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Phillips E, Picott K, Kümmel S, Bulka O, Edwards E, Wang P, Gehre M, Nijenhuis I, Lollar BS. Vitamin B 12 as a source of variability in isotope effects for chloroform biotransformation by Dehalobacter. Microbiologyopen 2024; 13:e1433. [PMID: 39190020 PMCID: PMC11348799 DOI: 10.1002/mbo3.1433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 08/28/2024] Open
Abstract
Carbon and chlorine isotope effects for biotransformation of chloroform by different microbes show significant variability. Reductive dehalogenases (RDase) enzymes contain different cobamides, affecting substrate preferences, growth yields, and dechlorination rates and extent. We investigate the role of cobamide type on carbon and chlorine isotopic signals observed during reductive dechlorination of chloroform by the RDase CfrA. Microcosm experiments with two subcultures of a Dehalobacter-containing culture expressing CfrA-one with exogenous cobamide (Vitamin B12, B12+) and one without (to drive native cobamide production)-resulted in a markedly smaller carbon isotope enrichment factor (εC, bulk) for B12- (-22.1 ± 1.9‰) compared to B12+ (-26.8 ± 3.2‰). Both cultures exhibited significant chlorine isotope fractionation, and although a lower εCl, bulk was observed for B12- (-6.17 ± 0.72‰) compared to B12+ (-6.86 ± 0.77‰) cultures, these values are not statistically different. Importantly, dual-isotope plots produced identical slopes of ΛCl/C (ΛCl/C, B12+ = 3.41 ± 0.15, ΛCl/C, B12- = 3.39 ± 0.15), suggesting the same reaction mechanism is involved in both experiments, independent of the lower cobamide bases. A nonisotopically fractionating masking effect may explain the smaller fractionations observed for the B12- containing culture.
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Affiliation(s)
- Elizabeth Phillips
- Department of Earth SciencesUniversity of TorontoTorontoOntarioCanada
- Present address:
Inorganic Chemistry LaboratoryUniversity of OxfordOxfordUK
| | - Katherine Picott
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Steffen Kümmel
- Department of Technical BiogeochemistryHelmholtz Centre for Environmental Research—UFZLeipzigGermany
| | - Olivia Bulka
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Elizabeth Edwards
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoOntarioCanada
| | - Po‐Hsiang Wang
- Department of Chemical Engineering and Applied ChemistryUniversity of TorontoTorontoOntarioCanada
- Present address:
Graduate Institute of Environmental EngineeringNational Central UniversityTaoyuan CityTaiwan
| | - Matthias Gehre
- Department of Technical BiogeochemistryHelmholtz Centre for Environmental Research—UFZLeipzigGermany
| | - Ivonne Nijenhuis
- Department of Technical BiogeochemistryHelmholtz Centre for Environmental Research—UFZLeipzigGermany
| | - Barbara S. Lollar
- Department of Earth SciencesUniversity of TorontoTorontoOntarioCanada
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2
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Bulka O, Picott K, Mahadevan R, Edwards EA. From mec cassette to rdhA: a key Dehalobacter genomic neighborhood in a chloroform and dichloromethane-transforming microbial consortium. Appl Environ Microbiol 2024; 90:e0073224. [PMID: 38819127 PMCID: PMC11218628 DOI: 10.1128/aem.00732-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-respiring bacteria that use reductive dehalogenases (RDases) to dechlorinate CF to DCM. In contrast, known DCM degraders use DCM as their electron donor, which is oxidized using a series of methyltransferases and associated proteins encoded by the mec cassette to facilitate the entry of DCM to the Wood-Ljungdahl pathway. The SC05 culture is an enrichment culture sold commercially for bioaugmentation, which transforms CF via DCM to CO2. This culture has the unique ability to dechlorinate CF to DCM using electron equivalents provided by the oxidation of DCM to CO2. Here, we use metagenomic and metaproteomic analyses to identify the functional genes involved in each of these transformations. Though 91 metagenome-assembled genomes were assembled, the genes for an RDase-named acdA-and a complete mec cassette were found to be encoded on a single contig belonging to Dehalobacter. AcdA and critical Mec proteins were also highly expressed by the culture. Heterologously expressed AcdA dechlorinated CF and other chloroalkanes but had 100-fold lower activity on DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest a Dehalobacter capable of dechlorination of CF to DCM and subsequent mineralization of DCM using the mec cassette. IMPORTANCE Chloroform (CF) and dichloromethane (DCM) are regulated groundwater contaminants. A cost-effective approach to remove these pollutants from contaminated groundwater is to employ microbes that transform CF and DCM as part of their metabolism, thus depleting the contamination as the microbes continue to grow. In this work, we investigate bioaugmentation culture SC05, a mixed microbial consortium that effectively and simultaneously degrades both CF and DCM coupled to the growth of Dehalobacter. We identified the functional genes responsible for the transformation of CF and DCM in SC05. These genetic biomarkers provide a means to monitor the remediation process in the field.
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Affiliation(s)
- Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Picott
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
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3
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Bulka O, Webb J, Dworatzek S, Mahadevan R, Edwards EA. A Multifunctional Dehalobacter? Tandem Chloroform and Dichloromethane Degradation in a Mixed Microbial Culture. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19912-19920. [PMID: 37962431 DOI: 10.1021/acs.est.3c06686] [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: 11/15/2023]
Abstract
Chloroform (CF) and dichloromethane (DCM) contaminate groundwater sites around the world but can be cleaned up through bioremediation. Although several strains of Dehalobacter restrictus can reduce CF to DCM and multiple Peptococcaceae can ferment DCM, these processes cannot typically happen simultaneously due to CF sensitivity in the known DCM-degraders or electron donor competition. Here, we present a mixed microbial culture that can simultaneously metabolize CF and DCM and create an additional enrichment culture fed only DCM. Through genus-specific quantitative polymerase chain reaction, we find that Dehalobacter grows while either CF alone or DCM alone is converted, indicating its involvement in both metabolic steps. Additionally, the culture was maintained for over 1400 days without the addition of an exogenous electron donor, and through electron balance calculations, we show that DCM metabolism would produce sufficient reducing equivalents (likely hydrogen) for CF respiration. Together, these results suggest intraspecies electron transfer could occur to continually reduce CF in the culture. Minimizing the addition of electron donor reduces the cost of bioremediation, and "self-feeding" could prolong bioremediation activity long after donor addition ends. Overall, understanding this mechanism informs strategies for culture maintenance and scale-up and benefits contaminated sites where the culture is employed for remediation worldwide.
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Affiliation(s)
- Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jennifer Webb
- SiREM, 130 Stone Road West, Guelph, Ontario N1G 3Z2, Canada
| | | | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
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4
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Wasmund K, Trueba-Santiso A, Vicent T, Adrian L, Vuilleumier S, Marco-Urrea E. Proteogenomics of the novel Dehalobacterium formicoaceticum strain EZ94 highlights a key role of methyltransferases during anaerobic dichloromethane degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:80602-80612. [PMID: 37300728 PMCID: PMC10344839 DOI: 10.1007/s11356-023-28144-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Dichloromethane (DCM, methylene chloride) is a toxic, high-volume industrial pollutant of long-standing. Anaerobic biodegradation is crucial for its removal from contaminated environments, yet prevailing mechanisms remain unresolved, especially concerning dehalogenation. In this study, we obtained an assembled genome of a novel DCM-degrading strain, Dehalobacterium formicoaceticum strain EZ94, from a stable DCM-degrading consortium, and we analyzed its proteome during degradation of DCM. A gene cluster recently predicted to play a major role in anaerobic DCM catabolism (the mec cassette) was found. Methyltransferases and other proteins encoded by the mec cassette were among the most abundant proteins produced, suggesting their involvement in DCM catabolism. Reductive dehalogenases were not detected. Genes and corresponding proteins for a complete Wood-Ljungdahl pathway, which could enable further metabolism of DCM carbon, were also found. Unlike for the anaerobic DCM degrader "Ca. F. warabiya," no genes for metabolism of the quaternary amines choline and glycine betaine were identified. This work provides independent and supporting evidence that mec-associated methyltransferases are key to anaerobic DCM metabolism.
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Affiliation(s)
- Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Alba Trueba-Santiso
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193, Cerdanyola del Valles, Spain
- Current address: Department of Chemical Engineering, CRETUS Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193, Cerdanyola del Valles, Spain
| | - Lorenz Adrian
- Department Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Chair for Geobiotechnology, Technische Universität Berlin, Berlin, Germany
| | - Stéphane Vuilleumier
- Université de Strasbourg, CNRS, GMGM UMR 7156, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193, Cerdanyola del Valles, Spain.
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Wackett LP. Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances. Microb Biotechnol 2022; 15:773-792. [PMID: 34570953 PMCID: PMC8913905 DOI: 10.1111/1751-7915.13928] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Poly- and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today's society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called 'forever chemicals' due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.
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Affiliation(s)
- Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaSt. PaulMN55108USA
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6
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Li Y, Zhao HP, Zhu L. Remediation of soil contaminated with organic compounds by nanoscale zero-valent iron: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 760:143413. [PMID: 33246720 DOI: 10.1016/j.scitotenv.2020.143413] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/22/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
In recent years, nanoscale zero-valent iron (nZVI) has been gradually applied in soil remediation due to its strong reducing ability and large specific surface area. Compared to conventional remediation solutions, in situ remediation using nZVI offers some unique advantages. In this review, respective merits and demerits of each approach to nZVI synthesis are summarized in detail, particularly the most commonly used aqueous-phase reduction method featuring surface modification. In order to overcome undesired oxidation and agglomeration of fresh nZVI due to its high reactivity, modifications of nZVI have been developed such as doping with transition metals, stabilization using macromolecules or surfactants, and sulfidation. Mechanisms underlying efficient removal of organic pollutants enabled by the modified nZVI lie in alleviative oxidation and agglomeration of nZVI and enhanced electron utilization efficiency. In addition to chemical modification, other assisting methods for further improving nZVI mobility and reactivity, such as electrokinetics and microbial technologies, are evaluated. The effects of different remediation technologies and soil physicochemical properties on remediation performance of nZVI are also summarized. Overall, this review offers an up-to-date comprehensive understanding of nZVI-driven soil remediation from scientific and practical perspectives.
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Affiliation(s)
- Yaru Li
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Organic Pollution Process and Control, Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - He-Ping Zhao
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Organic Pollution Process and Control, Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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7
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Yang MI, Previdsa M, Edwards EA, Sleep BE. Two distinct Dehalobacter strains sequentially dechlorinate 1,1,1-trichloroethane and 1,1-dichloroethane at a field site treated with granular zero valent iron and guar gum. WATER RESEARCH 2020; 186:116310. [PMID: 32858243 DOI: 10.1016/j.watres.2020.116310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/11/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
Chlorinated ethanes are environmental pollutants found frequently at many contaminated industrial sites. 1,1,1-Trichloroethane (1,1,1-TCA) can be dechlorinated and detoxified via abiotic transformation or biologically by the action of dechlorinating microorganisms such as Dehalobacter (Dhb). At a field site, it is challenging to distinguish abiotic vs. biotic mechanisms as both processes share common transformation products. In this study, we evaluated using the Dhb 16S rRNA gene and specific reductive dehalogenase genes as biomarkers for 1,1,1-TCA and 1,1-dichloroethane (1,1-DCA) dechlorination. We analyzed samples from laboratory groundwater microcosms and from an industrial site where a mixture of granular zero valent iron (ZVI) and guar gum was injected for 1,1,1-TCA remediation. Abiotic and biotic transformation products were monitored and the changes in dechlorinating organisms were tracked using quantitative PCR (qPCR) with primers targeting the Dhb 16S rRNA gene and two functional genes cfrA and dcrA encoding enzymes that dechlorinate 1,1,1-TCA to 1,1-DCA and 1,1-DCA to chloroethane (CA), respectively. The abundance of the cfrA- and dcrA-like genes confirmed that the two dechlorination steps were carried out by two distinct Dhb populations at the site. The biomarkers used in this study proved useful for monitoring different Dhb populations responsible for step-wise dechlorination and tracking biodegradation of 1,1,1-TCA and 1,1-DCA where both abiotic (e.g., with ZVI) and biotic processes co-occur.
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Affiliation(s)
- M Ivy Yang
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, M5S 1A4, Canada
| | - Michael Previdsa
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, M5S 1A4, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, M5S 3E5, Canada.
| | - Brent E Sleep
- Department of Civil & Mineral Engineering, University of Toronto, Toronto, M5S 1A4, Canada.
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8
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Schubert T, von Reuß SH, Kunze C, Paetz C, Kruse S, Brand‐Schön P, Nelly AM, Nüske J, Diekert G. Guided cobamide biosynthesis for heterologous production of reductive dehalogenases. Microb Biotechnol 2019; 12:346-359. [PMID: 30549216 PMCID: PMC6389850 DOI: 10.1111/1751-7915.13339] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/23/2018] [Accepted: 10/30/2018] [Indexed: 12/01/2022] Open
Abstract
Cobamides (Cbas) are essential cofactors of reductive dehalogenases (RDases) in organohalide-respiring bacteria (OHRB). Changes in the Cba structure can influence RDase function. Here, we report on the cofactor versatility or selectivity of Desulfitobacterium RDases produced either in the native organism or heterologously. The susceptibility of Desulfitobacterium hafniense strain DCB-2 to guided Cba biosynthesis (i.e. incorporation of exogenous Cba lower ligand base precursors) was analysed. Exogenous benzimidazoles, azabenzimidazoles and 4,5-dimethylimidazole were incorporated by the organism into Cbas. When the type of Cba changed, no effect on the turnover rate of the 3-chloro-4-hydroxy-phenylacetate-converting enzyme RdhA6 and the 3,5-dichlorophenol-dehalogenating enzyme RdhA3 was observed. The impact of the amendment of Cba lower ligand precursors on RDase function was also investigated in Shimwellia blattae, the Cba producer used for the heterologous production of Desulfitobacterium RDases. The recombinant tetrachloroethene RDase (PceAY51 ) appeared to be non-selective towards different Cbas. However, the functional production of the 1,2-dichloroethane-dihaloeliminating enzyme (DcaA) of Desulfitobacterium dichloroeliminans was completely prevented in cells producing 5,6-dimethylbenzimidazolyl-Cba, but substantially enhanced in cells that incorporated 5-methoxybenzimidazole into the Cba cofactor. The results of the study indicate the utilization of a range of different Cbas by Desulfitobacterium RDases with selected representatives apparently preferring distinct Cbas.
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Affiliation(s)
- Torsten Schubert
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Stephan H. von Reuß
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyHans‐Knöll‐Straße 8D‐07745JenaGermany
- Present address:
Laboratory for Bioanalytical ChemistryInstitute of ChemistryUniversity of NeuchâtelAvenue de Bellevaux 512000NeuchâtelSwitzerland
| | - Cindy Kunze
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
- Present address:
DECHEMA‐ForschungsinstitutTheodor‐Heuss‐Allee 25D‐60486Frankfurt am MainGermany
| | - Christian Paetz
- Research Group Biosynthesis/NMRMax Planck Institute for Chemical EcologyHans‐Knöll‐Straße 8D‐07745JenaGermany
| | - Stefan Kruse
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Peggy Brand‐Schön
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Anita Mac Nelly
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Jörg Nüske
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
| | - Gabriele Diekert
- Department of Applied and Ecological MicrobiologyInstitute of MicrobiologyFriedrich Schiller UniversityPhilosophenweg 12D‐07743JenaGermany
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9
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Türkowsky D, Jehmlich N, Diekert G, Adrian L, von Bergen M, Goris T. An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research. FEMS Microbiol Ecol 2019; 94:4830072. [PMID: 29390082 DOI: 10.1093/femsec/fiy013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/24/2018] [Indexed: 02/06/2023] Open
Abstract
Organohalide respiration (OHR) is a crucial process in the global halogen cycle and of interest for bioremediation. However, investigations on OHR are hampered by the restricted genetic accessibility and the poor growth yields of many organohalide-respiring bacteria (OHRB). Therefore, genomics, transcriptomics and proteomics are often used to investigate OHRB. In general, these gene expression studies are more useful when the data of the different 'omics' approaches are integrated and compared among a wide range of cultivation conditions and ideally involve several closely related OHRB. Despite the availability of a couple of proteomic and transcriptomic datasets dealing with OHRB, such approaches are currently not covered in reviews. Therefore, we here present an integrative and comparative overview of omics studies performed with the OHRB Sulfurospirillum multivorans, Dehalococcoides mccartyi, Desulfitobacterium spp. and Dehalobacter restrictus. Genes, transcripts, proteins and the regulatory and biochemical processes involved in OHR are discussed, and a comprehensive view on the unusual metabolism of D. mccartyi, which is one of the few bacteria possibly using a quinone-independent respiratory chain, is provided. Several 'omics'-derived theories on OHRB, e.g. the organohalide-respiratory chain, hydrogen metabolism, corrinoid biosynthesis or one-carbon metabolism are critically discussed on the basis of this integrative approach.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany.,Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
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10
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Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R, Edwards EA. An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. ISME JOURNAL 2019; 13:1042-1055. [PMID: 30607026 DOI: 10.1038/s41396-018-0333-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022]
Abstract
Microbes in ecosystems often develop coordinated metabolic interactions. Therefore, understanding metabolic interdependencies between microbes is critical to deciphering ecosystem function. In this study, we sought to deconstruct metabolic interdependencies in organohalide-respiring consortium ACT-3 containing Dehalobacter restrictus using a combination of metabolic modeling and experimental validation. D. restrictus possesses a complete set of genes for amino acid biosynthesis yet when grown in isolation requires amino acid supplementation. We reconciled this discrepancy using flux balance analysis considering cofactor availability, enzyme promiscuity, and shared protein expression patterns for several D. restrictus strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of D. restrictus strain PER-K23 cultures were performed to validate the model predictions. The model resolved that the amino acid dependency of D. restrictus resulted from restricted NADPH regeneration and predicted that malate supplementation would replenish intracellular NADPH. Interestingly, we observed unexpected export of pyruvate and glutamate in parallel to malate consumption in strain PER-K23 cultures. Further experimental analysis using the ACT-3 transfer cultures suggested the occurrence of an interspecies malate-pyruvate shuttle reconciling a redox imbalance, reminiscent of the mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study suggests that redox imbalance and metabolic complementarity are important driving forces for metabolite exchange in anaerobic microbial communities.
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Affiliation(s)
- Po-Hsiang Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kevin Correia
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Han-Chen Ho
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Kayla Nemr
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Robert Flick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.
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11
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Abstract
Organohalide respiration (OHR) is an anaerobic metabolism by which bacteria conserve energy with the use of halogenated compounds as terminal electron acceptors. Genes involved in OHR are organized in reductive dehalogenase (rdh) gene clusters and can be found in relatively high copy numbers in the genomes of organohalide-respiring bacteria (OHRB). The minimal rdh gene set is composed by rdhA and rdhB, encoding the catalytic enzyme involved in reductive dehalogenation and its putative membrane anchor, respectively. In this chapter, we present the major findings concerning the regulatory strategies developed by OHRB to control the expression of the rdh gene clusters. The first section focuses on the description of regulation patterns obtained from targeted transcriptional analyses, and from transcriptomic and proteomic studies, while the second section offers a detailed overview of the biochemically characterized OHR regulatory proteins identified so far. Depending on OHRB, transcriptional regulators belonging to three different protein families are found in the direct vicinity of rdh gene clusters, suggesting that they activate the transcription of their cognate gene cluster. In this chapter, strong emphasis was laid on the family of CRP/FNR-type RdhK regulators which belong to members of the genera Dehalobacter and Desulfitobacterium. Whereas only chlorophenols have been identified as effectors for RdhK regulators, the protein sequence diversity suggests a broader organohalide spectrum. Thus, effector identification of new regulators offers a promising alternative to elucidate the substrates of yet uncharacterized reductive dehalogenases. Future work investigating the possible cross-talk between OHR regulators and their possible use as biosensors is discussed.
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Wang S, Qiu L, Liu X, Xu G, Siegert M, Lu Q, Juneau P, Yu L, Liang D, He Z, Qiu R. Electron transport chains in organohalide-respiring bacteria and bioremediation implications. Biotechnol Adv 2018; 36:1194-1206. [DOI: 10.1016/j.biotechadv.2018.03.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/08/2023]
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Pérez-de-Mora A, Lacourt A, McMaster ML, Liang X, Dworatzek SM, Edwards EA. Chlorinated Electron Acceptor Abundance Drives Selection of Dehalococcoides mccartyi ( D. mccartyi) Strains in Dechlorinating Enrichment Cultures and Groundwater Environments. Front Microbiol 2018; 9:812. [PMID: 29867784 PMCID: PMC5968391 DOI: 10.3389/fmicb.2018.00812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/10/2018] [Indexed: 01/23/2023] Open
Abstract
Dehalococcoides mccartyi (D. mccartyi) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A (rdhA) genes within their respective genomes. While multiple rdhA genes have been sequenced, the activity of the corresponding proteins has been identified in only a few cases. Examples include the enzymes whose substrates are groundwater contaminants such as trichloroethene (TCE), cis-dichloroethene (cDCE) and vinyl chloride (VC). The associated rdhA genes, namely tceA, bvcA, and vcrA, along with the D. mccartyi 16S rRNA gene are often used as biomarkers of growth in field samples. In this study, we monitored an additional 12 uncharacterized rdhA sequences identified in the metagenome in the mixed D. mccartyi-containing culture KB-1 to monitor population shifts in more detail. Quantitative PCR (qPCR) assays were developed for 15 D. mccartyi rdhA genes and used to measure population diversity in 11 different sub-cultures of KB-1, each enriched on different chlorinated ethenes and ethanes. The proportion of rdhA gene copies relative to D. mccartyi 16S rRNA gene copies revealed the presence of multiple distinct D. mccartyi strains in each culture, many more than the two strains inferred from 16S rRNA analysis. The specific electron acceptor amended to each culture had a major influence on the distribution of D. mccartyi strains and their associated rdhA genes. We also surveyed the abundance of rdhA genes in samples from two bioaugmented field sites (Canada and United Kingdom). Growth of the dominant D. mccartyi strain in KB-1 was detected at the United Kingdom site. At both field sites, the measurement of relative rdhA abundances revealed D. mccartyi population shifts over time as dechlorination progressed from TCE through cDCE to VC and ethene. These shifts indicate a selective pressure of the most abundant chlorinated electron acceptor, as was also observed in lab cultures. These results also suggest that reductive dechlorination at contaminated sites is brought about by multiple strains of D. mccartyi whether or not the site is bioaugmented. Understanding the driving forces behind D. mccartyi population selection and activity is improving predictability of remediation performance at chlorinated solvent contaminated sites.
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Affiliation(s)
- Alfredo Pérez-de-Mora
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada.,Research Unit Analytical Biogeochemistry, Department of Environmental Sciences, Helmholtz Zentrum München, Neuherberg, Germany
| | - Anna Lacourt
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Xiaoming Liang
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | | | - Elizabeth A Edwards
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada
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Rodríguez-Fernández D, Torrentó C, Guivernau M, Viñas M, Hunkeler D, Soler A, Domènech C, Rosell M. Vitamin B 12 effects on chlorinated methanes-degrading microcosms: Dual isotope and metabolically active microbial populations assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 621:1615-1625. [PMID: 29054650 DOI: 10.1016/j.scitotenv.2017.10.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/21/2017] [Accepted: 10/08/2017] [Indexed: 06/07/2023]
Abstract
Field-derived anoxic microcosms were used to characterize chloroform (CF) and carbon tetrachloride (CT) natural attenuation to compare it with biostimulation scenarios in which vitamin B12 was added (B12/pollutant ratio of 0.01 and 0.1) by means of by-products, carbon and chlorine compound-specific stable-isotope analysis, and the active microbial community through 16S rRNA MiSeq high-throughput sequencing. Autoclaved slurry controls discarded abiotic degradation processes. B12 catalyzed CF and CT biodegradation without the accumulation of dichloromethane, carbon disulphide, or CF. The carbon isotopic fractionation value of CF (ƐCCF) with B12 was -14±4‰, and the value for chlorine (ƐClCF) was -2.4±0.4‰. The carbon isotopic fractionation values of CT (ƐCCT) were -16±6 with B12, and -13±2‰ without B12; and the chlorine isotopic fractionation values of CT (ƐClCT) were -6±3 and -4±2‰, respectively. Acidovorax, Ancylobacter, and Pseudomonas were the most metabolically active genera, whereas Dehalobacter and Desulfitobacterium were below 0.1% of relative abundance. The dual C-Cl element isotope slope (Λ=Δδ13C/Δδ37Cl) for CF biodegradation (only detected with B12, 7±1) was similar to that reported for CF reduction by Fe(0) (8±2). Several reductive pathways might be competing in the tested CT scenarios, as evidenced by the lack of CF accumulation when B12 was added, which might be linked to a major activity of Pseudomonas stutzeri; by different chlorine apparent kinetic isotope effect values and Λ which was statistically different with and without B12 (5±1 vs 6.1±0.5), respectively. Thus, positive B12 effects such as CT and CF degradation catalyst were quantified for the first time in isotopic terms, and confirmed with the major activity of species potentially capable of their degradation. Moreover, the indirect benefits of B12 on the degradation of chlorinated ethenes were proved, creating a basis for remediation strategies in multi-contaminant polluted sites.
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Affiliation(s)
- Diana Rodríguez-Fernández
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), c/Martí Franquès s/n, 08028 Barcelona, Spain.
| | - Clara Torrentó
- Centre d'hydrogéologie et de géothermie, Université de Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Miriam Guivernau
- GIRO Joint Research Unit IRTA-UPC, IRTA, Torre Marimon, Caldes de Montbui E-08140, Spain
| | - Marc Viñas
- GIRO Joint Research Unit IRTA-UPC, IRTA, Torre Marimon, Caldes de Montbui E-08140, Spain
| | - Daniel Hunkeler
- Centre d'hydrogéologie et de géothermie, Université de Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Albert Soler
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), c/Martí Franquès s/n, 08028 Barcelona, Spain
| | - Cristina Domènech
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), c/Martí Franquès s/n, 08028 Barcelona, Spain
| | - Mònica Rosell
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), c/Martí Franquès s/n, 08028 Barcelona, Spain
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Schubert T, Adrian L, Sawers RG, Diekert G. Organohalide respiratory chains: composition, topology and key enzymes. FEMS Microbiol Ecol 2018; 94:4923014. [DOI: 10.1093/femsec/fiy035] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/28/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
| | - Lorenz Adrian
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, D-04318 Leipzig, Germany
- Department of Geobiotechnology, Technische Universität Berlin, Ackerstraße 74, D-13355 Berlin, Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, D-07743 Jena, Germany
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Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates. ISME JOURNAL 2016; 11:626-640. [PMID: 27898054 DOI: 10.1038/ismej.2016.158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/25/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022]
Abstract
Two novel chlorinated alkane-respiring Dehalobacter restrictus strains CF and DCA were isolated from the same enrichment culture, ACT-3, and characterized. The closed genomes of these highly similar sister strains were previously assembled from metagenomic sequence data and annotated. The isolation of the strains enabled experimental verification of predicted annotations, particularly focusing on irregularities or predicted gaps in central metabolic pathways and cofactor biosynthesis. Similar to D. restrictus strain PER-K23, strains CF and DCA require arginine, histidine and threonine for growth, although the corresponding biosynthesis pathways are predicted to be functional. Using strain CF to experimentally verify annotations, we determined that the predicted defective serine biosynthesis pathway can be rescued with a promiscuous serine hydroxymethyltransferase. Strain CF grew without added thiamine although the thiamine biosynthesis pathway is predicted to be absent; intracellular thiamine diphosphate, the cofactor of carboxylases in central metabolism, was not detected in cell extracts. Thus, strain CF may use amino acids to replenish central metabolites, portending entangled metabolite exchanges in ACT-3. Consistent with annotation, strain CF possesses a functional corrinoid biosynthesis pathway, demonstrated by increasing corrinoid content during growth and guided cobalamin biosynthesis in corrinoid-free medium. Chloroform toxicity to corrinoid-producing methanogens and acetogens may drive the conservation of corrinoid autotrophy in Dehalobacter strains. Heme detection in strain CF cell extracts suggests the 'archaeal' heme biosynthesis pathway also functions in anaerobic Firmicutes. This study reinforces the importance of incorporating enzyme promiscuity and cofactor availability in genome-scale functional predictions and identifies essential nutrient interdependencies in anaerobic dechlorinating microbial communities.
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