Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer

Digabel, Yoann Le; Demanèche, Sandrine; Benoit, Yves; Vogel, Timothy M.; Fayolle-Guichard, Françoise

doi:10.1007/s00253-013-4803-3

Cited by 26 publications

(20 citation statements)

References 42 publications

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“…There are indeed several reports of syntrophic associations between two phyla for the complete degradation of recalcitrant compounds. 51 A Mycobacterium strain, EPa45, with the ability to degrade phenanthrene to TCA compounds, was isolated from the polluted soil at Week 15. Our genome sequencing of EPa45 suggested its phenanthrene degradation to protocatechaute 52 via the same route as used for mycobacterial phenanthrene degradation that was proposed by the Illumina metagenomic read analysis.…”

Section: Resultsmentioning

confidence: 99%

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance

Kato

Mori

Maruyama

et al. 2015

DNA Res

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Soil microbial communities have great potential for bioremediation of recalcitrant aromatic compounds. However, it is unclear which taxa and genes in the communities, and how they contribute to the bioremediation in the polluted soils. To get clues about this fundamental question here, time-course (up to 24 weeks) metagenomic analysis of microbial community in a closed soil microcosm artificially polluted with four aromatic compounds, including phenanthrene, was conducted to investigate the changes in the community structures and gene pools. The pollution led to drastic changes in the community structures and the gene sets for pollutant degradation. Complete degradation of phenanthrene was strongly suggested to occur by the syntrophic metabolism by Mycobacterium and the most proliferating genus, Burkholderia. The community structure at Week 24 (∼12 weeks after disappearance of the pollutants) returned to the structure similar to that before pollution. Our time-course metagenomic analysis of phage genes strongly suggested the involvement of the ‘kill-the-winner’ phenomenon (i.e. phage predation of Burkholderia cells) for the returning of the microbial community structure. The pollution resulted in a decrease in taxonomic diversity and a drastic increase in diversity of gene pools in the communities, showing the functional redundancy and robustness of the communities against chemical disturbance.

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Section: Resultsmentioning

confidence: 99%

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance

Kato

Mori

Maruyama

et al. 2015

DNA Res

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“…As a control, the compost sample alone was also incubated, both in suspension and as a solid culture. [19]. To avoid oxygen limitation, flasks were aerated for one hour under sterile conditions when CO 2 concentration reached 10% (v/v).…”

Section: Methodsmentioning

confidence: 99%

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

et al. 2016

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Cost-effective biofuel production from lignocellulosic biomass depends on efficient degradation of the plant cell wall. One of the major obstacles for the development of a cost-efficient process is the lack of resistance of currently used fungal enzymes to harsh conditions such as high temperature. Adapted, thermophilic microbial communities provide a huge reservoir of potentially interesting lignocellulose-degrading enzymes for improvement of the cellulose hydrolysis step. In order to identify such enzymes, a leaf and wood chip compost was enriched on a mixture of thermo-chemically pretreated wheat straw, poplar and Miscanthus under thermophile conditions, but in two different set-ups. Unexpectedly, metagenome sequencing revealed that incubation of the lignocellulosic substrate with compost as inoculum in a suspension culture resulted in an impoverishment of putative cellulase- and hemicellulase-encoding genes. However, mimicking composting conditions without liquid phase yielded a high number and diversity of glycoside hydrolase genes and an enrichment of genes encoding cellulose binding domains. These identified genes were most closely related to species from Actinobacteria, which seem to constitute important players of lignocellulose degradation under the applied conditions. The study highlights that subtle changes in an enrichment set-up can have an important impact on composition and functions of the microcosm. Composting-like conditions were found to be the most successful method for enrichment in species with high biomass degrading capacity.

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“…T3-1. This N-deethoxymethylase was encoded by the ethABCD gene cluster involved in methyl tertbutyl ether (MTBE) and ETBE degradation (16)(17)(18)(19)(20)(21)(22)(23)(24). The functions of EthABCD in bacteria were genetically verified by gene complementation in mutant strains.…”

Section: Discussionmentioning

confidence: 99%

“…Many strains harboring the ethRABCD gene cluster have been reported, and its function was also studied by genetic methods (16)(17)(18)(19)(20)(21)(22)(23)(24). The ethABCD cluster encoded a ferredoxin reductase (EthA), a cytochrome P450 (EthB), a ferredoxin (EthC), and a protein with an unknown function (EthD) (17).…”

Section: Discussionmentioning

confidence: 99%

Involvement of the Cytochrome P450 System EthBAD in the N -Deethoxymethylation of Acetochlor by Rhodococcus sp. Strain T3-1

Wang

Zhou

et al. 2015

Appl Environ Microbiol

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c 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. Chloroacetanilide herbicides are a class of important herbicides used worldwide. The chloroacetanilide herbicide acetochlor [2-chloro-N-(ethoxymethyl)-N-(2-ethyl-6-methylphenyl)-acetamide] is a selective preemergent herbicide that has been used to effectively control broadleaf weeds and annual grasses in corn fields for almost 40 years (1). The excessive and frequent application of acetochlor may result in high levels of acetochlor residues, which have been detected in ground and surface waters and negatively impact both the environment and agricultural ecosystems (2). The U.S. Environmental Protection Agency (EPA) has classified acetochlor as a B-2 carcinogen and a probable human carcinogen (3). Studies of different soil types treated with acetochlor have demonstrated that 2=-methyl-6=-ethyl-2-chloroacetanilide (CMEPA), a compound derived from acetochlor N-deethoxymethylation, is a major product of the microbial degradation process (1, 3-5).We previously isolated an efficient acetochlor N-deethoxymethylation strain, T3-1, from a microbial consortium that could mineralize acetochlor completely. The strain was identified as a Rhodococcus sp. (1). The biochemical pathway of acetochlor degradation by the three bacteria in the consortium was proposed to be as follows: acetochlor to CMEPA by Rhodococcus sp. strain T3-1, CMEPA to 2-methyl-6-ethyl aniline (MEA) by Delftia sp. strain T3-6, and MEA by Sphingobium sp. strain MEA3-1, based on the identified degradation intermediates (1). In this study, a three-...

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Ethyl tert-butyl ether (ETBE) biodegradation by a syntrophic association of Rhodococcus sp. IFP 2042 and Bradyrhizobium sp. IFP 2049 isolated from a polluted aquifer

Cited by 26 publications

References 42 publications

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance

Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

Involvement of the Cytochrome P450 System EthBAD in the N -Deethoxymethylation of Acetochlor by Rhodococcus sp. Strain T3-1

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