1
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Zhang C, Atashgahi S, Bosma TNP, Peng P, Smidt H. Organohalide respiration potential in marine sediments from Aarhus Bay. FEMS Microbiol Ecol 2022; 98:6605901. [PMID: 35689665 PMCID: PMC9303371 DOI: 10.1093/femsec/fiac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/09/2022] [Accepted: 06/08/2022] [Indexed: 11/14/2022] Open
Abstract
Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.
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Affiliation(s)
- Chen Zhang
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom N P Bosma
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109-2125, United States
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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2
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Aldas-Vargas A, Hauptfeld E, Hermes GDA, Atashgahi S, Smidt H, Rijnaarts HHM, Sutton NB. Selective pressure on microbial communities in a drinking water aquifer - Geochemical parameters vs. micropollutants. Environ Pollut 2022; 299:118807. [PMID: 35007672 DOI: 10.1016/j.envpol.2022.118807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/26/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Groundwater quality is crucial for drinking water production, but groundwater resources are increasingly threatened by contamination with pesticides. As pesticides often occur at micropollutant concentrations, they are unattractive carbon sources for microorganisms and typically remain recalcitrant. Exploring microbial communities in aquifers used for drinking water production is an essential first step towards understanding the fate of micropollutants in groundwater. In this study, we investigated the interaction between groundwater geochemistry, pesticide presence, and microbial communities in an aquifer used for drinking water production. Two groundwater monitoring wells in The Netherlands were sampled in 2014, 2015, and 2016. In both wells, water was sampled from five discrete depths ranging from 13 to 54 m and was analyzed for geochemical parameters, pesticide concentrations and microbial community composition using 16S rRNA gene sequencing and qPCR. Groundwater geochemistry was stable throughout the study period and pesticides were heterogeneously distributed at low concentrations (μg L-1 range). Microbial community composition was also stable throughout the sampling period. Integration of a unique dataset of chemical and microbial data showed that geochemical parameters and to a lesser extent pesticides exerted selective pressure on microbial communities. Microbial communities in both wells showed similar composition in the deeper aquifer, where pumping results in horizontal flow. This study provides insight into groundwater parameters that shape microbial community composition. This information can contribute to the future implementation of remediation technologies to guarantee safe drinking water production.
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Affiliation(s)
- Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, the Netherlands
| | - Ernestina Hauptfeld
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, the Netherlands; Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700, EH Wageningen, the Netherlands
| | - Gerben D A Hermes
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700, EH Wageningen, the Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700, EH Wageningen, the Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 8033, 6700, EH Wageningen, the Netherlands
| | - Huub H M Rijnaarts
- 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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3
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Shetty SA, Kuipers B, Atashgahi S, Aalvink S, Smidt H, de Vos WM. Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria. NPJ Biofilms Microbiomes 2022; 8:21. [PMID: 35395818 PMCID: PMC8993927 DOI: 10.1038/s41522-022-00275-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/18/2022] [Indexed: 12/13/2022] Open
Abstract
Knowledge of the functional roles and interspecies interactions are crucial for improving our understanding of the human intestinal microbiome in health and disease. However, the complexity of the human intestinal microbiome and technical challenges in investigating it pose major challenges. In this proof-of-concept study, we rationally designed, assembled and experimentally tested a synthetic Diet-based Minimal Microbiome (Db-MM) consisting of ten core intestinal bacterial species that together are capable of efficiently converting dietary fibres into short chain fatty acids (SCFAs). Despite their genomic potential for metabolic competition, all ten bacteria coexisted during growth on a mixture of dietary fibres, including pectin, inulin, xylan, cellobiose and starch. By integrated analyses of metabolite production, community composition and metatranscriptomics-based gene expression data, we identified interspecies metabolic interactions leading to production of key SCFAs such as butyrate and propionate. While public goods, such as sugars liberated from colonic fibres, are harvested by non-degraders, some species thrive by cross-feeding on energetically challenging substrates, including the butyrogenic conversion of acetate and lactate. Using a reductionist approach in an in-vitro system combined with functional measurements, our study provides key insights into the complex interspecies metabolic interactions between core intestinal bacterial species.
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Affiliation(s)
- Sudarshan A Shetty
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Department of Medical Microbiology and Infection prevention, Virology and Immunology Research Group, University Medical Center Groningen, Groningen, The Netherlands
| | - Ben Kuipers
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands. .,Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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4
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Atashgahi S, Oosterkamp MJ, Peng P, Frank J, Kraft B, Hornung B, Schleheck D, Lücker S, Jetten MSM, Stams AJM, Smidt H. Proteogenomic analysis of Georgfuchsia toluolica revealed unexpected concurrent aerobic and anaerobic toluene degradation. Environ Microbiol Rep 2021; 13:841-851. [PMID: 34374217 PMCID: PMC9290046 DOI: 10.1111/1758-2229.12996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Denitrifying Betaproteobacteria play a key role in the anaerobic degradation of monoaromatic hydrocarbons. We performed a multi-omics study to better understand the metabolism of the representative organism Georgfuchsia toluolica strain G5G6 known as a strict anaerobe coupling toluene oxidation with dissimilatory nitrate and Fe(III) reduction. Despite the genomic potential for degradation of different carbon sources, we did not find sugar or organic acid transporters, in line with the inability of strain G5G6 to use these substrates. Using a proteomics analysis, we detected proteins of fumarate-dependent toluene activation, membrane-bound nitrate reductase, and key components of the metal-reducing (Mtr) pathway under both nitrate- and Fe(III)-reducing conditions. High abundance of the multiheme cytochrome MtrC implied that a porin-cytochrome complex was used for respiratory Fe(III) reduction. Remarkably, strain G5G6 contains a full set of genes for aerobic toluene degradation, and we detected enzymes of aerobic toluene degradation under both nitrate- and Fe(III)-reducing conditions. We further detected an ATP-dependent benzoyl-CoA reductase, reactive oxygen species detoxification proteins, and cytochrome c oxidase indicating a facultative anaerobic lifestyle of strain G5G6. Correspondingly, we found diffusion through the septa a substantial source of oxygen in the cultures enabling concurrent aerobic and anaerobic toluene degradation by strain G5G6.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Margreet J. Oosterkamp
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Sub‐department of Environmental TechnologyWageningen University & Research, Bornse weilanden 9Wageningen6708 DWThe Netherlands
| | - Peng Peng
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Department of Civil and Environmental EngineeringUniversity of Michigan, 1351 Beal AvenueAnn ArborMI48109‐2125USA
| | - Jeroen Frank
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Beate Kraft
- Nordic Center for Earth EvolutionUniversity of Southern DenmarkOdenseDK‐5230Denmark
| | - Bastian Hornung
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, 163 avenue de Luminy13288 Aix Marseille UniversitéMarseilleFrance
| | - David Schleheck
- Department of BiologyUniversity of KonstanzKonstanz78457Germany
| | - Sebastian Lücker
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, IWWRRadboud UniversityHeyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
- Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135Nijmegen6525 AJThe Netherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de GualtarBraga4710‐057Portugal
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchWageningen6708 WEThe Netherlands
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5
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Brucha G, Aldas-Vargas A, Ross Z, Peng P, Atashgahi S, Smidt H, Langenhoff A, Sutton NB. 2,4-Dichlorophenoxyacetic acid degradation in methanogenic mixed cultures obtained from Brazilian Amazonian soil samples. Biodegradation 2021; 32:419-433. [PMID: 33877512 PMCID: PMC8260542 DOI: 10.1007/s10532-021-09940-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 03/31/2021] [Indexed: 01/23/2023]
Abstract
2,4-Dichlorophenoxyacetic acid (2,4-D) is the third most applied pesticide in Brazil to control broadleaf weeds in crop cultivation and pastures. Due to 2,4-D's high mobility and long half-life under anoxic conditions, this herbicide has high probability for groundwater contamination. Bioremediation is an attractive solution for 2,4-D contaminated anoxic environments, but there is limited understanding of anaerobic 2,4-D biodegradation. In this study, methanogenic enrichment cultures were obtained from Amazonian top soil (0-40 cm) and deep soil (50 -80 cm below ground) that biotransform 2,4-D (5 µM) to 4-chlorophenol and phenol. When these cultures were transferred (10% v/v) to fresh medium containing 40 µM or 160 µM 2,4-D, the rate of 2,4-D degradation decreased, and biotransformation did not proceed beyond 4-chlorophenol and 2,4-dichlorophenol in the top and deep soil cultures, respectively. 16S rRNA gene sequencing and qPCR of a selection of microbes revealed no significant enrichment of known organohalide-respiring bacteria. Furthermore, a member of the genus Cryptanaerobacter was identified as possibly responsible for phenol conversion to benzoate in the top soil inoculated culture. Overall, these results demonstrate the effect of 2,4-D concentration on biodegradation and microbial community composition, which are both important factors when developing pesticide bioremediation technologies.
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Affiliation(s)
- Gunther Brucha
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands
- Institute of Science and Technology, Universidade Federal de Alfenas, Alfenas, Brazil
| | - Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands
| | - Zacchariah Ross
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Alette Langenhoff
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, PO BOX 17, 6700 EV, Wageningen, The Netherlands.
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6
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Melkonian C, Fillinger L, Atashgahi S, da Rocha UN, Kuiper E, Olivier B, Braster M, Gottstein W, Helmus R, Parsons JR, Smidt H, van der Waals M, Gerritse J, Brandt BW, Röling WFM, Molenaar D, van Spanning RJM. Author Correction: High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. Commun Biol 2021; 4:774. [PMID: 34145385 PMCID: PMC8213818 DOI: 10.1038/s42003-021-02311-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Chrats Melkonian
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Lucas Fillinger
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Esther Kuiper
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brett Olivier
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martin Braster
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willi Gottstein
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Jan Gerritse
- Unit Subsurface and Groundwater Systems, Deltares, Utrecht, The Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wilfred F M Röling
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rob J M van Spanning
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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7
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Melkonian C, Fillinger L, Atashgahi S, da Rocha UN, Kuiper E, Olivier B, Braster M, Gottstein W, Helmus R, Parsons JR, Smidt H, van der Waals M, Gerritse J, Brandt BW, Röling WFM, Molenaar D, van Spanning RJM. High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. Commun Biol 2021; 4:530. [PMID: 33953314 PMCID: PMC8099898 DOI: 10.1038/s42003-021-01948-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.
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Affiliation(s)
- Chrats Melkonian
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Lucas Fillinger
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Esther Kuiper
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brett Olivier
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martin Braster
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willi Gottstein
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Jan Gerritse
- Unit Subsurface and Groundwater Systems, Deltares, Utrecht, The Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wilfred F M Röling
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rob J M van Spanning
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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8
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Alves JI, Salvador AF, Castro AR, Zheng Y, Nijsse B, Atashgahi S, Sousa DZ, Stams AJM, Alves MM, Cavaleiro AJ. Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of " Candidatus Desulfomonile Palmitatoxidans". Front Microbiol 2021; 11:539604. [PMID: 33391191 PMCID: PMC7773648 DOI: 10.3389/fmicb.2020.539604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 11/24/2020] [Indexed: 11/13/2022] Open
Abstract
Microbial communities with the ability to convert long-chain fatty acids (LCFA) coupled to sulfate reduction can be important in the removal of these compounds from wastewater. In this work, an enrichment culture, able to oxidize the long-chain fatty acid palmitate (C16 : 0) coupled to sulfate reduction, was obtained from anaerobic granular sludge. Microscopic analysis of this culture, designated HP culture, revealed that it was mainly composed of one morphotype with a typical collar-like cell wall invagination, a distinct morphological feature of the Desulfomonile genus. 16S rRNA gene amplicon and metagenome-assembled genome (MAG) indeed confirmed that the abundant phylotype in HP culture belong to Desulfomonile genus [ca. 92% 16S rRNA gene sequences closely related to Desulfomonile spp.; and ca. 82% whole genome shotgun (WGS)]. Based on similar cell morphology and average nucleotide identity (ANI) (77%) between the Desulfomonile sp. in HP culture and the type strain Desulfomonile tiedjei strain DCB-1T, we propose a novel species designated as "Candidatus Desulfomonile palmitatoxidans." This bacterium shares 94.3 and 93.6% 16S rRNA gene identity with Desulfomonile limimaris strain DCB-MT and D. tiedjei strain DCB-1T, respectively. Based on sequence abundance of Desulfomonile-morphotype in HP culture, its predominance in the microscopic observations, and presence of several genes coding for enzymes involved in LCFA degradation, the proposed species "Ca. Desulfomonile palmitatoxidans" most probably plays an important role in palmitate degradation in HP culture. Analysis of the growth of HP culture and D. tiedjei strain DCB-1T with short- (butyrate), medium- (caprylate) and long-chain fatty acids (palmitate, stearate, and oleate) showed that both cultures degraded all fatty acids coupled to sulfate reduction, except oleate that was only utilized by HP culture. In the absence of sulfate, neither HP culture, nor D. tiedjei strain DCB-1T degraded palmitate when incubated with Methanobacterium formicicum as a possible methanogenic syntrophic partner. Unlike D. tiedjei strain DCB-1T, "Ca. Desulfomonile palmitatoxidans" lacks reductive dehalogenase genes in its genome, and HP culture was not able to grow by organohalide respiration. An emended description of the genus Desulfomonile is proposed. Our study reveals an unrecognized LCFA degradation feature of the Desulfomonile genus.
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Affiliation(s)
- Joana I Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | | | - A Rita Castro
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ying Zheng
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Bart Nijsse
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands.,Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z Sousa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Alfons J M Stams
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ana J Cavaleiro
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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9
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Atashgahi S. Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS Microbiol Ecol 2020; 95:5426821. [PMID: 30942854 PMCID: PMC6797604 DOI: 10.1093/femsec/fiz048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Attempts for bioremediation of toxic organohalogens resulted in the identification of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases) enzymes. RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that does not have membrane-integral domains, and a small putative membrane anchor (RdhB, encoded by rdhB) that (presumably) locates the A subunit to the outside of the cytoplasmic membrane. Recent genomic studies identified a putative rdh gene in an uncultured deltaproteobacterial genome that was not accompanied by an rdhB gene, but contained transmembrane helixes in N-terminus. Therefore, rather than having a separate membrane anchor protein, this putative RDase is likely a hybrid of RdhA and RdhB, and directly connected to the membrane with transmembrane helixes. However, functionality of the hybrid putative RDase remains unknown. Further analysis showed that the hybrid putative rdh genes are present in the genomes of pure cultures and uncultured members of Bacteriodetes and Deltaproteobacteria, but also in the genomes of the candidate divisions. The encoded hybrid putative RDases have cytoplasmic or exoplasmic C-terminus localization, and cluster phylogenetically separately from the existing RDase groups. With increasing availability of (meta)genomes, more diverse and likely novel rdh genes are expected, but questions regarding their functionality and ecological roles remain open.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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10
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Luo Y, Atashgahi S, Rijnaarts HHM, Comans RNJ, Sutton NB. Influence of different redox conditions and dissolved organic matter on pesticide biodegradation in simulated groundwater systems. Sci Total Environ 2019; 677:692-699. [PMID: 31071671 DOI: 10.1016/j.scitotenv.2019.04.128] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Insights into the influence of redox conditions, that is the availability of electron acceptors, and dissolved organic matter (DOM) on pesticide biodegradation in groundwater are key to understanding the environmental fate of pesticides in natural groundwater systems. Here, the influence of redox conditions and supplemental DOM addition on biodegradation of pesticides, 2,4-dichlorophenoxyacetic acid (2,4-D), 2,6-dichlorobenzamide (BAM), mecoprop-p (MCPP) and bentazone, was tested in microcosm and subsequent column experiments. Pesticide degradation, functional genes and changes in specific fractions and quantity of DOM were systematically quantified. In aerobic microcosm experiments, the highest 2,4-D degradation rate was obtained with the presence of more assimilable DOM. In column experiments, minimal pesticide degradation (≤33.77%) in any anaerobic redox conditions was observed in the absence of DOM. However, in the presence of DOM, 2,4-D biodegradation was considerably enhanced under nitrate-reducing conditions (from 23.5 ± 10.2% to 82.3 ± 11.6%) and in a column without external electron acceptor amendment (from -6.3 ± 12.6% to 31.1 ± 36.3%). Observed preferential depletion of the fulvic acid fraction of DOM provides indications for specific functional DOM properties. The qPCR results show an increase in microbial biomass and functional genes (tfdA) in liquid phase after DOM addition. The results of this work provide insights into the interplays among DOM, redox geochemistry, and pesticide biodegradation, and show the potential of a novel approach - DOM addition to groundwater systems - for in situ biostimulation technology to remove pesticides from groundwater systems.
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Affiliation(s)
- Yujia Luo
- Sub-department of Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Huub H M Rijnaarts
- Sub-department of Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Rob N J Comans
- Department of Soil Quality, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Nora B Sutton
- Sub-department of Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands.
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11
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Peng P, Schneidewind U, Haest PJ, Bosma TNP, Danko AS, Smidt H, Atashgahi S. Reductive dechlorination of 1,2-dichloroethane in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants. Appl Microbiol Biotechnol 2019; 103:6837-6849. [PMID: 31250061 PMCID: PMC6667407 DOI: 10.1007/s00253-019-09985-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022]
Abstract
1,2-Dichloroethane (1,2-DCA) is one of the most abundant manmade chlorinated organic contaminants in the world. Reductive dechlorination of 1,2-DCA by organohalide-respiring bacteria (OHRB) can be impacted by other chlorinated contaminants such as chloroethenes and chloropropanes that can co-exist with 1,2-DCA at contaminated sites. The aim of this study was to evaluate the effect of chloroethenes and 1,2-dichloropropane (1,2-DCP) on 1,2-DCA dechlorination using sediment cultures enriched with 1,2-DCA as the sole chlorinated compound (EA culture) or with 1,2-DCA and tetrachloroethene (PCE) (EB culture), and to model dechlorination kinetics. Both cultures contained Dehalococcoides as most predominated OHRB, and Dehalogenimonas and Geobacter as other known OHRB. In sediment-free enrichments obtained from the EA and EB cultures, dechlorination of 1,2-DCA was inhibited in the presence of the same concentrations of either PCE, vinyl chloride (VC), or 1,2-DCP; however, concurrent dechlorination of dual chlorinated compounds was achieved. In contrast, 1,2-DCA dechlorination completely ceased in the presence of cis-dichloroethene (cDCE) and only occurred after cDCE was fully dechlorinated. In turn, 1,2-DCA did not affect dechlorination of PCE, cDCE, VC, and 1,2-DCP. In sediment-free enrichments obtained from the EA culture, Dehalogenimonas 16S rRNA gene copy numbers decreased 1–3 orders of magnitude likely due to an inhibitory effect of chloroethenes. Dechlorination with and without competitive inhibition fit Michaelis-Menten kinetics and confirmed the inhibitory effect of chloroethenes and 1,2-DCP on 1,2-DCA dechlorination. This study reinforces that the type of chlorinated substrate drives the selection of specific OHRB, and indicates that removal of chloroethenes and in particular cDCE might be necessary before effective removal of 1,2-DCA at sites contaminated with mixed chlorinated solvents.
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Affiliation(s)
- Peng Peng
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Uwe Schneidewind
- Department of Civil and Environmental Engineering, Western University, London, ON, Canada
| | - Pieter Jan Haest
- Advanced Groundwater Techniques (AGT), Aartselaar, Belgium
- Division of Geology, Department of Earth and Environmental Sciences, KU Leuven, Heverlee, Belgium
| | - Tom N P Bosma
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Anthony S Danko
- Centre for Natural Resources and the Environment (CERENA), Department of Mining Engineering, University of Porto (FEUP), Porto, Portugal
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
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12
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Atashgahi S, Liebensteiner MG, Janssen DB, Smidt H, Stams AJM, Sipkema D. Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds. Front Microbiol 2018; 9:3079. [PMID: 30619161 PMCID: PMC6299022 DOI: 10.3389/fmicb.2018.03079] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/29/2018] [Indexed: 12/26/2022] Open
Abstract
Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Dick B. Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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13
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Atashgahi S, Shetty SA, Smidt H, de Vos WM. Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut. Front Physiol 2018; 9:888. [PMID: 30042695 PMCID: PMC6048469 DOI: 10.3389/fphys.2018.00888] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 06/20/2018] [Indexed: 12/11/2022] Open
Abstract
Humans and their associated microbiomes are exposed to numerous xenobiotics through drugs, dietary components, personal care products as well as environmental chemicals. Most of the reciprocal interactions between the microbiota and xenobiotics, such as halogenated compounds, occur within the human gut harboring diverse and dense microbial communities. Here, we provide an overview of the flux of halogenated compounds in the environment, and diverse exposure routes of human microbiota to these compounds. Subsequently, we review the impact of halogenated compounds in perturbing the structure and function of gut microbiota and host cells. In turn, cultivation-dependent and metagenomic surveys of dehalogenating genes revealed the potential of the gut microbiota to chemically alter halogenated xenobiotics and impact their fate. Finally, we provide an outlook for future research to draw attention and attract interest to study the bidirectional impact of halogenated and other xenobiotic compounds and the gut microbiota.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Sudarshan A Shetty
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands.,Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Helsinki University, Helsinki, Finland
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14
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Atashgahi S, Sánchez-Andrea I, Heipieper HJ, van der Meer JR, Stams AJM, Smidt H. Prospects for harnessing biocide resistance for bioremediation and detoxification. Science 2018; 360:743-746. [DOI: 10.1126/science.aar3778] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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Weatherill JJ, Atashgahi S, Schneidewind U, Krause S, Ullah S, Cassidy N, Rivett MO. Natural attenuation of chlorinated ethenes in hyporheic zones: A review of key biogeochemical processes and in-situ transformation potential. Water Res 2018; 128:362-382. [PMID: 29126033 DOI: 10.1016/j.watres.2017.10.059] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 10/12/2017] [Accepted: 10/28/2017] [Indexed: 06/07/2023]
Abstract
Chlorinated ethenes (CEs) are legacy contaminants whose chemical footprint is expected to persist in aquifers around the world for many decades to come. These organohalides have been reported in river systems with concerning prevalence and are thought to be significant chemical stressors in urban water ecosystems. The aquifer-river interface (known as the hyporheic zone) is a critical pathway for CE discharge to surface water bodies in groundwater baseflow. This pore water system may represent a natural bioreactor where anoxic and oxic biotransformation process act in synergy to reduce or even eliminate contaminant fluxes to surface water. Here, we critically review current process understanding of anaerobic CE respiration in the competitive framework of hyporheic zone biogeochemical cycling fuelled by in-situ fermentation of natural organic matter. We conceptualise anoxic-oxic interface development for metabolic and co-metabolic mineralisation by a range of aerobic bacteria with a focus on vinyl chloride degradation pathways. The superimposition of microbial metabolic processes occurring in sediment biofilms and bulk solute transport delivering reactants produces a scale dependence in contaminant transformation rates. Process interpretation is often confounded by the natural geological heterogeneity typical of most riverbed environments. We discuss insights from recent field experience of CE plumes discharging to surface water and present a range of practical monitoring technologies which address this inherent complexity at different spatial scales. Future research must address key dynamics which link supply of limiting reactants, residence times and microbial ecophysiology to better understand the natural attenuation capacity of hyporheic systems.
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Affiliation(s)
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Uwe Schneidewind
- Department of Engineering Geology and Hydrogeology, RWTH Aachen University, Aachen, Germany
| | - Stefan Krause
- School of Geography, Earth and Environmental Science, University of Birmingham, UK
| | - Sami Ullah
- School of Geography, Earth and Environmental Science, University of Birmingham, UK
| | | | - Michael O Rivett
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, UK; GroundH(2)O Plus Ltd., Quinton, Birmingham, UK
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16
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Atashgahi S, Häggblom MM, Smidt H. Organohalide respiration in pristine environments: implications for the natural halogen cycle. Environ Microbiol 2017; 20:934-948. [PMID: 29215190 DOI: 10.1111/1462-2920.14016] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/29/2017] [Accepted: 12/01/2017] [Indexed: 11/29/2022]
Abstract
Halogenated organic compounds, also termed organohalogens, were initially considered to be of almost exclusively anthropogenic origin. However, over 5000 naturally synthesized organohalogens are known today. This has also fuelled the hypothesis that the natural and ancient origin of organohalogens could have primed development of metabolic machineries for their degradation, especially in microorganisms. Among these, a special group of anaerobic microorganisms was discovered that could conserve energy by reducing organohalogens as terminal electron acceptor in a process termed organohalide respiration. Originally discovered in a quest for biodegradation of anthropogenic organohalogens, these organohalide-respiring bacteria (OHRB) were soon found to reside in pristine environments, such as the deep subseafloor and Arctic tundra soil with limited/no connections to anthropogenic activities. As such, accumulating evidence suggests an important role of OHRB in local natural halogen cycles, presumably taking advantage of natural organohalogens. In this minireview, we integrate current knowledge regarding the natural origin and occurrence of industrially important organohalogens and the evolution and spread of OHRB, and describe potential implications for natural halogen and carbon cycles.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands
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17
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Doğan-Subaşı E, Elsner M, Qiu S, Cretnik S, Atashgahi S, Shouakar-Stash O, Boon N, Dejonghe W, Bastiaens L. Contrasting dual (C, Cl) isotope fractionation offers potential to distinguish reductive chloroethene transformation from breakdown by permanganate. Sci Total Environ 2017; 596-597:169-177. [PMID: 28431360 DOI: 10.1016/j.scitotenv.2017.03.292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/31/2017] [Accepted: 03/31/2017] [Indexed: 06/07/2023]
Abstract
cis-1,2-Dichloroethene (cis-DCE) and trichloroethene (TCE) are persistent, toxic and mobile pollutants in groundwater systems. They are both conducive to reductive dehalogenation and to oxidation by permanganate. In this study, the potential of dual element (C, Cl) compound specific isotope analyses (CSIA) for distinguishing between chemical oxidation and anaerobic reductive dechlorination of cis-DCE and TCE was investigated. Well-controlled cis-DCE degradation batch tests gave similar carbon isotope enrichment factors εC (‰), but starkly contrasting dual element isotope slopes Δδ13C/Δδ37Cl for permanganate oxidation (εC=-26‰±6‰, Δδ13C/Δδ37Cl≈-125±47) compared to reductive dechlorination (εC=-18‰±4‰, Δδ13C/Δδ37Cl≈4.5±3.4). The difference can be tracked down to distinctly different chlorine isotope fractionation: an inverse isotope effect during chemical oxidation (εCl=+0.2‰±0.1‰) compared to a large normal isotope effect in reductive dechlorination (εCl=-3.3‰±0.9‰) (p≪0.05). A similar trend was observed for TCE. The dual isotope approach was evaluated in the field before and up to 443days after a pilot scale permanganate injection in the subsurface. Our study indicates, for the first time, the potential of the dual element isotope approach for distinguishing cis-DCE (and TCE) concentration drops caused by dilution, oxidation by permanganate and reductive dechlorination both at laboratory and field scale.
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Affiliation(s)
- Eylem Doğan-Subaşı
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium; Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München-National Research Center for Environmental Health, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany
| | - Shiran Qiu
- Institute of Groundwater Ecology, Helmholtz Zentrum München-National Research Center for Environmental Health, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany
| | - Stefan Cretnik
- Institute of Groundwater Ecology, Helmholtz Zentrum München-National Research Center for Environmental Health, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany
| | - Siavash Atashgahi
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Orfan Shouakar-Stash
- Department of Earth Sciences, University of Waterloo, 200 University Avenue W., Waterloo, Ont. N2L 3G1, Canada
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Leen Bastiaens
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium.
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18
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van der Waals MJ, Atashgahi S, da Rocha UN, van der Zaan BM, Smidt H, Gerritse J. Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition. Appl Microbiol Biotechnol 2017; 101:5175-5188. [PMID: 28321487 PMCID: PMC5486827 DOI: 10.1007/s00253-017-8214-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/27/2017] [Accepted: 03/04/2017] [Indexed: 11/26/2022]
Abstract
Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions. Benzene was degraded at a rate of 0.15 μmol/mg protein/day and a first-order rate constant of 3.04/day which was fourfold higher than rates reported previously. Bacteria belonging to the Peptococcaceae were found to play an important role in this anaerobic benzene-degrading biofilm culture, but also members of the Anaerolineaceae were predicted to be involved in benzene degradation or benzene metabolite degradation based on Illumina MiSeq analysis of 16S ribosomal RNA genes. Biomass retention in the reactor using a filtration finger resulted in reduction of benzene degradation capacity. Detection of the benzene carboxylase encoding gene, abcA, and benzoic acid in the culture vessel indicated that benzene degradation proceeds through an initial carboxylation step.
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Affiliation(s)
- Marcelle J van der Waals
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands.
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Siavash Atashgahi
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- VU University of Amsterdam, Department of Molecular Cell Physiology, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Bas M van der Zaan
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jan Gerritse
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
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19
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Amoozegar MA, Siroosi M, Atashgahi S, Smidt H, Ventosa A. Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes. Microbiology (Reading) 2017; 163:623-645. [PMID: 28548036 DOI: 10.1099/mic.0.000463] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Halophilic archaea, also referred to as haloarchaea, dominate hypersaline environments. To survive under such extreme conditions, haloarchaea and their enzymes have evolved to function optimally in environments with high salt concentrations and, sometimes, with extreme pH and temperatures. These features make haloarchaea attractive sources of a wide variety of biotechnological products, such as hydrolytic enzymes, with numerous potential applications in biotechnology. The unique trait of haloarchaeal enzymes, haloenzymes, to sustain activity under hypersaline conditions has extended the range of already-available biocatalysts and industrial processes in which high salt concentrations inhibit the activity of regular enzymes. In addition to their halostable properties, haloenzymes can also withstand other conditions such as extreme pH and temperature. In spite of these benefits, the industrial potential of these natural catalysts remains largely unexplored, with only a few characterized extracellular hydrolases. Because of the applied impact of haloarchaea and their specific ability to live in the presence of high salt concentrations, studies on their systematics have intensified in recent years, identifying many new genera and species. This review summarizes the current status of the haloarchaeal genera and species, and discusses the properties of haloenzymes and their potential industrial applications.
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Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Siroosi
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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20
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Lu Y, Ramiro-Garcia J, Vandermeeren P, Herrmann S, Cichocka D, Springael D, Atashgahi S, Smidt H. Dechlorination of three tetrachlorobenzene isomers by contaminated harbor sludge-derived enrichment cultures follows thermodynamically favorable reactions. Appl Microbiol Biotechnol 2017; 101:2589-2601. [PMID: 27909745 PMCID: PMC5320011 DOI: 10.1007/s00253-016-8004-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/27/2023]
Abstract
Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers. Based on quantitative PCR analysis targeting 16S rRNA genes of known organohalide-respiring bacteria, the growth of Dehalococcoides was found to be associated with the reductive dechlorination of all three isomers, while growth of Dehalobacter, another known TeCB dechlorinator, was only observed in one 1,2,3,5-TeCB enriched microcosm among biological triplicates. Numbers of Desulfitobacterium and Geobacter as facultative dechlorinators were rather stable suggesting that they were not (directly) involved in the observed TeCB dechlorination. Bacterial community profiling suggested bacteria belonging to the phylum Bacteroidetes and the order Clostridiales as well as sulfate-reducing members of the class Deltaproteobacteria as putative stimulating guilds that provide electron donor and/or organic cofactors to fastidious dechlorinators. Our results provide a better understanding of thermodynamically preferred TeCB dechlorinating pathways in harbor environments and microbial guilds enriched and active in anoxic TeCB dechlorinating microcosms.
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Affiliation(s)
- Yue Lu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- College of Environmental Science and Engineering, Hunan University, Changsha, People's Republic of China
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | | | - Steffi Herrmann
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Danuta Cichocka
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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Atashgahi S, Lu Y, Ramiro-Garcia J, Peng P, Maphosa F, Sipkema D, Dejonghe W, Smidt H, Springael D. Geochemical Parameters and Reductive Dechlorination Determine Aerobic Cometabolic vs Aerobic Metabolic Vinyl Chloride Biodegradation at Oxic/Anoxic Interface of Hyporheic Zones. Environ Sci Technol 2017; 51:1626-1634. [PMID: 28004913 DOI: 10.1021/acs.est.6b05041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hyporheic zones mediate vinyl chloride (VC) biodegradation in groundwater discharging into surface waters. At the oxic/anoxic interface (OAI) of hyporheic zones subjected to redox oscillations, VC is degraded via coexisting aerobic ethenotrophic and anaerobic reductive dechlorination pathways. However, the identity of aerobic VC degradation pathways (cometabolic vs metabolic) and their interactions with reductive dechlorination in relation to riverbed sediment geochemistry remain ill-defined. We addressed this using microcosms containing OAI sediments incubated under fluctuating oxic/anoxic atmosphere. Under oxic atmosphere, aerobic metabolic VC oxidation was absent in sediments with high total organic carbon (TOC) and VC was reductively dechlorinated to ethene. Ethene was oxidized by ethenotrophs that can degrade VC cometabolically. Contrastingly, VC was metabolically oxidized by ethenotrophs in low-TOC sediments with low reductive dechlorination potential. Accordingly, enrichment and isolation of metabolic VC-oxidizing ethenotrophs was successful only from the low-TOC sediment. Sequence analysis of etnE genes from the microcosms as well phylogenetic typing of the isolates showed that ethenotrophs in the sediments were facultative anaerobic Proteobacteria capable of coping with OAI-associated redox fluctuations. Our results suggest that local sediment heterogeneity supports/selects divergent VC degradation processes at the OAI and that high reductive dechlorination potential suppresses development of aerobic metabolic VC oxidation potential.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
- KU Leuven , Division of Soil and Water Management, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
| | - Yue Lu
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Farai Maphosa
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Dirk Springael
- KU Leuven , Division of Soil and Water Management, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
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Atashgahi S, Lu Y, Zheng Y, Saccenti E, Suarez-Diez M, Ramiro-Garcia J, Eisenmann H, Elsner M, J.M. Stams A, Springael D, Dejonghe W, Smidt H. Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol. Environ Microbiol 2016; 19:968-981. [DOI: 10.1111/1462-2920.13531] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/12/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Siavash Atashgahi
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Yue Lu
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Ying Zheng
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Laboratory of Systems and Synthetic Biology; Wageningen University & Research; Wageningen The Netherlands
| | | | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München-National Research Center for Environmental Health; Ingolstädter Landstrasse 1 Neuherberg D-85764 Germany
| | - Alfons J.M. Stams
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
- Centre of Biological Engineering; University of Minho; Braga Portugal
| | - Dirk Springael
- Division of Soil and Water Management; KU Leuven; Kasteelpark Arenberg 20 Heverlee B-3001 Belgium
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology; Boeretang 200, 2400 Mol Belgium
| | - Hauke Smidt
- Laboratory of Microbiology; Wageningen University & Research; Wageningen The Netherlands
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23
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Sutton NB, Atashgahi S, Saccenti E, Grotenhuis T, Smidt H, Rijnaarts HHM. Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation. PLoS One 2015; 10:e0134615. [PMID: 26244346 PMCID: PMC4526698 DOI: 10.1371/journal.pone.0134615] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/12/2015] [Indexed: 11/19/2022] Open
Abstract
While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2-4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose-dependent changes of microbial composition and activity due to permanganate treatment provides insight into the mechanisms of OHR stimulation or disruption upon chemical oxidation.
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Affiliation(s)
- Nora B. Sutton
- Environmental Technology, Wageningen University, Wageningen, The Netherlands
- * E-mail:
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Tim Grotenhuis
- Environmental Technology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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24
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Oosterkamp MJ, Boeren S, Atashgahi S, Plugge CM, Schaap PJ, Stams AJM. Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC. FEMS Microbiol Lett 2015; 362:fnv080. [PMID: 25977262 DOI: 10.1093/femsle/fnv080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 11/13/2022] Open
Abstract
Alicycliphilus denitrificans strain BC grows anaerobically on acetone with nitrate as electron acceptor. Comparative proteomics of cultures of A. denitrificans strain BC grown on either acetone or acetate with nitrate was performed to study the enzymes involved in the acetone degradation pathway. In the proposed acetone degradation pathway, an acetone carboxylase converts acetone to acetoacetate, an AMP-dependent synthetase/ligase converts acetoacetate to acetoacetyl-CoA, and an acetyl-CoA acetyltransferase cleaves acetoacetyl-CoA to two acetyl-CoA. We also found a putative aldehyde dehydrogenase associated with acetone degradation. This enzyme functioned as a β-hydroxybutyrate dehydrogenase catalyzing the conversion of surplus acetoacetate to β-hydroxybutyrate that may be converted to the energy and carbon storage compound, poly-β-hydroxybutyrate. Accordingly, we confirmed the formation of poly-β-hydroxybutyrate in acetone-grown cells of strain BC. Our findings provide insight in nitrate-dependent acetone degradation that is activated by carboxylation of acetone. This will aid studies of similar pathways found in other microorganisms degrading acetone with nitrate or sulfate as electron acceptor.
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Affiliation(s)
- Margreet J Oosterkamp
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, Dreijenplein 3, 6703 HA Wageningen, the Netherlands
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, the Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands Centre of Biological Engineering, Campus de Gualtar, University of Minho, 4710-057, Braga, Portugal
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Sutton NB, Atashgahi S, van der Wal J, Wijn G, Grotenhuis T, Smidt H, Rijnaarts HHM. Microbial dynamics during and after in situ chemical oxidation of chlorinated solvents. Ground Water 2015; 53:261-270. [PMID: 24898385 DOI: 10.1111/gwat.12209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
In situ chemical oxidation (ISCO) followed by a bioremediation step is increasingly being considered as an effective biphasic technology. Information on the impact of chemical oxidants on organohalide respiring bacteria (OHRB), however, is largely lacking. Therefore, we used quantitative PCR (qPCR) to monitor the abundance of OHRB (Dehalococcoides mccartyi, Dehalobacter, Geobacter, and Desulfitobacterium) and reductive dehalogenase genes (rdh; tceA, vcrA, and bvcA) at a field location contaminated with chlorinated solvents prior to and following treatment with sodium persulfate. Natural attenuation of the contaminants tetrachloroethene (PCE) and trichloroethene (TCE) observed prior to ISCO was confirmed by the distribution of OHRB and rdh genes. In wells impacted by persulfate treatment, a 1 to 3 order of magnitude reduction in the abundances of OHRB and complete absence of rdh genes was observed 21 days after ISCO. Groundwater acidification (pH<3) and increase in the oxidation reduction potential (>500 mV) due to persulfate treatment were significant and contributed to disruption of the microbial community. In wells only mildly impacted by persulfate, a slight stimulation of the microbial community was observed, with more than 1 order of magnitude increase in the abundance of Geobacter and Desulfitobacterium 36 days after ISCO. After six months, regeneration of the OHRB community occurred, however, neither D. mccartyi nor any rdh genes were observed, indicating extended disruption of biological natural attenuation (NA) capacity following persulfate treatment. For full restoration of biological NA activity, additional time may prove sufficient; otherwise addition electron donor amendment or bioaugmentation may be required.
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Affiliation(s)
- Nora B Sutton
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
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26
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Schneidewind U, Haest PJ, Atashgahi S, Maphosa F, Hamonts K, Maesen M, Calderer M, Seuntjens P, Smidt H, Springael D, Dejonghe W. Kinetics of dechlorination by Dehalococcoides mccartyi using different carbon sources. J Contam Hydrol 2014; 157:25-36. [PMID: 24275111 DOI: 10.1016/j.jconhyd.2013.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 10/05/2013] [Accepted: 10/18/2013] [Indexed: 06/02/2023]
Abstract
Stimulated anaerobic dechlorination is generally considered a valuable step for the remediation of aquifers polluted with chlorinated ethenes (CEs). Correct simulation and prediction of this process in situ, however, require good knowledge of the associated biological reactions. The aim of this study was to evaluate the dechlorination reaction in an aquifer contaminated with trichloroethene (TCE) and its daughter products, discharging into the Zenne River. Different carbon sources were used in batch cultures and these were related to the dechlorination reaction, together with the monitored biomarkers. Appropriate kinetic formulations were assessed. Reductive dechlorination of TCE took place only when external carbon sources were added to microcosms, and occurred concomitant with a pronounced increase in the Dehalococcoides mccartyi cell count as determined by 16S rRNA gene-targeted qPCR. This indicates that native dechlorinating bacteria are present in the aquifer of the Zenne site and that the oligotrophic nature of the aquifer prevents a complete degradation to ethene. The type of carbon source, the cell number of D. mccartyi or the reductive dehalogenase genes, however, did not unequivocally explain the observed differences in degradation rates or the extent of dechlorination. Neither first-order, Michaelis-Menten nor Monod kinetics could perfectly simulate the dechlorination reactions in TCE spiked microcosms. A sensitivity analysis indicated that the inclusion of donor limitation would not significantly enhance the simulations without a clear process understanding. Results point to the role of the supporting microbial community but it remains to be verified how the complexity of the microbial (inter)actions should be represented in a model framework.
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Affiliation(s)
- Uwe Schneidewind
- Flemish Institute for Technological Research (VITO), Environmental Modeling Unit, Boeretang 200, 2400 Mol, Belgium; Ghent University, Department of Soil Management, Coupure Links 653, 9000 Ghent, Belgium
| | - Pieter Jan Haest
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Siavash Atashgahi
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium; Wageningen University, Laboratory of Microbiology, 6703 HB Wageningen, The Netherlands; KU Leuven, Division Soil and Water Management, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Farai Maphosa
- Wageningen University, Laboratory of Microbiology, 6703 HB Wageningen, The Netherlands
| | - Kelly Hamonts
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Miranda Maesen
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium
| | - Montse Calderer
- Manresa Technology Centre - CTM, Environmental Technology Area, Av. Bases de Manresa, 08242 Manresa, Spain
| | - Piet Seuntjens
- Flemish Institute for Technological Research (VITO), Environmental Modeling Unit, Boeretang 200, 2400 Mol, Belgium; Ghent University, Department of Soil Management, Coupure Links 653, 9000 Ghent, Belgium; University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Hauke Smidt
- Wageningen University, Laboratory of Microbiology, 6703 HB Wageningen, The Netherlands
| | - Dirk Springael
- KU Leuven, Division Soil and Water Management, Kasteelpark Arenberg 20, 3001 Heverlee, Belgium
| | - Winnie Dejonghe
- Flemish Institute for Technological Research (VITO), Separation and Conversion Technology, Boeretang 200, 2400 Mol, Belgium.
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Atashgahi S, Maphosa F, Doğan E, Smidt H, Springael D, Dejonghe W. Small-scale oxygen distribution determines the vinyl chloride biodegradation pathway in surficial sediments of riverbed hyporheic zones. FEMS Microbiol Ecol 2012; 84:133-42. [DOI: 10.1111/1574-6941.12044] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 10/18/2012] [Accepted: 11/07/2012] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Farai Maphosa
- Laboratory of Microbiology; Wageningen University; Wageningen; the Netherlands
| | - Eylem Doğan
- Separation and Conversion Technology; Flemish Institute for Technological Research (VITO); Mol; Belgium
| | - Hauke Smidt
- Laboratory of Microbiology; Wageningen University; Wageningen; the Netherlands
| | - Dirk Springael
- Division Soil and Water Management; KU Leuven; Heverlee; Belgium
| | - Winnie Dejonghe
- Separation and Conversion Technology; Flemish Institute for Technological Research (VITO); Mol; Belgium
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28
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Mollaei M, Abdollahpour S, Atashgahi S, Abbasi H, Masoomi F, Rad I, Lotfi AS, Zahiri HS, Vali H, Noghabi KA. Enhanced phenol degradation by Pseudomonas sp. SA01: gaining insight into the novel single and hybrid immobilizations. J Hazard Mater 2010; 175:284-292. [PMID: 19883975 DOI: 10.1016/j.jhazmat.2009.10.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 09/15/2009] [Accepted: 10/01/2009] [Indexed: 05/28/2023]
Abstract
In this work, Pseudomonas sp. SA01 cells were immobilized in a series of singular and hybrid immobilization techniques to achieve enhanced phenol removal. The singular immobilization strategies consisted of various concentrations of alginate (2-4%) and pectin (3-5%), while the hybrid strategies incorporated polyvinyl alcohol (PVA)-alginate and glycerol-alginate beads and alginate-chitosan-alginate (ACA) capsules. Immobilization protected cells against phenol and resulted in remarkable reduction (65%) in degradation time by cells immobilized in either alginate (3%) beads, in a hybrid PVA-alginate beads, or in ACA capsules compared to freely suspended cells. Cells immobilized in PVA-alginate and ACA provided the best performance in experiments using elevated phenol concentrations, up to 2000 mg/L, with complete degradation of 2000 mg/L phenol after 100 and 110 h, respectively. Electron microscopy examination indicated that cell loading capacity was increased in PVA-alginate hybrid beads through reduced cell leakage, resulting in higher activity of PVA-alginate hybrid beads compared to all other immobilization methods.
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Affiliation(s)
- Monir Mollaei
- National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
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