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Zhan M, Zeng W, Wu C, Chen G, Meng Q, Hao X, Peng Y. Impact of organic carbon on sulfide-driven autotrophic denitrification: Insights from isotope fractionation and functional genes. WATER RESEARCH 2024; 255:121507. [PMID: 38537490 DOI: 10.1016/j.watres.2024.121507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/15/2024] [Accepted: 03/22/2024] [Indexed: 04/24/2024]
Abstract
Additional organics are generally supplemented in the sulfide-driven autotrophic denitrification system to accelerate the denitrification rate and reduce sulfate production. In this study, different concentrations of sodium acetate (NaAc) were added to the sulfide-driven autotrophic denitrification reactor, and the S0 accumulation increased from 7.8% to 100% over a 120-day operation period. Batch experiments revealed a threefold increase in total nitrogen (TN) removal rate at an Ac--C/N ratio of 2.8 compared to a ratio of 0.5. Addition of organic carbon accelerated denitrification rate and nitrite consumption, which shortened the emission time of N2O, but increased the N2O production rate. The lowest N2O emissions were achieved at the Ac--C/N ratio of 1.3. Stable isotope fractionation is a powerful tool for evaluating different reaction pathways, with the 18ε/15ε values in nitrate reduction ranging from 0.5 to 1.0. This study further confirmed that isotope fractionation can reveal denitrifying nutrient types, with the 18ε (isotopic enrichment factor of oxygen)/15ε (isotopic enrichment factor of nitrogen) value approaching 1.0 for autotrophic denitrification and 0.5 for heterotrophic denitrification. Additionally, the 18ε/15ε values can indicate changes in nitrate reductase. There is a positive correlation between the 18ε/15ε values and the abundance of the functional gene napA, and a negative correlation with the abundance of the gene narG. Moreover, 18ε and 15ε were associated with changes in kinetic parameters during nitrate reduction. In summary, the combination of functional gene analysis and isotope fractionation effectively revealed the complexities of mixotrophic denitrification systems, providing insights for optimizing denitrification processes.
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Affiliation(s)
- Mengjia Zhan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Wei Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China.
| | - Congcong Wu
- Technology R&D Center of Beijing Drainage Group Co.,Ltd, Beijing 100124, China
| | - Gangxin Chen
- Technology R&D Center of Beijing Drainage Group Co.,Ltd, Beijing 100124, China
| | - Qingan Meng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Xiaojing Hao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing 100124, China
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Leavitt WD, Waldbauer J, Venceslau SS, Sim MS, Zhang L, Boidi FJ, Plummer S, Diaz JM, Pereira IAC, Bradley AS. Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles in Desulfovibrio vulgaris. GEOBIOLOGY 2024; 22:e12600. [PMID: 38725144 DOI: 10.1111/gbi.12600] [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: 08/23/2023] [Revised: 01/31/2024] [Accepted: 04/18/2024] [Indexed: 07/12/2024]
Abstract
Microbial sulfate reduction is central to the global carbon cycle and the redox evolution of Earth's surface. Tracking the activity of sulfate reducing microorganisms over space and time relies on a nuanced understanding of stable sulfur isotope fractionation in the context of the biochemical machinery of the metabolism. Here, we link the magnitude of stable sulfur isotopic fractionation to proteomic and metabolite profiles under different cellular energetic regimes. When energy availability is limited, cell-specific sulfate respiration rates and net sulfur isotope fractionation inversely covary. Beyond net S isotope fractionation values, we also quantified shifts in protein expression, abundances and isotopic composition of intracellular S metabolites, and lipid structures and lipid/water H isotope fractionation values. These coupled approaches reveal which protein abundances shift directly as a function of energy flux, those that vary minimally, and those that may vary independent of energy flux and likely do not contribute to shifts in S-isotope fractionation. By coupling the bulk S-isotope observations with quantitative proteomics, we provide novel constraints for metabolic isotope models. Together, these results lay the foundation for more predictive metabolic fractionation models, alongside interpretations of environmental sulfur and sulfate reducer lipid-H isotope data.
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Affiliation(s)
- William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Min Sub Sim
- School of Earth and Environmental Sciences, Seoul National University, Seoul, South Korea
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Flavia Jaquelina Boidi
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
- Centro de Investigaciones en Ciencias de la Tierra (CICTERRA), CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Sydney Plummer
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Julia M Diaz
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missouri, USA
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Pellerin A, Antler G, Marietou A, Turchyn AV, Jørgensen BB. The effect of temperature on sulfur and oxygen isotope fractionation by sulfate reducing bacteria (Desulfococcus multivorans). FEMS Microbiol Lett 2020; 367:5817845. [PMID: 32267916 DOI: 10.1093/femsle/fnaa061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 04/04/2020] [Indexed: 11/14/2022] Open
Abstract
Temperature influences microbiological growth and catabolic rates. Between 15 and 35 °C the growth rate and cell specific sulfate reduction rate of the sulfate reducing bacterium Desulfococcus multivorans increased with temperature. Sulfur isotope fractionation during sulfate reduction decreased with increasing temperature from 27.2 ‰ at 15 °C to 18.8 ‰ at 35 °C which is consistent with a decreasing reversibility of the metabolic pathway as the catabolic rate increases. Oxygen isotope fractionation, in contrast, decreased between 15 and 25 °C and then increased again between 25 and 35 °C, suggesting increasing reversibility in the first steps of the sulfate reducing pathway at higher temperatures. This points to a decoupling in the reversibility of sulfate reduction between the steps from the uptake of sulfate into the cell to the formation of sulfite, relative to the whole pathway from sulfate to sulfide. This observation is consistent with observations of increasing sulfur isotope fractionation when sulfate reducing bacteria are living near their upper temperature limit. The oxygen isotope decoupling may be a first signal of changing physiology as the bacteria cope with higher temperatures.
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Affiliation(s)
- André Pellerin
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark.,Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, P. O. Box 653, Beer-Sheva 84105, Israel
| | - Gilad Antler
- Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, P. O. Box 653, Beer-Sheva 84105, Israel.,The Interuniversity Institute for Marine Sciences of Eilat, PO Box 469, Eilat 88103, Israel
| | - Angeliki Marietou
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark
| | - Alexandra V Turchyn
- Cambridge University, Downing Street, Cambridge, CB2 3EQ, Departement of Earth Sciences, Cambridge, UK
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Ny Munkegade 116, Aarhus C 8000, Aarhus University, Department of Bioscience, Denmark
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Pellerin A, Antler G, Holm SA, Findlay AJ, Crockford PW, Turchyn AV, Jørgensen BB, Finster K. Large sulfur isotope fractionation by bacterial sulfide oxidation. SCIENCE ADVANCES 2019; 5:eaaw1480. [PMID: 31355330 PMCID: PMC6656534 DOI: 10.1126/sciadv.aaw1480] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/17/2019] [Indexed: 05/12/2023]
Abstract
A sulfide-oxidizing microorganism, Desulfurivibrio alkaliphilus (DA), generates a consistent enrichment of sulfur-34 (34 S) in the produced sulfate of +12.5 per mil or greater. This observation challenges the general consensus that the microbial oxidation of sulfide does not result in large 34 S enrichments and suggests that sedimentary sulfides and sulfates may be influenced by metabolic activity associated with sulfide oxidation. Since the DA-type sulfide oxidation pathway is ubiquitous in sediments, in the modern environment, and throughout Earth history, the enrichments and depletions in 34 S in sediments may be the combined result of three microbial metabolisms: microbial sulfate reduction, the disproportionation of external sulfur intermediates, and microbial sulfide oxidation.
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Affiliation(s)
- André Pellerin
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Gilad Antler
- Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 84105, Israel
- The Interuniversity Institute for Marine Sciences of Eilat, P.O. Box 469, Eilat 88103, Israel
| | - Simon Agner Holm
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Alyssa J. Findlay
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Peter W. Crockford
- Weizmann Institute of Science, Department of Earth and Planetary Science, Rehovot, Israel
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | | | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kai Finster
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019. [DOI: 10.10.3389/fmicb.2019.00849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019; 10:849. [PMID: 31105660 PMCID: PMC6492693 DOI: 10.3389/fmicb.2019.00849] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial dissimilatory sulfate reduction to sulfide is a predominant terminal pathway of organic matter mineralization in the anoxic seabed. Chemical or microbial oxidation of the produced sulfide establishes a complex network of pathways in the sulfur cycle, leading to intermediate sulfur species and partly back to sulfate. The intermediates include elemental sulfur, polysulfides, thiosulfate, and sulfite, which are all substrates for further microbial oxidation, reduction or disproportionation. New microbiological discoveries, such as long-distance electron transfer through sulfide oxidizing cable bacteria, add to the complexity. Isotope exchange reactions play an important role for the stable isotope geochemistry and for the experimental study of sulfur transformations using radiotracers. Microbially catalyzed processes are partly reversible whereby the back-reaction affects our interpretation of radiotracer experiments and provides a mechanism for isotope fractionation. We here review the progress and current status in our understanding of the sulfur cycle in the seabed with respect to its microbial ecology, biogeochemistry, and isotope geochemistry.
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Affiliation(s)
- Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
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Leavitt WD, Venceslau SS, Waldbauer J, Smith DA, Pereira IAC, Bradley AS. Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation. Front Microbiol 2019; 10:658. [PMID: 31031715 PMCID: PMC6470260 DOI: 10.3389/fmicb.2019.00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/15/2019] [Indexed: 11/30/2022] Open
Abstract
Dissimilatory sulfate reduction is a microbial energy metabolism that can produce sulfur isotopic fractionations over a large range in magnitude. Calibrating sulfur isotopic fractionation in laboratory experiments allows for better interpretations of sulfur isotopes in modern sediments and ancient sedimentary rocks. The proteins involved in sulfate reduction are expressed in response to environmental conditions, and are collectively responsible for the net isotopic fractionation between sulfate and sulfide. We examined the role of DsrC, a key component of the sulfate reduction pathway, by comparing wildtype Desulfovibrio vulgaris DSM 644T to strain IPFG07, a mutant deficient in DsrC production. Both strains were cultivated in parallel chemostat reactors at identical turnover times and cell specific sulfate reduction rates. Under these conditions, sulfur isotopic fractionations between sulfate and sulfide of 17.3 ± 0.5‰ or 12.6 ± 0.5‰ were recorded for the wildtype or mutant, respectively. The enzymatic machinery that produced these different fractionations was revealed by quantitative proteomics. Results are consistent with a cellular-level response that throttled the supply of electrons and sulfur supply through the sulfate reduction pathway more in the mutant relative to the wildtype, independent of rate. We conclude that the smaller fractionation observed in the mutant strain is a consequence of sulfate reduction that proceeded at a rate that consumed a greater proportion of the strains overall capacity for sulfate reduction. These observations have consequences for models of sulfate reducer metabolism and how it yields different isotopic fractionations, notably, the role of DsrC in central energy metabolism.
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Affiliation(s)
- William D. Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, United States
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
- Department of Chemistry, Dartmouth College, Hanover, NH, United States
| | - Sofia S. Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Jacob Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Derek A. Smith
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Inês A. Cardoso Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alexander S. Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, United States
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