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Franke S, Seidel K, Adrian L, Nijenhuis I. Dual Element (C/Cl) Isotope Analysis Indicates Distinct Mechanisms of Reductive Dehalogenation of Chlorinated Ethenes and Dichloroethane in Dehalococcoides mccartyi Strain BTF08 With Defined Reductive Dehalogenase Inventories. Front Microbiol 2020; 11:1507. [PMID: 32903289 PMCID: PMC7396605 DOI: 10.3389/fmicb.2020.01507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/10/2020] [Indexed: 02/02/2023] Open
Abstract
Dehalococcoides mccartyi strain BTF08 has the unique property to couple complete dechlorination of tetrachloroethene and 1,2-dichloroethane to ethene with growth by using the halogenated compounds as terminal electron acceptor. The genome of strain BTF08 encodes 20 genes for reductive dehalogenase homologous proteins (RdhA) including those described for dehalogenation of tetrachloroethene (PceA, PteA), trichloroethene (TceA) and vinyl chloride (VcrA). Thus far it is unknown under which conditions the different RdhAs are expressed, what their substrate specificity is and if different reaction mechanisms are employed. Here we found by proteomic analysis from differentially activated batches that PteA and VcrA were expressed during dechlorination of tetrachloroethene to ethene, while TceA was expressed during 1,2-dichloroethane dehalogenation. Carbon and chlorine compound-specific stable isotope analysis suggested distinct reaction mechanisms for the dechlorination of (i) cis-dichloroethene and vinyl chloride versus (ii) tetrachloroethene. This differentiation was observed independent of the expressed RdhA proteins. Differently, two stable isotope fractionation patterns were observed for 1,2-dichloroethane transformation, for cells with distinct RdhA inventories. Conclusively, we could link specific RdhA expression with functions and provide an insight into the apparently substrate-specific reaction mechanisms in the pathway of reductive dehalogenation in D. mccartyi strain BTF08. Data are available via ProteomeXchange with identifiers PXD018558 and PXD018595.
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Affiliation(s)
- Steffi Franke
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Katja Seidel
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Lorenz Adrian
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.,Chair of Geobiotechnology at TU Berlin, Berlin, Germany
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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Macaulay BM, Boothman C, van Dongen BE, Lloyd JR. A Novel "Microbial Bait" Technique for Capturing Fe(III)-Reducing Bacteria. Front Microbiol 2020; 11:330. [PMID: 32218773 PMCID: PMC7078115 DOI: 10.3389/fmicb.2020.00330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/14/2020] [Indexed: 11/29/2022] Open
Abstract
Microbial reduction of Fe(III) is a key geochemical process in anoxic environments, controlling the degradation of organics and the mobility of metals and radionuclides. To further understand these processes, it is vital to develop a reliable means of capturing Fe(III)-reducing microorganisms from the field for analysis and lab-based investigations. In this study, a novel method of capturing Fe(III)-reducing bacteria using Fe(III)-coated pumice "microbe-baits" was demonstrated. The methodology involved the coating of pumice (approximately diameter 4 to 6 mm) with a bioavailable Fe(III) mineral (akaganeite), and was verified by deployment into a freshwater spring for 2 months. On retrieval, the coated pumice baits were incubated in a series of lab-based microcosms, amended with and without electron donors (lactate and acetate), and incubated at 20°C for 8 weeks. 16S rRNA gene sequencing using the Illumina MiSeq platform showed that the Fe(III)-coated pumice baits, when incubated in the presence of lactate and acetate, enriched for Deltaproteobacteria (relative abundance of 52% of the sequences detected corresponded to Geobacter species and 24% to Desulfovibrio species). In the absence of added electron donors, Betaproteobacteria were the most abundant class detected, most heavily represented by a close relative to Rhodoferax ferrireducens (15% of species detected), that most likely used organic matter sequestered from the spring waters to support Fe(III) reduction. In addition, TEM-EDS analysis of the Fe(III)-coated pumice slurries amended with electron donors revealed that a biogenic Fe(II) mineral, magnetite, was formed at the end of the incubation period. These results demonstrate that Fe(III)-coated pumice "microbe baits" can potentially help target metal-reducing bacteria for culture-dependent studies, to further our understanding of the nano-scale microbe-mineral interactions in aquifers.
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Affiliation(s)
- Babajide Milton Macaulay
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
- Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Manchester, United Kingdom
- Environmental Biology and Public Health Unit, Department of Biology, The Federal University of Technology, Akure, Nigeria
| | - Christopher Boothman
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
- Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Manchester, United Kingdom
| | - Bart E. van Dongen
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
- Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Manchester, United Kingdom
| | - Jonathan Richard Lloyd
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, United Kingdom
- Williamson Research Centre for Molecular Environmental Science, The University of Manchester, Manchester, United Kingdom
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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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Türkowsky D, Esken J, Goris T, Schubert T, Diekert G, Jehmlich N, von Bergen M. A Retentive Memory of Tetrachloroethene Respiration in Sulfurospirillum halorespirans - involved Proteins and a possible link to Acetylation of a Two-Component Regulatory System. J Proteomics 2018; 181:36-46. [PMID: 29617628 DOI: 10.1016/j.jprot.2018.03.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/08/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
Abstract
Organohalide respiration (OHR), comprising the reductive dehalogenation of halogenated organic compounds, is subject to a unique memory effect and long-term transcriptional downregulation of the involved genes in Sulfurospirillum multivorans. Gene expression ceases slowly over approximately 100 generations in the absence of tetrachloroethene (PCE). However, the molecular mechanisms of this regulation process are not understood. We show here that Sulfurospirillum halorespirans undergoes the same type of regulation when cultivated without chlorinated ethenes for a long period of time. In addition, we compared the proteomes of S. halorespirans cells cultivated in the presence of PCE with those of cells long- and short-term cultivated with nitrate as the sole electron acceptor. Important OHR-related proteins previously unidentified in S. multivorans include a histidine kinase, a putative quinol dehydrogenase membrane protein, and a PCE-induced porin. Since for some regulatory proteins a posttranslational regulation of activity by lysine acetylations is known, we also analyzed the acetylome of S. halorespirans, revealing that 32% of the proteome was acetylated in at least one condition. The data indicate that the response regulator and the histidine kinase of a two-component system most probably involved in induction of PCE respiration are highly acetylated during short-term cultivation with nitrate in the absence of PCE. SIGNIFICANCE The so far unique long-term downregulation of organohalide respiration is now identified in a second species suggesting a broader distribution of this regulatory phenomenon. An improved protein extraction method allowed the identification of proteins most probably involved in transcriptional regulation of OHR in Sulfurospirillum spp. Our data indicate that acetylations of regulatory proteins are involved in this extreme, sustained standby-mode of metabolic enzymes in the absence of a substrate. This first published acetylome of Epsilonproteobacteria might help to study other ecologically or medically important species of this clade.
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Affiliation(s)
- Dominique Türkowsky
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Jens Esken
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - 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.
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Gadkari J, Goris T, Schiffmann CL, Rubick R, Adrian L, Schubert T, Diekert G. Reductive tetrachloroethene dehalogenation in the presence of oxygen by Sulfurospirillum multivorans: physiological studies and proteome analysis. FEMS Microbiol Ecol 2017; 94:4693833. [DOI: 10.1093/femsec/fix176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/02/2017] [Indexed: 11/14/2022] Open
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