In this study, a bacterial strain of Achromobacter sp. LZ35, which was capable of utilizing 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxy acetic acid (MCPA) as the sole sources of carbon and energy for growth, was isolated from the soil in a disused pesticide factory in Suzhou, China. The optimal 2,4-D degradation by strain LZ35 occurred at 30 °C and pH 8.0 when the initial 2,4-D concentration was 200 mg L−1. Strain LZ35 harbored the conserved 2,4-D/alpha-ketoglutarate dioxygenase (96%) and 2,4-dichlorophenol hydroxylase (99%), and catabolized 2,4-D via the intermediate 2,4-dichlorophenol. The inoculation of 7.8 × 106 CFU g−1 soil of strain LZ35 cells to 2,4-D-contaminated soil could efficiently remove over 75 and 90% of 100 and 50 mg L−1 2,4-D in 12 days and significantly released the phytotoxicity of maize caused by the 2,4-D residue. This is the first report of an Achromobacter sp. strain that was capable of mineralizing both 2,4-D and MCPA. This study provides us a promising candidate for its application in the bioremediation of 2,4-D- or MCPA-contaminated sites.

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.

An aerobic, Gram-stain negative, short rod-shaped, asporogenous, non-motile bacterium designated strain NK8T was isolated from a chlorobenzoate contaminated soil in China. Strain NK8T was observed to grow optimally at pH 7.0, 30 °C and in the absence of NaCl in LB medium. The G + C content of the total DNA of strain NK8T was found to be 65.5 mol%. The 16S rRNA gene sequence of strain NK8T showed high similarity to that of Aquamicrobium aerolatum Sa14T (97.3%), followed by Aquamicrobium lusatiense S1T (96.7%) and Mesorhizobium sangali SCAU7T (96.6%). The DNA–DNA relatedness between strain NK8T and A. aerolatum Sa14T was 35.5 ± 0.9%. The major fatty acids of strain NK8T were determined to be C19:0 cyclo ω8c (45.6%), C18:1ω7c (33.4%) and C16:0 (8.4%). The respiratory quinone was found to be ubiquinone Q-10. The major polyamine was found to be spermidine. The polar lipid profile include the major compounds phosphatidylcholine and diphosphatidylglycerol, and moderate amounts of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, aminolipid and phospholipid. Based on the differential biochemical and physiological characteristics, the geno-, chemo- and phenotypic characteristics, strain NK8T is proposed to represent a novel species of the genus Aquamicrobium, Aquamicrobium soli sp. nov. The type strain is NK8T (=KCTC 52165T=CCTCC AB2016045T).

•Three bacterial strains capable of utilizing three monochlorobenzoate isomers respectively were isolated.•The three monochlorobenzoate isomers were catabolized via three different dechlorination pathways in the three isolates, respectively.•2-Chlorobenzoate was catabolized by the hybrid 2-halobenzoate 1,2-dioxygenase system comprising of CbdAB and BenC.•Strain 4-CBA seemed to have a more compact gene cluster of fcbABC compared to previously reported strains.Three monochlorobenzoate isomer-utilizing bacterial strains, Pseudomonas sp. 2-CBA, Pseudomonas sp. 3-CBA, and Hydrogenophaga sp. 4-CBA, were isolated from a haloaromatic-contaminated soil in a disused chemical factory in Nanjing, China. Compared to strain 3-CBA and strain 4-CBA, which could only utilize its corresponding monochlorobenzoate isomer (3-chlorobenzoate and 4-chlorobenzoate) as the sole carbon source for growth, strain 2-CBA could utilize both 2-chlorobenzoate and 3-chlorobenzoate for growth. The three monochlorobenzoate isomers were catabolized via three different dechlorination pathways in the three isolates, respectively. 3-Chlorobenzoate was initially catabolized by the benzoate 1,2-dioxygenase (BenABCD) in strain 3-CBA, whereas 2-chlorobenzoate was catabolized by the hybrid 2-halobenzoate 1,2-dioxygenase system in strain 2-CBA, which comprised of the terminal oxygenase component of 2-halobenzoate dioxygenase system (CbdAB) and the reductase component of benzoate 1,2-dioxygenase system (BenC). For 4-chlorobenzoate, it was catabolized via the classic hydrolytic dehalogenation pathway in strain 4-CBA. While, strain 4-CBA seemed to have a more compact gene cluster of fcbABC compared to previously reported strains. This study provides new insights into the catabolic diversity of structurally similar isomers in a contaminated niche.

A Gram-negative, strictly aerobic, yellow-pigmented and rod-shaped bacterium, designated strain NSL10T, was isolated from the waste surface soil of a chemical factory in Hongan, China. Strain NSL10T was found to grow optimally at pH 7.0, 30 °C and in the absence of NaCl in modified LB medium. Cells were found to be positive for catalase and oxidase. The G+C content of the total DNA was determined to be 66.8 mol%. The 16S rRNA gene sequence of strain NSL10T showed the highest similarity to that of Devosia albogilva IPL15T (96.80 %), followed by Devosia geojensis BD-c194T (96.46 %) and Devosia chinhatensis IPL18T (96.27 %). The major cellular fatty acids of strain NSL10T were identified as C18:1ω7c/C18:1ω6c (48.2 %) and C16:0 (17.7 %). The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and an unidentified compound. Minor amounts of unidentified glycolipids and unidentified polar lipids were also detected. These chemotaxonomic data supported the affiliation of strain NSL10T to the genus Devosia. In conclusion, on the basis of biochemical, physiological characteristics and molecular properties, strain NSL10T represents a novel species within the genus Devosia, for which the name Devosia honganensis sp. nov., is proposed. The type strain is NSL10T (=KCTC 42281T = ACCC 19737T).

To confirm the reductive dehalogenation ability of the aerobic strain of Delftia sp. EOB-17, finding more evidences to support the hypothesis that reductive dehalogenation may occur extensively in aerobic bacteria.Delftia sp. EOB-17, isolated from terrestrial soil contaminated with halogenated aromatic compounds, completely degraded 0.2 mM DBHB in 28 h and released two equivalents of bromides under aerobic conditions in the presence of sodium succinate. LC–MS analysis revealed that DBHB was transformed to 4-hydroxybenzoate via 3-bromo-4-hydroxybenzoate by successive reductive dehalogenation. Highly conserved DBHB-degrading genes, including reductive dehalogenase gene (bhbA3) and the extra-cytoplasmic binding receptor gene (bhbB3), were also found in strain EOB-17 by genome sequencing. The optimal temperature and pH for DBHB reductive dehalogenation activity are 30 °C and 8, respectively, and 0.1 mM Cd2+, Cu2+, Hg2+ and Zn2+ strongly inhibited dehalogenation activity.The aerobic strain of Delftia sp. EOB-17 was confirmed to reductively dehalogenate DBHB under aerobic conditions, providing another evidence to support the hypothesis that reductive dehalogenation occurs extensively in aerobic bacteria.

A natural consortium of two bacterial strains (Sphingopyxis sp. OB-3 and Comamonas sp. 7D-2) was capable of utilizing bromoxynil octanoate as the sole source of carbon for its growth. Strain OB-3 was able to convert bromoxynil octanoate to bromoxynil but could not use the eight-carbon side chain as its sole carbon source. Strain 7D-2 could not degrade bromoxynil octanoate, although it was able to mineralize bromoxynil. An esterase (BroH) that is involved in the conversion of bromoxynil octanoate into bromoxynil and is essential for the mineralization of bromoxynil octanoate by the consortium was isolated from strain OB-3 and molecularly characterized. BroH encodes 304 amino acids and resembles α/β-hydrolase fold proteins. Recombinant BroH was overexpressed in Escherichia coli BL21 (DE3) and purified by Ni-NTA affinity chromatography. BroH was able to transform p-nitrophenyl esters (C2–C14) and showed the highest activity toward p-nitrophenyl caproate (C6) on the basis of the catalytic efficiency value (Vmax/Km). Additionally, BroH activity decreased when the aliphatic chain length increased. The optimal temperature and pH for BroH activity was found to be 35 °C and 7.5, respectively. On the basis of a phylogenetic analysis, BroH belongs to subfamily V of bacterial lipolytic enzymes.

Organophosphorus pesticide (OP) hydrolases play key roles in the degradation and decontamination of agricultural and household OPs and in the detoxification of chemical warfare agents. In this study, an isofenphos-methyl hydrolase gene (imh) was cloned from the isocarbophos-degrading strain of Arthrobacter sp. scl-2 using the polymerase chain reaction method. Isofenphos-methyl hydrolase (Imh) showed 98% sequence identity with the isofenphos hydrolase from Arthrobacter sp. strain B-5. Imh was highly expressed in Escherichia coli BL21 (DE3), and the His6-tagged Imh was purified (1.7 mg/ml) with a specific activity of 14.35 U/mg for the substrate isofenphos-methyl. The molecular mass of the denatured Imh is about 44 kDa, and the isoelectric point (pI) value was estimated to be 3.4. The optimal pH and temperature for hydrolysis of isofenphos-methyl were pH 8.0 and 35 °C, respectively. The secondary structure of Imh shows that Imh is a metallo-dependent hydrolase, and it was found that Imh was completely inhibited by the metalloprotease inhibitor 1,10-phenanthroline (0.5 mM), and the catalytic activity was restored by the subsequent addition of Zn2+. Interestingly, Imh had a relatively broader substrate specificity and was capable of hydrolyzing 12 of the tested oxon and thion OPs with the P–O–Z moiety instead of the P–S(C)–Z moiety. Furthermore, it was found that the existence of an aryl or heterocyclic group in the leaving group (Z) is also important in determining the substrate specificity. Among all the substrates hydrolyzed by Imh, it was assumed that Imh preferred P–O–Z substrates still with a phosphamide bond (P–N), such as isofenphos-methyl, isofenphos, isocarbophos, and butamifos. The newly characterized Imh has a great potential for use in the decontamination and detoxification of agricultural and household OPs and is a good candidate for the study of the catalytic mechanism and substrate specificity of OP hydrolases.

Buprofezin is a widely used insecticide that has caused environmental pollution in many areas. However, biodegradation of buprofezin by pure cultures has not been extensively studied, and the transformation pathway of buprofezin remains unclear. In this paper, a buprofezin co-metabolizing strain of DFS35-4 was isolated from a buprofezin-polluted soil in China. Strain DFS35-4 was preliminarily identified as Pseudomonas sp. based on its morphological, physiological, and biochemical properties, as well as 16S rRNA gene analysis. In the presence of 2.0 g l−1 sodium citrate, strain DFS35-4 degraded over 70% of 50 mg l−1 buprofezin in 3 days. Strain DFS35-4 efficiently degraded buprofezin in the pH range of 5.0–10.0 and at temperatures between 20 and 30°C. Three metabolites, 2-imino-5-phenyl-3-(propan-2-yl)-1,3,5-thiadiazinan-4-one, 2-imino-5-phenyl-1,3,5-thiadiazinan-4-one, and methyl(phenyl) carbamic acid, were identified during the degradation of buprofezin using gas chromatography–mass spectrometry (GC–MS) and tandem mass spectrometry (MS/MS). A partial transformation pathway of buprofezin in Pseudomonas sp. DFS35-4 was proposed based on these metabolites.

A bacterial strain, designated as CTN-11, capable of degrading chlorothalonil (CTN), was isolated from a chlorothalonil-contaminated soil in China. Based on the morphological, biochemical characteristics and comparative analysis of the 16S rRNA genes, strain CTN-11 was identified as Ochrobactrum sp. Strain CTN-11 could degrade 50 mg l−1 CTN to a non-detectable level within 48 h, and efficiently degrade CTN in a relatively broad range of temperatures from 20 to 40°C and initial pH values from 6.0 to 9.0. The new isolate differed from those previously reported CTN co-metabolic degraders by transforming CTN in the absence of other carbon sources. A glutathione S-transferase (GST) coding gene, which showed 88% sequence similarity with that from Ochrobactrum anthropi SH35B, was cloned from strain CTN-11. However, the gene was not functionally expressed in the presence of glutathione, indicating that CTN was not reductively dechlorinated by thiolytic substitution catalyzed by GST in strain CTN-11. The metabolite hydroxyl-trichloroisophthalonitrile (CTN-OH) produced during CTN anaerobic degradation was identified based on tandem MS/MS, confirming that hydrolytic dechlorination was involved in the CTN degradation. The removal of CTN by strain CTN-11 in sterile and non-sterile soils was also studied. In both soil samples, 50 mg kg−1 CTN could be degraded to an undetectable level within 3 days. This study highlights an important potential use of strain CTN-11 for the cleanup of CTN-contaminated sites and presents a hydrolytic dechlorination reaction of CTN by a pure culture.

Methamidophos is one of the most widely used organophosphorus insecticides usually detectable in the environment. A facultative methylotroph, Hyphomicrobium sp. MAP-1, capable of high efficiently degrading methamidophos, was isolated from methamidophos-contaminated soil in China. It was found that the addition of methanol significantly promoted the growth of strain MAP-1 and enhanced its degradation of methamidophos. Further, this strain could utilize methamidophos as its sole carbon, nitrogen and phosphorus source for growth and could completely degrade 3,000 mg l−1 methamidophos in 84 h under optimal conditions (pH 7.0, 30°C). The enzyme responsible for methamidophos degradation was mainly located on the cell inner membrane (90.4%). During methamidophos degradation, three metabolites were detected and identified based on tandem mass spectrometry (MS/MS) and gas chromatography-mass spectrometry (GC–MS) analysis. Using this information, a biochemical degradation pathway of methamidophos by Hyphomicrobium sp. MAP-1 was proposed for the first time. Methamidophos is first cleaved at the P–N bond to form O,S-dimethyl hydrogen thiophosphate and NH3. Subsequently, O,S-dimethyl hydrogen thiophosphate is hydrolyzed at the P–O bond to release –OCH3 and form S-methyl dihydrogen thiophosphate. O,S-dimethyl hydrogen thiophosphate can also be hydrolyzed at the P–S bond to release –SCH3 and form methyl dihydrogen phosphate. Finally, S-methyl dihydrogen thiophosphate and methyl dihydrogen phosphate are likely transformed into phosphoric acid.

The chloroacetamide herbicide butachlor is a widely used herbicide that has caused environmental pollution in many areas. The degradation mechanism of butachlor and bioremediation of butachlor contaminated-sites by bioaugmentation is of great concern. In this study, the novel strain Catellibacterium caeni sp. nov DCA-1T was found to degrade 81.2% of 50 mg l−1 butachlor in 84 h, and efficiently degrade butachlor in a relatively broad range of temperatures from 15 to 35 °C and initial pH values from 6.0 to 9.0. Five metabolites produced during butachlor degradation by strain DCA-1T were identified based on gas chromatography–mass spectrometry, and a different degradation pathway of butachlor was proposed. The removal of butachlor by bioaugmentation of strain DCA-1T in three different soils was also studied. The inoculation of DCA-1T cells significantly accelerated the degradation of butachlor in both sterile and non-sterile soils, with 57.2%–90.4% of 50 mg kg−1 butachlor removed in 5 days compared to 5.4%–36% in the controls. The removal rate of butachlor in the sterile red soil (pH 4.8) inoculated with strain DCA-1T was lower than that in the sterile fluvo-aquic soil (pH 6.3) and high sandy soil (pH 8.2), showing that soil type significantly affected the butachlor degradation. This study highlights an important potential use of strain DCA-1T for the cleanup of chloroacetamide herbicides contaminated-sites and presents a different degradation pathway of butachlor in a pure culture.Highlights► Strain DCA-1T efficiently degraded butachlor and other chloroacetamide herbicides. ► A different degradation pathway of butachlor was proposed in strain DCA-1T. ► Strain DCA-1T accelerated the degradation of butachlor in three different soils.

Bioremediation of pollutants in natural environments is affected by many factors, such as bacterial survival, motility, and chemotaxis. However, these roles in in-situ biodegradation of organophosphorus pesticides have not been examined extensively. In this paper, a highly effective methyl-parathion (MP) degrading strain, Pseudomonas putida DLL-1, which also demonstrates motile ability and chemotactic response toward MP, was selected as the research material. A leuB− auxotroph mutant A3-27 and fliC− non-motility mutant a4-8 were first constructed by random insertion of the kanamycin gene into the chromosome of P. putida DLL-1 with the mini-transposon system. Biodegradation of MP in liquid medium and soil microcosms by A3-27, a4-8 and a previously constructed cheA− non-chemotaxis mutant P. putida DAK were compared. The kinetic parameters for MP degradation were all similar in the well-mixed liquid systems. However, in soil microcosms, all the three mutants had lower degrading rates compared with wild-type P. putida DLL-1. The auxotroph mutant A3-27 had the lowest degrading rate and could only degrade 25.7–34.2% MP in 5 days, and the non-motility mutant a4-8 and non-chemotaxis mutant DAK could only degrade 53.5–68.1% and 64.3–85.7% MP, respectively. This paper emphasizes, for the first time, the use of non-auxotroph bacteria for efficient removal of organophosphorus pesticides in contaminated sites, and also points out the importance of select microorganisms with specific motile or chemotactic affinities in optimizing pesticide bioremediation.

Dimethoate is a widely used organophosphorus insecticide often detected in the environment. A highly effective dimethoate-degrading Paracoccus sp. strain Lgjj-3 was isolated from treatment wastewater. Strain Lgjj-3 can utilize dimethoate as its sole carbon source for growth and degrade an initial concentration of 100 mg l−1 dimethoate to non-detectable levels within 6 h in liquid culture. During the degradation of dimethoate, seven metabolites, including dimethoate carboxylic acid, 2-(hydroxy(methoxy)phosphorylthio)acetic acid, O,O,S-trimethyl thiophosphorothioate, O-methyl O,S-dihydrogen phosphorothioate, phosphorothioic O,O,S-acid, O,O,S-trimethylphosphorothiate and O,O,O-trimethyl phosphoric ester, were successfully detected and identified based on MS/MS and GC–MS analysis. A biochemical degradation pathway of dimethoate by Paracoccus sp. Lgjj-3 is proposed for the first time. Dimethoate is first hydrolyzed by the scission of the amide bond to form dimethoate carboxylic acid, which is subsequently decarboxylated into O,O,S-trimethyl thiophosphorothioate. The produced O,O,S-trimethyl thiophosphorothioate is oxidized to form O,O,S-trimethylphosphorothiate and then further oxidized to form O,O,O-trimethyl phosphoric ester. O,O,S-trimethylphosphorothiate can also be hydrolyzed at the C–O bond to release a CH3 group and cleavaged at the S–C bond through a hydrolytic pathway to form O-methyl O,S-dihydrogen phosphorothioate. Dimethoate carboxylic acid can also be oxidated at the PS bond to form the corresponding oxon derivative. Next, hydrolysis can occur at the C–O bond to form 2-(hydroxy(methoxy)phosphorylthio)acetic acid, which can be further hydrolyzed at the S–C bond to form O-methyl O,S-dihydrogen phosphorothioate. Phosphorothioic O,O,S-acid is finally formed by the hydrolysis of the C–O bond of O-methyl O,S-dihydrogen phosphorothioate to lose another CH3 group.

A bacterial strain, pcnb-21, capable of degrading pentachloronitrobenzene (PCNB) under aerobic and anoxic conditions, was isolated from a long-term PCNB-polluted soil by an enrichment culture technique and identified as Labrys portucalensis based upon its morphological, physiological and biochemical properties, as well as 16S rRNA gene sequence analysis. Effects of different factors, such as temperature and pH, on PCNB biodegradation were studied. Strain pcnb-21 efficiently degraded PCNB at temperatures from 20 to 30 °C and initial pH values from 4 to 7, which might be the first time that a Labrys strain was found capable of efficiently degrading PCNB. The degradation of PCNB was affected by oxygen, and the degradation decreased with increasing aeration. Exogenous electron donors such as glucose, lactic acid and succinic acid promoted the biodegradation of PCNB, while electron acceptors such as sodium nitrite, sodium sulfate, sodium nitrate and sodium sulfate inhibited PCNB biodegradation. The degradation of PCNB in sterile and non-sterile soils by a green fluorescent protein (GFP)-labeled strain, pcnb-21-gfp, was also studied. Cells of pcnb-21-gfp efficiently degraded 100 mg kg−1 PCNB in sterile and non-sterile soils and could not be detected after 42 days. Strain pcnb-21 might be useful in bioremediating PCNB-polluted soils and environment.