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Löffler M, Schwab L, Dethlefsen F, Lagmöller L, Vogt C, Richnow HH. Anaerobic dihydrogen consumption of nutrient-limited aquifer sediment microbial communities examined by stable isotope analysis. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2024; 60:103-121. [PMID: 38344763 DOI: 10.1080/10256016.2024.2306146] [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: 03/27/2023] [Accepted: 12/21/2023] [Indexed: 03/20/2024]
Abstract
The biogeochemical consequences of dihydrogen (H2) underground storage in porous aquifers are poorly understood. Here, the effects of nutrient limitations on anaerobic H2 oxidation of an aquifer microbial community in sediment microcosms were determined in order to evaluate possible responses to high H2 partial pressures. Hydrogen isotope analyses of H2 yielded isotope depletion in all biotic setups indicating microbial H2 consumption. Carbon isotope analyses of carbon dioxide (CO2) showed isotope enrichment in all H2-supplemented biotic setups indicating H2-dependent consumption of CO2 by methanogens or homoacetogens. Homoacetogenesis was indicated by the detection of acetate and formate. Consumption of CO2 and H2 varied along the differently nutrient-amended setups, as did the onset of methane production. Plotting carbon against hydrogen isotope signatures of CH4 indicated that CH4 was produced hydrogenotrophically and fermentatively. The putative hydrogenotrophic Methanobacterium sp. was the dominant methanogen. Most abundant phylotypes belonged to typical ferric iron reducers, indicating that besides CO2, Fe(III) was an important electron acceptor. In summary, our study provides evidence for the adaptability of subsurface microbial communities under different nutrient-deficient conditions to elevated H2 partial pressures.
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Affiliation(s)
- Michaela Löffler
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Laura Schwab
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Frank Dethlefsen
- Department of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy (KGE), University of Kiel, Kiel, Germany
| | - Louisa Lagmöller
- Department of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy (KGE), University of Kiel, Kiel, Germany
| | - Carsten Vogt
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Isodetect GmbH, Leipzig, Germany
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2
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Hessler T, Harrison ST, Banfield JF, Huddy RJ. Harnessing Fermentation May Enhance the Performance of Biological Sulfate-Reducing Bioreactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2830-2846. [PMID: 38301118 PMCID: PMC10867827 DOI: 10.1021/acs.est.3c04187] [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: 06/01/2023] [Revised: 12/28/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Biological sulfate reduction (BSR) represents a promising strategy for bioremediation of sulfate-rich waste streams, yet the impact of metabolic interactions on performance is largely unexplored. Here, genome-resolved metagenomics was used to characterize 17 microbial communities in reactors treating synthetic sulfate-contaminated solutions. Reactors were supplemented with lactate or acetate and a small amount of fermentable substrate. Of the 163 genomes representing all the abundant bacteria, 130 encode 321 NiFe and FeFe hydrogenases and all genomes of the 22 sulfate-reducing microorganisms (SRM) encode genes for H2 uptake. We observed lactate oxidation solely in the first packed bed reactor zone, with propionate and acetate oxidation in the middle and predominantly acetate oxidation in the effluent zone. The energetics of these reactions are very different, yet sulfate reduction kinetics were unaffected by the type of electron donor available. We hypothesize that the comparable rates, despite the typically slow growth of SRM on acetate, are a result of the consumption of H2 generated by fermentation. This is supported by the sustained performance of a predominantly acetate-supplemented stirred tank reactor dominated by diverse fermentative bacteria encoding FeFe hydrogenase genes and SRM capable of acetate and hydrogen consumption and CO2 assimilation. Thus, addition of fermentable substrates to stimulate syntrophic relationships may improve the performance of BSR reactors supplemented with inexpensive acetate.
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Affiliation(s)
- Tomas Hessler
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The
Innovative Genomics Institute at the University of California, Berkeley, California CA94720, United
States
- The
Department of Earth and Planetary Science, University of California, Berkeley, California CA94720, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California CA94720, United States
| | - Susan T.L. Harrison
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The Future
Water Institute, University of Cape Town, Cape Town 7700, South Africa
| | - Jillian F. Banfield
- The
Innovative Genomics Institute at the University of California, Berkeley, California CA94720, United
States
- The
Department of Earth and Planetary Science, University of California, Berkeley, California CA94720, United States
- The
Department of Environmental Science, Policy and Management, University of California, Berkeley, California CA94720, United States
| | - Robert J. Huddy
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The Future
Water Institute, University of Cape Town, Cape Town 7700, South Africa
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3
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Watanabe T, Yabe T, Tsuji JM, Fukui M. Desulfoferula mesophilus gen. nov. sp. nov., a mesophilic sulfate-reducing bacterium isolated from a brackish lake sediment. Arch Microbiol 2023; 205:368. [PMID: 37923857 DOI: 10.1007/s00203-023-03711-9] [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: 09/07/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 11/06/2023]
Abstract
A novel sulfate-reducing bacterium (strain 12FAKT) was isolated from sediment sampled from a brackish lake in Japan. Respiratory growth was observed with formate and pyruvate as an electron donor. Sulfate, thiosulfate, elemental sulfur and dimethyl sulfoxide were utilized as an electron acceptor. The isolate grew over a temperature range of 18-42 °C (optimum 35-37 °C), a NaCl concentration range of 50-450 mM (optimum 150-300 mM) and a pH range of 6.6-7.5. The 12FAKT genome consists of a circular chromosome with a length of 4.5 Mbp and G + C content of 63.6%. Based on 16S rRNA gene sequence similarity, the closest cultured relative was Desulfarculus baarsii 2st14T (92.2%). Genome-based phylogenetic analysis placed strain 12FAKT within the family Desulfarculaceae but did not affiliate the strain with any existing genus. Taken together, we propose a novel species of a novel genus, Desulfoferula mesophilus gen. nov. sp. nov. with the type strain 12FAKT (= DSM 115219T = JCM 39399T).
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Affiliation(s)
- Tomohiro Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan.
| | - Tatsuya Yabe
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
- Graduate School of Environmental Science, Hokkaido University, Kita-10, Nishi-5, Kita-ku, Sapporo, 060-0810, Japan
| | - Jackson M Tsuji
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
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4
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Sobieraj K, Stegenta-Dąbrowska S, Luo G, Koziel JA, Białowiec A. Biological treatment of biowaste as an innovative source of CO-The role of composting process. Front Bioeng Biotechnol 2023; 11:1126737. [PMID: 36845185 PMCID: PMC9947533 DOI: 10.3389/fbioe.2023.1126737] [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: 12/18/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Carbon monoxide (CO) is an essential "building block" for producing everyday chemicals on industrial scale. Carbon monoxide can also be generated though a lesser-known and sometimes forgotten biorenewable pathways that could be explored to advance biobased production from large and more sustainable sources such as bio-waste treatment. Organic matter decomposition can generate carbon monoxide both under aerobic and anaerobic conditions. While anaerobic carbon monoxide generation is relatively well understood, the aerobic is not. Yet many industrial-scale bioprocesses involve both conditions. This review summarizes the necessary basic biochemistry knowledge needed for realization of initial steps towards biobased carbon monoxide production. We analyzed for the first time, the complex information about carbon monoxide production during aerobic, anaerobic bio-waste treatment and storage, carbon monoxide-metabolizing microorganisms, pathways, and enzymes with bibliometric analysis of trends. The future directions recognizing limitations of combined composting and carbon monoxide production have been discussed in greater detail.
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Affiliation(s)
- Karolina Sobieraj
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Sylwia Stegenta-Dąbrowska
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, China,Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai, China,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Jacek A. Koziel
- USDA-ARS Conservation and Production Research Laboratory, Bushland, TX, United States,Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Andrzej Białowiec
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States,*Correspondence: Andrzej Białowiec,
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5
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Tong S, Zhao L, Zhu D, Chen W, Chen L, Li D. From formic acid to single-cell protein: genome-scale revealing the metabolic network of Paracoccus communis MA5. BIORESOUR BIOPROCESS 2022; 9:55. [PMID: 38647589 PMCID: PMC10992362 DOI: 10.1186/s40643-022-00544-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/29/2022] [Indexed: 11/10/2022] Open
Abstract
With the increase in population growth and environmental pollution, the daily protein supply is facing great challenges. Single-cell protein (SCP) produced by microorganism fermentation is a good alternative for substituting plant- and animal-derived proteins. In this study, Paracoccus communis MA5 isolated from soil previously demonstrated an excellent ability to synthesize SCP directly from sodium formate. To investigate the central metabolic network of formic acid assimilation and protein synthesis, genome-scale analyses were performed. Genomic analysis showed that complete tetrahydrofolate cycle-, serine cycle-, glycolytic pathway-, tricarboxylic acid (TCA) cycle- and nitrogen metabolism-relevant genes were annotated in the genome. These pathways play key roles in the conversion of formic acid into proteins. Transcriptional analysis showed that sodium formate stress could stimulate the metabolic pathway in response to environmental stress, but weaken the sulfur metabolic pathway to inhibit amino acid synthesis, resulting in a decrease in protein content (30% vs 44%). However, under culture conditions with ammonium sulfate, metabolic pathways associated with protein synthesis were accelerated, causing an increase in protein content (53% vs 44%); while the tetrahydrofolate cycle associated with formic acid assimilation was inhibited, causing a 62.5% decrease in growth rate (OD600: 0.21 vs 0.56). These results provide evidence of protein synthesis from sodium formate in strain MA5 at the gene level and lay a theoretical foundation for the optimization of fermentation systems using formic acid as a carbon source.
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Affiliation(s)
- Sheng Tong
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Innovation Centre for Synthetic Biology, Tianjin, 300308, China
| | - Lizhi Zhao
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-Utilization, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Daling Zhu
- Tianjin Key Laboratory of Brine Chemical Engineering and Resource Eco-Utilization, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Wuxi Chen
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Innovation Centre for Synthetic Biology, Tianjin, 300308, China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Innovation Centre for Synthetic Biology, Tianjin, 300308, China
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Innovation Centre for Synthetic Biology, Tianjin, 300308, China.
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6
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Jiang Q, Jing H, Jiang Q, Zhang Y. Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps. MARINE POLLUTION BULLETIN 2022; 176:113458. [PMID: 35217425 DOI: 10.1016/j.marpolbul.2022.113458] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 02/10/2022] [Indexed: 05/10/2023]
Abstract
Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior. At present, six pathways of autotrophic carbon fixation have been found: the Calvin cycle, the reductive Acetyl-CoA or Wood-Ljungdahl pathway (rAcCoA), the reductive tricarboxylic acid cycle (rTCA), the 3-hydroxypropionate bicycle (3HP), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB), and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB). Although our knowledge about carbon fixation pathways in the ocean has increased significantly, carbon fixation pathways in the cold seeps are still unknown. In this study, we collected sediment samples from two cold seeps and one trough in the south China sea (SCS), and investigated with metagenomic and metagenome assembled genomes (MAGs). We found that six autotrophic carbon fixation pathways present in the cold seeps and trough with rTCA cycle was the most common pathway, whose genes were particularly high in the cold seeps and increased with sediment depths; the rAcCoA cycle mainly occurred in the cold seep regions, and the abundance of module genes increased with sediment depths. We also elucidated members of chemoautotrophic microorganisms involved in these six carbon-fixation pathways. The rAcCoA, rTCA and DC/4-HB cycles required significantly less energy probably play an important role in the deep-sea environments, especially in the cold seeps. This study provided metabolic insights into the carbon fixation pathways in the cold seeps, and laid the foundation for future detailed study on processes and rates of carbon fixation in the deep-sea ecosystems.
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Affiliation(s)
- QiuYun Jiang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya 572000, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China.
| | - QiuLong Jiang
- The College of Information, Mechanical and Electrical Engineering, Shanghai Normal University, Shanghai 201400, China
| | - Yue Zhang
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Izadi P, Schröder U. What is the Role of Individual Species within Bidirectional Electroactive Microbial Biofilms: A Case Study on
Desulfarculus baarsii
and
Desulfurivibrio alkaliphilus. ChemElectroChem 2022. [DOI: 10.1002/celc.202101116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Paniz Izadi
- Institute of Environmental and Sustainable Chemistry Technische Universität Braunschweig Hagenring 30 38106 Braunschweig Germany
- Now at: Helmholtz Centre for Environmental Research – UFZ Permoserstr. 15 04318 Leipzig Germany
| | - Uwe Schröder
- Institute of Environmental and Sustainable Chemistry Technische Universität Braunschweig Hagenring 30 38106 Braunschweig Germany
- Now at: Institute for Biochemistry University of Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Germany
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8
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Coskun ÖK, Vuillemin A, Schubotz F, Klein F, Sichel SE, Eisenreich W, Orsi WD. Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks. ISME JOURNAL 2021; 16:257-271. [PMID: 34312482 PMCID: PMC8692406 DOI: 10.1038/s41396-021-01066-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022]
Abstract
Thermodynamic models predict that H2 is energetically favorable for seafloor microbial life, but how H2 affects anabolic processes in seafloor-associated communities is poorly understood. Here, we used quantitative 13C DNA stable isotope probing (qSIP) to quantify the effect of H2 on carbon assimilation by microbial taxa synthesizing 13C-labeled DNA that are associated with partially serpentinized peridotite rocks from the equatorial Mid-Atlantic Ridge. The rock-hosted seafloor community was an order of magnitude more diverse compared to the seawater community directly above the rocks. With added H2, peridotite-associated taxa increased assimilation of 13C-bicarbonate and 13C-acetate into 16S rRNA genes of operational taxonomic units by 146% (±29%) and 55% (±34%), respectively, which correlated with enrichment of H2-oxidizing NiFe-hydrogenases encoded in peridotite-associated metagenomes. The effect of H2 on anabolism was phylogenetically organized, with taxa affiliated with Atribacteria, Nitrospira, and Thaumarchaeota exhibiting the most significant increases in 13C-substrate assimilation in the presence of H2. In SIP incubations with added H2, an order of magnitude higher number of peridotite rock-associated taxa assimilated 13C-bicarbonate, 13C-acetate, and 13C-formate compared to taxa that were not associated with peridotites. Collectively, these findings indicate that the unique geochemical nature of the peridotite-hosted ecosystem has selected for H2-metabolizing, rock-associated taxa that can increase anabolism under high H2 concentrations. Because ultramafic rocks are widespread in slow-, and ultraslow-spreading oceanic lithosphere, continental margins, and subduction zones where H2 is formed in copious amounts, the link between H2 and carbon assimilation demonstrated here may be widespread within these geological settings.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany
| | - Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany.,GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Frieder Klein
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Susanna E Sichel
- Departamento de Geologia e Geofísica/LAGEMAR-Universidade Federal Fluminense-Brazil, Niterói, RJ, Brazil
| | - Wolfgang Eisenreich
- Department of Chemistry, Bavarian NMR Center-Structural Membrane Biochemistry, Technische Universität München, Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Munich, Germany. .,GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany.
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9
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Sánchez-Andrea I, Guedes IA, Hornung B, Boeren S, Lawson CE, Sousa DZ, Bar-Even A, Claassens NJ, Stams AJM. The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans. Nat Commun 2020; 11:5090. [PMID: 33037220 PMCID: PMC7547702 DOI: 10.1038/s41467-020-18906-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 09/14/2020] [Indexed: 12/30/2022] Open
Abstract
Six CO2 fixation pathways are known to operate in photoautotrophic and chemoautotrophic microorganisms. Here, we describe chemolithoautotrophic growth of the sulphate-reducing bacterium Desulfovibrio desulfuricans (strain G11) with hydrogen and sulphate as energy substrates. Genomic, transcriptomic, proteomic and metabolomic analyses reveal that D. desulfuricans assimilates CO2 via the reductive glycine pathway, a seventh CO2 fixation pathway. In this pathway, CO2 is first reduced to formate, which is reduced and condensed with a second CO2 to generate glycine. Glycine is further reduced in D. desulfuricans by glycine reductase to acetyl-P, and then to acetyl-CoA, which is condensed with another CO2 to form pyruvate. Ammonia is involved in the operation of the pathway, which is reflected in the dependence of the autotrophic growth rate on the ammonia concentration. Our study demonstrates microbial autotrophic growth fully supported by this highly ATP-efficient CO2 fixation pathway.
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Affiliation(s)
- Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Iame Alves Guedes
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Bastian Hornung
- Leids Universitair Medisch Centrum (LUMC), Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Christopher E Lawson
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Center of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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10
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Gupta D, Guzman MS, Bose A. Extracellular electron uptake by autotrophic microbes: physiological, ecological, and evolutionary implications. ACTA ACUST UNITED AC 2020; 47:863-876. [DOI: 10.1007/s10295-020-02309-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/07/2020] [Indexed: 02/05/2023]
Abstract
Abstract
Microbes exchange electrons with their extracellular environment via direct or indirect means. This exchange is bidirectional and supports essential microbial oxidation–reduction processes, such as respiration and photosynthesis. The microbial capacity to use electrons from insoluble electron donors, such as redox-active minerals, poised electrodes, or even other microbial cells is called extracellular electron uptake (EEU). Autotrophs with this capability can thrive in nutrient and soluble electron donor-deficient environments. As primary producers, autotrophic microbes capable of EEU greatly impact microbial ecology and play important roles in matter and energy flow in the biosphere. In this review, we discuss EEU-driven autotrophic metabolisms, their mechanism and physiology, and highlight their ecological, evolutionary, and biotechnological implications.
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Affiliation(s)
- Dinesh Gupta
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
| | - Michael S Guzman
- grid.250008.f 0000 0001 2160 9702 Biosciences and Biotechnology Division Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory Livermore CA USA
| | - Arpita Bose
- grid.4367.6 0000 0001 2355 7002 Department of Biology Washington University in St. Louis One Brookings Drive 63130 St. Louis MO USA
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11
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Recent progress in metabolic engineering of microbial formate assimilation. Appl Microbiol Biotechnol 2020; 104:6905-6917. [PMID: 32566995 DOI: 10.1007/s00253-020-10725-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/25/2020] [Accepted: 06/07/2020] [Indexed: 12/27/2022]
Abstract
Formate can be efficiently produced via electrochemical or photochemical catalytic conversion of CO2, and it can be directly used as an organic carbon source by microorganisms. In theory, formate can be used as the sole carbon source for the microbial production of high-value-added chemicals. Consequently, the construction of efficient formate-assimilation pathways in microorganisms is essential for the utilization of cheap, renewable one-carbon compounds. This paper summarizes new methods of formate synthesis, as well as the natural formate utilization pathways of microorganisms with their advantages and disadvantages. Furthermore, it reviews recent progress in the design of utilization pathways for formate in microbial cells through metabolic engineering and synthetic biology. Besides, we also use the pathway-prediction algorithm comb-FBA to rationally design completely new one-carbon compounds utilization pathways. The pathway with the highest efficiency, named GAA, was corroborated by the in vitro experiments showing a carbon molar yield up to 88%. Finally, it discusses the main problems and challenges presently existing in the pathway design and strain improvement for microbial utilization of formate. KEY POINTS: • Natural and artificial design pathways of formate-assimilation was summarized. • Recent progresses in different hosts and approaches of using one-carbon compounds was reviewed. • Metabolic engineering and synthetic biology methods to improve formate utilization were discussed.
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12
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Lang SQ, Brazelton WJ. Habitability of the marine serpentinite subsurface: a case study of the Lost City hydrothermal field. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20180429. [PMID: 31902336 PMCID: PMC7015304 DOI: 10.1098/rsta.2018.0429] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
The Lost City hydrothermal field is a dramatic example of the biological potential of serpentinization. Microbial life is prevalent throughout the Lost City chimneys, powered by the hydrogen gas and organic molecules produced by serpentinization and its associated geochemical reactions. Microbial life in the serpentinite subsurface below the Lost City chimneys, however, is unlikely to be as dense or active. The marine serpentinite subsurface poses serious challenges for microbial activity, including low porosities, the combination of stressors of elevated temperature, high pH and a lack of bioavailable ∑CO2. A better understanding of the biological opportunities and challenges in serpentinizing systems would provide important insights into the total habitable volume of Earth's crust and for the potential of the origin and persistence of life in Earth's subsurface environments. Furthermore, the limitations to life in serpentinizing subsurface environments on Earth have significant implications for the habitability of subsurface environments on ocean worlds such as Europa and Enceladus. Here, we review the requirements and limitations of life in serpentinizing systems, informed by our research at the Lost City and the underwater mountain on which it resides, the Atlantis Massif. This article is part of a discussion meeting issue 'Serpentinite in the Earth System'.
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Affiliation(s)
- Susan Q. Lang
- School of the Earth, Ocean, and Environment, University of South Carolina, Columbia, SC 29208, USA
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13
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Bird LR, Dawson KS, Chadwick GL, Fulton JM, Orphan VJ, Freeman KH. Carbon isotopic heterogeneity of coenzyme F430 and membrane lipids in methane-oxidizing archaea. GEOBIOLOGY 2019; 17:611-627. [PMID: 31364272 DOI: 10.1111/gbi.12354] [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: 08/20/2018] [Revised: 06/17/2019] [Accepted: 06/23/2019] [Indexed: 06/10/2023]
Abstract
Archaeal ANaerobic MEthanotrophs (ANME) facilitate the anaerobic oxidation of methane (AOM), a process that is believed to proceed via the reversal of the methanogenesis pathway. Carbon isotopic composition studies indicate that ANME are metabolically diverse and able to assimilate metabolites including methane, methanol, acetate, and dissolved inorganic carbon (DIC). Our data support the interpretation that ANME in marine sediments at methane seeps assimilate both methane and DIC, and the carbon isotopic compositions of the tetrapyrrole coenzyme F430 and the membrane lipids archaeol and hydroxy-archaeol reflect their relative proportions of carbon from these substrates. Methane is assimilated via the methyl group of CH3 -tetrahydromethanopterin (H4 MPT) and DIC from carboxylation reactions that incorporate free intracellular DIC. F430 was enriched in 13 C (mean δ13 C = -27‰ for Hydrate Ridge and -80‰ for the Santa Monica Basin) compared to the archaeal lipids (mean δ13 C = -97‰ for Hydrate Ridge and -122‰ for the Santa Monica Basin). We propose that depending on the side of the tricarboxylic acid (TCA) cycle used to synthesize F430, its carbon was derived from 76% DIC and 24% methane via the reductive side or 57% DIC and 43% methane via the oxidative side. ANME lipids are predicted to contain 42% DIC and 58% methane, reflecting the amount of each assimilated into acetyl-CoA. With isotope models that include variable fractionation during biosynthesis for different carbon substrates, we show the estimated amounts of DIC and methane can result in carbon isotopic compositions of - 73‰ to - 77‰ for F430 and - 105‰ for archaeal lipids, values close to those for Santa Monica Basin. The F430 δ13 C value for Hydrate Ridge was 13 C-enriched compared with the modeled value, suggesting there is divergence from the predicted two carbon source models.
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Affiliation(s)
- Laurence R Bird
- Department of Geosciences, the Pennsylvania State University, University Park, PA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Grayson L Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - James M Fulton
- Department of Geosciences, the Pennsylvania State University, University Park, PA, USA
- Department of Geosciences, Baylor University, Waco, TX, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Katherine H Freeman
- Department of Geosciences, the Pennsylvania State University, University Park, PA, USA
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14
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Abstract
Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood-Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.
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15
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Xavier JC, Preiner M, Martin WF. Something special about CO-dependent CO 2 fixation. FEBS J 2018; 285:4181-4195. [PMID: 30240136 PMCID: PMC6282760 DOI: 10.1111/febs.14664] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/08/2018] [Accepted: 09/19/2018] [Indexed: 01/02/2023]
Abstract
Carbon dioxide enters metabolism via six known CO2 fixation pathways, of which only one is linear, exergonic in the direction of CO2‐assimilation, and present in both bacterial and archaeal anaerobes – the Wood‐Ljungdahl (WL) or reductive acetyl‐CoA pathway. Carbon monoxide (CO) plays a central role in the WL pathway as an energy rich intermediate. Here, we scan the major biochemical reaction databases for reactions involving CO and CO2. We identified 415 reactions corresponding to enzyme commission (EC) numbers involving CO2, which are non‐randomly distributed across different biochemical pathways. Their taxonomic distribution, reversibility under physiological conditions, cofactors and prosthetic groups are summarized. In contrast to CO2, only 15 reaction classes involving CO were detected. Closer inspection reveals that CO interfaces with metabolism and the carbon cycle at only two enzymes: anaerobic carbon monoxide dehydrogenase (CODH), a Ni‐ and Fe‐containing enzyme that generates CO for CO2 fixation in the WL pathway, and aerobic CODH, a Mo‐ and Cu‐containing enzyme that oxidizes environmental CO as an electron source. The CO‐dependent reaction of the WL pathway involves carbonyl insertion into a methyl carbon‐nickel at the Ni‐Fe‐S A‐cluster of acetyl‐CoA synthase (ACS). It appears that no alternative mechanisms to the CO‐dependent reaction of ACS have evolved in nearly 4 billion years, indicating an ancient and mechanistically essential role for CO at the onset of metabolism.
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Affiliation(s)
- Joana C Xavier
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - Martina Preiner
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - William F Martin
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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Cerqueira T, Barroso C, Froufe H, Egas C, Bettencourt R. Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields. MICROBIAL ECOLOGY 2018; 76:387-403. [PMID: 29354879 DOI: 10.1007/s00248-018-1144-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/02/2018] [Indexed: 05/25/2023]
Abstract
The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.
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Affiliation(s)
- Teresa Cerqueira
- Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, 9901-862, Horta, Portugal.
- MARE - Marine and Environmental Sciences Centre, 9901-862, Horta, Portugal.
- OKEANOS Research Unit, Faculty of Science and Technology, University of the Azores, 9901-862, Horta, Portugal.
| | - Cristina Barroso
- Next Generation Sequencing Unit - UC-Biotech, Center for Neuroscience and Cell Biology, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Hugo Froufe
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit - UC-Biotech, Center for Neuroscience and Cell Biology, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Raul Bettencourt
- MARE - Marine and Environmental Sciences Centre, 9901-862, Horta, Portugal
- OKEANOS Research Unit, Faculty of Science and Technology, University of the Azores, 9901-862, Horta, Portugal
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Deeply-sourced formate fuels sulfate reducers but not methanogens at Lost City hydrothermal field. Sci Rep 2018; 8:755. [PMID: 29335466 PMCID: PMC5768773 DOI: 10.1038/s41598-017-19002-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 12/19/2017] [Indexed: 01/15/2023] Open
Abstract
Hydrogen produced during water-rock serpentinization reactions can drive the synthesis of organic compounds both biotically and abiotically. We investigated abiotic carbon production and microbial metabolic pathways at the high energy but low diversity serpentinite-hosted Lost City hydrothermal field. Compound-specific 14C data demonstrates that formate is mantle-derived and abiotic in some locations and has an additional, seawater-derived component in others. Lipids produced by the dominant member of the archaeal community, the Lost City Methanosarcinales, largely lack 14C, but metagenomic evidence suggests they cannot use formate for methanogenesis. Instead, sulfate-reducing bacteria may be the primary consumers of formate in Lost City chimneys. Paradoxically, the archaeal phylotype that numerically dominates the chimney microbial communities appears ill suited to live in pure hydrothermal fluids without the co-occurrence of organisms that can liberate CO2. Considering the lack of dissolved inorganic carbon in such systems, the ability to utilize formate may be a key trait for survival in pristine serpentinite-hosted environments.
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18
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Brewster ET, Pozo G, Batstone DJ, Freguia S, Ledezma P. A modelling approach to assess the long-term stability of a novel microbial/electrochemical system for the treatment of acid mine drainage. RSC Adv 2018; 8:18682-18689. [PMID: 35541131 PMCID: PMC9080545 DOI: 10.1039/c8ra03153c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/14/2018] [Indexed: 11/21/2022] Open
Abstract
Microbial electrochemical processes have potential to remediate acid mine drainage (AMD) wastewaters which are highly acidic and rich in sulfate and heavy metals, without the need for extensive chemical dosing. In this manuscript, a novel hybrid microbial/electrochemical remediation process which uses a 3-reactor system – a precipitation vessel, an electrochemical reactor and a microbial electrochemical reactor with a sulfate-reducing biocathode – was modelled. To evaluate the long-term operability of this system, a dynamic model for the fluxes of 140 different ionic species was developed and calibrated using laboratory-scale experimental data. The model identified that when the reactors are operating in the desired state, the coulombic efficiency of sulfate removal from AMD is high (91%). Modelling also identified that a periodic electrolyte purge is required to prevent the build-up of Cl− ions in the microbial electrochemical reactor. The model furthermore studied the fate of sulfate and carbon in the system. For sulfate, it was found that only 29% can be converted into elemental sulfur, with the rest complexating with metals in the precipitation vessel. Finally, the model shows that the flux of inorganic carbon under the current operational strategy is insufficient to maintain the autotrophic sulfate-reducing biomass. The modelling approach demonstrates that a change in system operational strategies plus close monitoring of overlooked ionic species (such as Cl− and HCO3−) are key towards the scaling-up of this technology. Microbial electrochemical processes have potential to remediate acid mine drainage (AMD) wastewaters which are highly acidic and rich in sulfate and heavy metals, without the need for extensive chemical dosing.![]()
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Affiliation(s)
| | - Guillermo Pozo
- Advanced Water Management Centre
- The University of Queensland
- Australia
| | | | - Stefano Freguia
- Advanced Water Management Centre
- The University of Queensland
- Australia
| | - Pablo Ledezma
- Advanced Water Management Centre
- The University of Queensland
- Australia
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19
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Davidova IA, Wawrik B, Callaghan AV, Duncan K, Marks CR, Suflita JM. Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae. Int J Syst Evol Microbiol 2015; 66:1242-1248. [PMID: 26704417 DOI: 10.1099/ijsem.0.000864] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic deltaproteobacterium, designated strain SPRT, was isolated from a methanogenic consortium capable of degrading long-chain paraffins. Cells were motile, vibrio-shaped, and occurred singly, in pairs or in clusters. Strain SPRT did not metabolize hydrocarbons but grew fermentatively on pyruvate and oxaloacetate and autotrophically with H2 and CO2. Thiosulfate served as a terminal electron acceptor, but sulfate or sulfite did not. The organism required at least 10 g NaCl l- 1 and a small amount of yeast extract (0.001%) for growth. Optimal growth was observed between 30 and 37 °C and a pH range from 6.0 to 7.2. The DNA G+C content of SPRT's genome was 52.02 mol%. Based on 16S rRNA gene sequence analysis, strain SPRT was distinct from previously described Deltaproteobacteria, exhibiting the closest affiliation to Desulfarculus baarsii DSM 2075T and Desulfocarbo indianensis SCBMT, with only 91% similarity between their respective 16S gene sequences. In silico genome comparison supported the distinctiveness between strain SPRT and both Desulfocarbo indianensis SCBMT and Desulfarculus baarsii DSM 2075T. Based on physiological differences, as well as phylogenetic and genomic comparisons, we propose to classify SPRT as the type strain ( = DSM 100305T = JCM 30857T) of a novel species of a new genus with the name Dethiosulfatarculus sandiegensis gen. nov., sp. nov.
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Affiliation(s)
- Irene A Davidova
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA.,Institute for Energy and the Environment, The University of Oklahoma, 100 East Boyd Street, Room 1510, Norman, OK 73019-1015, USA
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA
| | - Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA
| | - Kathleen Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA.,Institute for Energy and the Environment, The University of Oklahoma, 100 East Boyd Street, Room 1510, Norman, OK 73019-1015, USA
| | - Christopher R Marks
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA.,Institute for Energy and the Environment, The University of Oklahoma, 100 East Boyd Street, Room 1510, Norman, OK 73019-1015, USA
| | - Joseph M Suflita
- Department of Microbiology and Plant Biology, University of Oklahoma, George Lynn Cross Hall, 770 Van Vleet Oval, Norman, OK 73019, USA.,Institute for Energy and the Environment, The University of Oklahoma, 100 East Boyd Street, Room 1510, Norman, OK 73019-1015, USA
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20
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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21
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Hao TW, Xiang PY, Mackey HR, Chi K, Lu H, Chui HK, van Loosdrecht MCM, Chen GH. A review of biological sulfate conversions in wastewater treatment. WATER RESEARCH 2014; 65:1-21. [PMID: 25086411 DOI: 10.1016/j.watres.2014.06.043] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/26/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Treatment of waters contaminated with sulfur containing compounds (S) resulting from seawater intrusion, the use of seawater (e.g. seawater flushing, cooling) and industrial processes has become a challenging issue since around two thirds of the world's population live within 150 km of the coast. In the past, research has produced a number of bioengineered systems for remediation of industrial sulfate containing sewage and sulfur contaminated groundwater utilizing sulfate reducing bacteria (SRB). The majority of these studies are specific with SRB only or focusing on the microbiology rather than the engineered application. In this review, existing sulfate based biotechnologies and new approaches for sulfate contaminated waters treatment are discussed. The sulfur cycle connects with carbon, nitrogen and phosphorus cycles, thus a new platform of sulfur based biotechnologies incorporating sulfur cycle with other cycles can be developed, for the removal of sulfate and other pollutants (e.g. carbon, nitrogen, phosphorus and metal) from wastewaters. All possible electron donors for sulfate reduction are summarized for further understanding of the S related biotechnologies including rates and benefits/drawbacks of each electron donor. A review of known SRB and their environmental preferences with regard to bioreactor operational parameters (e.g. pH, temperature, salinity etc.) shed light on the optimization of sulfur conversion-based biotechnologies. This review not only summarizes information from the current sulfur conversion-based biotechnologies for further optimization and understanding, but also offers new directions for sulfur related biotechnology development.
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Affiliation(s)
- Tian-wei Hao
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peng-yu Xiang
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hamish R Mackey
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Kun Chi
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hui Lu
- SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China
| | - Ho-kwong Chui
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China.
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22
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An TT, Picardal FW. Desulfocarbo indianensis gen. nov., sp. nov., a benzoate-oxidizing, sulfate-reducing bacterium isolated from water extracted from a coal bed. Int J Syst Evol Microbiol 2014; 64:2907-2914. [PMID: 24876241 DOI: 10.1099/ijs.0.064873-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A novel, strictly anaerobic, sulfate-reducing bacterium, designated strain SCBM(T), was isolated from water extracted from a coal bed in Indiana, USA. The isolate was characterized by a polyphasic taxonomic approach that included phenotypic and genotypic characterizations. Cells of strain SCBM(T) were vibrio-shaped, polarly flagellated, Gram-negative, motile, oxidase-negative and weakly catalase-positive. Growth of strain SCBM(T) was observed at NaCl concentrations ranging from 0 to 300 mM. However, no growth was observed when 1 M or more NaCl was present. Growth was observed at 16-37 °C, with optimal growth at 30 °C. The optimum pH for growth was 7, although growth was observed from pH 6.5 to 8. The doubling time under optimal growth conditions (30 °C, pH 7, 2.5 mM benzoate, 14 mM sulfate) was 2.7 days. Bicarbonate, HEPES, PIPES and MES were effective buffers for growth of strain SCBM(T), but citrate inhibited growth. When sulfate was provided as the electron acceptor, strain SCBM(T) grew autotrophically with hydrogen as the electron donor and heterotrophically on benzoate, formate, acetate, pyruvate, butyrate, fumarate, succinate and palmitate. None of the substrates tested supported fermentative growth. Thiosulfate and sulfate were used as electron acceptors coupled to benzoate oxidation, but sulfite, elemental sulfur, DMSO, anthraquinone 2,6-disulfonate, nitrate, nitrite, ferric citrate, hydrous iron oxide and oxygen were not. The G+C content of genomic DNA was 62.5 mol%. The major cellular fatty acids were anteiso-C(15 : 0) and C(18 : 1)ω7c. Phylogenetic analysis based on 16S rRNA gene sequencing placed strain SCBM(T) into a distinct lineage within the class Deltaproteobacteria. The closest, cultivated phylogenetic relative of strain SCBM(T) was Desulfarculus baarsii DSM 2075(T), with only 91.7% 16S rRNA gene sequence identity. On the basis of phenotypic and genotypic analyses, strain SCBM(T) represents a novel genus and species of sulfate-reducing bacteria, for which the name Desulfocarbo indianensis gen. nov., sp. nov. is proposed. The type strain of Desulfocarbo indianensis is SCBM(T) ( = DSM 28127(T) = JCM 19826(T)). Desulfocarbo is the second genus of the order Desulfarculales.
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Affiliation(s)
- Thuy T An
- School of Public and Environmental Affairs, Indiana University, MSBII, 702 N. Walnut Grove Ave, Bloomington, IN 47405-2204, USA
| | - Flynn W Picardal
- School of Public and Environmental Affairs, Indiana University, MSBII, 702 N. Walnut Grove Ave, Bloomington, IN 47405-2204, USA
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23
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Glass JB, Yu H, Steele JA, Dawson KS, Sun S, Chourey K, Pan C, Hettich RL, Orphan VJ. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments. Environ Microbiol 2013; 16:1592-611. [DOI: 10.1111/1462-2920.12314] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 10/13/2013] [Indexed: 01/17/2023]
Affiliation(s)
- Jennifer B. Glass
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
| | - Hang Yu
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
| | - Joshua A. Steele
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
| | - Katherine S. Dawson
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
| | - Shulei Sun
- The CAMERA Project; University of California San Diego; San Diego CA 92093 USA
| | - Karuna Chourey
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Chongle Pan
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Robert L. Hettich
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge TN 37831 USA
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences; California Institute of Technology; Pasadena CA 91125 USA
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24
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Bar-Even A, Noor E, Flamholz A, Milo R. Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:1039-47. [PMID: 23123556 DOI: 10.1016/j.bbabio.2012.10.013] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/05/2012] [Accepted: 10/25/2012] [Indexed: 11/29/2022]
Abstract
Electrosynthesis is a promising approach that enables the biological production of commodities, like fuels and fine chemicals, using renewably produced electricity. Several techniques have been proposed to mediate the transfer of electrons from the cathode to living cells. Of these, the electroproduction of formate as a mediator seems especially promising: formate is readily soluble, of low toxicity and can be produced at relatively high efficiency and at reasonable current density. While organisms that are capable of formatotrophic growth, i.e. growth on formate, exist naturally, they are generally less suitable for bulk cultivation and industrial needs. Hence, it may be helpful to engineer a model organism of industrial relevance, such as E. coli, for growth on formate. There are numerous metabolic pathways that can potentially support formatotrophic growth. Here we analyze these diverse pathways according to various criteria including biomass yield, thermodynamic favorability, chemical motive force, kinetics and the practical challenges posed by their expression. We find that the reductive glycine pathway, composed of the tetrahydrofolate system, the glycine cleavage system, serine hydroxymethyltransferase and serine deaminase, is a promising candidate to support electrosynthesis in E. coli. The approach presented here exemplifies how combining different computational approaches into a systematic analysis methodology provides assistance in redesigning metabolism. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Arren Bar-Even
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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25
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Hügler M, Sievert SM. Beyond the Calvin cycle: autotrophic carbon fixation in the ocean. ANNUAL REVIEW OF MARINE SCIENCE 2011; 3:261-89. [PMID: 21329206 DOI: 10.1146/annurev-marine-120709-142712] [Citation(s) in RCA: 329] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Organisms capable of autotrophic metabolism assimilate inorganic carbon into organic carbon. They form an integral part of ecosystems by making an otherwise unavailable form of carbon available to other organisms, a central component of the global carbon cycle. For many years, the doctrine prevailed that the Calvin-Benson-Bassham (CBB) cycle is the only biochemical autotrophic CO2 fixation pathway of significance in the ocean. However, ecological, biochemical, and genomic studies carried out over the last decade have not only elucidated new pathways but also shown that autotrophic carbon fixation via pathways other than the CBB cycle can be significant. This has ramifications for our understanding of the carbon cycle and energy flow in the ocean. Here, we review the recent discoveries in the field of autotrophic carbon fixation, including the biochemistry and evolution of the different pathways, as well as their ecological relevance in various oceanic ecosystems.
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Affiliation(s)
- Michael Hügler
- Microbiology Department, Water Technology Center, 76139 Karlsruhe, Germany.
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26
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Sun H, Spring S, Lapidus A, Davenport K, Del Rio TG, Tice H, Nolan M, Copeland A, Cheng JF, Lucas S, Tapia R, Goodwin L, Pitluck S, Ivanova N, Pagani I, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Hauser L, Chang YJ, Jeffries CD, Detter JC, Han C, Rohde M, Brambilla E, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Land M. Complete genome sequence of Desulfarculus baarsii type strain (2st14). Stand Genomic Sci 2010; 3:276-84. [PMID: 21304732 PMCID: PMC3035298 DOI: 10.4056/sigs.1243258] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the genus Desulfarculus, which represents the family Desulfarculaceae and the order Desulfarculales. This species is a mesophilic sulfate-reducing bacterium with the capability to oxidize acetate and fatty acids of up to 18 carbon atoms completely to CO(2). The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is used by this species for the complete oxidation of carbon sources and autotrophic growth on formate. The type strain 2st14(T) was isolated from a ditch sediment collected near the University of Konstanz, Germany. This is the first completed genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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27
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Carbon monoxide as an electron donor for the biological reduction of sulphate. Int J Microbiol 2010; 2010:319527. [PMID: 20628586 PMCID: PMC2901600 DOI: 10.1155/2010/319527] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 03/10/2010] [Accepted: 03/31/2010] [Indexed: 11/17/2022] Open
Abstract
Several strains of Gram-negative and Gram-positive sulphate-reducing bacteria (SRB) are able to use carbon monoxide (CO) as a carbon source and electron donor for biological sulphate reduction. These strains exhibit variable resistance to CO toxicity. The most resistant SRB can grow and use CO as an electron donor at concentrations up to 100%, whereas others are already severely inhibited at CO concentrations as low as 1-2%. Here, the utilization, inhibition characteristics, and enzymology of CO metabolism as well as the current state of genomics of CO-oxidizing SRB are reviewed. Carboxydotrophic sulphate-reducing bacteria can be applied for biological sulphate reduction with synthesis gas (a mixture of hydrogen and carbon monoxide) as an electron donor.
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28
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Sipma J, Henstra AM, Parshina SM, Lens PN, Lettinga G, Stams AJM. Microbial CO conversions with applications in synthesis gas purification and bio-desulfurization. Crit Rev Biotechnol 2006; 26:41-65. [PMID: 16594524 DOI: 10.1080/07388550500513974] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Recent advances in the field of microbial physiology demonstrate that carbon monoxide is a readily used substrate by a wide variety of anaerobic micro-organisms, and may be employed in novel biotechnological processes for production of bulk and fine chemicals or in biological treatment of waste streams. Synthesis gas produced from fossil fuels or biomass is rich in hydrogen and carbon monoxide. Conversion of carbon monoxide to hydrogen allows use of synthesis gas in existing hydrogen utilizing processes and is interesting in view of a transition from hydrogen production from fossil fuels to sustainable (CO2-neutral) biomass. The conversion of CO with H2O to CO2 and H2 is catalyzed by a rapidly increasing group of micro-organisms. Hydrogen is a preferred electron donor in biotechnological desulfurization ofwastewaters and flue gases. Additionally, CO is a good alternative electron donor considering the recent isolation of a CO oxidizing, sulfate reducing bacterium. Here we review CO utilization by various anaerobic micro-organisms and their possible role in biotechnological processes, with a focus on hydrogen production and bio-desulfurization.
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Affiliation(s)
- Jan Sipma
- Sub-department of Environmental Technology, Wageningen University, Wageningen, The Netherlands
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29
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Lovell CR, Leaphart AB. Community-level analysis: key genes of CO2-reductive acetogenesis. Methods Enzymol 2005; 397:454-69. [PMID: 16260309 DOI: 10.1016/s0076-6879(05)97028-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
CO2-reductive acetogenic bacteria are ubiquitous in anaerobic habitats and are physiologically and phylogenetically diverse. The latter characteristics have rendered their diversity in natural environments, their distributions, and their ecological function(s) difficult to assess. Recently introduced polymerase chain reaction (PCR) primers for specific amplification of the structural gene encoding formyltetrahydrofolate synthetase (FTHFS, EC 6.3.4.3), a key enzyme in the acetyl-CoA pathway of acetogenesis, have facilitated studies of acetogen diversity and ecology. These primers amplify an approximately 1100-bp segment of the FTHFS gene. FTHFS sequences have been recovered from authentic acetogens, from sulfate reducing bacteria, and from a variety of other nonacetogenic bacteria. Phylogenetic analyses segregated these sequences into distinct clusters, only one of which contained sequences from known acetogens. This chapter describes the PCR primers, defines conditions for successful amplification of FTHFS sequences, and details the phylogenetic analysis of the FTHFS sequences. Information on the types of sequences that have been recovered from natural acetogen habitats and how they have been interpreted is also included.
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Affiliation(s)
- Charles R Lovell
- Department of Biological Sciences, University of South Carolina, Columbia 29208, USA
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30
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Lovell CR. Belowground interactions among salt marsh plants and microorganisms. COASTAL AND ESTUARINE STUDIES 2005. [DOI: 10.1029/ce060p0061] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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31
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Leaphart AB, Friez MJ, Lovell CR. Formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups. Appl Environ Microbiol 2003; 69:693-6. [PMID: 12514064 PMCID: PMC152474 DOI: 10.1128/aem.69.1.693-696.2003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sixty-two partial formyltetrahydrofolate synthetase (FTHFS) structural gene sequences were recovered from roots of salt marsh plants, including Spartina alterniflora, Salicornia virginica, and Juncus roemerianus. Only S. alterniflora roots yielded sequences grouping with FTHFS sequences from known acetogens. Most other FTHFS or FTHFS-like sequences grouped with those from sulfate-reducing bacteria. Several sequences that grouped with Sphingomonas paucimobilis ligH were also recovered.
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Affiliation(s)
- A B Leaphart
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA
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32
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Louie TM, Mohn WW. Evidence for a chemiosmotic model of dehalorespiration in Desulfomonile tiedjei DCB-1. J Bacteriol 1999; 181:40-6. [PMID: 9864310 PMCID: PMC103529 DOI: 10.1128/jb.181.1.40-46.1999] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/1998] [Accepted: 10/19/1998] [Indexed: 11/20/2022] Open
Abstract
Desulfomonile tiedjei DCB-1, a sulfate-reducing bacterium, conserves energy for growth from reductive dehalogenation of 3-chlorobenzoate by an uncharacterized chemiosmotic process. Respiratory electron transport components were examined in D. tiedjei cells grown under conditions for reductive dehalogenation, pyruvate fermentation, and sulfate reduction. Reductive dehalogenation was inhibited by the respiratory quinone inhibitor 2-heptyl-4-hydroxyquinoline N-oxide, suggesting that a respiratory quinoid is a component of the electron transport chain coupled to reductive dehalogenation. Moreover, reductive dehalogenation activity was dependent on 1, 4-naphthoquinone, a possible precursor for a respiratory quinoid. However, no ubiquinone or menaquinone could be extracted from D. tiedjei. Rather, a UV-absorbing quinoid which is different from common respiratory quinones in chemical structure according to mass spectrometric and UV absorption spectroscopic analyses was extracted. ATP sulfurylase, adenosine phosphosulfate reductase, and desulfoviridin sulfite reductase, enzymes involved in sulfate reduction, were constitutively expressed in the cytoplasm of D. tiedjei cells grown under all three metabolic conditions. A periplasmic hydrogenase was detected in cells grown under reductive-dehalogenating and pyruvate-fermenting conditions. A membrane-bound, periplasm-oriented formate dehydrogenase was detected only in cells grown with formate as electron donor, while a cytoplasmic formate dehydrogenase was detected in cells grown under reductive-dehalogenating and pyruvate-fermenting conditions. Results from dehalogenation assays with D. tiedjei whole-cell suspensions and cell extracts suggest that the membrane-bound reductive dehalogenase is cytoplasm oriented. The data clearly demonstrate an enzyme topology in D. tiedjei which produces protons directly in the periplasm, generating a proton motive force by a scalar mechanism.
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Affiliation(s)
- T M Louie
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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33
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Pianzzola MJ, Soubes M, Touati D. Overproduction of the rbo gene product from Desulfovibrio species suppresses all deleterious effects of lack of superoxide dismutase in Escherichia coli. J Bacteriol 1996; 178:6736-42. [PMID: 8955290 PMCID: PMC178569 DOI: 10.1128/jb.178.23.6736-6742.1996] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In an attempt to isolate the superoxide dismutase (SOD) gene from the anaerobic sulfate-reducing bacterium Desulfoarculus baarsii, a DNA fragment was isolated which functionally complemented an Escherichia coli mutant (sodA sodB) deficient in cytoplasmic SODs. This region carries two open reading frames with sequences which are very similar to that of the rbo-rub operon from Desulfovibrio vulgaris. Independent expression of the rbo and rub genes from ptac showed that expression of rbo was responsible for the observed phenotype. rbo overexpression suppressed all deleterious effects of SOD deficiency in E. coli, including inactivation by superoxide of enzymes containing 4Fe-4S clusters and DNA damage produced via the superoxide-enhanced Fenton reaction. Thus, rbo restored to the sodA sodB mutant the ability to grow on minimal medium without the addition of branched amino acids, and growth on gluconate and succinate carbon sources was no longer impaired. The spontaneous mutation rate, which is elevated in SOD-deficient mutants, returned to the wild-type level in the presence of Rbo, which also restored aerobic viability of sodA sodB recA mutants. Rbo from Desulfovibrio vulgaris, but not Desulfovibrio gigas desulforedoxin, which corresponds to the NH2-terminal domain of Rbo, complemented sod mutants. The physiological role of Rbo in sulfate-reducing bacteria is unknown. In E. coli, Rbo may permit the bacterium to avoid superoxide stress by maintaining functional (reduced) superoxide sensitive 4Fe-4S clusters. It would thereby restore enzyme activities and prevent the release of iron that occurs after cluster degradation and presumably leads to DNA damage.
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Affiliation(s)
- M J Pianzzola
- Facultad de Quimica, Catedra de Microbiologia, Montevideo, Uruguay
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Hanselmann K, Kaiser J, Wenk M, Schön R, Bachofen R. Growth on methanol and conversion of methoxylated aromatic substrates by Desulfotomaculum orientis in the presence and absence of sulfate. Microbiol Res 1995. [DOI: 10.1016/s0944-5013(11)80021-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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35
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Colleran E, Finnegan S, Lens P. Anaerobic treatment of sulphate-containing waste streams. Antonie Van Leeuwenhoek 1995; 67:29-46. [PMID: 7741527 DOI: 10.1007/bf00872194] [Citation(s) in RCA: 179] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Sulphate-containing wastewaters from the paper and board industry, molasses-based fermentation industries and edible oil refineries present difficulties during anaerobic treatment, leading to problems of toxicity, reduction in methane yield, odour and corrosion. The microbiology and biochemistry of dissimilatory sulphate reduction are reviewed in order to illustrate the potential competition between sulphate reducers and other anaerobes involved in the sequential anaerobic mineralisation process. The theoretical considerations which influence the outcome of competition between sulphate reducers and fermentative, syntrophic, homoacetogenic and methanogenic bacteria are discussed. The actual outcome, under the varying influent organic composition and strength and sulfate concentrations which prevail during digestion of industrial wastewaters, may be quite different to that predicted by thermodynamic or kinetic considerations. The factors governing competitive interactions between SRB and other anaerobes involved in methanogenesis is discussed in the context of literature data on sulphate wastewater treatment and with particular reference to laboratory and full-scale digestion of citric acid production wastewater.
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Affiliation(s)
- E Colleran
- Department of Microbiology, University College, Galway, Ireland
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36
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Choi SC, Chase T, Bartha R. Metabolic Pathways Leading to Mercury Methylation in
Desulfovibrio desulfuricans
LS. Appl Environ Microbiol 1994; 60:4072-7. [PMID: 16349435 PMCID: PMC201938 DOI: 10.1128/aem.60.11.4072-4077.1994] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The synthesis of methylmercury by
Desulfovibrio desulfuricans
LS was investigated on the basis of
14
C incorporation from precursors and the measurement of relevant enzyme activities in cell extracts. The previously observed incorporation of C-3 from serine into methylmercury was confirmed by measurement of relatively high activities of serine hydroxymethyltransferase and other enzymes of this pathway. High rates of label incorporation into methylmercury from H
14
COO
-
and H
14
CO
3
-
prompted the assay of enzymes of the acetyl coenzyme A (CoA) synthase pathway. These enzymes were found to be present but at activity levels much lower than those reported for acetogens. Propyl iodide inhibited methylmercury and acetyl-CoA syntheses to similar extents, and methylmercury synthesis was found to compete with acetyl-CoA synthesis for methyl groups. On the basis of these findings, we propose that in methylmercury synthesis by
D. desulfuricans
LS the methyl group is transferred from CH
3
-tetrahydrofolate via methylcobalamin. The methyl group may originate from C-3 of serine or from formate via the acetyl-CoA synthase pathway. These pathways are not unique to
D. desulfuricans
LS, and thus the ability of this bacterium to methylate mercury is most likely associated with the substrate specificity of its enzymes.
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Affiliation(s)
- S C Choi
- Department of Biochemistry and Microbiology, Cook College, Rutgers University, New Brunswick, New Jersey 08903-0231
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37
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Ensign S, Ludden P. Characterization of the CO oxidation/H2 evolution system of Rhodospirillum rubrum. Role of a 22-kDa iron-sulfur protein in mediating electron transfer between carbon monoxide dehydrogenase and hydrogenase. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)55283-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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38
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Philp JC, Taylor KJ, Christofi N. Consequences of sulphate-reducing bacterial growth in a lab-simulated waste disposal regime. ACTA ACUST UNITED AC 1991. [DOI: 10.1007/bf01949877] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
In anaerobic ecosystems, acyl lipids are initially hydrolyzed by microbial lipases with the release of free fatty acids. Glycerol, galactose, choline, and other non-fatty acid components released during hydrolysis are fermented to volatile fatty acids by the fermentative bacteria. Fatty acids are not degraded further in the rumen or other parts of the digestive tract but are subjected to extensive biohydrogenation especially in the rumen. However, in environments such as sediments and waste digestors, which have long retention times, both long and short chain fatty acids are beta-oxidized to acetate by a special group of bacteria, the H2-producing syntrophs. Long chain fatty acids can also be degraded by alpha-oxidation. Biotransformation of bile acids, cholesterol, and steroids by intestinal microorganisms is extensive. Many rumen bacteria have specific growth requirements for fatty acids such as n-valeric, iso-valeric, 2-methylbutyric, and iso-butyric acids. Some species have requirements for C13 to C18 straight-chain saturated or monoenoic fatty acids for growth.
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Affiliation(s)
- R I Mackie
- Department of Animal Sciences, University of Illinois, Urbana-Champaign 61801
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40
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Gibson GR. Physiology and ecology of the sulphate-reducing bacteria. THE JOURNAL OF APPLIED BACTERIOLOGY 1990; 69:769-97. [PMID: 2286579 DOI: 10.1111/j.1365-2672.1990.tb01575.x] [Citation(s) in RCA: 151] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- G R Gibson
- Medical Research Council, Dunn Clinical Nutrition Centre, Cambridge, UK
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41
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Oxidative and reductive acetyl CoA/carbon monoxide dehydrogenase pathway in Desulfobacterium autotrophicum. Arch Microbiol 1988. [DOI: 10.1007/bf00444673] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Oxidative and reductive acetyl CoA/carbon monoxide dehydrogenase pathway in Desulfobacterium autotrophicum. Arch Microbiol 1988. [DOI: 10.1007/bf00444674] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Acetyl-CoA pathway of autotrophic growth. Identification of the methyl-binding site of the CO dehydrogenase. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)37548-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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44
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Thauer RK. Citric-acid cycle, 50 years on. Modifications and an alternative pathway in anaerobic bacteria. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 176:497-508. [PMID: 3049083 DOI: 10.1111/j.1432-1033.1988.tb14307.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Many anaerobic bacteria can completely oxidize organic matter to CO2 with either sulfur, sulfate, or protons as electron acceptor. The sulfur-reducing bacteria and one genus of sulfate reducers use a modified citric-acid cycle with a novel anaplerotic sequence as pathway of terminal respiration. All other anaerobes use an alternative pathway, in which carbon monoxide dehydrogenase is a key enzyme and in which acetyl-CoA is cleaved into two C1 units at the oxidation level of CH3OH and CO. Thus almost 50 years after the discovery of the citric acid cycle by Hans Krebs in 1937, a second pathway for acetyl-CoA oxidation was found.
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Affiliation(s)
- R K Thauer
- Laboratorium für Mikrobiologie, Philipps-Universität, Marburg, Federal Republic of Germany
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Abstract
To detect autotrophic CO2 assimilation in cell extracts of Methanococcus maripaludis, lactate dehydrogenase and NADH were added to convert pyruvate formed from autotrophically synthesized acetyl coenzyme A to lactate. The lactate produced was determined spectrophotometrically. When CO2 fixation was pulled in the direction of lactate synthesis, CO2 reduction to methane was inhibited. Bromoethanesulfonate (BES), a potent inhibitor of methanogenesis, enhanced lactate synthesis, and methyl coenzyme M inhibited it in the absence of BES. Lactate synthesis was dependent on CO2 and H2, but H2 + CO2-independent synthesis was also observed. In cell extracts, the rate of lactate synthesis was about 1.2 nmol min-1 mg of protein-1. When BES was added, the rate of lactate synthesis increased to 2.3 nmol min-1 mg of protein-1. Because acetyl coenzyme A did not stimulate lactate synthesis, pyruvate synthase may have been the limiting activity in these assays. Radiolabel from 14CO2 was incorporated into lactate. The percentages of radiolabel in the C-1, C-2, and C-3 positions of lactate were 73, 33, and 11%, respectively. Both carbon monoxide and formaldehyde stimulated lactate synthesis. 14CH2O was specifically incorporated into the C-3 of lactate, and 14CO was incorporated into the C-1 and C-2 positions. Low concentrations of cyanide also inhibited autotrophic growth, CO dehydrogenase activity, and autotrophic lactate synthesis. These observations are in agreement with the acetogenic pathway of autotrophic CO2 assimilation.
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Affiliation(s)
- J Shieh
- Department of Microbiology, University of Georgia, Athens 30602
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47
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48
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Lithoautotrophic growth of sulfate-reducing bacteria, and description of Desulfobacterium autotrophicum gen. nov., sp. nov. Arch Microbiol 1987. [DOI: 10.1007/bf00456703] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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49
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Schauder R, Widdel F, Fuchs G. Carbon assimilation pathways in sulfate-reducing bacteria II. Enzymes of a reductive citric acid cycle in the autotrophic Desulfobacter hydrogenophilus. Arch Microbiol 1987. [DOI: 10.1007/bf00414815] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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50
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Blair NE, Martens CS, Des Marais DJ. Natural abundances of carbon isotopes in acetate from a coastal marine sediment. Science 1987; 236:66-8. [PMID: 11539717 DOI: 10.1126/science.11539717] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Measurements of the natural abundances of carbon isotopes were made in acetate samples isolated from the anoxic marine sediment of Cape Lookout Bight, North Carolina. The typical value of the total acetate carbon isotope ratio (delta 13C) was -16.1 +/- 0.2 per mil. The methyl and carboxyl groups were determined to be -26.4 +/- 0.3 and -6.0 +/- 0.3 per mil, respectively, for one sample. The isotopic composition of the acetate is thought to have resulted from isotopic discriminations that occurred during the cycling of that molecule. Measurements of this type, which have not been made previously in the natural environment, may provide information about the dominant microbial pathways in anoxic sediments as well as the processes that influence the carbon isotopic composition of biogenic methane from many sources.
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Affiliation(s)
- N E Blair
- Department of Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh 27695, USA
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