. littoralis were illustrated with high throughput sequencing of the V3-V4 region of the bacterial 16S rRNA. The results resolved that the diversity and richness of endophytic bacteria were significantly higher in root than in leaf and stem. The operational taxonomic units (OTU) analysis demonstrated that the Actinobacteria and Proteobacteria were dominant in all the samples at the phylum level, and Pseudomonas, Bacillus, Rhizobium were the dominant genera. Our results unraveled that the bacterial communities differed among different tissues of G. littoralis. Endophytic bacterial communities in leaf and stem shared more similarity than that in the root. Furthermore, the difference of bacteria community and structure among different tissues were also detected by principal coordinate analysis. Taken altogether, we can conclude that the bacterial communities of different tissues are unique, which could facilitate understanding the diversity of endophytic bacteria in G. littoralis.

Characterization of a Linuron-Specific Amidohydrolase from the Newly Isolated Bacterium Sphingobium sp. Strain SMB

The phenylurea herbicide linuron is globally used and has caused considerable concern because it leads to environmental pollution. In this study, a highly efficient linuron-transforming strain Sphingobium sp. SMB was isolated, and a gene (lahB) responsible for the hydrolysis of linuron to 3,4-dichloroaniline and N,O-dimethylhydroxylamine was cloned from the genome of strain SMB. The lahB gene encodes an amidohydrolase, which shares 20-53% identity with other biochemically characterized amidohydrolases, except for the newly reported linuron hydrolase Phh (75%). The optimal conditions for the hydrolysis of linuron by LahB were determined to be pH 7.0 and 30 °C, and the K_m value of LahB for linuron was 37.3 ± 1.2 μM. Although LahB and Phh shared relatively high identity, LahB exhibited a narrow substrate spectrum (specific for linuron) compared to Phh (active for linuron, diuron, chlortoluron, etc.). Sequence analysis and site-directed mutagenesis revealed that Ala261 of Phh was the key amino acid residue affecting the substrate specificity. Our study provides a new amidohydrolase for the specific hydrolysis of linuron.

Mineralization of the herbicide swep by a two-strain consortium and characterization of a new amidase for hydrolyzing swep

BACKGROUND

Swep is an excellent carbamate herbicide that kills weeds by interfering with metabolic processes and inhibiting cell division at the growth point. Due to the large amount of use, swep residues in soil and water not only cause environmental pollution but also accumulate through the food chain, ultimately pose a threat to human health. This herbicide is degraded in soil mainly by microbial activity, but no studies on the biotransformation of swep have been reported.

RESULTS

In this study, a consortium consisting of two bacterial strains, Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34, was enriched from a contaminated soil sample and shown to be capable of mineralizing swep. Swep was first transformed by Comamonas sp. SWP-3 to the intermediate 3,4-dichloroaniline (3,4-DCA), after which 3,4-DCA was mineralized by Alicycliphilus sp. PH-34. An amidase gene, designated as ppa, responsible for the transformation of swep into 3,4-DCA was cloned from strain SWP-3. The expressed Ppa protein efficiently hydrolyzed swep and a number of other structural analogues, such as propanil, chlorpropham and propham. Ppa shared less than 50% identity with previously reported arylamidases and displayed maximal activity at 30 °C and pH 8.6. Gly449 and Val266 were confirmed by sequential error prone PCR to be the key catalytic sites for Ppa in the conversion of swep.

CONCLUSIONS

These results provide additional microbial resources for the potential remediation of swep-contaminated sites and add new insights into the catalytic mechanism of amidase in the hydrolysis of swep.

Mitigation of environmental pollution by genetically engineered bacteria - Current challenges and future perspectives

Industries are the paramount driving force for the economic and technological development of society. However, the flourishing industrialization and unimpeded growth of current production unit's result in widespread environmental pollution due to increased discharge of wastes loaded with baleful, hazardous, and carcinogenic contaminants. Physicochemical-based remediation means are costly, create a secondary disposal problem and remain inadequate for pollution mitigating because of the continuous emergence of new recalcitrant pollutants. Due to eco-friendly, social acceptance, and lesser health hazards, microbial bioremediation has received considerable global attention for pollution abatement. Moreover, with the recent advancement in biotechnology and microbiology, genetically engineered bacteria with high ability to remove environmental pollutants are widely used in the fields of environmental restoration, resulting in the bioremediation in a more viable and eco-friendly way. This review summarized the advantages of genetically engineered bacteria and their application in the treatment of a wide variety of environmental contaminants such as synthetic dyestuff, heavy metal, petroleum hydrocarbons, polychlorinated biphenyls, phenazines and agricultural chemicals which will include herbicides, pesticides, and fertilizers. Considering the risk of genetic material exchange by using genetically engineered bacteria, the challenges and limitations associated with the application of recombinant bacteria on contaminated sites are also discussed. An integrated microbiological, biological and ecological acquaintance accompanied by field engineering designs are the desired features for effective in situ bioremediation of hazardous waste polluted sites by recombinant bacteria.

Comparative genome analysis reveals the evolution of chloroacetanilide herbicide mineralization in Sphingomonas wittichii DC-6

The environmental fate of the extensively used chloroacetanilide herbicides (CH) has been a cause of increasing concern in the past decade because of their carcinogenic properties. Although microbes play important roles in CH degradation, Sphingomonas wittichii DC-6 was the first reported CH-mineralizing bacterium. In this study, the complete genome of strain DC-6 was sequenced and comparative genomic analysis was performed using strain DC-6 and other three partial CH-degrading bacteria, Sphingobium quisquiliarum DC-2, Sphingobium baderi DE-13, and Sphingobium sp. MEA3-1. 16S rDNA phylogenetic analysis indicated that strain DC-2, MEA3-1, and DE-13 are closely related and DC-6 has relatively distant genetic relationship with the other three strains. The identified CH degradation genes responsible for the upstream and downstream pathway, including cndA, cmeH, meaXY, and meaAB, were all located in conserved DNA fragments (or genetic islands) in the vicinity of mobile element proteins. Protein BLAST in the NCBI database showed that cndA and cmeH were present in the genomes of other sequenced strains isolated from various habitats; however, the gene compositions in these host strains were completely different from those of other sphingomonads, and codon usage of genes for upstream pathway were also different from that of downstream pathway. These results showed that the upstream and downstream pathways of CH degradation in strain DC-6 have evolved by horizontal gene transfer and gene combination. In addition, the genes of the ring-cleavage pathway were not conserved and may have evolved directly from bacterial degradation of hydroxyquinol. The present study provides insights into the evolutionary strategy and microbial catabolic pathway of CH mineralization.

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

Naturally occurring plasmids constitute a major category of mobile genetic elements responsible for harboring and transferring genes important in survival and fitness. A targeted evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We developed a model system to optimize plasmid DNA isolation procedures targeted to groundwater samples which are typically characterized by low cell density (and likely variations in the plasmid size and copy numbers). The optimized method resulted in successful identification of several hundred circular plasmids, including some large plasmids (11 plasmids more than 50 kb in size, with the largest being 1.7 Mb in size). Several interesting observations were made from the analysis of plasmid DNA isolated in this study. The plasmid pool (plasmidome) was more conserved than the corresponding microbiome distribution (16S rRNA based). The circular plasmids were diverse as represented by the presence of seven plasmid incompatibility groups. The genes carried on these groundwater plasmids were highly enriched in metal resistance. Results from this study confirmed that traits such as metal, antibiotic, and phage resistance along with toxin-antitoxin systems are encoded on abundant circular plasmids, all of which could confer novel and advantageous traits to their hosts. This study confirms the ecological role of the plasmidome in maintaining the latent capacity of a microbiome, enabling rapid adaptation to environmental stresses.IMPORTANCE Plasmidomes have been typically studied in environments abundant in bacteria, and this is the first study to explore plasmids from an environment characterized by low cell density. We specifically target groundwater, a significant source of water for human/agriculture use. We used samples from a well-studied site and identified hundreds of circular plasmids, including one of the largest sizes reported in plasmidome studies. The striking similarity of the plasmid-borne ORFs in terms of taxonomical and functional classifications across several samples suggests a conserved plasmid pool, in contrast to the observed variability in the 16S rRNA-based microbiome distribution. Additionally, the stress response to environmental factors has stronger conservation via plasmid-borne genes as marked by abundance of metal resistance genes. Last, identification of novel and diverse plasmids enriches the existing plasmid database(s) and serves as a paradigm to increase the repertoire of biological parts that are available for modifying novel environmental strains.

Characterization of an arylamidase from a newly isolated propanil-transforming strain of Ochrobactrum sp. PP-2

Propanil, one of the most extensively used post-emergent contact herbicides, has also been reported to have adverse effect on environmental safety. A bacterial strain of Ochrobactrum sp. PP-2, which was capable of transforming propanil, was isolated from a propanil-contaminated soil collected from a chemical factory. An arylamidase gene mah responsible for transforming propanil to 3,4-dichloroaniline (3,4-DCA) was cloned from strain PP-2 by shotgun method and subsequently confirmed by function expression. The arylamidase Mah shares low amino acid sequence identity (27-50%) with other biochemically characterized amidases and shows less than 30% identities to other reported propanil hydrolytic enzymes. Mah was most active at pH 8 and 35 °C. Mah had a remarkable activity toward propanil (K_m = 6.3 ± 1.2 µM), showing the highest affinity efficiency for propanil as compared with other reported propanil hydrolytic enzymes. Our study also provides a new arylamidase for the hydrolysis of propanil.

Optimization of fed-batch fermentation and direct spray drying in the preparation of microbial inoculant of acetochlor-degrading strain Sphingomonas sp. DC-6

Microbial inoculant preparation is a prerequisite for its application in large-scale bioremediation. In the present study, Sphingomonas sp. DC-6, an efficient acetochlor-degrading strain, was used to investigate the process of preparing the inoculant. Optimization of submerged fermentation (SmF) by response surface methodology (RSM) resulted in a first 22% increase in biomass of liquid inoculant. Then, a biomass increase of 2.18 times with 14.58% shortened incubation period was further obtained in optimized medium using a 7.5-l bioreactor. However, less than 0.4% viable cells in liquid inoculant survived after 180-days storage. Thus, optimized spray drying conditions were subsequently employed for the production of high viability powder (2.11 × 10¹² cfu g^- 1 powder) without additive and its survival ratio (SR) after 180-days storage was still maintained at 90.5%. Both the 180-days stored powder and the original powder showed the same degradation performance, being able to completely degrade 200 mg l^- 1 acetochlor within 48 h. This study demonstrated that strain DC-6 was suitable for industrial production of bacteria powder and provided a potential approach for the preparation of pesticide-degrading microbial inoculant.

Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales

The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C₄₀ carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales. Comparative analyses of the genomes of 41 strains of this order revealed that there were different patterns of clustering of carotenoid biosynthesis (crt) ORFs, with four ORF clusters being the most common. The analyses also revealed that co-occurrence of crtY and crtI is an evolutionarily conserved feature in Sphingomonadales and other carotenogenic bacteria. The comparisons facilitated the categorisation of bacteria of this order into four groups based on the presence of different crt ORFs. Yellow coloured strains most likely accumulate nostoxanthin, and contain six ORFs (group I: crtE, crtB, crtI, crtY, crtZ, crtG). Orange coloured strains may produce adonixanthin, astaxanthin, canthaxanthin and erythroxanthin, and contain seven ORFs (group II: crtE, crtB, crtI, crtY, crtZ, crtG, crtW). Red coloured strains may accumulate astaxanthin, and contain six ORFs (group III: crtE, crtB, crtI, crtY, crtZ, crtW). Non-pigmented strains may contain a smaller subset of crt ORFs, and thus fail to produce any carotenoids (group IV). The functions of many of these ORFs remain to be characterised.

Expression and characterization of the key enzymes involved in 2-benzoxazolinone degradation by Pigmentiphaga sp. DL-8

In this study, the key enzymes involved in 2-benzoxazolinone (BOA) degradation by Pigmentiphaga sp. DL-8 were further verified and characterized in Escherichia coli. By codon optimization and co-expression of molecular chaperones in a combined strategy, recombinant BOA amidohydrolase (rCbaA) and 2-aminophenol (2-AP) 1,2-dioxygenase (rCnbC_αC_β) were expressed and purified with the highest activity of 1934.6U·mgprotein^-1 and 32.80U·mgprotein^-1, respectively. BOA could be hydrolyzed to 2AP by rCbaA, which was further transformed to picolinic acid by rCnbC_αC_β based on identified catalytic product. The optimal pH and temperature for rCbaA are 9.0 and 55°C with excellent stability for catalytic environments, and the residual activity was >50% after incubation at temperatures <45°C or at pH between 6.0 and 10.0 for 24h. On the contrary, rCnbC_αC_β composed of α-subunit (33kDa) and β-subunit (38kDa) showed poor stability against environmental factors, including temperature, pH, metal ions and chemicals.

Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica

Halophytes play important roles in coastal ecosystems. However, few reports have described bacterial communities related to halophytes, and the distribution patterns of these bacteria in different plant tissues have been rarely compared. This paper mainly studied the diversity and community structure of endophytic and rhizosphere (Rh) bacteria related to the halophyte Messerschmidia sibirica, a dominant species in the coastal zone of Shandong Peninsula, China. We collected leaf (Lf), stem (Sm), root (Rt), Rh, and bulk (Bl) control soil samples, and sequenced the V5–V7 region of the bacterial 16S rRNA gene using the Illumina HiSeq platform to identify bacterial communities originating from different plant habitats. We found that the bacterial richness and diversity in Rh were significantly higher than those in the leaves, Sm, and Rt, but lower than those of the Bl control soil. In total, 37 phyla and 438 genera were identified. Microbial-diversity analysis showed that Proteobacteria and Actinobacteria were the dominant phyla and that Pseudomonas, Bacillus, Sphingomonas, Streptomyces, Microbacterium, Rhizobium, and Nocardioides were the dominant genera. However, there were clear differences in community diversity and structure among the samples. Endophytic bacteria community in Lf, Sm, and Rt shared more similarity than those in Rh and Bl control soil. The numbers of operational taxonomic units exclusive to the Lf, stem, Rt, Rh, and Bl control soil samples were 51, 43, 122, 139, and 922, respectively, implying habitat-specific patterns. Principal coordinate analysis demonstrated differences were apparent in the bacterial communities associated with habitats. On the whole, M. sibirica affected bacterial diversity and structured the bacterial community. This study provides insight into the complex microbial compositions of coastal halophytes.

Microbial catabolism of chemical herbicides: Microbial resources, metabolic pathways and catabolic genes

Chemical herbicides are widely used to control weeds and are frequently detected as contaminants in the environment. Due to their toxicity, the environmental fate of herbicides is of great concern. Microbial catabolism is considered the major pathway for the dissipation of herbicides in the environment. In recent decades, there have been an increasing number of reports on the catabolism of various herbicides by microorganisms. This review presents an overview of the recent advances in the microbial catabolism of various herbicides, including phenoxyacetic acid, chlorinated benzoic acid, diphenyl ether, tetra-substituted benzene, sulfonamide, imidazolinone, aryloxyphenoxypropionate, phenylurea, dinitroaniline, s-triazine, chloroacetanilide, organophosphorus, thiocarbamate, trazinone, triketone, pyrimidinylthiobenzoate, benzonitrile, isoxazole and bipyridinium herbicides. This review highlights the microbial resources that are capable of catabolizing these herbicides and the mechanisms involved in the catabolism. Furthermore, the application of herbicide-degrading strains to clean up herbicide-contaminated sites and the construction of genetically modified herbicide-resistant crops are discussed.

The Two-Component Monooxygenase MeaXY Initiates the Downstream Pathway of Chloroacetanilide Herbicide Catabolism in Sphingomonads

Due to the extensive use of chloroacetanilide herbicides over the past 60 years, bacteria have evolved catabolic pathways to mineralize these compounds. In the upstream catabolic pathway, chloroacetanilide herbicides are transformed into the two common metabolites 2-methyl-6-ethylaniline (MEA) and 2,6-diethylaniline (DEA) through N-dealkylation and amide hydrolysis. The pathway downstream of MEA is initiated by the hydroxylation of aromatic rings, followed by its conversion to a substrate for ring cleavage after several steps. Most of the key genes in the pathway have been identified. However, the genes involved in the initial hydroxylation step of MEA are still unknown. As a special aniline derivative, MEA cannot be transformed by the aniline dioxygenases that have been characterized. Sphingobium baderi DE-13 can completely degrade MEA and use it as a sole carbon source for growth. In this work, an MEA degradation-deficient mutant of S. baderi DE-13 was isolated. MEA catabolism genes were predicted through comparative genomic analysis. The results of genetic complementation and heterologous expression demonstrated that the products of meaX and meaY are responsible for the initial step of MEA degradation in S. baderi DE-13. MeaXY is a two-component flavoprotein monooxygenase system that catalyzes the hydroxylation of MEA and DEA using NADH and flavin mononucleotide (FMN) as cofactors. Nuclear magnetic resonance (NMR) analysis confirmed that MeaXY hydroxylates MEA and DEA at the para-position. Transcription of meaX was enhanced remarkably upon induction of MEA or DEA in S. baderi DE-13. Additionally, meaX and meaY were highly conserved among other MEA-degrading sphingomonads. This study fills a gap in our knowledge of the biochemical pathway that carries out mineralization of chloroacetanilide herbicides in sphingomonads.IMPORTANCE Much attention has been paid to the environmental fate of chloroacetanilide herbicides used for the past 60 years. Microbial degradation is considered an important mechanism in the degradation of these compounds. Bacterial degradation of chloroacetanilide herbicides has been investigated in many recent studies. Pure cultures or consortia able to mineralize these herbicides have been obtained. The catabolic pathway has been proposed, and most key genes involved have been identified. However, the genes responsible for the initiation step (from MEA to hydroxylated MEA or from DEA to hydroxylated DEA) of the downstream pathway have not been reported. The present study demonstrates that a two-component flavin-dependent monooxygenase system, MeaXY, catalyzes the para-hydroxylation of MEA or DEA in sphingomonads. Therefore, this work finds a missing link in the biochemical pathway that carries out the mineralization of chloroacetanilide herbicides in sphingomonads. Additionally, the results expand our understanding of the degradation of a special kind of aniline derivative.

Isolation, identification, and acetochlor-degrading potential of a novel Rhodococcus sp. MZ-3

A new species of Rhodococcus, designated strain MZ-3, which could degrade acetochlor efficiently were isolated and identified. The isolate could degrade and utilize acetochlor as the sole source of carbon, nitrogen, and energy for growth. The optimal conditions for the degradation and growth of MZ-3 were pH 7.0 and 30°C. Under these conditions, this strain could completely degrade 200 mg/L of acetochlor within 12 h of incubation. During the biodegradation process, the enantioselectivity of the strain was investigated using a chiral high-performance liquid chromatography (HPLC) system. However, no obvious enantioselectivities were found. 2-chloro-N-(2-methyl-6-ethylphenyl) acetamide (CMEPA) was detected as the intermediate using liquid chromatography-mass spectrometry (LC-MS) analyses. Our results suggest that strain MZ-3 might be a promising microorganism for the bioremediation of acetochlor-contaminated environments because of its acetochlor-degrading performance.

A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site

1,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was determined in three aerobic DCA-degrading bacteria (Starkeya novella strain EL1, Xanthobacter autotrophicus strain EL4, and Xanthobacter flavus strain EL8) isolated from a groundwater treatment plant (GTP). A haloalkane dehalogenase gene (dhlA) identical to the canonical dhlA gene from Xanthobacter sp. strain GJ10 was present in all three isolates, and, in each case, the dhlA gene was carried on a variant of a 37-kb circular plasmid, which was named pDCA. Sequence analysis of the repA replication initiator gene indicated that pDCA was a member of the pTAR plasmid family, related to catabolic plasmids from the Alphaproteobacteria, which enable growth on aromatics, dimethylformamide, and tartrate. Genes for plasmid replication, mobilization, and stabilization were identified, along with two insertion sequences (ISXa1 and ISPme1) which were likely to have mobilized dhlA and dhlB and played a role in the evolution of aerobic DCA-degrading bacteria. Two haloacid dehalogenase genes (dhlB1 and dhlB2) were detected in the GTP isolates; dhlB1 was most likely chromosomal and was similar to the canonical dhlB gene from strain GJ10, while dhlB2 was carried on pDCA and was not closely related to dhlB1 Heterologous expression of the DhlB2 protein confirmed that this plasmid-borne dehalogenase was capable of chloroacetate dechlorination.

IMPORTANCE

Earlier studies on the DCA-degrading Xanthobacter sp. strain GJ10 indicated that the key dehalogenases dhlA and dhlB were carried on a 225-kb linear plasmid and on the chromosome, respectively. The present study has found a dramatically different gene organization in more recently isolated DCA-degrading Xanthobacter strains from Australia, in which a relatively small circular plasmid (pDCA) carries both dhlA and dhlB homologs. pDCA represents a true organochlorine-catabolic plasmid, first because its only obvious metabolic phenotype is dehalogenation of organochlorines, and second because acquisition of this plasmid provides both key enzymes required for carbon-chlorine bond cleavage. The discovery of the alternative haloacid dehalogenase dhlB2 in pDCA increases the known genetic diversity of bacterial chloroacetate-hydrolyzing enzymes.

Effects of Selected Herbicides on Growth and Nitrogen Fixing Activity of Stenotrophomonas maltophilia (Sb16)

A study was carried out to determine the effects of paraquat, pretilachlor and 2, 4-D on growth and nitrogen fixing activity of Stenotrophomonas maltophilia (Sb16) and pH of Jensen's N-free medium. The growth of Sb16 and pH of medium were significantly reduced with full (X) and double (2X) doses of tested herbicides, but nitrogen fixing activity was decreased by 2X doses. The nitrogenase activity had the highest value in samples treated with 1/2X of 2, 4-D on fifth incubation day, but 2X of 2, 4-D had the most adverse effect. An inhibition in the growth and nitrogenase activity was recovered on the last days of incubation.

Characterization of a Novel Butachlor Biodegradation Pathway and Cloning of the Debutoxylase (Dbo) Gene Responsible for Debutoxylation of Butachlor in Bacillus sp. hys-1

Bacillus sp. strain hys-1, which was isolated from active sludge, could degrade >90% butachlor at a concentration of 100 mg/L within 7 days. The present work revealed that strain hys-1 could mineralize butachlor via the following pathway: butachlor was initially metabolized to 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide by debutoxylation and then transformed to form 2-chloro-N-(2,6-diethylphenyl)acetamide by N-demethylation. Subsequently, it was converted to 2,6-diethylaniline and further mineralized into CO2 and H2O. In addition, the catalytic efficiency of crude cell extracts descended as follows: alachlor > acetochlor > butachlor. Furthermore, a novel 744 bp gene responsible for transforming butachlor into 2-chloro-N-(2,6-diethylphenyl)-N-methylacetamide was cloned from strain hys-1 and the encoding debutoxylase was designated Dbo. Then Dbo was expressed in Escherichia coli BL21 (DE3) and purified using Ni-nitrilotriacetic acid affinity chromatography. Dbo displayed the highest activity against butachlor at pH 6.5 and 30 °C. Metal ions played an important role in Dbo activity. To the best of the authors' knowledge, this is the first report that strain hys-1 can mineralize butachlor by a novel metabolic mechanism and the first identification of a gene encoding butachlor debutoxylase.

Metabolic pathway involved in 2-methyl-6-ethylaniline degradation by Sphingobium sp. strain MEA3-1 and cloning of the novel flavin-dependent monooxygenase system meaBA

2-Methyl-6-ethylaniline (MEA) is the main microbial degradation intermediate of the chloroacetanilide herbicides acetochlor and metolachlor. Sphingobium sp. strain MEA3-1 can utilize MEA and various alkyl-substituted aniline and phenol compounds as sole carbon and energy sources for growth. We isolated the mutant strain MEA3-1Mut, which converts MEA only to 2-methyl-6-ethyl-hydroquinone (MEHQ) and 2-methyl-6-ethyl-benzoquinone (MEBQ). MEA may be oxidized by the P450 monooxygenase system to 4-hydroxy-2-methyl-6-ethylaniline (4-OH-MEA), which can be hydrolytically spontaneously deaminated to MEBQ or MEHQ. The MEA microbial metabolic pathway was reconstituted based on the substrate spectra and identification of the intermediate metabolites in both the wild-type and mutant strains. Plasmidome sequencing indicated that both strains harbored 7 plasmids with sizes ranging from 6,108 bp to 287,745 bp. Among the 7 plasmids, 6 were identical, and pMEA02' in strain MEA3-1Mut lost a 37,000-bp fragment compared to pMEA02 in strain MEA3-1. Two-dimensional electrophoresis (2-DE) and protein mass fingerprinting (PMF) showed that MEA3-1Mut lost the two-component flavin-dependent monooxygenase (TC-FDM) MeaBA, which was encoded by a gene in the lost fragment of pMEA02. MeaA shared 22% to 25% amino acid sequence identity with oxygenase components of some TC-FDMs, whereas MeaB showed no sequence identity with the reductase components of those TC-FDMs. Complementation with meaBA in MEA3-1Mut and heterologous expression in Pseudomonas putida strain KT2440 resulted in the production of an active MEHQ monooxygenase.

Mechanism study of alachlor biodegradation by Paecilomyces marquandii with proteomic and metabolomic methods

Alachlor is an herbicide that is widely used worldwide to protect plant crops against broadleaf weeds and annual grasses. However, due to its endocrine-disrupting activity, its application had been banned in the European Union. As described in our earlier work, Paecilomyces marquandii is a microscopic fungus capable of alachlor removal by N-acetyl oxidation. Our current work uses proteomics and metabolomics to gain a better understanding of alachlor biodegradation by the microscopic fungus P. marquandii. The data revealed that the addition of alachlor reduced the culture growth and glucose consumption rates. Moreover, the rates of glycolysis and the tricarboxylic acids (TCA) cycle increased during the initial stage of growth, and there was a shift toward the formation of supplementary materials (UDP-glucose/galactose) and reactive oxygen species (ROS) scavengers (ascorbate). Proteomic analysis revealed that the presence of xenobiotics resulted in a strong upregulation of enzymes related to energy, sugar metabolism and ROS production. However, the unique overexpression of cyanide hydratase in alachlor-containing cultures may implicate this enzyme as the key protein involved in the alachlor biodegradation pathway. The characterization of P. marquandii-mediated alachlor removal in terms of cell structure and function provides a deeper insight into the strategies of microorganisms toward xenobiotic biodegradation.

Biodegradation of fenoxaprop-P-ethyl (FE) by Acinetobacter sp. strain DL-2 and cloning of FE hydrolase gene afeH

Fenoxaprop-P-ethyl (FE) is widely used as a post-emergence aryloxyphenoxy propionate (AOPP) herbicide in agriculture. An efficient FE-degrading strain DL-2 was isolated from the enrichment culture and identified as Acinetobacter sp. and the metabolite fenoxaprop acid (FA) was identified by HPLC/MS analysis. The strain DL-2 could also degrade a wide range of other AOPP herbicides. A novel FE hydrolase esterase gene afeH was cloned from strain DL-2 and functionally expressed in Escherichia coli BL21(DE3). The specific activities of recombinant AfeH was 216.39 U mg(-1) for FE with Km and Vmax values of 0.82 μM and 7.94 μmol min(-1) mg(-1). AfeH could also hydrolyze various AOPP herbicides, p-nitrophenyl esters and triglycerides. The optimal pH and temperature for recombinant AfeH were 9.0 and 50°C, respectively; the enzyme was activated by Co(2+) and inhibited by Ca(2+), Zn(2+), Ba(2+). AfeH was inhibited strongly by phenylmethylsulfonyl and SDS and weakly by dimethyl sulfoxide.

Involvement of the cytochrome P450 system EthBAD in the N-deethoxymethylation of acetochlor by Rhodococcus sp. strain T3-1

Acetochlor [2-chloro-N-(ethoxymethyl)-N-(2-ethyl-6-methylphenyl)-acetamide] is a widely applied herbicide with potential carcinogenic properties. N-Deethoxymethylation is the key step in acetochlor biodegradation. N-Deethoxymethylase is a multicomponent enzyme that catalyzes the conversion of acetochlor to 2'-methyl-6'-ethyl-2-chloroacetanilide (CMEPA). Fast detection of CMEPA by a two-enzyme (N-deethoxymethylase-amide hydrolase) system was established in this research. Based on the fast detection method, a three-component enzyme was purified from Rhodococcus sp. strain T3-1 using ammonium sulfate precipitation and hydrophobic interaction chromatography. The molecular masses of the components of the purified enzyme were estimated to be 45, 43, and 11 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Based on the results of peptide mass fingerprint analysis, acetochlor N-deethoxymethylase was identified as a cytochrome P450 system, composed of a cytochrome P450 oxygenase (43-kDa component; EthB), a ferredoxin (45 kDa; EthA), and a reductase (11 kDa; EthD), that is involved in the degradation of methyl tert-butyl ether. The gene cluster ethABCD was cloned by PCR amplification and expressed in Escherichia coli BL21(DE3). Resting cells of a recombinant E. coli strain showed deethoxymethylation activity against acetochlor. Subcloning of ethABCD showed that ethABD expressed in E. coli BL21(DE3) has the activity of acetochlor N-deethoxymethylase and is capable of converting acetochlor to CMEPA.

Metabolic fate of the (14)C-labeled herbicide clodinafop-propargyl in a sediment-water system

The metabolic fate of (14)C-phenyl-labeled herbicide clodinafop-propargyl ((14)C-CfP) was studied for 28 days in lab assays using a sediment-water system derived from a German location. Mineralization was 5.21% of applied (14)C after 28 days exhibiting a distinct lag phase until day 14 of incubation. Portions of radioactivity remaining in water phases decreased at moderate rate to 18.48% after 28 days; 62.46% were still detected in water after 14 days. Soxhlet extraction of the sediment using acetonitrile released 35.56% of applied (14)C with day 28, while 33.99% remained as non-extractable residues. A remarkable increase of bound (14)C was observed between 14 and 28 days correlating with the distinct increase of mineralization. No correlation was found throughout incubation with microbial activity of the sediment as determined by dimethyl sulfoxide reduction. Dissolved oxygen and pH value of water phases remained almost constant for 28 days. Analyses of Soxhlet extracts of the sediment and ethyl acetate extracts of water phases by radio-TLC and radio-HPLC revealed that CfP was rapidly cleaved to free acid clodinafop (Cf), which was further (bio-) transformed. DT50 values (based on radio-HPLC) were below 1 day (CfP) and slightly above 28 days (Cf). Further metabolites were not detected. Fractionation of humic and non-humic components of the sediment demonstrated that CfP's non-extractable residues were predominantly associated with fulvic acids up to 14 days of incubation (3.36%), whereas after 28 days, the majority of radioactivity was found in the humin/mineral fraction (13.30% of applied (14)C). Due to high-performance size-exclusion chromatography of the fulvic acids fraction derived from assays incubated for 28 days, this portion of (14)C was firmly, possibly covalently bound to fulvic acids and did not consist of CfP or Cf. Using an isolation strategy comprising preincubation of sediment with CfP and mineralization of (14)C-CfP as criterion, a microorganism was isolated from the sediment examined. It grew on (14)C-CfP as sole carbon source with evolution of (14)CO2. The bacterium was characterized by growth on commonly used carbon sources and 16S rDNA sequence analysis. Its sequence exhibited high similarity with that of Nocardioides aromaticivorans strain H-1 (98.85%; DSM 15131, JCM 11674).

Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide–degrading bacterium isolated from activated sludge

Strain BUT-14T, a Gram-reaction-negative, non-spore-forming, ellipse-shaped bacterium, was isolated from activated sludge of a chloroacetamide-herbicides-manufacturing wastewater treatment facility. The strain was able to degrade more than 90 % of butachlor, acetochlor and alachlor (100 mg l−1) within 5 days of incubation. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-14T was a member of the genus Novosphingobium and showed the highest sequence similarities to Novosphingobium soli DSM 22821T (97.9 %), N. naphthalenivorans KACC 15258T (97.4 %), N. pentaromativorans JCM 12182T (97.4 %) and N. barchaimii DSM 25411T (97.1 %) and lower (<97 %) sequence similarities to all other species of the genus Novosphingobium . Chemotaxonomic analysis revealed that strain BUT-14T possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine and C18 : 1ω7c (46.9 %), C17 : 1ω6c (17.9 %), summed feature 3, C14 : 0 2-OH (4.4 %), C15 : 0 2-OH (3.1 %) and C16 : 0 (5.51 %) as the major fatty acids. The polar lipids included lipid, glycolipid, phosphatidylglycerol, phospholipid, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and phospatidyldimethylethanolamine. Strain BUT-14T showed low DNA–DNA relatedness with N. soli DSM 22821T (41.5±2.9 %), N. naphthalenivorans JCM 12182T (49.2±4.2 %), N. pentaromativorans KACC 12295T (53.2±1.9 %) and N. barchaimii DSM 25411 (51.2±4.5 %). The DNA G+C content was 66±0.3 mol%. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic data and DNA–DNA hybridization supports the suggestion that strain BUT-14T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium chloroacetimidivorans sp. nov. is proposed. The type strain is BUT-14T ( = CCTCC AB 2013086T = KACC 17147T = JCM 19923T).

Novel three-component Rieske non-heme iron oxygenase system catalyzing the N-dealkylation of chloroacetanilide herbicides in sphingomonads DC-6 and DC-2

Sphingomonads DC-6 and DC-2 degrade the chloroacetanilide herbicides alachlor, acetochlor, and butachlor via N-dealkylation. In this study, we report a three-component Rieske non-heme iron oxygenase (RHO) system catalyzing the N-dealkylation of these herbicides. The oxygenase component gene cndA is located in a transposable element that is highly conserved in the two strains. CndA shares 24 to 42% amino acid sequence identities with the oxygenase components of some RHOs that catalyze N- or O-demethylation. Two putative [2Fe-2S] ferredoxin genes and one glutathione reductase (GR)-type reductase gene were retrieved from the genome of each strain. These genes were not located in the immediate vicinity of cndA. The four ferredoxins share 64 to 72% amino acid sequence identities to the ferredoxin component of dicamba O-demethylase (DMO), and the two reductases share 62 to 65% amino acid sequence identities to the reductase component of DMO. cndA, the four ferredoxin genes, and the two reductases genes were expressed in Escherichia coli, and the recombinant proteins were purified using Ni-affinity chromatography. The individual components or the components in pairs displayed no activity; the enzyme mixture showed N-dealkylase activities toward alachlor, acetochlor, and butachlor only when CndA-His6 was combined with one of the four ferredoxins and one of the two reductases, suggesting that the enzyme consists of three components, a homo-oligomer oxygenase, a [2Fe-2S] ferredoxin, and a GR-type reductase, and CndA has a low specificity for the electron transport component (ETC). The N-dealkylase utilizes NADH, but not NADPH, as the electron donor.

A novel angular dioxygenase gene cluster encoding 3-phenoxybenzoate 1',2'-dioxygenase in Sphingobium wenxiniae JZ-1

Sphingobium wenxiniae JZ-1 utilizes a wide range of pyrethroids and their metabolic product, 3-phenoxybenzoate, as sources of carbon and energy. A mutant JZ-1 strain, MJZ-1, defective in the degradation of 3-phenoxybenzoate was obtained by successive streaking on LB agar. Comparison of the draft genomes of strains JZ-1 and MJZ-1 revealed that a 29,366-bp DNA fragment containing a putative angular dioxygenase gene cluster (pbaA1A2B) is missing in strain MJZ-1. PbaA1, PbaA2, and PbaB share 65%, 52%, and 10% identity with the corresponding α and β subunits and the ferredoxin component of dioxin dioxygenase from Sphingomonas wittichii RW1, respectively. Complementation of pbaA1A2B in strain MJZ-1 resulted in the active 3-phenoxybenzoate 1',2'-dioxygenase, but the enzyme activity in Escherichia coli was achieved only through the coexpression of pbaA1A2B and a glutathione reductase (GR)-type reductase gene, pbaC, indicating that the 3-phenoxybenzoate 1',2'-dioxygenase belongs to a type IV Rieske non-heme iron aromatic ring-hydroxylating oxygenase system consisting of a hetero-oligomeric oxygenase, a [2Fe-2S]-type ferredoxin, and a GR-type reductase. The pbaC gene is not located in the immediate vicinity of pbaA1A2B. 3-Phenoxybenzoate 1',2'-dioxygenase catalyzes the hydroxylation in the 1' and 2' positions of the benzene moiety of 3-phenoxybenzoate, yielding 3-hydroxybenzoate and catechol. Transcription of pbaA1A2B and pbaC was induced by 3-phenoxybenzoate, but the transcriptional level of pbaC was far less than that of pbaA1A2B, implying the possibility that PbaC may not be the only reductase that can physiologically transfer electrons to PbaA1A2B in strain JZ-1. Some GR-type reductases from other sphingomonad strains could also transfer electrons to PbaA1A2B, suggesting that PbaA1A2B has a low specificity for reductase.