1
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Raes B, Wang J, Horemans B, Dirckx L, Waldherr S, Kohler HPE, Springael D. The Growth Yield of Aminobacter niigataensis MSH1 on the Micropollutant 2,6-Dichlorobenzamide Decreases Substantially at Trace Substrate Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2859-2869. [PMID: 38289638 DOI: 10.1021/acs.est.3c06883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
2,6-Dichlorobenzamide (BAM) is an omnipresent micropollutant in European groundwaters. Aminobacter niigataensis MSH1 is a prime candidate for biologically treating BAM-contaminated groundwater since this organism is capable of utilizing BAM as a carbon and energy source. However, detailed information on the BAM degradation kinetics by MSH1 at trace concentrations is lacking, while this knowledge is required for predicting and optimizing the degradation process. Contaminating assimilable organic carbon (AOC) in media makes the biodegradation experiment a mixed-substrate assay and hampers exploration of pollutant degradation at trace concentrations. In this study, we examined how the BAM concentration affects MSH1 growth and BAM substrate utilization kinetics in a AOC-restricted background to avoid mixed-substrate conditions. Conventional Monod kinetic models were unable to predict kinetic parameters at low concentrations from kinetics determined at high concentrations. Growth yields on BAM were concentration-dependent and decreased substantially at trace concentrations; i.e., growth of MSH1 diminished until undetectable levels at BAM concentrations below 217 μg-C/L. Nevertheless, BAM degradation continued. Decreasing growth yields at lower BAM concentrations might relate to physiological adaptations to low substrate availability or decreased expression of downstream steps of the BAM catabolic pathway beyond 2,6-dichlorobenzoic acid (2,6-DCBA) that ultimately leads to Krebs cycle intermediates for growth and energy conservation.
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Affiliation(s)
- Bart Raes
- Division of Soil and Water Management, KU Leuven, Heverlee B-3001, Belgium
| | - Jinsong Wang
- Division of Soil and Water Management, KU Leuven, Heverlee B-3001, Belgium
| | - Benjamin Horemans
- Division of Soil and Water Management, KU Leuven, Heverlee B-3001, Belgium
| | - Lode Dirckx
- Division of Soil and Water Management, KU Leuven, Heverlee B-3001, Belgium
| | - Steffen Waldherr
- Chemical Reactor Engineering and Safety (CREaS), KU Leuven, Heverlee B-3001, Belgium
| | - Hans-Peter E Kohler
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Heverlee B-3001, Belgium
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2
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Zhang L, Yao G, Mao Z, Song M, Zhao R, Zhang X, Chen C, Zhang H, Liu Y, Wang G, Li F, Wu X. Experimental and computational approaches to characterize a novel amidase that initiates the biodegradation of the herbicide propanil in Bosea sp. P5. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131155. [PMID: 36893600 DOI: 10.1016/j.jhazmat.2023.131155] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
The herbicide propanil and its major metabolite 3,4-dichloroaniline (3,4-DCA) are difficult to biodegrade and pose great health and environmental risks. However, studies on the sole or synergistic mineralization of propanil by pure cultured strains are limited. A two-strain consortium (Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34), obtained from a swep-mineralizing enrichment culture that can synergistically mineralize propanil, has been previously reported. Here, another propanil degradation strain, Bosea sp. P5, was successfully isolated from the same enrichment culture. A novel amidase, PsaA, responsible for initial propanil degradation, was identified from strain P5. PsaA shared low sequence identity (24.0-39.7 %) with other biochemically characterized amidases. PsaA exhibited optimal activity at 30 °C and pH 7.5 and had kcat and Km values of 5.7 s-1 and 125 μM, respectively. PsaA could convert the herbicide propanil to 3,4-DCA but exhibited no activity toward other herbicide structural analogs. This catalytic specificity was explained by using propanil and swep as substrates and then analyzed by molecular docking, molecular dynamics simulation and thermodynamic calculations, which revealed that Tyr138 is the key residue that affects the substrate spectrum of PsaA. This is the first propanil amidase with a narrow substrate spectrum identified, providing new insights into the catalytic mechanism of amidase in propanil hydrolysis.
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Affiliation(s)
- Long Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China; Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China.
| | - Gui Yao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Zhenbo Mao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Man Song
- College of Chemistry and Materials Science, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Ruiqi Zhao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Xiaochun Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China; School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Chun Chen
- Institute of Biomedicine, Jinan University, Guangzhou, 510632, PR China
| | - Huijun Zhang
- Anhui Bio-breeding Engineering Research Center for Watermelon and Melon, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Yuan Liu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Guangli Wang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Feng Li
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, School of Life Sciences, Huaibei Normal University, Huaibei, Anhui, 235000, PR China.
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3
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Aldas-Vargas A, Poursat BAJ, Sutton NB. Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil. World J Microbiol Biotechnol 2022; 38:240. [PMID: 36261779 PMCID: PMC9581840 DOI: 10.1007/s11274-022-03426-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022]
Abstract
Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.
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Affiliation(s)
- Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Baptiste A J Poursat
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700 EV, Wageningen, The Netherlands.
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4
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Schostag MD, Gobbi A, Fini MN, Ellegaard-Jensen L, Aamand J, Hansen LH, Muff J, Albers CN. Combining reverse osmosis and microbial degradation for remediation of drinking water contaminated with recalcitrant pesticide residue. WATER RESEARCH 2022; 216:118352. [PMID: 35358881 DOI: 10.1016/j.watres.2022.118352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Groundwater contamination by recalcitrant organic micropollutants such as pesticide residues poses a great threat to the quality of drinking water. One way to remediate drinking water containing micropollutants is to bioaugment with specific pollutant degrading bacteria. Previous attempts to augment sand filters with the 2,6-dichlorobenzamide (BAM) degrading bacterium Aminobacter niigataensis MSH1 to remediate BAM-polluted drinking water initially worked well, but the efficiency rapidly decreased due to loss of degrader bacteria. Here, we use pilot-scale augmented sand filters to treat retentate of reverse osmosis treatment, thus increasing residence time in the biofilters and potentially nutrient availability. In a first pilot-scale experiment, BAM and most of the measured nutrients were concentrated 5-10 times in the retentate. This did not adversely affect the abundances of inoculated bacteria and the general prokaryotic community of the sand filter presented only minor differences. On the other hand, the high degradation activity was not prolonged compared to the filter receiving non-concentrated water at the same residence time. Using laboratory columns, it was shown that efficient BAM degradation could be achieved for >100 days by increasing the residence time in the sand filter. A slower flow may have practical implications for the treatment of large volumes of water, however this can be circumvented when treating only the retentate water equalling 10-15% of the volume of inlet water. We therefore conducted a second pilot-scale experiment with two inoculated sand filters receiving membrane retentate operated with different residence times (22 versus 133 min) for 65 days. While the number of MSH1 in the biofilters was not affected, the effect on degradation was significant. In the filter with short residence time, BAM degradation decreased from 86% to a stable level of 10-30% degradation within the first two weeks. The filter with the long residence time initially showed >97% BAM degradation, which only slightly decreased with time (88% at day 65). Our study demonstrates the advantage of combining membrane filtration with bioaugmented filters in cases where flow rate is of high importance.
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Affiliation(s)
- Morten D Schostag
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mahdi Nikbakht Fini
- Center for Membrane Technology, Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jens Muff
- Center for Membrane Technology, Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Christian N Albers
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark.
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5
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Sun F, Mellage A, Wang Z, Bakkour R, Griebler C, Thullner M, Cirpka OA, Elsner M. Toward Improved Bioremediation Strategies: Response of BAM-Degradation Activity to Concentration and Flow Changes in an Inoculated Bench-Scale Sediment Tank. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4050-4061. [PMID: 35263099 PMCID: PMC8988295 DOI: 10.1021/acs.est.1c05259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/24/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Compound-specific isotope analysis (CSIA) can reveal mass-transfer limitations during biodegradation of organic pollutants by enabling the detection of masked isotope fractionation. Here, we applied CSIA to monitor the adaptive response of bacterial degradation in inoculated sediment to low contaminant concentrations over time. We characterized Aminobacter sp. MSH1 activity in a flow-through sediment tank in response to a transient supply of elevated 2,6-dichlorobenzamide (BAM) concentrations as a priming strategy and took advantage of an inadvertent intermittence to investigate the effect of short-term flow fluctuations. Priming and flow fluctuations yielded improved biodegradation performance and increased biodegradation capacity, as evaluated from bacterial activity and residual concentration time series. However, changes in isotope ratios in space and over time evidenced that mass transfer became increasingly limiting for degradation of BAM at low concentrations under such stimulated conditions, and that activity decreased further due to bacterial adaptation at low BAM (μg/L) levels. Isotope ratios, in conjunction with residual substrate concentrations, therefore helped identifying underlying limitations of biodegradation in such a stimulated system, offering important insight for future optimization of remediation schemes.
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Affiliation(s)
- Fengchao Sun
- Institute
of Groundwater Ecology, Helmholtz Zentrum München, Ingolstadter Landstrasse 1 85764 Neuherberg, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Adrian Mellage
- Center
for Applied Geoscience, University of Tübingen, Schnarrenbergstraße 94, 72076, Tübingen, Germany
| | - Zhe Wang
- Institute
of Groundwater Ecology, Helmholtz Zentrum München, Ingolstadter Landstrasse 1 85764 Neuherberg, Germany
- Chair
of Ecological Microbiology, University of
Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95448 Bayreuth, Germany
- School
of Life Sciences, Technical University of
Munich, Alte Akademie 8, 85354 Freising, Germany
| | - Rani Bakkour
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Christian Griebler
- Department
of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Martin Thullner
- Department
of Environmental Microbiology, UFZ—Helmholtz
Centre for Environmental Research, Permoserstr. 15, 30418 Leipzig, Germany
| | - Olaf A. Cirpka
- Center
for Applied Geoscience, University of Tübingen, Schnarrenbergstraße 94, 72076, Tübingen, Germany
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum München, Ingolstadter Landstrasse 1 85764 Neuherberg, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
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6
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Nielsen TK, Horemans B, Lood C, T'Syen J, van Noort V, Lavigne R, Ellegaard-Jensen L, Hylling O, Aamand J, Springael D, Hansen LH. The complete genome of 2,6-dichlorobenzamide (BAM) degrader Aminobacter sp. MSH1 suggests a polyploid chromosome, phylogenetic reassignment, and functions of plasmids. Sci Rep 2021; 11:18943. [PMID: 34556718 PMCID: PMC8460812 DOI: 10.1038/s41598-021-98184-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/03/2021] [Indexed: 11/14/2022] Open
Abstract
Aminobacter sp. MSH1 (CIP 110285) can use the pesticide dichlobenil and its recalcitrant transformation product, 2,6-dichlorobenzamide (BAM), as sole source of carbon, nitrogen, and energy. The concentration of BAM in groundwater often exceeds the threshold limit for drinking water, requiring additional treatment in drinking water treatment plants or closure of the affected abstraction wells. Biological treatment with MSH1 is considered a potential sustainable alternative to remediate BAM-contamination in drinking water production. We present the complete genome of MSH1, which was determined independently in two institutes at Aarhus University and KU Leuven. Divergences were observed between the two genomes, i.e. one of them lacked four plasmids compared to the other. Besides the circular chromosome and the two previously described plasmids involved in BAM catabolism, pBAM1 and pBAM2, the genome of MSH1 contained two megaplasmids and three smaller plasmids. The MSH1 substrain from KU Leuven showed a reduced genome lacking a megaplasmid and three smaller plasmids and was designated substrain MK1, whereas the Aarhus variant with all plasmids was designated substrain DK1. A plasmid stability experiment indicate that substrain DK1 may have a polyploid chromosome when growing in R2B medium with more chromosomes than plasmids per cell. Finally, strain MSH1 is reassigned as Aminobacter niigataensis MSH1.
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Affiliation(s)
- Tue Kjærgaard Nielsen
- Section for Microbiology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Copenhagen, Denmark
| | - Benjamin Horemans
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20 bus 2459, 3001, Leuven, Belgium.,Sustainable Materials Unit, BAT Knowledge Centre, Vlaams Instituut voor Technologisch Onderzoek, Mol, Belgium
| | - Cédric Lood
- Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Jeroen T'Syen
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20 bus 2459, 3001, Leuven, Belgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems (M2S), Faculty of Bioscience Engineering, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Lea Ellegaard-Jensen
- Section of Environmental Microbiology and Circular Resource Flow, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Ole Hylling
- Section of Environmental Microbiology and Circular Resource Flow, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, Denmark
| | - Dirk Springael
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 20 bus 2459, 3001, Leuven, Belgium.
| | - Lars Hestbjerg Hansen
- Section for Microbiology and Biotechnology, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Copenhagen, Denmark.
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7
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Artuso I, Turrini P, Pirolo M, Lugli GA, Ventura M, Visca P. Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter. Microorganisms 2021; 9:1332. [PMID: 34205374 PMCID: PMC8235418 DOI: 10.3390/microorganisms9061332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/01/2022] Open
Abstract
Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all Aminobacter species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462T contains a symbiosis island implicated in nodulation and nitrogen fixation.
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Affiliation(s)
- Irene Artuso
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; (I.A.); (P.T.)
| | - Paolo Turrini
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; (I.A.); (P.T.)
| | - Mattia Pirolo
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark;
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy; (G.A.L.); (M.V.)
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy; (G.A.L.); (M.V.)
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, 43124 Parma, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy; (I.A.); (P.T.)
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8
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Sun F, Mellage A, Gharasoo M, Melsbach A, Cao X, Zimmermann R, Griebler C, Thullner M, Cirpka OA, Elsner M. Mass-Transfer-Limited Biodegradation at Low Concentrations-Evidence from Reactive Transport Modeling of Isotope Profiles in a Bench-Scale Aquifer. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:7386-7397. [PMID: 33970610 PMCID: PMC8173607 DOI: 10.1021/acs.est.0c08566] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Organic contaminant degradation by suspended bacteria in chemostats has shown that isotope fractionation decreases dramatically when pollutant concentrations fall below the (half-saturation) Monod constant. This masked isotope fractionation implies that membrane transfer is slow relative to the enzyme turnover at μg L-1 substrate levels. Analogous evidence of mass transfer as a bottleneck for biodegradation in aquifer settings, where microbes are attached to the sediment, is lacking. A quasi-two-dimensional flow-through sediment microcosm/tank system enabled us to study the aerobic degradation of 2,6-dichlorobenzamide (BAM), while collecting sufficient samples at the outlet for compound-specific isotope analysis. By feeding an anoxic BAM solution through the center inlet port and dissolved oxygen (DO) above and below, strong transverse concentration cross-gradients of BAM and DO yielded zones of low (μg L-1) steady-state concentrations. We were able to simulate the profiles of concentrations and isotope ratios of the contaminant plume using a reactive transport model that accounted for a mass-transfer limitation into bacterial cells, where apparent isotope enrichment factors *ε decreased strongly below concentrations around 600 μg/L BAM. For the biodegradation of organic micropollutants, mass transfer into the cell emerges as a bottleneck, specifically at low (μg L-1) concentrations. Neglecting this effect when interpreting isotope ratios at field sites may lead to a significant underestimation of biodegradation.
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Affiliation(s)
- Fengchao Sun
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, Neuherberg 85764, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, Munich 81377, Germany
| | - Adrian Mellage
- Center
for Applied Geoscience, University of Tübingen, Schnarrenbergstrasse 94−96, Tübingen 72076, Germany
| | - Mehdi Gharasoo
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, Neuherberg 85764, Germany
- Department
of Earth and Environmental Sciences, Ecohydrology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Canada
| | - Aileen Melsbach
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, Neuherberg 85764, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, Munich 81377, Germany
| | - Xin Cao
- Joint
Mass Spectrometry Centre, Comprehensive
Molecular Analytics (CMA) Cooperation Group Helmholtz Zentrum, Gmunderstrasse 37, Munich 81379, Germany
| | - Ralf Zimmermann
- Joint
Mass Spectrometry Centre, Comprehensive
Molecular Analytics (CMA) Cooperation Group Helmholtz Zentrum, Gmunderstrasse 37, Munich 81379, Germany
| | - Christian Griebler
- Department
of Functional and Evolutionary Ecology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Martin Thullner
- Department
of Environmental Microbiology, UFZ—Helmholtz
Centre for Environmental Research, Permoserstrasse 15, Leipzig 30418, Germany
| | - Olaf A. Cirpka
- Center
for Applied Geoscience, University of Tübingen, Schnarrenbergstrasse 94−96, Tübingen 72076, Germany
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, Neuherberg 85764, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, Munich 81377, Germany
- Phone: +49 89 2180-78232
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9
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Maucourt B, Vuilleumier S, Bringel F. Transcriptional regulation of organohalide pollutant utilisation in bacteria. FEMS Microbiol Rev 2020; 44:189-207. [PMID: 32011697 DOI: 10.1093/femsre/fuaa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.
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Affiliation(s)
- Bruno Maucourt
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Stéphane Vuilleumier
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Françoise Bringel
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
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10
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Posselt M, Mechelke J, Rutere C, Coll C, Jaeger A, Raza M, Meinikmann K, Krause S, Sobek A, Lewandowski J, Horn MA, Hollender J, Benskin JP. Bacterial Diversity Controls Transformation of Wastewater-Derived Organic Contaminants in River-Simulating Flumes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:5467-5479. [PMID: 32251587 PMCID: PMC7304871 DOI: 10.1021/acs.est.9b06928] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/21/2020] [Accepted: 04/06/2020] [Indexed: 05/22/2023]
Abstract
Hyporheic zones are the water-saturated flow-through subsurfaces of rivers which are characterized by the simultaneous occurrence of multiple physical, biological, and chemical processes. Two factors playing a role in the hyporheic attenuation of organic contaminants are sediment bedforms (a major driver of hyporheic exchange) and the composition of the sediment microbial community. How these factors act on the diverse range of organic contaminants encountered downstream from wastewater treatment plants is not well understood. To address this knowledge gap, we investigated dissipation half-lives (DT50s) of 31 substances (mainly pharmaceuticals) under different combinations of bacterial diversity and bedform-induced hyporheic flow using 20 recirculating flumes in a central composite face factorial design. By combining small-volume pore water sampling, targeted analysis, and suspect screening, along with quantitative real-time PCR and time-resolved amplicon Illumina MiSeq sequencing, we determined a comprehensive set of DT50s, associated bacterial communities, and microbial transformation products. The resulting DT50s of parent compounds ranged from 0.5 (fluoxetine) to 306 days (carbamazepine), with 20 substances responding significantly to bacterial diversity and four to both diversity and hyporheic flow. Bacterial taxa that were associated with biodegradation included Acidobacteria (groups 6, 17, and 22), Actinobacteria (Nocardioides and Illumatobacter), Bacteroidetes (Terrimonas and Flavobacterium) and diverse Proteobacteria (Pseudomonadaceae, Sphingomonadaceae, and Xanthomonadaceae). Notable were the formation of valsartan acid from irbesartan and valsartan, the persistence of N-desmethylvenlafaxine across all treatments, and the identification of biuret as a novel transformation product of metformin. Twelve additional target transformation products were identified, which were persistent in either pore or surface water of at least one treatment, indicating their environmental relevance.
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Affiliation(s)
- Malte Posselt
- Department
of Environmental Science (ACES), Stockholm
University, Svante Arrhenius väg 8, SE-11418 Stockholm, Sweden
| | - Jonas Mechelke
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, Überlandstr. 133, CH 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zürich, Switzerland
| | - Cyrus Rutere
- Department
of Ecological Microbiology, University of
Bayreuth, Bayreuth, Germany
| | - Claudia Coll
- Department
of Environmental Science (ACES), Stockholm
University, Svante Arrhenius väg 8, SE-11418 Stockholm, Sweden
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, Überlandstr. 133, CH 8600 Dübendorf, Switzerland
| | - Anna Jaeger
- Department
Ecohydrology, Leibniz-Institute of Freshwater
Ecology and Inland Fisheries, Berlin, Germany
- Geography
Department, Humboldt University Berlin, Berlin, Germany
| | - Muhammad Raza
- Technical
University of Darmstadt, Institute of Applied
Geosciences, Darmstadt, Germany
- IWW
Water Centre, Mülheim an
der Ruhr, Germany
| | - Karin Meinikmann
- Department
Ecohydrology, Leibniz-Institute of Freshwater
Ecology and Inland Fisheries, Berlin, Germany
- Julius
Kühn-Institute, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
| | - Stefan Krause
- School
of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, U.K.
| | - Anna Sobek
- Department
of Environmental Science (ACES), Stockholm
University, Svante Arrhenius väg 8, SE-11418 Stockholm, Sweden
| | - Jörg Lewandowski
- Department
Ecohydrology, Leibniz-Institute of Freshwater
Ecology and Inland Fisheries, Berlin, Germany
- Geography
Department, Humboldt University Berlin, Berlin, Germany
| | - Marcus A. Horn
- Department
of Ecological Microbiology, University of
Bayreuth, Bayreuth, Germany
- Institute
of Microbiology, Leibniz University of Hannover, Herrenhäuser Str. 2, DE-30167 Hannover, Germany
| | - Juliane Hollender
- Eawag,
Swiss Federal Institute of Aquatic Science and Technology, Überlandstr. 133, CH 8600 Dübendorf, Switzerland
- Institute
of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zürich, Switzerland
| | - Jonathan P. Benskin
- Department
of Environmental Science (ACES), Stockholm
University, Svante Arrhenius väg 8, SE-11418 Stockholm, Sweden
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11
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Mineralization of the herbicide swep by a two-strain consortium and characterization of a new amidase for hydrolyzing swep. Microb Cell Fact 2020; 19:4. [PMID: 31910844 PMCID: PMC6945715 DOI: 10.1186/s12934-020-1276-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 01/02/2020] [Indexed: 11/10/2022] Open
Abstract
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.
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12
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Poursat BAJ, van Spanning RJM, Braster M, Helmus R, de Voogt P, Parsons JR. Biodegradation of metformin and its transformation product, guanylurea, by natural and exposed microbial communities. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 182:109414. [PMID: 31301597 DOI: 10.1016/j.ecoenv.2019.109414] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 05/25/2023]
Abstract
Metformin (MET) is a pharmaceutical product mostly biotransformed in the environment to a transformation product, guanylurea (GUA). In ready biodegradability tests (RBTs), however, contrasting results have been observed for metformin. The objective of this study was to measure the biodegradation of MET and GUA in RBTs, using activated sludge from the local wastewater treatment plant, either directly or after pre-exposure to MET, in a chemostat. The activated sludge community was cultivated in chemostats, in presence or absence of MET, for a period of nine months, and was used in RBT after one, three and nine months. The results of this study showed that the original activated sludge was able to completely remove MET (15 mg/l) and the newly produced GUA (50% of C0MET) under the test conditions. Inoculation of the chemostat led to a rapid shift in the community composition and abundance. The community exposed to 1.5 mg/l of MET was still able to completely consume MET in the RBTs after one-month exposure, but three- and nine-months exposure resulted in reduced removal of MET in the RBTs. The ability of the activated sludge community to degrade MET and GUA is the result of environmental exposure to these chemicals as well as of conditions that could not be reproduced in the laboratory system. A MET-degrading strain belonging to the genus Aminobacter has been isolated from the chemostat community. This strain was able to completely consume 15 mg/l of MET within three days in the test. However, community analysis revealed that the fluctuation in relative abundance of this genus (<1%) could not be correlated to the fluctuation in biodegradation capacity of the chemostat community.
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Affiliation(s)
- Baptiste A J Poursat
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098, XH Amsterdam, the Netherlands; Department of Molecular Cell Biology, Vrije Universteit, de Boelelaan 1108, 1081, HZ Amsterdam, the Netherlands.
| | - Rob J M van Spanning
- Department of Molecular Cell Biology, Vrije Universteit, de Boelelaan 1108, 1081, HZ Amsterdam, the Netherlands
| | - Martin Braster
- Department of Molecular Cell Biology, Vrije Universteit, de Boelelaan 1108, 1081, HZ Amsterdam, the Netherlands
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098, XH Amsterdam, the Netherlands
| | - Pim de Voogt
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098, XH Amsterdam, the Netherlands; KWR Watercycle Research Institute, Nieuwegein, the Netherlands
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098, XH Amsterdam, the Netherlands
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13
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Raes B, Horemans B, Rentsch D, T'Syen J, Ghequire MGK, De Mot R, Wattiez R, Kohler HPE, Springael D. Aminobacter sp. MSH1 Mineralizes the Groundwater Micropollutant 2,6-Dichlorobenzamide through a Unique Chlorobenzoate Catabolic Pathway. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:10146-10156. [PMID: 31386350 DOI: 10.1021/acs.est.9b02021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
2,6-Dichlorobenzamide (BAM) is a major groundwater micropollutant posing problems for drinking water treatment plants (DWTPs) that depend on groundwater intake. Aminobacter sp. MSH1 uses BAM as the sole source of carbon, nitrogen, and energy and is considered a prime biocatalyst for groundwater bioremediation in DWTPs. Its use in bioremediation requires knowledge of its BAM-catabolic pathway, which is currently restricted to the amidase BbdA converting BAM into 2,6-dichlorobenzoic acid (2,6-DCBA) and the monooxygenase BbdD transforming 2,6-DCBA into 2,6-dichloro-3-hydroxybenzoic acid. Here, we show that the 2,6-DCBA catabolic pathway is unique and differs substantially from catabolism of other chlorobenzoates. BbdD catalyzes a second hydroxylation, forming 2,6-dichloro-3,5-dihydroxybenzoic acid. Subsequently, glutathione-dependent dehalogenases (BbdI and BbdE) catalyze the thiolytic removal of the first chlorine. The remaining chlorine is then removed hydrolytically by a dehalogenase of the α/β hydrolase superfamily (BbdC). BbdC is the first enzyme in that superfamily associated with dehalogenation of chlorinated aromatics and appears to represent a new subtype within the α/β hydrolase dehalogenases. The activity of BbdC yields a unique trihydroxylated aromatic intermediate for ring cleavage that is performed by an extradiol dioxygenase (BbdF) producing 2,4,6-trioxoheptanedioic acid, which is likely converted to Krebs cycle intermediates by BbdG.
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Affiliation(s)
| | | | - Daniel Rentsch
- Laboratory for Functional Polymers , Empa, Swiss Federal Laboratories for Materials Science and Technology , Dübendorf 8600 , Switzerland
| | | | | | | | - Ruddy Wattiez
- Department of Proteomics and Microbiology , University of Mons , Mons 7000 , Belgium
| | - Hans-Peter E Kohler
- Department of Environmental Microbiology , Eawag, Swiss Federal Institute of Aquatic Science and Technology , Dübendorf 8600 , Switzerland
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14
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Catabolism of the groundwater micropollutant 2,6-dichlorobenzamide beyond 2,6-dichlorobenzoate is plasmid encoded in Aminobacter sp. MSH1. Appl Microbiol Biotechnol 2018; 102:7963-7979. [PMID: 29984394 DOI: 10.1007/s00253-018-9189-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 01/01/2023]
Abstract
Aminobacter sp. MSH1 uses the groundwater micropollutant 2,6-dichlorobenzamide (BAM) as sole source of carbon and energy. In the first step, MSH1 converts BAM to 2,6-dichlorobenzoic acid (2,6-DCBA) by means of the BbdA amidase encoded on the IncP-1β plasmid pBAM1. Information about the genes and degradation steps involved in 2,6-DCBA metabolism in MSH1 or any other organism is currently lacking. Here, we show that the genes for 2,6-DCBA degradation in strain MSH1 reside on a second catabolic plasmid in MSH1, designated as pBAM2. The complete sequence of pBAM2 was determined revealing that it is a 53.9 kb repABC family plasmid. The 2,6-DCBA catabolic genes on pBAM2 are organized in two main clusters bordered by IS elements and integrase genes and encode putative functions like Rieske mono-/dioxygenase, meta-cleavage dioxygenase, and reductive dehalogenases. The putative mono-oxygenase encoded by the bbdD gene was shown to convert 2,6-DCBA to 3-hydroxy-2,6-dichlorobenzoate (3-OH-2,6-DCBA). 3-OH-DCBA was degraded by wild-type MSH1 and not by a pBAM2-free MSH1 variant indicating that it is a likely intermediate in the pBAM2-encoded DCBA catabolic pathway. Based on the activity of BbdD and the putative functions of the other catabolic genes on pBAM2, a metabolic pathway for BAM/2,6-DCBA in strain MSH1 was suggested.
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15
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Groundwater contamination with 2,6-dichlorobenzamide (BAM) and perspectives for its microbial removal. Appl Microbiol Biotechnol 2017; 101:5235-5245. [PMID: 28616645 DOI: 10.1007/s00253-017-8362-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 01/26/2023]
Abstract
The pesticide metabolite 2,6-dichlorobenzamide (BAM) is very persistent in both soil and groundwater and has become one of the most frequently detected groundwater micropollutants. BAM is not removed by the physico-chemical treatment techniques currently used in drinking water treatment plants (DWTP); therefore, if concentrations exceed the legal threshold limit, it represents a sizeable problem for the stability and quality of drinking water production, especially in places that depend on groundwater for drinking water. Bioremediation is suggested as a valuable strategy for removing BAM from groundwater by deploying dedicated BAM-degrading bacteria in DWTP sand filters. Only a few bacterial strains with the capability to degrade BAM have been isolated, and of these, only three isolates belonging to the Aminobacter genus are able to mineralise BAM. Considerable effort has been made to elucidate degradation pathways, kinetics and degrader genes, and research has recently been presented on the application of strain Aminobacter sp. MSH1 for the purification of BAM-contaminated water. The aim of the present review was to provide insight into the issue of BAM contamination and to report on the current status and knowledge with regard to the application of microorganisms for purification of BAM-contaminated water resources. This paper discusses the prospects and challenges for bioaugmentation of DWTP sand filters with specific BAM-degrading bacteria and identifies relevant perspectives for future research.
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16
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Genetic (In)stability of 2,6-Dichlorobenzamide Catabolism in Aminobacter sp. Strain MSH1 Biofilms under Carbon Starvation Conditions. Appl Environ Microbiol 2017; 83:AEM.00137-17. [PMID: 28363960 DOI: 10.1128/aem.00137-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/24/2017] [Indexed: 01/07/2023] Open
Abstract
Aminobacter sp. strain MSH1 grows on and mineralizes the groundwater micropollutant 2,6-dichlorobenzamide (BAM) and is of interest for BAM removal in drinking water treatment plants (DWTPs). The BAM-catabolic genes in MSH1 are located on plasmid pBAM1, carrying bbdA, which encodes the conversion of BAM to 2,6-dichlorobenzoic acid (2,6-DCBA) (BbdA+ phenotype), and plasmid pBAM2, carrying gene clusters encoding the conversion of 2,6-DCBA to tricarboxylic acid (TCA) cycle intermediates (Dcba+ phenotype). There are indications that MSH1 easily loses its BAM-catabolic phenotype. We obtained evidence that MSH1 rapidly develops a population that lacks the ability to mineralize BAM when grown on nonselective (R2B medium) and semiselective (R2B medium with BAM) media. Lack of mineralization was explained by loss of the Dcba+ phenotype and corresponding genes. The ecological significance of this instability for the use of MSH1 for BAM removal in the oligotrophic environment of DWTPs was explored in lab and pilot systems. A higher incidence of BbdA+ Dcba- MSH1 cells was also observed when MSH1 was grown as a biofilm in flow chambers under C and N starvation conditions due to growth on nonselective residual assimilable organic carbon. Similar observations were made in experiments with a pilot sand filter reactor bioaugmented with MSH1. BAM conversion to 2,6-DCBA was not affected by loss of the DCBA-catabolic genes. Our results show that MSH1 is prone to BAM-catabolic instability under the conditions occurring in a DWTP. While conversion of BAM to 2,6-DCBA remains unaffected, BAM mineralization activity is at risk, and monitoring of metabolites is warranted.IMPORTANCE Bioaugmentation of dedicated biofiltration units with bacterial strains that grow on and mineralize micropollutants was suggested as an alternative for treating micropollutant-contaminated water in drinking water treatment plants (DWTPs). Organic-pollutant-catabolic genes in bacteria are often easily lost, especially under nonselective conditions, which affects the bioaugmentation success. In this study, we provide evidence that Aminobacter sp. strain MSH1, which uses the common groundwater micropollutant 2,6-dichlorobenzamide (BAM) as a C source, shows a high frequency of loss of its BAM-mineralizing phenotype due to the loss of genes that convert 2,6-DCBA to Krebs cycle intermediates when nonselective conditions occur. Moreover, we show that catabolic-gene loss also occurs in the oligotrophic environment of DWTPs, where growth of MSH1 depends mainly on the high fluxes of low concentrations of assimilable organic carbon, and hence show the ecological relevance of catabolic instability for using strain MSH1 for BAM removal in DWTPs.
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17
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Horemans B, Raes B, Vandermaesen J, Simanjuntak Y, Brocatus H, T'Syen J, Degryse J, Boonen J, Wittebol J, Lapanje A, Sørensen SR, Springael D. Biocarriers Improve Bioaugmentation Efficiency of a Rapid Sand Filter for the Treatment of 2,6-Dichlorobenzamide-Contaminated Drinking Water. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:1616-1625. [PMID: 28027645 DOI: 10.1021/acs.est.6b05027] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Aminobacter sp. MSH1 immobilized in an alginate matrix in porous stones was tested in a pilot system as an alternative inoculation strategy to the use of free suspended cells for biological removal of micropollutant concentrations of 2,6-dichlorobenzamide (BAM) in drinking water treatment plants (DWTPs). BAM removal rates and MSH1 cell numbers were recorded during operation and assessed with specific BAM degradation rates obtained in lab conditions using either freshly grown cells or starved cells to explain reactor performance. Both reactors inoculated with either suspended or immobilized cells showed immediate BAM removal under the threshold of 0.1 μg/L, but the duration of sufficient BAM removal was 2-fold (44 days) longer for immobilized cells. The longer sufficient BAM removal in case of immobilized cells compared to suspended cells was mainly explained by a lower initial loss of MSH1 cells at operational start due to volume replacement and shear. Overall loss of activity in the reactors though was due to starvation, and final removal rates did not differ between reactors inoculated with immobilized and suspended cells. Management of assimilable organic carbon, in addition to cell immobilization, appears crucial for guaranteeing long-term BAM degradation activity of MSH1 in DWTP units.
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Affiliation(s)
- Benjamin Horemans
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven , Kasteelpark Arenberg 20 bus 2459, 3001 Heverlee, Belgium
| | - Bart Raes
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven , Kasteelpark Arenberg 20 bus 2459, 3001 Heverlee, Belgium
| | - Johanna Vandermaesen
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven , Kasteelpark Arenberg 20 bus 2459, 3001 Heverlee, Belgium
| | - Yanti Simanjuntak
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven , Kasteelpark Arenberg 20 bus 2459, 3001 Heverlee, Belgium
| | - Hannelore Brocatus
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven , Kasteelpark Arenberg 20 bus 2459, 3001 Heverlee, Belgium
| | - Jeroen T'Syen
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven , Kasteelpark Arenberg 20 bus 2459, 3001 Heverlee, Belgium
| | - Julie Degryse
- De Watergroep , Vooruitgangstraat 189, 1030 Brussels, Belgium
| | - Jos Boonen
- De Watergroep , Vooruitgangstraat 189, 1030 Brussels, Belgium
| | | | - Ales Lapanje
- Josef Stefan Institute , Jamova 49, 1000 Ljubljana, Slovenia
- National Research Saratov State University , Astrakhanskaya 83, 410012 Saratov, Russian Federation
| | - Sebastian R Sørensen
- Department of Geochemistry, Geological Survey of Denmark and Greenland , Øster Voldgade 10, 1350 Copenhagen K, Denmark
| | - Dirk Springael
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, Faculty of Bioscience Engineering, KU Leuven , Kasteelpark Arenberg 20 bus 2459, 3001 Heverlee, Belgium
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Yun H, Liang B, Qiu J, Zhang L, Zhao Y, Jiang J, Wang A. Functional Characterization of a Novel Amidase Involved in Biotransformation of Triclocarban and its Dehalogenated Congeners in Ochrobactrum sp. TCC-2. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:291-300. [PMID: 27966913 DOI: 10.1021/acs.est.6b04885] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Haloaromatic antimicrobial triclocarban (3,4,4'-trichlorocarbanilide, TCC) is a refractory contaminant which is frequently detected in various aquatic and sediment environments globally. However, few TCC-degrading communities or pure cultures have been documented, and functional enzymes involved in TCC biodegradation hitherto have not yet been characterized. In this study, a bacterial strain, Ochrobactrum sp. TCC-2, capable of degrading TCC under both aerobic and anaerobic conditions was isolated from a sediment sample. A novel amidase gene (tccA), responsible for the hydrolysis of the two amide bonds of TCC and its dehalogenated congeners 4,4'-dichlorocarbanilide (DCC) and carbanilide (NCC) to more biodegradable chloroaniline or aniline products, was cloned and characterized. TccA shares low amino acid sequence identity (27 to 38%) with other biochemically characterized amidases and contains the conserved catalytic triad (Ser-Ser-Lys) of the amidase signature enzyme family. TccA was stable over a pH range of 5.0 to 10.0 and at temperatures lower than 60 °C, and it was constitutively expressed in strain TCC-2. In contrast to the halogenated TCC and DCC, the nonchlorinated NCC was the preferred substrate for TccA. TccA also had hydrolysis activity to a broad spectrum of amide bonds in herbicides, insecticides, and chemical intermediates. The constitutive expression and broad substrate spectrum of TccA suggested strain TCC-2 may be potentially useful for bioremediation applications.
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Affiliation(s)
- Hui Yun
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, 100085, China
- University of Chinese Academy of Sciences , Beijing, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, 100085, China
| | - Jiguo Qiu
- Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University , 210095, Nanjing, China
| | - Long Zhang
- Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University , 210095, Nanjing, China
| | - Youkang Zhao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology , Harbin, 150090, China
| | - Jiandong Jiang
- Key Lab of Microbiological Engineering of Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University , 210095, Nanjing, China
| | - Aijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, 100085, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology , Harbin, 150090, China
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Vandermaesen J, Horemans B, Degryse J, Boonen J, Walravens E, Springael D. Mineralization of the Common Groundwater Pollutant 2,6-Dichlorobenzamide (BAM) and its Metabolite 2,6-Dichlorobenzoic Acid (2,6-DCBA) in Sand Filter Units of Drinking Water Treatment Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:10114-22. [PMID: 27533590 DOI: 10.1021/acs.est.6b01352] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The intrinsic capacity to mineralize the groundwater pollutant 2,6-dichlorobenzamide (BAM) and its metabolite 2,6-dichlorobenzoic acid (2,6-DCBA) was evaluated in samples from sand filters (SFs) of drinking water treatment plants (DWTPs). Whereas BAM mineralization occurred rarely and only in SFs exposed to BAM, 2,6-DCBA mineralization was common in SFs, including those treating uncontaminated water. Nevertheless, SFs treating BAM contaminated water showed the highest 2,6-DCBA mineralization rates. For comparison, 2,6-DCBA and BAM mineralization were determined in various topsoil samples. As in SF samples, BAM mineralization was rare, whereas 2,6-DCBA mineralization capacity appeared widespread, with high mineralization rates found especially in forest soils. Multivariate analysis showed that in both SF and soil samples, high 2,6-DCBA mineralization correlated with high organic carbon content. Adding a 2,6-DCBA degradation deficient mutant of the BAM mineralizing Aminobacter sp. MSH1 confirmed that 2,6-DCBA produced from BAM is rapidly mineralized by the endogenous microbial community in SFs showing intrinsic 2,6-DCBA mineralization. This study demonstrates that (i) 2,6-DCBA mineralization is widely established in SFs of DWTPs, allowing the mineralization of 2,6-DCBA produced during BAM degradation and (ii) the first metabolic step in BAM mineralization is rare in microbial communities, rather than its further degradation beyond 2,6-DCBA.
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Affiliation(s)
- Johanna Vandermaesen
- KU Leuven, Division of Soil and Water Management, Kasteelpark Arenberg 20 bus 2459, B-3001 Heverlee, Belgium
| | - Benjamin Horemans
- KU Leuven, Division of Soil and Water Management, Kasteelpark Arenberg 20 bus 2459, B-3001 Heverlee, Belgium
| | - Julie Degryse
- Centraal laboratorium, De Watergroep, Researchpark Haasrode Leuven 1834 - Technologielaan 23, B-3001 Heverlee, Belgium
| | - Jos Boonen
- Centraal laboratorium, De Watergroep, Researchpark Haasrode Leuven 1834 - Technologielaan 23, B-3001 Heverlee, Belgium
| | - Eddy Walravens
- Centraal laboratorium, De Watergroep, Researchpark Haasrode Leuven 1834 - Technologielaan 23, B-3001 Heverlee, Belgium
| | - Dirk Springael
- KU Leuven, Division of Soil and Water Management, Kasteelpark Arenberg 20 bus 2459, B-3001 Heverlee, Belgium
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Sekhar A, Horemans B, Aamand J, Sørensen SR, Vanhaecke L, Bussche JV, Hofkens J, Springael D. Surface Colonization and Activity of the 2,6-Dichlorobenzamide (BAM) Degrading Aminobacter sp. Strain MSH1 at Macro- and Micropollutant BAM Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:10123-33. [PMID: 27537851 DOI: 10.1021/acs.est.6b01978] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Aminobacter sp. MSH1 uses the groundwater micropollutant 2,6-dichlorobenzamide (BAM) as a C and N source and is a potential catalyst for biotreatment of BAM-contaminated groundwater in filtration units of drinking water treatment plants (DWTPs). The oligotrophic environment of DWTPs including trace pollutant concentrations, and the high flow rates impose challenges for micropollutant biodegradation in DWTPs. To understand how trace BAM concentrations affect MSH1 surface colonization and BAM degrading activity, MSH1 was cultivated in flow channels fed continuously with BAM macro- and microconcentrations in a N- and C-limiting medium. At all BAM concentrations, MSH1 colonized the flow channel. BAM degradation efficiencies were concentration-dependent, ranging between 70 and 95%. Similarly, BAM concentration affected surface colonization, but at 100 μg/L BAM and lower, colonization was similar to that in systems without BAM, suggesting that assimilable organic carbon and nitrogen other than those supplied by BAM sustained colonization at BAM microconcentrations. Comparison of specific BAM degradation rates in flow channels and in cultures of suspended freshly grown cells indicated that starvation conditions in flow channels receiving BAM microconcentrations resulted into MSH1 biomasses with 10-100-times reduced BAM degrading activity and provided a kinetic model for predicting BAM degradation under continuous C and N starvation.
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Affiliation(s)
- Aswini Sekhar
- Division of Soil and Water Management, KU Leuven , Kasteelpark Arenberg 20, BE-3001 Leuven, Belgium
| | - Benjamin Horemans
- Division of Soil and Water Management, KU Leuven , Kasteelpark Arenberg 20, BE-3001 Leuven, Belgium
| | - Jens Aamand
- Department of Geochemistry, Geological Survey of Greenland and Denmark (GEUS) , DK-1350 Copenhagen, Denmark
| | - Sebastian R Sørensen
- Department of Geochemistry, Geological Survey of Greenland and Denmark (GEUS) , DK-1350 Copenhagen, Denmark
| | - Lynn Vanhaecke
- Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, UGent , BE-9000 Ghent, Belgium
| | - Julie Vanden Bussche
- Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, UGent , BE-9000 Ghent, Belgium
| | - Johan Hofkens
- Molecular Imaging and Photonics, KU Leuven , Celestijnenlaan 200 F, BE-3001 Leuven, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven , Kasteelpark Arenberg 20, BE-3001 Leuven, Belgium
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Öztürk B, Ghequire M, Nguyen TPO, De Mot R, Wattiez R, Springael D. Expanded insecticide catabolic activity gained by a single nucleotide substitution in a bacterial carbamate hydrolase gene. Environ Microbiol 2016; 18:4878-4887. [PMID: 27312345 DOI: 10.1111/1462-2920.13409] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/05/2016] [Accepted: 06/06/2016] [Indexed: 01/29/2023]
Abstract
Carbofuran-mineralizing strain Novosphingobium sp. KN65.2 produces the CfdJ enzyme that converts the N-methylcarbamate insecticide to carbofuran phenol. Purified CfdJ shows a remarkably low KM towards carbofuran. Together with the carbaryl hydrolase CehA of Rhizobium sp. strain AC100, CfdJ represents a new protein family with several uncharacterized bacterial members outside the proteobacteria. Although both enzymes differ by only four amino acids, CehA does not recognize carbofuran as a substrate whereas CfdJ also hydrolyzes carbaryl. None of the CfdJ amino acids that differ from CehA were shown to be silent regarding carbofuran hydrolytic activity but one particular amino acid substitution, i.e., L152 to F152, proved crucial. CfdJ is more efficient in degrading methylcarbamate pesticides with an aromatic side chain whereas CehA is more efficient in degrading the oxime carbamate nematicide oxamyl. The presence of common flanking sequences suggest that the cfdJ gene is located on a remnant of the mobile genetic element Tnceh carrying cehA. Our results suggest that these enzymes can be acquired through horizontal gene transfer and can evolve to degrade new carbamate substrates by limited amino acid substitutions. We demonstrate that a carbaryl hydrolase can gain the additional capacity to degrade carbofuran by a single nucleotide transversion.
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Affiliation(s)
- Başak Öztürk
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Maarten Ghequire
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Thi Phi Oanh Nguyen
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium.,Department of Biology, College of Natural Sciences, Cantho University, Vietnam
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, Mons, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
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