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Yang L, Tang C, Cui Y, Zhang J. A High-Throughput Screening Strategy for Bacillus subtilis Producing Menaquinone-7 Based on Fluorescence-Activated Cell Sorting. Microorganisms 2025; 13:536. [PMID: 40142429 PMCID: PMC11946230 DOI: 10.3390/microorganisms13030536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 03/28/2025] Open
Abstract
Menaquinone-7 (MK-7) is recognized for its important biological activity, and Bacillus subtilis is the preferred strain for its fermentative production. However, the limited phenotypic diversity among high-yielding strains complicates the development of rapid screening methods. To address this, we utilized the effect of MK-7 on transmembrane potential to develop a high-throughput screening (HTS) strategy for efficiently identifying strains with improved MK-7 production. Among various membrane potential fluorescent dyes tested, Rhodamine 123 was selected for quantifying intracellular MK-7 levels due to its effective staining and minimal impact on cell growth. By optimizing pretreatment protocols and staining conditions, we established an HTS protocol that combines fluorescence-activated cell sorting with HPLC to identify strains with increased MK-7 production. A linear correlation was observed between mean MK-7 content and average fluorescence intensity (R2 = 0.9646). This approach was applied to mutant libraries generated through atmospheric room temperature plasma mutagenesis. After three cycles of mutagenesis and screening, the mutant AR03-27 was identified, showing an 85.65% increase in MK-7 yield compared to the original SJTU2 strain. Resequencing analysis revealed that the top three mutants contained mutations in genes related to membrane transport, suggesting their potential role in enhancing MK-7 yield.
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Affiliation(s)
- Lina Yang
- School of Agriculture and Biology, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai 200240, China; (L.Y.); (C.T.); (Y.C.)
| | - Can Tang
- School of Agriculture and Biology, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai 200240, China; (L.Y.); (C.T.); (Y.C.)
| | - Yan Cui
- School of Agriculture and Biology, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai 200240, China; (L.Y.); (C.T.); (Y.C.)
| | - Jianhua Zhang
- School of Agriculture and Biology, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai 200240, China; (L.Y.); (C.T.); (Y.C.)
- NMPA Key Laboratory for Testing Technology of Pharmaceutical, Shanghai Institute for Food and Drug Control, Shanghai 201203, China
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2
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Hilpmann S, Jeschke I, Hübner R, Deev D, Zugan M, Rijavec T, Lapanje A, Schymura S, Cherkouk A. Uranium (VI) reduction by an iron-reducing Desulfitobacterium species as single cells and in artificial multispecies bio-aggregates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 955:177210. [PMID: 39471942 DOI: 10.1016/j.scitotenv.2024.177210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 10/22/2024] [Accepted: 10/23/2024] [Indexed: 11/01/2024]
Abstract
Microbial U(VI) reduction plays a major role in new bioremediation strategies for radionuclide-contaminated environments and can potentially affect the safe disposal of high-level radioactive waste in a deep geological repository. Desulfitobacterium sp. G1-2, isolated from a bentonite sample, was used to investigate its potential to reduce U(VI) in different background electrolytes: bicarbonate buffer, where a uranyl(VI)‑carbonate complex predominates, and synthetic Opalinus Clay pore water, where a uranyl(VI)-lactate complex occurs, as confirmed by time-resolved laser-induced fluorescence spectroscopic measurements. While Desulfitobacterium sp. G1-2 rapidly removed almost all U from the supernatants in bicarbonate buffer, only a low amount of U was removed in Opalinus Clay pore water. UV/Vis measurements suggest a speciation-dependent reduction by the microorganism. Scanning transmission electron microscopy coupled with energy-dispersive X-ray spectroscopy revealed the formation of two different U-containing nanoparticles inside the cells. In a subsequent step, artificial multispecies bio-aggregates were formed using derivatized polyelectrolytes with cells of Desulfitobacterium sp. G1-2 and Cobetia marina DSM 50416 to assess their potential for U(VI) reduction under aerobic and anaerobic conditions. These findings provide new perspectives on microbial U(VI) reduction and contribute to the development of a safety concept for high-level radioactive waste repositories, as well as to new bioremediation strategies.
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Affiliation(s)
- Stephan Hilpmann
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - Isabelle Jeschke
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - René Hübner
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Ion Beam Physics and Materials Research, Dresden, Germany
| | - Dmitrii Deev
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Maja Zugan
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Tomaž Rijavec
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
| | - Aleš Lapanje
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
| | - Stefan Schymura
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Research Site Leipzig, Leipzig, Germany
| | - Andrea Cherkouk
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Dresden, Germany.
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Zhang F, Ge R, Wan Z, Li G, Cao L. Dual effects of PFOA or PFOS on reductive dechlorination of trichloroethylene (TCE). WATER RESEARCH 2023; 240:120093. [PMID: 37210970 DOI: 10.1016/j.watres.2023.120093] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 05/02/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
PFASs and chlorinated solvents are the common co-contaminants in soil and groundwater at firefighter training areas (FTAs). Although PFASs mixtures could have adverse impacts on bioremediation of trichloroethylene (TCE) by inhibiting Dehalococcoides (Dhc), little is known about the effect and contribution of PFOA or PFOS on dechlorination of TCE by non-Dhc organohalide-respiring bacteria (OHRB). To study this, PFOA and PFOS were amended to the growth medium of a non-Dhc OHRB-containing enrichment culture to determine the impact on dechlorination. This study demonstrated that high levels of PFOA or PFOS (100 mg L-1) inhibited TCE dechlorination in four non-Dhc OHRB-containing community including Geobacter, Desulfuromonas, Desulfitobacterium, and Dehalobacter, but low levels of PFOA or PFOS (≤10 mg L-1) enhanced TCE dechlorination. Four non-Dhc OHRB were less inhibited by PFOA than that by PFOS, and high level of PFOS killed Desulfitobacterium and Dehalobacter and decreased the biodiversity of bacterial community. Although most fermenters were killed by the presence of 100 mg L-1 PFOS, two important co-cultures (Desulfovibrio and Sedimentibacter) of OHRB were enriched, indicating that the syntrophic relationships between OHRB and co-cultures still remained, and PFOA or PFOS inhibited TCE dechlorination by directly repressing non-Dhc OHRB. Our results highlight that the bioattenuation of chloroethene contamination could be confounded by non-Dhc OHRB in high levels of PFOS contaminated subsurface environments at FTAs.
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Affiliation(s)
- Fang Zhang
- School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, China State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Runlei Ge
- School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, China State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Ziren Wan
- School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, China State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Guanghe Li
- School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, China State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing 100084, China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, China
| | - Lifeng Cao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China.
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Wu Z, Yu X, Liu G, Li W, Lu L, Li P, Xu X, Jiang J, Wang B, Qiao W. Sustained detoxification of 1,2-dichloroethane to ethylene by a symbiotic consortium containing Dehalococcoides species. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 325:121443. [PMID: 36921661 DOI: 10.1016/j.envpol.2023.121443] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/19/2023] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
1,2-Dichloroethane (1,2-DCA) is a ubiquitous volatile halogenated organic pollutant in groundwater and soil, which poses a serious threat to the ecosystem and human health. Microbial reductive dechlorination has been recognized as an environmentally-friendly strategy for the remediation of sites contaminated with 1,2-DCA. In this study, we obtained an anaerobic microbiota derived from 1,2-DCA contaminated groundwater, which was able to sustainably convert 1,2-DCA into non-toxic ethylene with an average dechlorination rate of 30.70 ± 11.06 μM d-1 (N = 6). The microbial community profile demonstrated that the relative abundance of Dehalococcoides species increased from 0.53 ± 0.08% to 44.68 ± 3.61% in parallel with the dechlorination of 1,2-DCA. Quantitative PCR results showed that the Dehalococcoides species 16S rRNA gene increased from 2.40 ± 1.71 × 108 copies∙mL-1 culture to 4.07 ± 2.45 × 108 copies∙mL-1 culture after dechlorinating 110.69 ± 30.61 μmol of 1,2-DCA with a growth yield of 1.55 ± 0.93 × 108 cells per μmol Cl- released (N = 6), suggesting that Dehalococcoides species used 1,2-DCA for organohalide respiration to maintain cell growth. Notably, the relative abundances of Methanobacterium sp. (p = 0.0618) and Desulfovibrio sp. (p = 0.0001995) also increased significantly during the dechlorination of 1,2-DCA and were clustered in the same module with Dehalococcoides species in the co-occurrence network. These results hinted that Dehalococcoides species, the obligate organohalide-respiring bacterium, exhibited potential symbiotic relationships with Methanobacterium and Desulfovibrio species. This study illustrates the importance of microbial interactions within functional microbiota and provides a promising microbial resource for in situ bioremediation in sites contaminated with 1,2-DCA.
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Affiliation(s)
- Zhiming Wu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin Yu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guiping Liu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lianghua Lu
- Jiangsu Provincial Key Laboratory of Environmental Engineering, Jiangsu Provincial Academy of Environmental Science, Nanjing 210036, China
| | - Pengfa Li
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Baozhan Wang
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Qiao
- Department of Microbiology, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Willemin MS, Hamelin R, Armand F, Holliger C, Maillard J. Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms. Front Microbiol 2023; 14:1058127. [PMID: 36733918 PMCID: PMC9888536 DOI: 10.3389/fmicb.2023.1058127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023] Open
Abstract
Introduction Desulfitobacterium hafniense was isolated for its ability to use organohalogens as terminal electron acceptors via organohalide respiration (OHR). In contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy metabolism with the capacity to use different electron donors and acceptors and to grow fermentatively. Desulfitobacterium genomes display numerous and apparently redundant members of redox enzyme families which confirm their metabolic potential. Nonetheless, the enzymes responsible for many metabolic traits are not yet identified. Methods In the present work, we conducted an extended proteomic study by comparing the proteomes of Desulfitobacterium hafniense strain DCB-2 cultivated in combinations of electron donors and acceptors, triggering five alternative respiratory metabolisms that include OHR, as well as fermentation. Tandem Mass Tag labelling proteomics allowed us to identify and quantify almost 60% of the predicted proteome of strain DCB-2 (2,796 proteins) in all six growth conditions. Raw data are available via ProteomeXchange with identifier PXD030393. Results and discussion This dataset was analyzed in order to highlight the proteins that were significantly up-regulated in one or a subset of growth conditions and to identify possible key players in the different energy metabolisms. The addition of sodium sulfide as reducing agent in the medium - a very widespread practice in the cultivation of strictly anaerobic bacteria - triggered the expression of the dissimilatory sulfite reduction pathway in relatively less favorable conditions such as fermentative growth on pyruvate, respiration with H2 as electron donor and OHR conditions. The presence of H2, CO2 and acetate in the medium induced several metabolic pathways involved in carbon metabolism including the Wood-Ljungdahl pathway and two pathways related to the fermentation of butyrate that rely on electron-bifurcating enzymes. While the predicted fumarate reductase appears to be constitutively expressed, a new lactate dehydrogenase and lactate transporters were identified. Finally, the OHR metabolism with 3-chloro-4-hydroxyphenylacetate as electron acceptor strongly induced proteins encoded in several reductive dehalogenase gene clusters, as well as four new proteins related to corrinoid metabolism. We believe that this extended proteomic database represents a new landmark in understanding the metabolic versatility of Desulfitobacterium spp. and provides a solid basis for addressing future research questions.
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Affiliation(s)
- Mathilde Stéphanie Willemin
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Romain Hamelin
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Armand
- Proteomic Core Facility (PCF), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology (LBE), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland,*Correspondence: Julien Maillard, ✉
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Cimmino L, Schmid AW, Holliger C, Maillard J. Stoichiometry of the Gene Products From the Tetrachloroethene Reductive Dehalogenase Operon pceABCT. Front Microbiol 2022; 13:838026. [PMID: 35283847 PMCID: PMC8905343 DOI: 10.3389/fmicb.2022.838026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Organohalide respiration (OHR) is a bacterial anaerobic process that uses halogenated compounds, e.g., tetrachloroethene (PCE), as terminal electron acceptors. Our model organisms are Dehalobacter restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and Desulfitobacterium hafniense strain TCE1, a bacterium with a versatile metabolism. The key enzyme is the PCE reductive dehalogenase (PceA) that is encoded in the highly conserved gene cluster (pceABCT) in both above-mentioned strains, and in other Firmicutes OHRB. To date, the functions of PceA and PceT, a dedicated molecular chaperone for the maturation of PceA, are well defined. However, the role of PceB and PceC are still not elucidated. We present a multilevel study aiming at deciphering the stoichiometry of pceABCT individual gene products. The investigation was assessed at RNA level by reverse transcription and (quantitative) polymerase chain reaction, while at protein level, proteomic analyses based on parallel reaction monitoring were performed to quantify the Pce proteins in cell-free extracts as well as in soluble and membrane fractions of both strains using heavy-labeled reference peptides. At RNA level, our results confirmed the co-transcription of all pce genes, while the quantitative analysis revealed a relative stoichiometry of the gene transcripts of pceA, pceB, pceC, and pceT at ~ 1.0:3.0:0.1:0.1 in D. restrictus. This trend was not observed in D. hafniense strain TCE1, where no substantial difference was measured for the four genes. At proteomic level, an apparent 2:1 stoichiometry of PceA and PceB was obtained in the membrane fraction, and a low abundance of PceC in comparison to the other two proteins. In the soluble fraction, a 1:1 stoichiometry of PceA and PceT was identified. In summary, we show that the pce gene cluster is transcribed as an operon with, however, a level of transcription that differs for individual genes, an observation that could be explained by post-transcriptional events. Despite challenges in the quantification of integral membrane proteins such as PceB and PceC, the similar abundance of PceA and PceB invites to consider them as forming a membrane-bound PceA2B protein complex, which, in contrast to the proposed model, seems to be devoid of PceC.
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Affiliation(s)
- Lorenzo Cimmino
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Adrien W Schmid
- Protein Core Facility, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Yang X, Liu P, Yao M, Sun H, Liu R, Xie J, Zhao Y. Mechanism and enhancement of Cr(VI) contaminated groundwater remediation by molasses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146580. [PMID: 34030333 DOI: 10.1016/j.scitotenv.2021.146580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
The remediation of Cr(VI)-contaminated groundwater with molasses has many advantages compared with traditional in-situ chemical methods, including high cost-effectiveness and negligible secondary contamination. Hence, the reaction conditions and mechanisms of molasses were investigated in this study. The results showed that Cr(VI) was chemically reduced by molasses at acidic pH (3.0), wherein the dominant active components were the hydroxyl and carbonyl groups of molasses. At neutral pH (7.0), molasses mainly acted as an electron donor for direct or indirect reduction of Cr(VI) by microorganisms. The main functional microorganisms were Bacillus and Clostridium Sensu Stricto. Compared with chemical reduction, bio-reduction could completely reduce higher concentrations of Cr(VI) when molasses was added at a concentration of 3 g/L. Ascorbic acid was added to promote the removal rate of bioremediation. Owing to the antioxidant properties of ascorbic acid, the reaction rate increased by 9.3% and 37.5% when 0.05 g/L of ascorbic acid was added to the 50 and 100 mg/L Cr(VI) bioremediation systems, respectively. Due to the decrease in pH during bioremediation, NaHCO3 was added to buffer the pH changes and promote Cr(III) precipitation. Compared with the addition of NaHCO3 and molasses simultaneously, separate additions were more effective for precipitation. Furthermore, X-ray absorption near-edge structure analysis revealed that after chemical reduction and biological reduction, Cr was attached to the solid medium in the form of Cr(III).
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Affiliation(s)
- Xinru Yang
- Key Laboratory of Groundwater Resources and Environment of Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130021, China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun 130021, China
| | - Peng Liu
- School of Environmental Studies, China University of Geosciences, 388 Lumo Rd., Wuhan, Hubei 430074, China
| | - Meng Yao
- Key Laboratory of Groundwater Resources and Environment of Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130021, China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun 130021, China
| | - He Sun
- Key Laboratory of Groundwater Resources and Environment of Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130021, China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun 130021, China
| | - Ruxue Liu
- Key Laboratory of Groundwater Resources and Environment of Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130021, China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun 130021, China
| | - Jiayin Xie
- Key Laboratory of Groundwater Resources and Environment of Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130021, China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun 130021, China
| | - Yongsheng Zhao
- Key Laboratory of Groundwater Resources and Environment of Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130021, China; Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun 130021, China; National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun 130021, China.
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8
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Esken J, Goris T, Gadkari J, Bischler T, Förstner KU, Sharma CM, Diekert G, Schubert T. Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two-component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies. Microbiologyopen 2020; 9:e1138. [PMID: 33242236 PMCID: PMC7755780 DOI: 10.1002/mbo3.1138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022] Open
Abstract
Energy conservation via organohalide respiration (OHR) in dehalogenating Sulfurospirillum species is an inducible process. However, the gene products involved in tetrachloroethene (PCE) sensing and signal transduction have not been unambiguously identified. Here, genome sequencing of Sulfurospirillum strains defective in PCE respiration and comparative genomics, which included the PCE-respiring representatives of the genus, uncovered the genetic inactivation of a two-component system (TCS) in the OHR gene region of the natural mutants. The assumption that the TCS gene products serve as a PCE sensor that initiates gene transcription was supported by the constitutive low-level expression of the TCS operon in fumarate-adapted cells of Sulfurospirillum multivorans. Via RNA sequencing, eight transcriptional units were identified in the OHR gene region, which includes the TCS operon, the PCE reductive dehalogenase operon, the gene cluster for norcobamide biosynthesis, and putative accessory genes with unknown functions. The OmpR-family response regulator (RR) encoded in the TCS operon was functionally characterized by promoter-binding assays. The RR bound a cis-regulatory element that contained a consensus sequence of a direct repeat (CTATW) separated by 17 bp. Its location either overlapping the -35 box or 50 bp further upstream indicated different regulatory mechanisms. Sequence variations in the regulator binding sites identified in the OHR gene region were in accordance with differences in the transcript levels of the respective gene clusters forming the PCE regulon. The results indicate the presence of a fine-tuned regulatory network controlling PCE metabolism in dehalogenating Sulfurospirillum species, a group of metabolically versatile organohalide-respiring bacteria.
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Affiliation(s)
- Jens Esken
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.,Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Tobias Goris
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Jennifer Gadkari
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Konrad U Förstner
- ZB MED - Information Center for Life Sciences, Cologne, Germany.,TH Köln - University of Applied Sciences, Institute of Information Science, Cologne, Germany
| | - Cynthia M Sharma
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Gabriele Diekert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Torsten Schubert
- Department of Applied and Ecological Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.,Research Group Anaerobic Microbiology, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
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9
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He WJ, Shi MM, Yang P, Huang T, Yuan QS, Yi SY, Wu AB, Li HP, Gao CB, Zhang JB, Liao YC. Novel Soil Bacterium Strain Desulfitobacterium sp. PGC-3-9 Detoxifies Trichothecene Mycotoxins in Wheat via De-Epoxidation under Aerobic and Anaerobic Conditions. Toxins (Basel) 2020; 12:toxins12060363. [PMID: 32492959 PMCID: PMC7354494 DOI: 10.3390/toxins12060363] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/24/2020] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Trichothecenes are the most common mycotoxins contaminating small grain cereals worldwide. The C12,13 epoxide group in the trichothecenes was identified as a toxic group posing harm to humans, farm animals, and plants. Aerobic biological de-epoxidation is considered the ideal method of controlling these types of mycotoxins. In this study, we isolated a novel trichothecene mycotoxin-de-epoxidating bacterium, Desulfitobacterium sp. PGC-3-9, from a consortium obtained from the soil of a wheat field known for the occurrence of frequent Fusarium head blight epidemics under aerobic conditions. Along with MMYPF media, a combination of two antibiotics (sulfadiazine and trimethoprim) substantially increased the relative abundance of Desulfitobacterium species from 1.55% (aerobic) to 29.11% (aerobic) and 28.63% (anaerobic). A single colony purified strain, PGC-3-9, was isolated and a 16S rRNA sequencing analysis determined that it was Desulfitobacterium. The PGC-3-9 strain completely de-epoxidated HT-2, deoxynivalenol (DON), nivalenol and 15-acetyl deoxynivalenol, and efficiently eliminated DON in wheat grains under aerobic and anaerobic conditions. The strain PGC-3-9 exhibited high DON de-epoxidation activity at a wide range of pH (6–10) and temperature (15–50 °C) values under both conditions. This strain may be used for the development of detoxification agents in the agriculture and feed industries and the isolation of de-epoxidation enzymes.
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Affiliation(s)
- Wei-Jie He
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan 430064, China; (W.-J.H.); (C.-B.G.)
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (M.-M.S.); (P.Y.); (T.H.); (Q.-S.Y.); (S.-Y.Y.); (H.-P.L.)
| | - Meng-Meng Shi
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (M.-M.S.); (P.Y.); (T.H.); (Q.-S.Y.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Peng Yang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (M.-M.S.); (P.Y.); (T.H.); (Q.-S.Y.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Huang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (M.-M.S.); (P.Y.); (T.H.); (Q.-S.Y.); (S.-Y.Y.); (H.-P.L.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing-Song Yuan
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (M.-M.S.); (P.Y.); (T.H.); (Q.-S.Y.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shu-Yuan Yi
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (M.-M.S.); (P.Y.); (T.H.); (Q.-S.Y.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ai-Bo Wu
- Key Laboratory of Food Safety Research Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China;
| | - He-Ping Li
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (M.-M.S.); (P.Y.); (T.H.); (Q.-S.Y.); (S.-Y.Y.); (H.-P.L.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chun-Bao Gao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences/Hubei Engineering and Technology Research Center of Wheat/Wheat Disease Biology Research Station for Central China, Wuhan 430064, China; (W.-J.H.); (C.-B.G.)
| | - Jing-Bo Zhang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (M.-M.S.); (P.Y.); (T.H.); (Q.-S.Y.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (J.-B.Z.); (Y.-C.L.); Tel.: +86-27-87283008 (Y.-C.L.)
| | - Yu-Cai Liao
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan 430070, China; (M.-M.S.); (P.Y.); (T.H.); (Q.-S.Y.); (S.-Y.Y.); (H.-P.L.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (J.-B.Z.); (Y.-C.L.); Tel.: +86-27-87283008 (Y.-C.L.)
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10
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Büsing J, Buchner D, Behrens S, Haderlein SB. Deciphering the Variability of Stable Isotope (C, Cl) Fractionation of Tetrachloroethene Biotransformation by Desulfitobacterium strains Carrying Different Reductive Dehalogenases Enzymes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1593-1602. [PMID: 31880148 DOI: 10.1021/acs.est.9b05606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Kinetic isotope effects have been used successfully to prove and characterize organic contaminant transformation on various scales including field and laboratory studies. For tetrachloroethene (PCE) biotransformation, however, causes for the substantial variability of reported isotope enrichment factors (ε) are still not deciphered (εC = -0.4 to -19.0‰). Factors such as different reaction mechanisms and masking of isotope fractionation by either limited intracellular mass transfer or rate-limitations within the enzymatic multistep reaction are under discussion. This study evaluated the contribution of these factors to the magnitude of carbon and chlorine isotope fractionation of Desulfitobacterium strains harboring three different PCE-transforming enzymes (PCE-RdhA). Despite variable single element isotope fractionation (εC = -5.0 to -19.7‰; εCl = -1.9 to -6.3‰), similar slopes of dual element isotope plots (ΛC/Cl values of 2.4 ± 0.1 to 3.6 ± 0.1) suggest a common reaction mechanism for different PCE-RdhAs. Cell envelope properties of the Desulfitobacterium strains allowed to exclude masking effects due to PCE mass transfer limitation. Our results thus revealed that different rate-limiting steps (e.g., substrate channel diffusion) in the enzymatic multistep reactions of individual PCE-RdhAs rather than different reaction mechanisms determine the extent of PCE isotope fractionation in the Desulfitobacterium genus.
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Affiliation(s)
- Johannes Büsing
- Center for Applied Geoscience , University of Tübingen , 72074 Tübingen , Germany
| | - Daniel Buchner
- Center for Applied Geoscience , University of Tübingen , 72074 Tübingen , Germany
| | - Sebastian Behrens
- Department of Civil, Environmental, and Geo-Engineering , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Stefan B Haderlein
- Center for Applied Geoscience , University of Tübingen , 72074 Tübingen , Germany
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11
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Organohalide-respiring Desulfoluna species isolated from marine environments. ISME JOURNAL 2020; 14:815-827. [PMID: 31896791 PMCID: PMC7031245 DOI: 10.1038/s41396-019-0573-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1T and D. butyratoxydans MSL71T, of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third strain, designated D. spongiiphila strain DBB, from marine intertidal sediment using 1,4-dibromobenzene and sulfate as the electron acceptors and lactate as the electron donor. Each strain harbors three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes, and dehalogenated brominated but not chlorinated organohalogens. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect other organohalide-respiring bacteria. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed expression of rdhA1 with 1,4-dibromobenzene, and revealed a partially shared electron transport chain from lactate to 1,4-dibromobenzene and sulfate, which may explain accelerated OHR during concurrent sulfate reduction. Versatility in using electron donors, de novo corrinoid biosynthesis, resistance to sulfate, sulfide and oxygen, and concurrent sulfate reduction and OHR may confer an advantage to marine Desulfoluna strains.
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12
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Bacterial nitrous oxide respiration: electron transport chains and copper transfer reactions. Adv Microb Physiol 2019; 75:137-175. [PMID: 31655736 DOI: 10.1016/bs.ampbs.2019.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biologically catalyzed nitrous oxide (N2O, laughing gas) reduction to dinitrogen gas (N2) is a desirable process in the light of ever-increasing atmospheric concentrations of this important greenhouse gas and ozone depleting substance. A diverse range of bacterial species produce the copper cluster-containing enzyme N2O reductase (NosZ), which is the only known enzyme that converts N2O to N2. Based on phylogenetic analyses, NosZ enzymes have been classified into clade I or clade II and it has turned out that this differentiation is also applicable to nos gene clusters (NGCs) and some physiological traits of the corresponding microbial cells. The NosZ enzyme is the terminal reductase of anaerobic N2O respiration, in which electrons derived from a donor substrate are transferred to NosZ by means of an electron transport chain (ETC) that conserves energy through proton motive force generation. This chapter presents models of the ETCs involved in clade I and clade II N2O respiration as well as of the respective NosZ maturation and maintenance processes. Despite differences in NGCs and growth yields of N2O-respiring microorganisms, the deduced bioenergetic framework in clade I and clade II N2O respiration is assumed to be equivalent. In both cases proton motive quinol oxidation by N2O is thought to be catalyzed by the Q cycle mechanism of a membrane-bound Rieske/cytochrome bc complex. However, clade I and clade II organisms are expected to differ significantly in terms of auxiliary electron transport processes as well as NosZ active site maintenance and repair.
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13
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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: 1.8] [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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14
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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: 4.7] [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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15
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Türkowsky D, Lohmann P, Mühlenbrink M, Schubert T, Adrian L, Goris T, Jehmlich N, von Bergen M. Thermal proteome profiling allows quantitative assessment of interactions between tetrachloroethene reductive dehalogenase and trichloroethene. J Proteomics 2019; 192:10-17. [DOI: 10.1016/j.jprot.2018.05.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 05/29/2018] [Indexed: 01/22/2023]
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16
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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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17
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Lechner U, Türkowsky D, Dinh TTH, Al‐Fathi H, Schwoch S, Franke S, Gerlach M, Koch M, von Bergen M, Jehmlich N, Dang TCH. Desulfitobacterium contributes to the microbial transformation of 2,4,5-T by methanogenic enrichment cultures from a Vietnamese active landfill. Microb Biotechnol 2018; 11:1137-1156. [PMID: 30117290 PMCID: PMC6196390 DOI: 10.1111/1751-7915.13301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/07/2018] [Indexed: 12/17/2022] Open
Abstract
The herbicide 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) was a major component of Agent Orange, which was used as a defoliant in the Vietnam War. Little is known about its degradation under anoxic conditions. Established enrichment cultures using soil from an Agent Orange bioremediation plant in southern Vietnam with pyruvate as potential electron donor and carbon source were shown to degrade 2,4,5-T via ether cleavage to 2,4,5-trichlorophenol (2,4,5-TCP), which was further dechlorinated to 3,4-dichlorophenol. Pyruvate was initially fermented to hydrogen, acetate and propionate. Hydrogen was then used as the direct electron donor for ether cleavage of 2,4,5-T and subsequent dechlorination of 2,4,5-TCP. 16S rRNA gene amplicon sequencing indicated the presence of bacteria and archaea mainly belonging to the Firmicutes, Bacteroidetes, Spirochaetes, Chloroflexi and Euryarchaeota. Desulfitobacterium hafniense was identified as the dechlorinating bacterium. Metaproteomics of the enrichment culture indicated higher protein abundances of 60 protein groups in the presence of 2,4,5-T. A reductive dehalogenase related to RdhA3 of D. hafniense showed the highest fold change, supporting its function in reductive dehalogenation of 2,4,5-TCP. Despite an ether-cleaving enzyme not being detected, the inhibition of ether cleavage but not of dechlorination, by 2-bromoethane sulphonate, suggested that the two reactions are catalysed by different organisms.
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Affiliation(s)
- Ute Lechner
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Dominique Türkowsky
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Thi Thu Hang Dinh
- Vietnamese Academy of Science and TechnologyInstitute of BiotechnologyHanoiVietnam
- Present address:
Vietnamese Academy of Science and TechnologyGraduate University of Science and TechnologyHanoiVietnam
| | - Hassan Al‐Fathi
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Stefan Schwoch
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Stefan Franke
- Institute of Biology/MicrobiologyMartin‐Luther University Halle‐WittenbergHalleGermany
| | | | - Mandy Koch
- Institute of Chemistry/Food and Environmental ChemistryMartin‐Luther University Halle‐WittenbergHalleGermany
| | - Martin von Bergen
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Nico Jehmlich
- Department of Molecular Systems BiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Thi Cam Ha Dang
- Vietnamese Academy of Science and TechnologyInstitute of BiotechnologyHanoiVietnam
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18
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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: 4.1] [Reference Citation Analysis] [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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19
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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: 8.1] [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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20
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Marozava S, Vargas-López R, Tian Y, Merl-Pham J, Braster M, Meckenstock RU, Smidt H, Röling WFM, Westerhoff HV. Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats. Environ Microbiol 2018; 20:2652-2669. [PMID: 29921035 DOI: 10.1111/1462-2920.14295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 05/19/2018] [Indexed: 11/30/2022]
Abstract
Desulfitobacterium hafniense Y51 has been widely used in investigations of perchloroethylene (PCE) biodegradation, but limited information exists on its other physiological capabilities. We investigated how D. hafniense Y51 confronts the debilitating limitations of not having enough electron donor (lactate), or electron acceptor (fumarate) during cultivation in chemostats. The residual concentrations of the substrates supplied in excess were much lower than expected. Transcriptomics, proteomics and fluxomics were integrated to investigate how this phenomenon was regulated. Through diverse regulation at both transcriptional and translational levels, strain Y51 turned to fermenting the excess lactate and disproportionating the excess fumarate under fumarate- and lactate-limiting conditions respectively. Genes and proteins related to the utilization of a variety of alternative electron donors and acceptors absent from the medium were induced, apparently involving the Wood-Ljungdahl pathway. Through this metabolic flexibility, D. hafniense Y51 may be able to switch between different metabolic capabilities under limiting conditions.
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Affiliation(s)
- Sviatlana Marozava
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Raquel Vargas-López
- Molecular Cell Physiology, Faculty of Science, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Ye Tian
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Juliane Merl-Pham
- Core Facility Proteomics, Helmholtz Zentrum München, Heidemannstraße 1, 80939, München, Germany
| | - Martin Braster
- Molecular Cell Physiology, Faculty of Science, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Rainer U Meckenstock
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Wilfred F M Röling
- Molecular Cell Physiology, Faculty of Science, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Hans V Westerhoff
- Molecular Cell Physiology, Faculty of Science, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands.,Synthetic Systems Biology, SILS, University of Amsterdam, Amsterdam, The Netherlands.,Manchester Centre for Integrative Systems Biology, School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, UK
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21
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Buttet GF, Willemin MS, Hamelin R, Rupakula A, Maillard J. The Membrane-Bound C Subunit of Reductive Dehalogenases: Topology Analysis and Reconstitution of the FMN-Binding Domain of PceC. Front Microbiol 2018; 9:755. [PMID: 29740408 PMCID: PMC5928378 DOI: 10.3389/fmicb.2018.00755] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/04/2018] [Indexed: 12/15/2022] Open
Abstract
Organohalide respiration (OHR) is the energy metabolism of anaerobic bacteria able to use halogenated organic compounds as terminal electron acceptors. While the terminal enzymes in OHR, so-called reductive dehalogenases, are well-characterized, the identity of proteins potentially involved in electron transfer to the terminal enzymes remains elusive. Among the accessory genes identified in OHR gene clusters, the C subunit (rdhC) could well code for the missing redox protein between the quinol pool and the reductive dehalogenase, although it was initially proposed to act as transcriptional regulator. RdhC sequences are characterized by the presence of multiple transmembrane segments, a flavin mononucleotide (FMN) binding motif and two conserved CX3CP motifs. Based on these features, we propose a curated selection of RdhC proteins identified in general sequence databases. Beside the Firmicutes from which RdhC sequences were initially identified, the identified sequences belong to three additional phyla, the Chloroflexi, the Proteobacteria, and the Bacteriodetes. The diversity of RdhC sequences mostly respects the phylogenetic distribution, suggesting that rdhC genes emerged relatively early in the evolution of the OHR metabolism. PceC, the C subunit of the tetrachloroethene (PCE) reductive dehalogenase is encoded by the conserved pceABCT gene cluster identified in Dehalobacter restrictus PER-K23 and in several strains of Desulfitobacterium hafniense. Surfaceome analysis of D. restrictus cells confirmed the predicted topology of the FMN-binding domain (FBD) of PceC that is the exocytoplasmic face of the membrane. Starting from inclusion bodies of a recombinant FBD protein, strategies for successful assembly of the FMN cofactor and refolding were achieved with the use of the flavin-trafficking protein from D. hafniense TCE1. Mass spectrometry analysis and site-directed mutagenesis of rFBD revealed that threonine-168 of PceC is binding FMN covalently. Our results suggest that PceC, and more generally RdhC proteins, may play a role in electron transfer in the metabolism of OHR.
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Affiliation(s)
- Géraldine F Buttet
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Mathilde S Willemin
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Romain Hamelin
- Protein Core Facility, Faculty of Life Sciences, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Aamani Rupakula
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, Institute for Environmental Engineering, Swiss Federal Institute of Technology in Lausanne, Lausanne, Switzerland
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22
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Holliger C, Nijenhuis I. Editorial: Special issue on anaerobic biological dehalogenation. FEMS Microbiol Ecol 2018; 94:4953414. [PMID: 29590392 DOI: 10.1093/femsec/fiy054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/23/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Christof Holliger
- School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 6, CH-1015 Lausanne, Switzerland
| | - Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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