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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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2
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Allais L, Thibodeau B, Khan NS, Crowe SA, Cannicci S, Not C. Salinity, mineralogy, porosity, and hydrodynamics as drivers of carbon burial in urban mangroves from a megacity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168955. [PMID: 38056642 DOI: 10.1016/j.scitotenv.2023.168955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023]
Abstract
Mangrove ecosystems are an important blue carbon store but exhibit considerable variation in soil carbon stocks globally. Unravelling the conditions controlling carbon stock is critical for assessing current and future carbon budgets. Mangrove soil biogeochemical cycles can strongly influence carbon storage capacities. We thus investigated carbon sequestration and the environmental parameters shaping variability in biogeochemical cycling and carbon storage in sediment samples from four mangrove sites along an estuarine-to-marine gradient in Hong Kong, a megacity. Our results showed that organic matter in Hong Kong mangroves is sourced principally from autochthonous mangrove plants. Total nitrogen was higher in the freshwater-influenced sites and supplied from different sources. Marine-influenced sites had larger sulfur fractionations, reflecting higher marine-sourced sulfate concentrations and indicating a relatively open sulfate system. We estimated an average organic carbon stock of 115 ± 8 Mg C ha-1 in the upper 100 cm soil layer placing Hong Kong mangroves at the lower end of the global spectrum of the soil carbon stock. Carbon accumulation was found to be driven by a combination of higher total organic matter inputs, soil fluxes, and porosity. Notably, despite having the highest mass-specific soil organic carbon contents, Mai Po had the lowest integrated soil organic carbon storage (77 ± 3 Mg C ha-1). This was primarily due to lower sediment density and higher tidal pumping leading to a decrease in carbon retention. Total organic matter input, sediment characteristics, and hydrodynamics were the main factors influencing soil organic carbon storage. Overall, our results suggest that (1) while multiple parameters can enhance soil organic carbon content and increase carbon storage capacities, (2) hydrodynamics and sediment characteristics can increase the potential for leakage of carbon, and (3) high carbon content does not always equal high carbon sequestration and stock.
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Affiliation(s)
- Laetitia Allais
- Department of Earth Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Swire Institute of Marine Science, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region.
| | - Benoit Thibodeau
- Earth and Environmental Sciences Programme & School of Life Sciences, Chinese University of Hong Kong, Hong Kong Special Administrative Region.
| | - Nicole S Khan
- Department of Earth Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Swire Institute of Marine Science, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Sean A Crowe
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada; Department of Earth, Ocean, Atmospheric Sciences, University of British Columbia, BC, Canada
| | | | - Christelle Not
- Department of Earth Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Swire Institute of Marine Science, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
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3
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Martocello DE, Wankel SD. Physiological Influence of Fe and Cu Availability on Nitrogen Isotope Fractionation during Ammonia Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:421-431. [PMID: 38147309 DOI: 10.1021/acs.est.3c05964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Microbially mediated cycling processes play central roles in regulating the speciation and availability of nitrogen, a vital nutrient with wide implications for agriculture, water quality, wastewater treatment, ecosystem health, and climate change. Ammonia oxidation, the first and rate-limiting step of nitrification, is carried out by bacteria (AOB) and archaea (AOA) that require the trace metal micronutrients copper (Cu) and iron (Fe) for growth and metabolic catalysis. While stable isotope analyses for constraining nitrogen cycling are commonly used, it is unclear whether metal availability may modulate expression of stable isotope fractionation during ammonia oxidation, by varying growth or through regulation of metabolic metalloenzymes. We present the first study examining the influence of Fe and Cu availability on the kinetic nitrogen isotope effect in ammonia oxidation (15εAO). We report a general independence of 15εAO from the growth rate in AOB, except at a low temperature (10 °C). With AOA Nitrosopumilus maritimus SCM1, however, 15εAO decreases nonlinearly at lower oxidation rates. We examine assumptions involved in the interpretation of 15εAO values and suggest these dynamics may arise from physiological constraints that push the system toward isotopic equilibrium. These results suggest important links between isotope fractionation and environmental constraints on physiology in these key N cycling microorganisms.
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Affiliation(s)
- Donald E Martocello
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Scott D Wankel
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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4
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Halevy I, Fike DA, Pasquier V, Bryant RN, Wenk CB, Turchyn AV, Johnston DT, Claypool GE. Sedimentary parameters control the sulfur isotope composition of marine pyrite. Science 2023; 382:946-951. [PMID: 37995229 DOI: 10.1126/science.adh1215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023]
Abstract
Reconstructions of coupled carbon, oxygen, and sulfur cycles rely heavily on sedimentary pyrite sulfur isotope compositions (δ34Spyr). With a model of sediment diagenesis, paired with global datasets of sedimentary parameters, we show that the wide range of δ34Spyr (~100 per mil) in modern marine sediments arises from geographic patterns in the relative rates of diffusion, burial, and microbial reduction of sulfate. By contrast, the microbial sulfur isotope fractionation remains large and relatively uniform. Over Earth history, the effect of increasing seawater sulfate and oxygen concentrations on sulfate and sulfide transport and reaction may explain the corresponding increase observed in the δ34S offset between sulfate and pyrite. More subtle variations may be related to changes in depositional environments associated with sea level fluctuations and supercontinent cycles.
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Affiliation(s)
- I Halevy
- Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - D A Fike
- Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130-4899, USA
| | - V Pasquier
- Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - R N Bryant
- Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130-4899, USA
- Earth, Atmospheric and Planetary Sciences, Purdue University, W. Lafayette, IN 47907, USA
| | - C B Wenk
- Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - A V Turchyn
- Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK
| | - D T Johnston
- Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
| | - G E Claypool
- 8910 West Jewell Avenue, Unit 209, Lakewood, CO 80232, USA
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5
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Li M, Xu Y, Sun L, Chen J, Zhang K, Li D, Farquhar J, Zhang X, Sun R, Macdonald FA, Grasby SE, Fu Y, Shen Y. Deglacial volcanism and reoxygenation in the aftermath of the Sturtian Snowball Earth. SCIENCE ADVANCES 2023; 9:eadh9502. [PMID: 37672591 PMCID: PMC10482342 DOI: 10.1126/sciadv.adh9502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/02/2023] [Indexed: 09/08/2023]
Abstract
The Cryogenian Sturtian and Marinoan Snowball Earth glaciations bracket a nonglacial interval during which Demosponge and green-algal biomarkers first appear. To understand the relationships between environmental perturbations and early animal evolution, we measured sulfur and mercury isotopes from the Datangpo Formation from South China. Hg enrichment with positive Δ199Hg excursion suggests enhanced volcanism, potentially due to depressurization of terrestrial magma chambers during deglaciation. A thick stratigraphic interval of negative Δ33Spy indicates that the nonglacial interlude was characterized by low but rising sulfate levels. Model results reveal a mechanism to produce the Δ33S anomalies down to -0.284‰ through Rayleigh distillation. We propose that extreme temperatures and anoxia contributed to the apparent delay in green algal production in the aftermath of the Sturtian glaciation and the subsequent reoxygenation of the iron-rich and sulfate-depleted ocean paved the way for evolution of animals.
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Affiliation(s)
- Menghan Li
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yilun Xu
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Lilin Sun
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Jiubin Chen
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300350, China
| | - Ke Zhang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300350, China
| | - Dandan Li
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - James Farquhar
- Department of Geology and ESSIC, University of Maryland, College Park, MD 20742, USA
| | - Xiaolin Zhang
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Ruoyu Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300350, China
| | - Francis A. Macdonald
- Department of Earth Science, University of California–Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stephen E. Grasby
- Geological Survey of Canada, Natural Resources Canada, Calgary, Alberta T2L 2A7, Canada
| | - Yong Fu
- College of Resource and Environmental Engineering, Guizhou University, Guiyang 550012, China
| | - Yanan Shen
- School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
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6
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Wang H, Peng Y, Li C, Cao X, Cheng M, Bao H. Sulfate triple-oxygen-isotope evidence confirming oceanic oxygenation 570 million years ago. Nat Commun 2023; 14:4315. [PMID: 37463883 DOI: 10.1038/s41467-023-39962-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
The largest negative inorganic carbon isotope excursion in Earth's history, namely the Ediacaran Shuram Excursion (SE), closely followed by early animal radiation, has been widely interpreted as a consequence of oceanic oxidation. However, the primary nature of the signature, source of oxidants, and tempo of the event remain contested. Here, we show that carbonate-associated sulfate (CAS) from three different paleocontinents all have conspicuous negative 17O anomalies (Δ'17OCAS values down to -0.53‰) during the SE. Furthermore, the Δ'17OCAS varies in correlation with its corresponding δ34SCAS and δ18OCAS as well as the carbonate δ13Ccarb, decreasing initially followed by a recovery over the ~7-Myr SE duration. In a box-model examination, we argue for a period of sustained water-column ventilation and consequently enhanced sulfur oxidation in the SE ocean. Our findings reveal a direct involvement of mass-anomalously 17O-depleted atmospheric O2 in marine sulfate formation and thus a primary global oceanic oxygenation event during the SE.
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Affiliation(s)
- Haiyang Wang
- International Center for Isotope Effects Research, Nanjing University, Nanjing, China
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation & Institute of Sedimentary Geology, Chengdu University of Technology, Chengdu, China
- International Center for Sedimentary Geochemistry and Biogeochemistry Research, Chengdu University of Technology, Chengdu, China
| | - Yongbo Peng
- International Center for Isotope Effects Research, Nanjing University, Nanjing, China.
- Frontiers Science Center for Critical Earth Material Cycling and State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, China.
| | - Chao Li
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation & Institute of Sedimentary Geology, Chengdu University of Technology, Chengdu, China.
- International Center for Sedimentary Geochemistry and Biogeochemistry Research, Chengdu University of Technology, Chengdu, China.
- Key Laboratory of Deep-time Geography and Environment Reconstruction and Applications of Ministry of Natural Resources, Chengdu University of Technology, Chengdu, China.
| | - Xiaobin Cao
- International Center for Isotope Effects Research, Nanjing University, Nanjing, China
- Frontiers Science Center for Critical Earth Material Cycling and State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, China
| | - Meng Cheng
- State Key Laboratory of Oil and Gas Reservoir Geology and Exploitation & Institute of Sedimentary Geology, Chengdu University of Technology, Chengdu, China
- International Center for Sedimentary Geochemistry and Biogeochemistry Research, Chengdu University of Technology, Chengdu, China
- Key Laboratory of Deep-time Geography and Environment Reconstruction and Applications of Ministry of Natural Resources, Chengdu University of Technology, Chengdu, China
| | - Huiming Bao
- International Center for Isotope Effects Research, Nanjing University, Nanjing, China.
- Frontiers Science Center for Critical Earth Material Cycling and State Key Laboratory for Mineral Deposits Research, School of Earth Sciences and Engineering, Nanjing University, Nanjing, China.
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7
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Fan K, Wang W, Xu X, Yuan Y, Ren N, Lee DJ, Chen C. Recent Advances in Biotechnologies for the Treatment of Environmental Pollutants Based on Reactive Sulfur Species. Antioxidants (Basel) 2023; 12:antiox12030767. [PMID: 36979016 PMCID: PMC10044940 DOI: 10.3390/antiox12030767] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The definition of reactive sulfur species (RSS) is inspired by the reactivity and variable chemical valence of sulfur. Sulfur is an essential element for life and is a part of global geochemical cycles. Wastewater treatment bioreactors can be divided into two major categories: sulfur reduction and sulfur oxidation. We review the origins of the definition of RSS and related biotechnological processes in environmental management. Sulfate reduction, sulfide oxidation, and sulfur-based redox reactions are key to driving the coupled global carbon, nitrogen, and sulfur co-cycles. This shows the coupling of the sulfur cycle with the carbon and nitrogen cycles and provides insights into the global material-chemical cycle. We also review the biological classification and RSS metabolic mechanisms of functional microorganisms involved in the biological processes, such as sulfate-reducing and sulfur-oxidizing bacteria. Developments in molecular biology and genomic technologies have allowed us to obtain detailed information on these bacteria. The importance of RSS in environmental technologies requires further consideration.
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Affiliation(s)
- Kaili Fan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wei Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xijun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yuan Yuan
- College of Biological Engineering, Beijing Polytechnic, Beijing 100176, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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8
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Sim MS, Woo DK, Kim B, Jeong H, Joo YJ, Hong YW, Choi JY. What Controls the Sulfur Isotope Fractionation during Dissimilatory Sulfate Reduction? ACS ENVIRONMENTAL AU 2023; 3:76-86. [PMID: 37102088 PMCID: PMC10125365 DOI: 10.1021/acsenvironau.2c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 04/28/2023]
Abstract
Sulfate often behaves conservatively in the oxygenated environments but serves as an electron acceptor for microbial respiration in a wide range of natural and engineered systems where oxygen is depleted. As a ubiquitous anaerobic dissimilatory pathway, therefore, microbial reduction of sulfate to sulfide has been of continuing interest in the field of microbiology, ecology, biochemistry, and geochemistry. Stable isotopes of sulfur are an effective tool for tracking this catabolic process as microorganisms discriminate strongly against heavy isotopes when cleaving the sulfur-oxygen bond. Along with its high preservation potential in environmental archives, a wide variation in the sulfur isotope effects can provide insights into the physiology of sulfate reducing microorganisms across temporal and spatial barriers. A vast array of parameters, including phylogeny, temperature, respiration rate, and availability of sulfate, electron donor, and other essential nutrients, has been explored as a possible determinant of the magnitude of isotope fractionation, and there is now a broad consensus that the relative availability of sulfate and electron donors primarily controls the magnitude of fractionation. As the ratio shifts toward sulfate, the sulfur isotope fractionation increases. The results of conceptual models, centered on the reversibility of each enzymatic step in the dissimilatory sulfate reduction pathway, are in qualitative agreement with the observations, although the underlying intracellular mechanisms that translate the external stimuli into the isotopic phenotype remain largely unexplored experimentally. This minireview offers a snapshot of our current understanding of the sulfur isotope effects during dissimilatory sulfate reduction as well as their potential quantitative applications. It emphasizes the importance of sulfate respiration as a model system for the isotopic investigation of other respiratory pathways that utilize oxyanions as terminal electron acceptors.
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Affiliation(s)
- Min Sub Sim
- School
of Earth and Environmental Sciences, Seoul
National University, Seoul08826, Korea
- . Tel: +82 2 880 6632
| | - Dong Kyun Woo
- School
of Earth and Environmental Sciences, Seoul
National University, Seoul08826, Korea
| | - Bokyung Kim
- School
of Earth and Environmental Sciences, Seoul
National University, Seoul08826, Korea
| | - Hyeonjeong Jeong
- School
of Earth and Environmental Sciences, Seoul
National University, Seoul08826, Korea
| | - Young Ji Joo
- Department
of Earth and Environmental Sciences, Pukyong
National University, Busan48513, Korea
| | - Yeon Woo Hong
- School
of Earth and Environmental Sciences, Seoul
National University, Seoul08826, Korea
| | - Jy Young Choi
- School
of Earth and Environmental Sciences, Seoul
National University, Seoul08826, Korea
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9
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Yu Q, Mao H, Yang B, Zhu Y, Sun C, Zhao Z, Li Y, Zhang Y. Electro-polarization of protein-like substances accelerates trans-cell-wall electron transfer in microbial extracellular respiration. iScience 2023; 26:106065. [PMID: 36818305 PMCID: PMC9929677 DOI: 10.1016/j.isci.2023.106065] [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: 08/25/2022] [Revised: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Electrical stimulation has been used to strengthen microbial extracellular electron transfer (EET), however, the deep-seated reasons remain unclear. Here we reported that Bacillus subtilis, a typical gram-positive bacterium capable of extracellular respiration, obtained a higher EET capacity after the electrical domestication. After the electrical domestication, the current generated by the EET of B. subtilis was 23.4-fold that of the control group without pre-domestication. Multiple lines of evidence in bacterial cells of B. subtilis, their cell walls, and a model tripeptide indicated that the polarization of amide groups after the electrical stimulation forwarded the H-bonds recombination and radical generation of protein-like substances to develop extracellular electron transfer via the proton-coupled pattern. The improved electrochemical properties of protein-like substances benefited the trans-cell-wall electron transfer and strengthen extracellular respiration. This study was the first exploration to promote microbial extracellular respiration by improving the electrochemical properties of protein-like substances in cell envelopes.
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Affiliation(s)
- Qilin Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Haohao Mao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bowen Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yahui Zhu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Cheng Sun
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yang Li
- School of Ocean Science and Technology, Dalian University of Technology, Panjin, Liaoning 124221, China
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China,Corresponding author
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10
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A Cristae-Like Microcompartment in Desulfobacterota. mBio 2022; 13:e0161322. [PMID: 36321837 PMCID: PMC9764997 DOI: 10.1128/mbio.01613-22] [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] [Indexed: 01/25/2023] Open
Abstract
Some Alphaproteobacteria contain intracytoplasmic membranes (ICMs) and proteins homologous to those responsible for the mitochondrial cristae, an observation which has given rise to the hypothesis that the Alphaproteobacteria endosymbiont had already evolved cristae-like structures and functions. However, our knowledge of microbial fine structure is still limited, leaving open the possibility of structurally homologous ICMs outside the Alphaproteobacteria. Here, we report on the detailed characterization of lamellar cristae-like ICMs in environmental sulfate-reducing Desulfobacterota that form syntrophic partnerships with anaerobic methane-oxidizing (ANME) archaea. These structures are junction-bound to the cytoplasmic membrane and resemble the form seen in the lamellar cristae of opisthokont mitochondria. Extending these observations, we also characterized similar structures in Desulfovibrio carbinolicus, a close relative of the magnetotactic D. magneticus, which does not contain magnetosomes. Despite a remarkable structural similarity, the key proteins involved in cristae formation have not yet been identified in Desulfobacterota, suggesting that an analogous, but not a homologous, protein organization system developed during the evolution of some members of Desulfobacterota. IMPORTANCE Working with anaerobic consortia of methane oxidizing ANME archaea and their sulfate-reducing bacterial partners recovered from deep sea sediments and with the related sulfate-reducing bacterial isolate D. carbinolicus, we discovered that their intracytoplasmic membranes (ICMs) appear remarkably similar to lamellar cristae. Three-dimensional electron microscopy allowed for the novel analysis of the nanoscale attachment of ICMs to the cytoplasmic membrane, and these ICMs are structurally nearly identical to the crista junction architecture seen in metazoan mitochondria. However, the core junction-forming proteins must be different. The outer membrane vesicles were observed to bud from syntrophic Desulfobacterota, and darkly stained granules were prominent in both Desulfobacterota and D. carbinolicus. These findings expand the taxonomic breadth of ICM-producing microorganisms and add to our understanding of three-dimensional microbial fine structure in environmental microorganisms.
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11
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Novel sulfur isotope analyses constrain sulfurized porewater fluxes as a minor component of marine dissolved organic matter. Proc Natl Acad Sci U S A 2022; 119:e2209152119. [PMID: 36201540 PMCID: PMC9565371 DOI: 10.1073/pnas.2209152119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Marine dissolved organic matter (DOM) is a major reservoir that links global carbon, nitrogen, and phosphorus. DOM is also important for marine sulfur biogeochemistry as the largest water column reservoir of organic sulfur. Dissolved organic sulfur (DOS) can originate from phytoplankton-derived biomolecules in the surface ocean or from abiotically "sulfurized" organic matter diffusing from sulfidic sediments. These sources differ in 34S/32S isotope ratios (δ34S values), with phytoplankton-produced DOS tracking marine sulfate (21‰) and sulfurized DOS mirroring sedimentary porewater sulfide (∼0 to -10‰). We measured the δ34S values of solid-phase extracted (SPE) DOM from marine water columns and porewater from sulfidic sediments. Marine DOMSPE δ34S values ranged from 14.9‰ to 19.9‰ and C:S ratios from 153 to 303, with lower δ34S values corresponding to higher C:S ratios. Marine DOMSPE samples showed consistent trends with depth: δ34S values decreased, C:S ratios increased, and δ13C values were constant. Porewater DOMSPE was 34S-depleted (∼-0.6‰) and sulfur-rich (C:S ∼37) compared with water column samples. We interpret these trends as reflecting at most 20% (and on average ∼8%) contribution of abiotic sulfurized sources to marine DOSSPE and conclude that sulfurized porewater is not a main component of oceanic DOS and DOM. We hypothesize that heterogeneity in δ34S values and C:S ratios reflects the combination of sulfurized porewater inputs and preferential microbial scavenging of sulfur relative to carbon without isotope fractionation. Our findings strengthen links between oceanic sulfur and carbon cycling, supporting a realization that organic sulfur, not just sulfate, is important to marine biogeochemistry.
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12
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Peng Y, Bao H, Jiang G, Crockford P, Feng D, Xiao S, Kaufman AJ, Wang J. A transient peak in marine sulfate after the 635-Ma snowball Earth. Proc Natl Acad Sci U S A 2022; 119:e2117341119. [PMID: 35500113 PMCID: PMC9171640 DOI: 10.1073/pnas.2117341119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/24/2022] [Indexed: 11/18/2022] Open
Abstract
SignificanceEarth system's response to major perturbations is of paramount interest. On the basis of multiple isotope compositions for pyrite, carbonate-associated sulfate, carbonates, and organics within, we inferred that the much-debated, enigmatic, extremely 13C-depleted calcite cements in the ∼635-Ma cap carbonates in South China preserve geochemical evidence for marine microbial sulfate reduction coupled to anaerobic oxidation of methane. This interpretation implies the existence of a brief interval of modern-level marine sulfate. We determined that this interval coincides with the earliest Ediacaran 17O-depletion episode, and both likely occurred within ∼50 ky since the onset of the 635-Ma meltdown, revealing an astonishing pace of transformation of the Earth system in the aftermath of Earth's latest snowball glaciation.
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Affiliation(s)
- Yongbo Peng
- International Center for Isotope Effects Research, Nanjing University, Nanjing 210023, China
- School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Huiming Bao
- International Center for Isotope Effects Research, Nanjing University, Nanjing 210023, China
- School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Ganqing Jiang
- Department of Geoscience, University of Nevada, Las Vegas, NV 89154
| | - Peter Crockford
- Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dong Feng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA 24061
| | - Alan Jay Kaufman
- Department of Geology, University of Maryland, College Park, MD 20742
| | - Jiasheng Wang
- State Key Laboratory of Biogeology and Environment Geology, China University of Geosciences, Wuhan 430074, China
- Hubei Key Laboratory of Marine Geological Resources, China University of Geosciences, Wuhan 430074, China
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13
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Maiti BK. Cross‐talk Between (Hydrogen)Sulfite and Metalloproteins: Impact on Human Health. Chemistry 2022; 28:e202104342. [DOI: 10.1002/chem.202104342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Indexed: 12/28/2022]
Affiliation(s)
- Biplab K Maiti
- Department of Chemistry National Institute of Technology Sikkim, Ravangla Campus Barfung Block, Ravangla Sub Division South Sikkim 737139 India
- Department of Chemistry Cluster University of Jammu Canal Road Jammu 180001
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14
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Gropp J, Jin Q, Halevy I. Controls on the isotopic composition of microbial methane. SCIENCE ADVANCES 2022; 8:eabm5713. [PMID: 35385305 PMCID: PMC8985922 DOI: 10.1126/sciadv.abm5713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Microbial methane production (methanogenesis) is responsible for more than half of the annual emissions of this major greenhouse gas to the atmosphere. Although the stable isotopic composition of methane is often used to characterize its sources and sinks, strictly empirical descriptions of the isotopic signature of methanogenesis currently limit these attempts. We developed a metabolic-isotopic model of methanogenesis by carbon dioxide reduction, which predicts carbon and hydrogen isotopic fractionations, and clumped isotopologue distributions, as functions of the cell's environment. We mechanistically explain multiple isotopic patterns in laboratory and natural settings and show that these patterns constrain the in situ energetics of methanogenesis. Combining our model with data from environments in which methanogenic activity is energy-limited, we provide predictions for the biomass-specific methanogenesis rates and the associated isotopic effects.
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Affiliation(s)
- Jonathan Gropp
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Qusheng Jin
- Department of Earth Sciences, University of Oregon, Eugene, OR, USA
| | - Itay Halevy
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
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15
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Pasquier V, Fike DA, Halevy I. Sedimentary pyrite sulfur isotopes track the local dynamics of the Peruvian oxygen minimum zone. Nat Commun 2021; 12:4403. [PMID: 34285238 PMCID: PMC8292381 DOI: 10.1038/s41467-021-24753-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/25/2021] [Indexed: 11/25/2022] Open
Abstract
Sulfur cycling is ubiquitous in sedimentary environments, where it mediates organic carbon remineralization, impacting both local and global redox budgets, and leaving an imprint in pyrite sulfur isotope ratios (δ34Spyr). It is unclear to what extent stratigraphic δ34Spyr variations reflect local aspects of the depositional environment or microbial activity versus global sulfur-cycle variations. Here, we couple carbon-nitrogen-sulfur concentrations and stable isotopes to identify clear influences on δ34Spyr of local environmental changes along the Peru margin. Stratigraphically coherent glacial-interglacial δ34Spyr fluctuations (>30‰) were mediated by Oxygen Minimum Zone intensification/expansion and local enhancement of organic matter deposition. The higher resulting microbial sulfate reduction rates led to more effective drawdown and 34S-enrichment of residual porewater sulfate and sulfide produced from it, some of which is preserved in pyrite. We identify organic carbon loading as a major influence on δ34Spyr, adding to the growing body of evidence highlighting the local controls on these records. To explore the importance of local vs. global sulfur-cycle controls on variations in pyrite sulfur isotopes, the authors couple carbon-nitrogen-sulfur concentrations and stable isotopes of sediments from the Peruvian oxygen minimum zone, identifying a major role for the local organic carbon loading.
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Affiliation(s)
- Virgil Pasquier
- Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - David A Fike
- Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Itay Halevy
- Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
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16
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Sun F, Mellage A, Gharasoo M, Melsbach A, Cao X, Zimmermann R, Griebler C, Thullner M, Cirpka OA, Elsner M. Mass-Transfer-Limited Biodegradation at Low Concentrations-Evidence from Reactive Transport Modeling of Isotope Profiles in a Bench-Scale Aquifer. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:7386-7397. [PMID: 33970610 PMCID: PMC8173607 DOI: 10.1021/acs.est.0c08566] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Organic contaminant degradation by suspended bacteria in chemostats has shown that isotope fractionation decreases dramatically when pollutant concentrations fall below the (half-saturation) Monod constant. This masked isotope fractionation implies that membrane transfer is slow relative to the enzyme turnover at μg L-1 substrate levels. Analogous evidence of mass transfer as a bottleneck for biodegradation in aquifer settings, where microbes are attached to the sediment, is lacking. A quasi-two-dimensional flow-through sediment microcosm/tank system enabled us to study the aerobic degradation of 2,6-dichlorobenzamide (BAM), while collecting sufficient samples at the outlet for compound-specific isotope analysis. By feeding an anoxic BAM solution through the center inlet port and dissolved oxygen (DO) above and below, strong transverse concentration cross-gradients of BAM and DO yielded zones of low (μg L-1) steady-state concentrations. We were able to simulate the profiles of concentrations and isotope ratios of the contaminant plume using a reactive transport model that accounted for a mass-transfer limitation into bacterial cells, where apparent isotope enrichment factors *ε decreased strongly below concentrations around 600 μg/L BAM. For the biodegradation of organic micropollutants, mass transfer into the cell emerges as a bottleneck, specifically at low (μg L-1) concentrations. Neglecting this effect when interpreting isotope ratios at field sites may lead to a significant underestimation of biodegradation.
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Affiliation(s)
- Fengchao Sun
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, Neuherberg 85764, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, Munich 81377, Germany
| | - Adrian Mellage
- Center
for Applied Geoscience, University of Tübingen, Schnarrenbergstrasse 94−96, Tübingen 72076, Germany
| | - Mehdi Gharasoo
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, Neuherberg 85764, Germany
- Department
of Earth and Environmental Sciences, Ecohydrology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Canada
| | - Aileen Melsbach
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, Neuherberg 85764, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, Munich 81377, Germany
| | - Xin Cao
- Joint
Mass Spectrometry Centre, Comprehensive
Molecular Analytics (CMA) Cooperation Group Helmholtz Zentrum, Gmunderstrasse 37, Munich 81379, Germany
| | - Ralf Zimmermann
- Joint
Mass Spectrometry Centre, Comprehensive
Molecular Analytics (CMA) Cooperation Group Helmholtz Zentrum, Gmunderstrasse 37, Munich 81379, Germany
| | - Christian Griebler
- Department
of Functional and Evolutionary Ecology, University of Vienna, Althanstrasse 14, Vienna 1090, Austria
| | - Martin Thullner
- Department
of Environmental Microbiology, UFZ—Helmholtz
Centre for Environmental Research, Permoserstrasse 15, Leipzig 30418, Germany
| | - Olaf A. Cirpka
- Center
for Applied Geoscience, University of Tübingen, Schnarrenbergstrasse 94−96, Tübingen 72076, Germany
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, Neuherberg 85764, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, Munich 81377, Germany
- Phone: +49 89 2180-78232
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17
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Ward LM, Bertran E, Johnston DT. Expanded Genomic Sampling Refines Current Understanding of the Distribution and Evolution of Sulfur Metabolisms in the Desulfobulbales. Front Microbiol 2021; 12:666052. [PMID: 34093483 PMCID: PMC8170396 DOI: 10.3389/fmicb.2021.666052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
The reconstruction of modern and paleo-sulfur cycling relies on understanding the long-term relative contribution of its main actors; these include microbial sulfate reduction (MSR) and microbial sulfur disproportionation (MSD). However, a unifying theory is lacking for how MSR and MSD, with the same enzyme machinery and intimately linked evolutionary histories, perform two drastically different metabolisms. Here, we aim at shedding some light on the distribution, diversity, and evolutionary histories of MSR and MSD, with a focus on the Desulfobulbales as a test case. The Desulfobulbales is a diverse and widespread order of bacteria in the Desulfobacterota (formerly Deltaproteobacteria) phylum primarily composed of sulfate reducing bacteria. Recent culture- and sequence-based approaches have revealed an expanded diversity of organisms and metabolisms within this clade, including the presence of obligate and facultative sulfur disproportionators. Here, we present draft genomes of previously unsequenced species of Desulfobulbales, substantially expanding the available genomic diversity of this clade. We leverage this expanded genomic sampling to perform phylogenetic analyses, revealing an evolutionary history defined by vertical inheritance of sulfur metabolism genes with numerous convergent instances of transition from sulfate reduction to sulfur disproportionation.
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Affiliation(s)
- Lewis M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Emma Bertran
- Princeton Environmental Institute, Princeton University, Princeton, NJ, United States
| | - David T. Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
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18
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Liu Y, Liu Y, Jiao D, Lu C, Lou Y, Li N, Wang G, Wang H. Synthesis and release of fatty acids under the interaction of Ulva pertusa and Heterosigma akashiwo by stable isotope analysis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 210:111852. [PMID: 33418155 DOI: 10.1016/j.ecoenv.2020.111852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Symbiosis of marine algae is inevitable in the marine environment, and species may occur interaction on the growth. In this study, the macroalgae Ulva pertusa and marine microalgae Heterosigma akashiwo were selected as target species to study the interaction mechanism between them. After the 8 days of co-cultivation, the inhibition on growth was observed for both of U. pertusa and H. akashiwo. Eight fatty acids in U. pertusa was detected, with the significant decrease in contents of polyunsaturated fatty acids (PUFAs) especially for C18:2, C18:3n-3 and C18:3n-6. Twelve fatty acids in H. akashiwo was detected, with the significant change for PUFAs. PUFA concentrations in the co-culture group were less than those in the mono-culture. Meanwhile the principal component analysis was conducted to insight into the interaction between U. pertusa and H. akashiwo by fatty acids content and carbon stable isotope ratio of fatty acids (δ13CFAs). Fatty acid content could not distinguish mono and co-culture. However, δ13CFAs could distinguish not only the culture time of algae, but also the living environment of algae. In addition, this study combined fatty acids content and δ13CFAs to explore the release of fatty acids by algae into the seawater. The C18:3n-3 was identified as the allelochemical released by U. pertusa to inhibit the growth of H. akashiwo. The ratio of δ13CFAs in seawater decreased. This study provides a theoretical basis for the symbiosis of marine algae, and a new method of compound-specific stable carbon isotopes was used to better explore the metabolism of fatty acids in algae.
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Affiliation(s)
- Yuxin Liu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yu Liu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; Environmental Information Institute, Dalian Maritime University, Dalian 116026, China.
| | - Dian Jiao
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Chao Lu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yadi Lou
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Na Li
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Guoguang Wang
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Haixia Wang
- Navigation College, Dalian Maritime University, Dalian 116026, China
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19
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Sim MS, Skennerton CT, Orphan VJ. Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus. PLoS One 2021; 16:e0245069. [PMID: 33444327 PMCID: PMC7808614 DOI: 10.1371/journal.pone.0245069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/21/2020] [Indexed: 11/25/2022] Open
Abstract
Methanol is often considered as a non-competitive substrate for methanogenic archaea, but an increasing number of sulfate-reducing microorganisms (SRMs) have been reported to be capable of respiring with methanol as an electron donor. A better understanding of the fate of methanol in natural or artificial anaerobic systems thus requires knowledge of the methanol dissimilation by SRMs. In this study, we describe the growth kinetics and sulfur isotope effects of Desulfovibrio carbinolicus, a methanol-oxidizing sulfate-reducing deltaproteobacterium, together with its genome sequence and annotation. D. carbinolicus can grow with a series of alcohols from methanol to butanol. Compared to longer-chain alcohols, however, specific growth and respiration rates decrease by several fold with methanol as an electron donor. Larger sulfur isotope fractionation accompanies slowed growth kinetics, indicating low chemical potential at terminal reductive steps of respiration. In a medium containing both ethanol and methanol, D. carbinolicus does not consume methanol even after the cessation of growth on ethanol. Among the two known methanol dissimilatory systems, the genome of D. carbinolicus contains the genes coding for alcohol dehydrogenase but lacks enzymes analogous to methanol methyltransferase. We analyzed the genomes of 52 additional species of sulfate-reducing bacteria that have been tested for methanol oxidation. There is no apparent relationship between phylogeny and methanol metabolizing capacity, but most gram-negative methanol oxidizers grow poorly, and none carry homologs for methyltransferase (mtaB). Although the amount of available data is limited, it is notable that more than half of the known gram-positive methanol oxidizers have both enzymatic systems, showing enhanced growth relative to the SRMs containing only alcohol dehydrogenase genes. Thus, physiological, genomic, and sulfur isotopic results suggest that D. carbinolicus and close relatives have the ability to metabolize methanol but likely play a limited role in methanol degradation in most natural environments.
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Affiliation(s)
- Min Sub Sim
- School of Earth and Environmental Sciences, Seoul National University, Seoul, South Korea
- * E-mail:
| | - Connor T. Skennerton
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
| | - Victoria J. Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
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20
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Smith DA, Fike DA, Johnston DT, Bradley AS. Isotopic Fractionation Associated With Sulfate Import and Activation by Desulfovibrio vulgaris str. Hildenborough. Front Microbiol 2020; 11:529317. [PMID: 33072004 PMCID: PMC7531388 DOI: 10.3389/fmicb.2020.529317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/14/2020] [Indexed: 11/13/2022] Open
Abstract
The use of stable isotopes to trace biogeochemical sulfur cycling relies on an understanding of how isotopic fractionation is imposed by metabolic networks. We investigated the effects of the first two enzymatic steps in the dissimilatory sulfate reduction (DSR) network - sulfate permease and sulfate adenylyl transferase (Sat) - on the sulfur and oxygen isotopic composition of residual sulfate. Mutant strains of Desulfovibrio vulgaris str. Hildenborough (DvH) with perturbed expression of these enzymes were grown in batch culture, with a subset grown in continuous culture, to examine the impact of these enzymatic steps on growth rate, cell specific sulfate reduction rate and isotopic fractionations in comparison to the wild type strain. Deletion of several permease genes resulted in only small (∼1‰) changes in sulfur isotope fractionation, a difference that approaches the uncertainties of the measurement. Mutants that perturb Sat expression show higher fractionations than the wild type strain. This increase probably relates to an increased material flux between sulfate and APS, allowing an increase in the expressed fractionation of rate-limiting APS reductase. This work illustrates that flux through the initial steps of the DSR pathway can affect the fractionation imposed by the overall pathway, even though these steps are themselves likely to impose only small fractionations.
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Affiliation(s)
- Derek A Smith
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - David A Fike
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - 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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21
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Huang Y, Zheng H, Tan K, Sun X, Ye J, Zhang Y. Circulating metabolomics profiling reveals novel pathways associated with cognitive decline in patients with hypertension. Ther Adv Neurol Disord 2020; 13:1756286420947973. [PMID: 32952614 PMCID: PMC7476355 DOI: 10.1177/1756286420947973] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/16/2020] [Indexed: 12/30/2022] Open
Abstract
Background: Hypertension is a significant risk factor for cardiovascular disease, and it is associated with dementia, including Alzheimer’s disease (AD). Although it may be correlated with AD in terms of symptoms, the link between hypertension and AD pathological biomarkers, and the potential underlying mechanism of hypertension with cognitive decline, are still not well understood. Methods: The Mini-Mental State Examination (MMSE) scores were used to evaluate cognitive function. Enzyme-linked immunosorbent assays were used to examine plasma amyloid-beta (Aβ)40, Aβ42, and tau concentration in hypertensive patients. Metabolomics and metagenomics were performed to identify the significantly changed circulating metabolites and microbiota between healthy individuals and hypertensive patients. Pearson’s correlation was used to examine the association between cognitive indicators and differential metabolites. Results: We found significantly decreased MMSE scores, elevated plasma Aβ40, and decreased Aβ42/Aβ40 ratio in hypertensive patients, which are critically associated with AD pathology. Based on metabolomics, we found that significantly altered metabolites in the plasma of hypertensive patients were enriched in the benzoate degradation and phenylpropanoid biosynthesis pathways, and they were also correlated with changes in MMSE scores and Aβ42/Aβ40 ratio. In addition, metabolomics signaling pathway analysis suggested that microbial metabolism was altered in hypertensive patients. We also identified altered blood microbiota in hypertensive patients compared with the controls. Conclusions: Our study provides a novel metabolic and microbial mechanism, which may underlie the cognitive impairment in hypertensive patients.
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Affiliation(s)
- Yuli Huang
- Department of Cardiology, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, China
| | - Haoxiao Zheng
- Department of Cardiology, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, China
| | - Kuan Tan
- Department of Cardiology, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan, China
| | - Xiangdong Sun
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
| | - Jinshao Ye
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, China
| | - Yunlong Zhang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Panyu District, Xinzao, Guangzhou, 510260, China
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22
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Nabhan S, Marin-Carbonne J, Mason PRD, Heubeck C. In situ S-isotope compositions of sulfate and sulfide from the 3.2 Ga Moodies Group, South Africa: A record of oxidative sulfur cycling. GEOBIOLOGY 2020; 18:426-444. [PMID: 32301171 DOI: 10.1111/gbi.12393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/12/2020] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
Sulfate minerals are rare in the Archean rock record and largely restricted to the occurrence of barite (BaSO4 ). The origin of this barite remains controversially debated. The mass-independent fractionation of sulfur isotopes in these and other Archean sedimentary rocks suggests that photolysis of volcanic aerosols in an oxygen-poor atmosphere played an important role in their formation. Here, we report on the multiple sulfur isotopic composition of sedimentary anhydrite in the ca. 3.22 Ga Moodies Group of the Barberton Greenstone Belt, southern Africa. Anhydrite occurs, together with barite and pyrite, in regionally traceable beds that formed in fluvial settings. Variable abundances of barite versus anhydrite reflect changes in sulfate enrichment by evaporitic concentration across orders of magnitude in an arid, nearshore terrestrial environment, periodically replenished by influxes of seawater. The multiple S-isotope compositions of anhydrite and pyrite are consistent with microbial sulfate reduction. S-isotope signatures in barite suggest an additional oxidative sulfate source probably derived from continental weathering of sulfide possibly enhanced by microbial sulfur oxidation. Although depositional environments of Moodies sulfate minerals differ strongly from marine barite deposits, their sulfur isotopic composition is similar and most likely reflects a primary isotopic signature. The data indicate that a constant input of small portions of oxidized sulfur from the continents into the ocean may have contributed to the observed long-term increase in Δ33 Ssulfate values through the Paleoarchean.
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Affiliation(s)
- Sami Nabhan
- Department for Geosciences, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Johanna Marin-Carbonne
- Laboratoire Magma et Volcans, Univ Lyon, UJM Saint Etienne, UBP, CNRS, IRD, St Etienne, France
- Institute of Earth Sciences, Universitè of Lausanne, Lausanne, Switzerland
| | - Paul R D Mason
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Christoph Heubeck
- Department for Geosciences, Friedrich-Schiller-Universität Jena, Jena, Germany
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23
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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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24
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Bertran E, Waldeck A, Wing BA, Halevy I, Leavitt WD, Bradley AS, Johnston DT. Oxygen isotope effects during microbial sulfate reduction: applications to sediment cell abundances. ISME JOURNAL 2020; 14:1508-1519. [PMID: 32152390 PMCID: PMC7242377 DOI: 10.1038/s41396-020-0618-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 01/31/2020] [Accepted: 02/17/2020] [Indexed: 12/13/2022]
Abstract
The majority of anaerobic biogeochemical cycling occurs within marine sediments. To understand these processes, quantifying the distribution of active cells and gross metabolic activity is essential. We present an isotope model rooted in thermodynamics to draw quantitative links between cell-specific sulfate reduction rates and active sedimentary cell abundances. This model is calibrated using data from a series of continuous culture experiments with two strains of sulfate reducing bacteria (freshwater bacterium Desulfovibrio vulgaris strain Hildenborough, and marine bacterium Desulfovibrio alaskensis strain G-20) grown on lactate across a range of metabolic rates and ambient sulfate concentrations. We use a combination of experimental sulfate oxygen isotope data and nonlinear regression fitting tools to solve for unknown kinetic, step-specific oxygen isotope effects. This approach enables identification of key isotopic reactions within the metabolic pathway, and defines a new, calibrated framework for understanding oxygen isotope variability in sulfate. This approach is then combined with porewater sulfate/sulfide concentration data and diagenetic modeling to reproduce measured 18O/16O in porewater sulfate. From here, we infer cell-specific sulfate reduction rates and predict abundance of active cells of sulfate reducing bacteria, the result of which is consistent with direct biological measurements.
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Affiliation(s)
- E Bertran
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA.
| | - A Waldeck
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA
| | - B A Wing
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA
| | - I Halevy
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - W D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA.,Department of Chemistry, Dartmouth College, Hanover, NH, USA.,Department of Biological Science, Dartmouth College, Hanover, NH, USA
| | - A S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, USA.,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - D T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA.
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25
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Colangelo-Lillis J, Pelikan C, Herbold CW, Altshuler I, Loy A, Whyte LG, Wing BA. Diversity decoupled from sulfur isotope fractionation in a sulfate-reducing microbial community. GEOBIOLOGY 2019; 17:660-675. [PMID: 31328364 DOI: 10.1111/gbi.12356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/25/2019] [Indexed: 06/10/2023]
Abstract
The extent of fractionation of sulfur isotopes by sulfate-reducing microbes is dictated by genomic and environmental factors. A greater understanding of species-specific fractionations may better inform interpretation of sulfur isotopes preserved in the rock record. To examine whether gene diversity influences net isotopic fractionation in situ, we assessed environmental chemistry, sulfate reduction rates, diversity of putative sulfur-metabolizing organisms by 16S rRNA and dissimilatory sulfite reductase (dsrB) gene amplicon sequencing, and net fractionation of sulfur isotopes along a sediment transect of a hypersaline Arctic spring. In situ sulfate reduction rates yielded minimum cell-specific sulfate reduction rates < 0.3 × 10-15 moles cell-1 day-1 . Neither 16S rRNA nor dsrB diversity indices correlated with relatively constant (38‰-45‰) net isotope fractionation (ε34 Ssulfide-sulfate ). Measured ε34 S values could be reproduced in a mechanistic fractionation model if 1%-2% of the microbial community (10%-60% of Deltaproteobacteria) were engaged in sulfate respiration, indicating heterogeneous respiratory activity within sulfate-reducing populations. This model indicated enzymatic kinetic diversity of Apr was more likely to correlate with sulfur fractionation than DsrB. We propose that, above a threshold Shannon diversity value of 0.8 for dsrB, the influence of the specific composition of the microbial community responsible for generating an isotope signal is overprinted by the control exerted by environmental variables on microbial physiology.
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Affiliation(s)
- Jesse Colangelo-Lillis
- Department of Geological Sciences, University of Colorado, Boulder, CO, USA
- Institute for Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
- Department of Earth and Planetary Science, McGill University, Montreal, Quebec, Canada
- McGill Space Institute, McGill University, Montreal, Quebec, Canada
| | - Claus Pelikan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Ianina Altshuler
- McGill Space Institute, McGill University, Montreal, Quebec, Canada
- Department of Natural Resource Science, McGill University, Montreal, Quebec, Canada
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Lyle G Whyte
- McGill Space Institute, McGill University, Montreal, Quebec, Canada
- Department of Natural Resource Science, McGill University, Montreal, Quebec, Canada
| | - Boswell A Wing
- Department of Geological Sciences, University of Colorado, Boulder, CO, USA
- Department of Earth and Planetary Science, McGill University, Montreal, Quebec, Canada
- McGill Space Institute, McGill University, Montreal, Quebec, Canada
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26
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Hodgskiss MSW, Crockford PW, Peng Y, Wing BA, Horner TJ. A productivity collapse to end Earth's Great Oxidation. Proc Natl Acad Sci U S A 2019; 116:17207-17212. [PMID: 31405980 PMCID: PMC6717284 DOI: 10.1073/pnas.1900325116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been hypothesized that the overall size of-or efficiency of carbon export from-the biosphere decreased at the end of the Great Oxidation Event (GOE) (ca. 2,400 to 2,050 Ma). However, the timing, tempo, and trigger for this decrease remain poorly constrained. Here we test this hypothesis by studying the isotope geochemistry of sulfate minerals from the Belcher Group, in subarctic Canada. Using insights from sulfur and barium isotope measurements, combined with radiometric ages from bracketing strata, we infer that the sulfate minerals studied here record ambient sulfate in the immediate aftermath of the GOE (ca. 2,018 Ma). These sulfate minerals captured negative triple-oxygen isotope anomalies as low as ∼ -0.8‰. Such negative values occurring shortly after the GOE require a rapid reduction in primary productivity of >80%, although even larger reductions are plausible. Given that these data imply a collapse in primary productivity rather than export efficiency, the trigger for this shift in the Earth system must reflect a change in the availability of nutrients, such as phosphorus. Cumulatively, these data highlight that Earth's GOE is a tale of feast and famine: A geologically unprecedented reduction in the size of the biosphere occurred across the end-GOE transition.
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Affiliation(s)
| | - Peter W Crockford
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 761000 Rehovot, Israel;
- Department of Geoscience, Princeton University, Princeton, NJ 08544
| | - Yongbo Peng
- School of Earth Sciences and Engineering, Nanjing University, 210023 Nanjing, China
| | - Boswell A Wing
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO 80309
| | - Tristan J Horner
- Non-traditional Isotope Research on Various Advanced Novel Applications (NIRVANA) Labs, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
- Department of Marine Chemistry & Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543
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27
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Johnson JE. From minerals to metabolisms: Evidence for life before oxygen from the geological record. Free Radic Biol Med 2019; 140:126-137. [PMID: 30743045 DOI: 10.1016/j.freeradbiomed.2019.01.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/18/2018] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Jena E Johnson
- Dept. of Earth and Environmental Sciences, University of Michigan, 1100 N. University Ave, Ann Arbor, MI, 48109, USA.
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28
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Reactivity of Small Oxoacids of Sulfur. Molecules 2019; 24:molecules24152768. [PMID: 31366103 PMCID: PMC6696132 DOI: 10.3390/molecules24152768] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 01/01/2023] Open
Abstract
Oxidation of sulfide to sulfate is known to consist of several steps. Key intermediates in this process are the so-called small oxoacids of sulfur (SOS)—sulfenic HSOH (hydrogen thioperoxide, oxadisulfane, or sulfur hydride hydroxide) and sulfoxylic S(OH)2 acids. Sulfur monoxide can be considered as a dehydrated form of sulfoxylic acid. Although all of these species play an important role in atmospheric chemistry and in organic synthesis, and are also invoked in biochemical processes, they are quite unstable compounds so much so that their physical and chemical properties are still subject to intense studies. It is well-established that sulfoxylic acid has very strong reducing properties, while sulfenic acid is capable of both oxidizing and reducing various substrates. Here, in this review, the mechanisms of sulfide oxidation as well as data on the structure and reactivity of small sulfur-containing oxoacids, sulfur monoxide, and its precursors are discussed.
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29
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Iron MA, Gropp J. Cost-effective density functional theory (DFT) calculations of equilibrium isotopic fractionation in large organic molecules. Phys Chem Chem Phys 2019; 21:17555-17570. [PMID: 31342034 DOI: 10.1039/c9cp02975c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of stable isotopes to address a wide range of biochemical, microbiological and environmental problems is hindered by the experimental difficulty and the computational cost of determining equilibrium isotopic fractionations (EIF) of large organic molecules. Here, we evaluate the factors that impact the accuracy of computed EIFs and develop a framework for cost-effective and accurate computation of EIFs by density functional theory (DFT). We generated two benchmark databases of experimentally determined EIFs, one for H isotopes and another for the isotopes of the heavy atoms C, N and O. The accuracy of several DFT exchange-correlation functionals in calculating EIFs was then evaluated by comparing the computational results to these experimental datasets. We find that with the def2-TZVP basis set, O3LYP had the lowest mean absolute deviation (21‰ and 3.9‰ for the isotopic fractionation of H and the heavier atoms, respectively), but the GGA/meta-GGA functionals τHCTHD3BJ, τHCTH and HCTH have similar performances (22‰ and 4.1‰, respectively, for τHCTHD3BJ). Leveraging the good performance of computationally efficient functionals, we provide a robust, practical, experimentally validated framework for using DFT to accurately predict EIFs of large organic molecules, including uncertainty estimates.
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Affiliation(s)
- Mark A Iron
- Computational Chemistry Unit, Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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30
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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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31
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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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32
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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: 203] [Impact Index Per Article: 40.6] [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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33
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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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34
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Ehrl B, Kundu K, Gharasoo M, Marozava S, Elsner M. Rate-Limiting Mass Transfer in Micropollutant Degradation Revealed by Isotope Fractionation in Chemostat. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:1197-1205. [PMID: 30514083 PMCID: PMC6365907 DOI: 10.1021/acs.est.8b05175] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 05/05/2023]
Abstract
Biodegradation of persistent micropollutants like pesticides often slows down at low concentrations (μg/L) in the environment. Mass transfer limitations or physiological adaptation are debated to be responsible. Although promising, evidence from compound-specific isotope fractionation analysis (CSIA) remains unexplored for bacteria adapted to this low concentration regime. We accomplished CSIA for degradation of a persistent pesticide, atrazine, during cultivation of Arthrobacter aurescens TC1 in chemostat under four different dilution rates leading to 82, 62, 45, and 32 μg/L residual atrazine concentrations. Isotope analysis of atrazine in chemostat experiments with whole cells revealed a drastic decrease in isotope fractionation with declining residual substrate concentration from ε(C) = -5.36 ± 0.20‰ at 82 μg/L to ε(C) = -2.32 ± 0.28‰ at 32 μg/L. At 82 μg/L ε(C) represented the full isotope effect of the enzyme reaction. At lower residual concentrations smaller ε(C) indicated that this isotope effect was masked indicating that mass transfer across the cell membrane became rate-limiting. This onset of mass transfer limitation appeared in a narrow concentration range corresponding to about 0.7 μM assimilable carbon. Concomitant changes in cell morphology highlight the opportunity to study the role of this onset of mass transfer limitation on the physiological level in cells adapted to low concentrations.
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Affiliation(s)
- Benno
N. Ehrl
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Kankana Kundu
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Mehdi Gharasoo
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Sviatlana Marozava
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, 81377 Munich, Germany
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35
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Labrado AL, Brunner B, Bernasconi SM, Peckmann J. Formation of Large Native Sulfur Deposits Does Not Require Molecular Oxygen. Front Microbiol 2019; 10:24. [PMID: 30740094 PMCID: PMC6355691 DOI: 10.3389/fmicb.2019.00024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/09/2019] [Indexed: 01/05/2023] Open
Abstract
Large native (i.e., elemental) sulfur deposits can be part of caprock assemblages found on top of or in lateral position to salt diapirs and as stratabound mineralization in gypsum and anhydrite lithologies. Native sulfur is formed when hydrocarbons come in contact with sulfate minerals in presence of liquid water. The prevailing model for native sulfur formation in such settings is that sulfide produced by sulfate-reducing bacteria is oxidized to zero-valent sulfur in presence of molecular oxygen (O2). Although possible, such a scenario is problematic because: (1) exposure to oxygen would drastically decrease growth of microbial sulfate-reducing organisms, thereby slowing down sulfide production; (2) on geologic timescales, excess supply with oxygen would convert sulfide into sulfate rather than native sulfur; and (3) to produce large native sulfur deposits, enormous amounts of oxygenated water would need to be brought in close proximity to environments in which ample hydrocarbon supply sustains sulfate reduction. However, sulfur stable isotope data from native sulfur deposits emplaced at a stage after the formation of the host rocks indicate that the sulfur was formed in a setting with little solute exchange with the ambient environment and little supply of dissolved oxygen. We deduce that there must be a process for the formation of native sulfur in absence of an external oxidant for sulfide. We hypothesize that in systems with little solute exchange, sulfate-reducing organisms, possibly in cooperation with other anaerobic microbial partners, drive the formation of native sulfur deposits. In order to cope with sulfide stress, microbes may shift from harmful sulfide production to non-hazardous native sulfur production. We propose four possible mechanisms as a means to form native sulfur: (1) a modified sulfate reduction process that produces sulfur compounds with an intermediate oxidation state, (2) coupling of sulfide oxidation to methanogenesis that utilizes methylated compounds, acetate or carbon dioxide, (3) ammonium oxidation coupled to sulfate reduction, and (4) sulfur comproportionation of sulfate and sulfide. We show these reactions are thermodynamically favorable and especially useful in environments with multiple stressors, such as salt and dissolved sulfide, and provide evidence that microbial species functioning in such environments produce native sulfur. Integrating these insights, we argue that microbes may form large native sulfur deposits in absence of light and external oxidants such as O2, nitrate, and metal oxides. The existence of such a process would not only explain enigmatic occurrences of native sulfur in the geologic record, but also provide an explanation for cryptic sulfur and carbon cycling beneath the seabed.
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Affiliation(s)
- Amanda L. Labrado
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | - Benjamin Brunner
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Jörn Peckmann
- Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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36
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Sulphur and carbon isotopes as tracers of past sub-seafloor microbial activity. Sci Rep 2019; 9:604. [PMID: 30679710 PMCID: PMC6345876 DOI: 10.1038/s41598-018-36943-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/27/2018] [Indexed: 11/09/2022] Open
Abstract
Microbial life below the seafloor has changed over geological time, but these changes are often not obvious, as they are not recorded in the sediment. Sulphur (S) isotope values in pyrite extracted from a Plio- to Holocene sequence of the Peru Margin (Ocean Drilling Program, ODP, Site 1229) show a down-core pattern that correlates with the pattern of carbon (C) isotopes in diagenetic dolomite. Early formation of the pyrite is indicated by the mineralogical composition of iron, showing a high degree of pyritization throughout the sedimentary sequence. Hence, the S-record could not have been substantially overprinted by later pyrite formation. The S- and C-isotope profiles show, thus, evidence for two episodes of enhanced microbial methane production with a very shallow sulphate-methane transition zone. The events of high activity are correlated with zones of elevated organic C content in the stratigraphic sequence. Our results demonstrate how isotopic signatures preserved in diagenetic mineral phases provide information on changes of past biogeochemical activity in a dynamic sub-seafloor biosphere.
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37
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Sim MS, Ogata H, Lubitz W, Adkins JF, Sessions AL, Orphan VJ, McGlynn SE. Role of APS reductase in biogeochemical sulfur isotope fractionation. Nat Commun 2019; 10:44. [PMID: 30626879 PMCID: PMC6327049 DOI: 10.1038/s41467-018-07878-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022] Open
Abstract
Sulfur isotope fractionation resulting from microbial sulfate reduction (MSR) provides some of the earliest evidence of life, and secular variations in fractionation values reflect changes in biogeochemical cycles. Here we determine the sulfur isotope effect of the enzyme adenosine phosphosulfate reductase (Apr), which is present in all known organisms conducting MSR and catalyzes the first reductive step in the pathway and reinterpret the sedimentary sulfur isotope record over geological time. Small fractionations may be attributed to low sulfate concentrations and/or high respiration rates, whereas fractionations greater than that of Apr require a low chemical potential at that metabolic step. Since Archean sediments lack fractionation exceeding the Apr value of 20‰, they are indicative of sulfate reducers having had access to ample electron donors to drive their metabolisms. Large fractionations in post-Archean sediments are congruent with a decline of favorable electron donors as aerobic and other high potential metabolic competitors evolved.
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Affiliation(s)
- Min Sub Sim
- School of Earth and Environmental Sciences, Seoul National University, Seoul, 08826, South Korea. .,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Hideaki Ogata
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany.,Institute of Low Temperature Science, Hokkaido University, Sapporo, 060-0819, Japan
| | - Wolfgang Lubitz
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany
| | - Jess F Adkins
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shawn E McGlynn
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA. .,Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, 152-8550, Japan.
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38
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Bertran E, Leavitt WD, Pellerin A, Zane GM, Wall JD, Halevy I, Wing BA, Johnston DT. Deconstructing the Dissimilatory Sulfate Reduction Pathway: Isotope Fractionation of a Mutant Unable of Growth on Sulfate. Front Microbiol 2018; 9:3110. [PMID: 30619187 PMCID: PMC6302107 DOI: 10.3389/fmicb.2018.03110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/30/2018] [Indexed: 11/13/2022] Open
Abstract
The sulfur isotope record provides key insight into the history of Earth's redox conditions. A detailed understanding of the metabolisms driving this cycle, and specifically microbial sulfate reduction (MSR), is crucial for accurate paleoenvironmental reconstructions. This includes a precise knowledge of the step-specific sulfur isotope effects during MSR. In this study, we aim at resolving the cellular-level fractionation factor during dissimilatory sulfite reduction to sulfide within MSR, and use this measured isotope effect as a calibration to enhance our understanding of the biochemistry of sulfite reduction. For this, we merge measured isotope effects associated with dissimilatory sulfite reduction with a quantitative model that explicitly links net fractionation, reaction reversibility, and intracellular metabolite levels. The highly targeted experimental aspect of this study was possible by virtue of the availability of a deletion mutant strain of the model sulfate reducer Desulfovibrio vulgaris (strain Hildenborough), in which the sulfite reduction step is isolated from the rest of the metabolic pathway owing to the absence of its QmoABC complex (ΔQmo). This deletion disrupts electron flux and prevents the reduction of adenosine phosphosulfate (APS) to sulfite. When grown in open-system steady-state conditions at 10% maximum growth rate in the presence of sulfite and lactate as electron donor, sulfur isotope fractionation factors averaged -15.9‰ (1 σ = 0.4), which appeared to be statistically indistinguishable from a pure enzyme study with dissimilatory sulfite reductase. We coupled these measurements with an understanding of step-specific equilibrium and kinetic isotope effects, and furthered our mechanistic understanding of the biochemistry of sulfite uptake and ensuing reduction. Our metabolically informed isotope model identifies flavodoxin as the most likely electron carrier performing the transfer of electrons to dissimilatory sulfite reductase. This is in line with previous work on metabolic strategies adopted by sulfate reducers under different energy regimes, and has implications for our understanding of the plasticity of this metabolic pathway at the center of our interpretation of modern and palaeo-environmental records.
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Affiliation(s)
- Emma Bertran
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MD, United States
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Cambridge, MD, United States.,Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
| | - Andre Pellerin
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Grant M Zane
- Department of Biochemistry, University of Missouri, Columbia, SC, United States
| | - Judy D Wall
- Department of Biochemistry, University of Missouri, Columbia, SC, United States
| | - Itay Halevy
- Department of Environmental Sciences and Energy Research, Weizmann Institute of Science, Rehovot, Israel
| | - Boswell A Wing
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, United States
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MD, United States
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Diamond CW, Planavsky NJ, Wang C, Lyons TW. What the ~1.4 Ga Xiamaling Formation can and cannot tell us about the mid-Proterozoic ocean. GEOBIOLOGY 2018; 16:219-236. [PMID: 29577549 DOI: 10.1111/gbi.12282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Despite a surge of recent work, the evolution of mid-Proterozoic oceanic-atmospheric redox remains heavily debated. Constraining the dynamics of Proterozoic redox evolution is essential to determine the role, if any, that anoxia played in protracting the development of eukaryotic diversity. We present a multiproxy suite of high-resolution geochemical measurements from a drill core capturing the ~1.4 Ga Xiamaling Formation, North China Craton. Specifically, we analyzed major and trace element concentrations, sulfur and molybdenum isotopes, and iron speciation not only to better understand the local redox conditions but also to establish how relevant our data are to understanding the contemporaneous global ocean. Our results suggest that throughout deposition of the Xiamaling Formation, the basin experienced varying degrees of isolation from the global ocean. During deposition of the lower organic-rich shales (130-85 m depth), the basin was extremely restricted, and the reservoirs of sulfate and trace metals were drawn down almost completely. Above a depth of 85 m, shales were deposited in dominantly euxinic waters that more closely resembled a marine system and thus potentially bear signatures of coeval seawater. In the most highly enriched sample from this upper interval, the concentration of molybdenum is 51 ppm with a δ98 Mo value of +1.7‰. Concentrations of Mo and other redox-sensitive elements in our samples are consistent with a deep ocean that was largely anoxic on a global scale. Our maximum δ98 Mo value, in contrast, is high compared to published mid-Proterozoic data. This high value raises the possibility that the Earth's surface environments were transiently more oxygenated at ~1.4 Ga compared to preceding or postdating times. More broadly, this study demonstrates the importance of integrating all available data when attempting to reconstruct surface O2 dynamics based on rocks of any age.
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Affiliation(s)
- C W Diamond
- Department of Earth Sciences, University of California, Riverside, CA, USA
| | - N J Planavsky
- Department of Geology and Geophysics, Yale University, New Haven, CT, USA
| | - C Wang
- State Key Laboratory of Petroleum Resources and Prospecting, China University of Petroleum, Beijing, China
| | - T W Lyons
- Department of Earth Sciences, University of California, Riverside, CA, USA
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40
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Antler G, Pellerin A. A Critical Look at the Combined Use of Sulfur and Oxygen Isotopes to Study Microbial Metabolisms in Methane-Rich Environments. Front Microbiol 2018; 9:519. [PMID: 29681890 PMCID: PMC5898156 DOI: 10.3389/fmicb.2018.00519] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
Separating the contributions of anaerobic oxidation of methane and organoclastic sulfate reduction in the overall sedimentary sulfur cycle of marine sediments has benefited from advances in isotope biogeochemistry. Particularly, the coupling of sulfur and oxygen isotopes measured in the residual sulfate pool (δ18OSO4 vs. δ34SSO4). Yet, some important questions remain. Recent works have observed patterns that are inconsistent with previous interpretations. We differentiate the contributions of oxygen and sulfur isotopes to separating the anaerobic oxidation of methane and organoclastic sulfate reduction into three phases; first evidence from conventional high methane vs. low methane sites suggests a clear relationship between oxygen and sulfur isotopes in porewater and the metabolic process taking place. Second, evidence from pure cultures and organic matter rich sites with low levels of methane suggest the signatures of both processes overlap and cannot be differentiated. Third, we take a critical look at the use of oxygen and sulfur isotopes to differentiate metabolic processes (anaerobic oxidation of methane vs. organoclastic sulfate reduction). We identify that it is essential to develop a better understanding of the oxygen kinetic isotope effect, the degree of isotope exchange with sulfur intermediates as well as establishing their relationships with the cell-specific metabolic rates if we are to develop this proxy into a reliable tool to study the sulfur cycle in marine sediments and the geological record.
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Affiliation(s)
- Gilad Antler
- Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom.,Department of Geological and Environmental Sciences, Ben-Gurion University of the Negev, Beersheba, Israel.,The Interuniversity Institute for Marine Sciences, Eilat, Israel
| | - André Pellerin
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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41
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Pellerin A, Wenk CB, Halevy I, Wing BA. Sulfur Isotope Fractionation by Sulfate-Reducing Microbes Can Reflect Past Physiology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:4013-4022. [PMID: 29505248 DOI: 10.1021/acs.est.7b05119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sulfur (S) isotope fractionation by sulfate-reducing microorganisms is a direct manifestation of their respiratory metabolism. This fractionation is apparent in the substrate (sulfate) and waste (sulfide) produced. The sulfate-reducing metabolism responds to variability in the local environment, with the response determined by the underlying genotype, resulting in the expression of an "isotope phenotype". Sulfur isotope phenotypes have been used as a diagnostic tool for the metabolic activity of sulfate-reducing microorganisms in the environment. Our experiments with Desulfovibrio vulgaris Hildenborough (DvH) grown in batch culture suggest that the S isotope phenotype of sulfate respiring microbes may lag environmental changes on time scales that are longer than generational. When inocula from different phases of growth are assayed under the same environmental conditions, we observed that DvH exhibited different net apparent fractionations of up to -9‰. The magnitude of fractionation was weakly correlated with physiological parameters but was strongly correlated to the age of the initial inoculum. The S isotope fractionation observed between sulfate and sulfide showed a positive correlation with respiration rate, contradicting the well-described negative dependence of fractionation on respiration rate. Quantitative modeling of S isotope fractionation shows that either a large increase (≈50×) in the abundance of sulfate adenylyl transferase (Sat) or a smaller increase in sulfate transport proteins (≈2×) is sufficient to account for the change in fractionation associated with past physiology. Temporal transcriptomic studies with DvH imply that expression of sulfate permeases doubles over the transition from early exponential to early stationary phase, lending support to the transport hypothesis proposed here. As it is apparently maintained for multiple generations (≈1-6) of subsequent growth in the assay environment, we suggest that this fractionation effect acts as a sort of isotopic "memory" of a previous physiological and environmental state. Whatever its root cause, this physiological hysteresis effect can explain variations in fractionations observed in many environments. It may also enable new insights into life at energetic limits, especially if its historical footprint extends deeper than generational.
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Affiliation(s)
- André Pellerin
- Center for Geomicrobiology, Department of Bioscience , Aarhus University , Ny Munkegade 114 , Aarhus C 8000 , Denmark
| | - Christine B Wenk
- Department of Earth and Planetary Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Itay Halevy
- Department of Earth and Planetary Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Boswell A Wing
- Geological Sciences , University of Colorado Boulder , UCB 399, Boulder , Colorado 80309-0399 , United States
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42
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Ehrl B, Gharasoo M, Elsner M. Isotope Fractionation Pinpoints Membrane Permeability as a Barrier to Atrazine Biodegradation in Gram-negative Polaromonas sp. Nea-C. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:4137-4144. [PMID: 29495658 PMCID: PMC6331012 DOI: 10.1021/acs.est.7b06599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Biodegradation of persistent pesticides like atrazine often stalls at low concentrations in the environment. While mass transfer does not limit atrazine degradation by the Gram-positive Arthrobacter aurescens TC1 at high concentrations (>1 mg/L), evidence of bioavailability limitations is emerging at trace concentrations (<0.1 mg/L). To assess the bioavailability constraints on biodegradation, the roles of cell wall physiology and transporters remain imperfectly understood. Here, compound-specific isotope analysis (CSIA) demonstrates that cell wall physiology (i.e., the difference between Gram-negative and Gram-positive bacteria) imposes mass transfer limitations in atrazine biodegradation even at high concentrations. Atrazine biodegradation by Gram-negative Polaromonas sp. Nea-C caused significantly less isotope fractionation (ε(C) = -3.5 ‰) than expected for hydrolysis by the enzyme TrzN (ε(C) = -5.0 ‰) and observed in Gram-positive Arthrobacter aurescens TC1 (ε(C) = -5.4 ‰). Isotope fractionation was recovered in cell-free extracts (ε(C) = -5.3 ‰) where no cell envelope restricted pollutant uptake. When active transport was inhibited with cyanide, atrazine degradation rates remained constant demonstrating that atrazine mass transfer across the cell envelope does not depend on active transport but is a consequence of passive cell wall permeation. Taken together, our results identify the cell envelope of the Gram-negative bacterium Polaromonas sp. Nea-C as a relevant barrier for atrazine biodegradation.
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Affiliation(s)
- Benno
N. Ehrl
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Mehdi Gharasoo
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
- Chair
of Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, 81377 Munich, Germany
- E-mail: . Tel.: +49 89 2180-78232
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43
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Dalby FR, Hansen MJ, Feilberg A. Application of Proton-Transfer-Reaction Mass Spectrometry (PTR-MS) and 33S Isotope Labeling for Monitoring Sulfur Processes in Livestock Waste. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:2100-2107. [PMID: 29338206 DOI: 10.1021/acs.est.7b04570] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Reduced sulfur compounds emitted from livestock production cause odor nuisance for local residents. The microbial processes responsible for this are not well described in swine manure and a method for monitoring the biological processes is necessary to develop strategic abatement technologies. In this study, Proton-Transfer-Reaction Mass Spectrometry and isotope-labeled sulfate were combined and applied to elucidate the sulfur processes in swine manure with high time resolution. We successfully monitored reduction of isotope 33S labeled sulfate into corresponding 33S hydrogen sulfide and found that some of the 33S hydrogen sulfide was further methylated into 33S methanethiol. The isotope patterns in reduced sulfur compounds together with usage of inhibitors enabled us to calculate a sulfate reduction rate of 1.03 ± 0.18 mM/day equivalent to 76.9 ± 3.0% of total hydrogen sulfide emissions. Cysteine degradation constituted 20.2 ± 2.7% of the total hydrogen sulfide produced and the remaining hydrogen sulfide came from demethylation of methanethiol and dimethyl sulfide. Another source to methanethiol, besides hydrogen sulfide methylation, was methionine degradation, which contributed with 78.3 ± 2.5% of the methanethiol production, whereas the remaining 21.7 ± 2.5% came from hydrogen sulfide methylation. This study suggests, therefore, that emissions of odorous sulfur compounds from swine manure can be reduced by inhibiting methionine degradation and sulfate reduction.
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Affiliation(s)
- Frederik R Dalby
- Department of Engineering, Aarhus University , Hangøvej 2, 8200 Aarhus N, Denmark
| | - Michael J Hansen
- Department of Engineering, Aarhus University , Hangøvej 2, 8200 Aarhus N, Denmark
| | - Anders Feilberg
- Department of Engineering, Aarhus University , Hangøvej 2, 8200 Aarhus N, Denmark
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44
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Wenk CB, Wing BA, Halevy I. Electron carriers in microbial sulfate reduction inferred from experimental and environmental sulfur isotope fractionations. THE ISME JOURNAL 2018; 12:495-507. [PMID: 29087380 PMCID: PMC5776465 DOI: 10.1038/ismej.2017.185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/26/2017] [Accepted: 09/24/2017] [Indexed: 01/29/2023]
Abstract
Dissimilatory sulfate reduction (DSR) has been a key process influencing the global carbon cycle, atmospheric composition and climate for much of Earth's history, yet the energy metabolism of sulfate-reducing microbes remains poorly understood. Many organisms, particularly sulfate reducers, live in low-energy environments and metabolize at very low rates, requiring specific physiological adaptations. We identify one such potential adaptation-the electron carriers selected for survival under energy-limited conditions. Employing a quantitative biochemical-isotopic model, we find that the large S isotope fractionations (>55‰) observed in a wide range of natural environments and culture experiments at low respiration rates are only possible when the standard-state Gibbs free energy (ΔG'°) of all steps during DSR is more positive than -10 kJ mol-1. This implies that at low respiration rates, only electron carriers with modestly negative reduction potentials are involved, such as menaquinone, rubredoxin, rubrerythrin or some flavodoxins. Furthermore, the constraints from S isotope fractionation imply that ferredoxins with a strongly negative reduction potential cannot be the direct electron donor to S intermediates at low respiration rates. Although most sulfate reducers have the genetic potential to express a variety of electron carriers, our results suggest that a key physiological adaptation of sulfate reducers to low-energy environments is to use electron carriers with modestly negative reduction potentials.
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Affiliation(s)
- Christine B Wenk
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel.
| | - Boswell A Wing
- Department of Geological Sciences, University of Colorado, Boulder, CO, USA
| | - Itay Halevy
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel.
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45
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Gomes ML, Fike DA, Bergmann KD, Jones C, Knoll AH. Environmental insights from high-resolution (SIMS) sulfur isotope analyses of sulfides in Proterozoic microbialites with diverse mat textures. GEOBIOLOGY 2018; 16:17-34. [PMID: 29047210 DOI: 10.1111/gbi.12265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 09/01/2017] [Indexed: 06/07/2023]
Abstract
In modern microbial mats, hydrogen sulfide shows pronounced sulfur isotope (δ34 S) variability over small spatial scales (~50‰ over <4 mm), providing information about microbial sulfur cycling within different ecological niches in the mat. In the geological record, the location of pyrite formation, overprinting from mat accretion, and post-depositional alteration also affect both fine-scale δ34 S patterns and bulk δ34 Spyrite values. We report μm-scale δ34 S patterns in Proterozoic samples with well-preserved microbial mat textures. We show a well-defined relationship between δ34 S values and sulfide mineral grain size and type. Small pyrite grains (<25 μm) span a large range, tending toward high δ34 S values (-54.5‰ to 11.7‰, mean: -14.4‰). Larger pyrite grains (>25 μm) have low but equally variable δ34 S values (-61.0‰ to -10.5‰, mean: -44.4‰). In one sample, larger sphalerite grains (>35 μm) have intermediate and essentially invariant δ34 S values (-22.6‰ to -15.6‰, mean: -19.4‰). We suggest that different sulfide mineral populations reflect separate stages of formation. In the first stage, small pyrite grains form near the mat surface along a redox boundary where high rates of sulfate reduction, partial closed-system sulfate consumption in microenvironments, and/or sulfide oxidation lead to high δ34 S values. In another stage, large sphalerite grains with low δ34 S values grow along the edges of pore spaces formed from desiccation of the mat. Large pyrite grains form deeper in the mat at slower sulfate reduction rates, leading to low δ34 Ssulfide values. We do not see evidence for significant 34 S-enrichment in bulk pore water sulfide at depth in the mat due to closed-system Rayleigh fractionation effects. On a local scale, Rayleigh fractionation influences the range of δ34 S values measured for individual pyrite grains. Fine-scale analyses of δ34 Spyrite patterns can thus be used to extract environmental information from ancient microbial mats and aid in the interpretation of bulk δ34 Spyrite records.
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Affiliation(s)
- M L Gomes
- Washington University, Saint Louis, MO, USA
- Harvard University, Cambridge, MA, USA
| | - D A Fike
- Washington University, Saint Louis, MO, USA
| | - K D Bergmann
- Massachusettes Institute of Technology, Cambridge, MA, USA
| | - C Jones
- Washington University, Saint Louis, MO, USA
| | - A H Knoll
- Harvard University, Cambridge, MA, USA
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46
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Pontefract A, Zhu TF, Walker VK, Hepburn H, Lui C, Zuber MT, Ruvkun G, Carr CE. Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars. Front Microbiol 2017; 8:1819. [PMID: 29018418 PMCID: PMC5623196 DOI: 10.3389/fmicb.2017.01819] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/06/2017] [Indexed: 11/13/2022] Open
Abstract
Life can persist under severe osmotic stress and low water activity in hypersaline environments. On Mars, evidence for the past presence of saline bodies of water is prevalent and resulted in the widespread deposition of sulfate and chloride salts. Here we investigate Spotted Lake (British Columbia, Canada), a hypersaline lake with extreme (>3 M) levels of sulfate salts as an exemplar of the conditions thought to be associated with ancient Mars. We provide the first characterization of microbial structure in Spotted Lake sediments through metagenomic sequencing, and report a bacteria-dominated community with abundant Proteobacteria, Firmicutes, and Bacteroidetes, as well as diverse extremophiles. Microbial abundance and functional comparisons reveal similarities to Ace Lake, a meromictic Antarctic lake with anoxic and sulfidic bottom waters. Our analysis suggests that hypersaline-associated species occupy niches characterized foremost by differential abundance of Archaea, uncharacterized Bacteria, and Cyanobacteria. Potential biosignatures in this environment are discussed, specifically the likelihood of a strong sulfur isotopic fractionation record within the sediments due to the presence of sulfate reducing bacteria. With its high sulfate levels and seasonal freeze-thaw cycles, Spotted Lake is an analog for ancient paleolakes on Mars in which sulfate salt deposits may have offered periodically habitable environments, and could have concentrated and preserved organic materials or their biomarkers over geologic time.
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Affiliation(s)
- Alexandra Pontefract
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Ting F Zhu
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | - Holli Hepburn
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Clarissa Lui
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Maria T Zuber
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Christopher E Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
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47
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Zaarur S, Wang DT, Ono S, Bosak T. Influence of Phosphorus and Cell Geometry on the Fractionation of Sulfur Isotopes by Several Species of Desulfovibrio during Microbial Sulfate Reduction. Front Microbiol 2017; 8:890. [PMID: 28611734 PMCID: PMC5447228 DOI: 10.3389/fmicb.2017.00890] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/02/2017] [Indexed: 12/02/2022] Open
Abstract
We investigated the influence of organic substrates and phosphate concentration on the rates of dissimilatory microbial sulfate reduction and the 34S/32S isotopic fractionation produced by several Desulfovibrio species. Our experiments corroborate the previously reported species-specific correlation between sulfur isotope fractionation and cell-specific sulfate reduction rates. We also identify cell size as a key factor that contributes to the species-effect of this correlation. Phosphate limitation results in larger cells and contributes to a small decrease in sulfur isotope fractionation concomitant with an apparent increase in cell-specific sulfate reduction rates. Sulfur isotope fractionation in phosphate-limited cultures asymptotically approaches a lower limit of approximately 5‰ as cell-specific sulfate reduction rates increase to >100 fmol cell−1 day−1. These experimental results test models that link the reversibilities of enzymatic steps in dissimilatory sulfate reduction to sulfur isotope fractionation and show that these models can provide consistent predictions across large variations in physiological states experienced by sulfate reducing bacteria.
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Affiliation(s)
- Shikma Zaarur
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of TechnologyCambridge, MA, United States
| | - David T Wang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of TechnologyCambridge, MA, United States
| | - Shuhei Ono
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of TechnologyCambridge, MA, United States
| | - Tanja Bosak
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of TechnologyCambridge, MA, United States
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48
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Guo H, Zhou Y, Jia Y, Tang X, Li X, Shen M, Lu H, Han S, Wei C, Norra S, Zhang F. Sulfur Cycling-Related Biogeochemical Processes of Arsenic Mobilization in the Western Hetao Basin, China: Evidence from Multiple Isotope Approaches. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:12650-12659. [PMID: 27797497 DOI: 10.1021/acs.est.6b03460] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The role of sulfur cycling in arsenic behavior under reducing conditions is not well-understood in previous investigations. This study provides observations of sulfur and oxygen isotope fractionation in sulfate and evaluation of sulfur cycling-related biogeochemical processes controlling dissolved arsenic groundwater concentrations using multiple isotope approaches. As a typical basin hosting high arsenic groundwater, the western Hetao basin was selected as the study area. Results showed that, along the groundwater flow paths, groundwater δ34SSO4, δ18OSO4, and δ13CDOC increased with increases in arsenic, dissolved iron, hydrogen sulfide and ammonium concentrations, while δ13CDIC decreased with decreasing Eh and sulfate/chloride. Bacterial sulfate reduction (BSR) was responsible for many of these observed changes. The δ34SSO4 indicated that dissolved sulfate was mainly sourced from oxidative weathering of sulfides in upgradient alluvial fans. The high oxygen-sulfur isotope fractionation ratio (0.60) may result from both slow sulfate reduction rates and bacterial disproportionation of sulfur intermediates (BDSI). Data indicate that both the sulfide produced by BSR and the overall BDSI reduce arsenic-bearing iron(III) oxyhydroxides, leading to the release of arsenic into groundwater. These results suggest that sulfur-related biogeochemical processes are important in mobilizing arsenic in aquifer systems.
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Affiliation(s)
- Huaming Guo
- State Key Laboratory of Biogeology and Environmental Geology, School of Water Resources and Environment, China University of Geosciences (Beijing) , Beijing 100083, China
| | - Yinzhu Zhou
- State Key Laboratory of Biogeology and Environmental Geology, School of Water Resources and Environment, China University of Geosciences (Beijing) , Beijing 100083, China
| | - Yongfeng Jia
- State Key Laboratory of Biogeology and Environmental Geology, School of Water Resources and Environment, China University of Geosciences (Beijing) , Beijing 100083, China
| | - Xiaohui Tang
- Institute of Applied Geosciences, Karlsruhe Institute of Technology , Karlsruhe 76131, Germany
| | - Xiaofeng Li
- State Key Laboratory of Biogeology and Environmental Geology, School of Water Resources and Environment, China University of Geosciences (Beijing) , Beijing 100083, China
| | - Mengmeng Shen
- State Key Laboratory of Biogeology and Environmental Geology, School of Water Resources and Environment, China University of Geosciences (Beijing) , Beijing 100083, China
| | - Hai Lu
- The National Institute of Metrology , Beijing 100013, P.R. China
| | - Shuangbao Han
- Center for Hydrogeology and Environmental Geology, China Geological Survey , Baoding 071051, Hebei China
| | - Chao Wei
- The National Institute of Metrology , Beijing 100013, P.R. China
| | - Stefan Norra
- Institute of Applied Geosciences, Karlsruhe Institute of Technology , Karlsruhe 76131, Germany
| | - Fucun Zhang
- Center for Hydrogeology and Environmental Geology, China Geological Survey , Baoding 071051, Hebei China
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49
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Leavitt WD, Venceslau SS, Pereira IAC, Johnston DT, Bradley AS. Fractionation of sulfur and hydrogen isotopes in Desulfovibrio vulgaris with perturbed DsrC expression. FEMS Microbiol Lett 2016; 363:fnw226. [PMID: 27702753 DOI: 10.1093/femsle/fnw226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2016] [Indexed: 12/11/2022] Open
Abstract
Dissimilatory sulfate reduction is the central microbial metabolism in global sulfur cycling. Understanding the importance of sulfate reduction to Earth's biogeochemical S cycle requires aggregating single-cell processes with geochemical signals. For sulfate reduction, these signals include the ratio of stable sulfur isotopes preserved in minerals, as well as the hydrogen isotope ratios and structures of microbial membrane lipids preserved in organic matter. In this study, we cultivated the model sulfate reducer, Desulfovibrio vulgaris DSM 644T, to investigate how these parameters were perturbed by changes in expression of the protein DsrC. DsrC is critical to the final metabolic step in sulfate reduction to sulfide. S and H isotopic fractionation imposed by the wild type was compared to three mutants. Discrimination against 34S in sulfate, as calculated from the residual reactant, did not discernibly differ among all strains. However, a closed-system sulfur isotope distillation model, based on accumulated sulfide, produced inconsistent results in one mutant strain IPFG09. Lipids produced by IPFG09 were also slightly enriched in 2H. These results suggest that DsrC alone does not have a major impact on sulfate-S, though may influence sulfide-S and lipid-H isotopic compositions. While intriguing, a mechanistic explanation requires further study under continuous culture conditions.
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Affiliation(s)
- William D Leavitt
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA .,Department of Earth Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA .,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
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50
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Cui H, Kaufman AJ, Xiao S, Peek S, Cao H, Min X, Cai Y, Siegel Z, Liu XM, Peng Y, Schiffbauer JD, Martin AJ. Environmental context for the terminal Ediacaran biomineralization of animals. GEOBIOLOGY 2016; 14:344-363. [PMID: 27038407 DOI: 10.1111/gbi.12178] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/19/2016] [Indexed: 06/05/2023]
Abstract
In terminal Ediacaran strata of South China, the onset of calcareous biomineralization is preserved in the paleontological transition from Conotubus to Cloudina in repetitious limestone facies of the Dengying Formation. Both fossils have similar size, funnel-in-funnel construction, and epibenthic lifestyle, but Cloudina is biomineralized, whereas Conotubus is not. To provide environmental context for this evolutionary milestone, we conducted a high-resolution elemental and stable isotope study of the richly fossiliferous Gaojiashan Member. Coincident with the first appearance of Cloudina is a significant positive carbonate carbon isotope excursion (up to +6‰) and an increase in the abundance and (34) S composition of pyrite. In contrast, δ(34) S values of carbonate-associated sulfate remain steady throughout the succession, resulting in anomalously large (>70‰) sulfur isotope fractionations in the lower half of the member. The fractionation trend likely relates to changes in microbial communities, with sulfur disproportionation involved in the lower interval, whereas microbial sulfate reduction was the principal metabolic pathway in the upper. We speculate that the coupled paleontological and biogeochemical anomalies may have coincided with an increase in terrestrial weathering fluxes of sulfate, alkalinity, and nutrients to the depositional basin, which stimulated primary productivity, the spread of an oxygen minimum zone, and the development of euxinic conditions in subtidal and basinal environments. Enhanced production and burial of organic matter is thus directly connected to the carbon isotope anomaly, and likely promoted pyritization as the main taphonomic pathway for Conotubus and other soft-bodied Ediacara biotas. Our studies suggest that the Ediacaran confluence of ecological pressures from predation and environmental pressures from an increase in seawater alkalinity set the stage for an unprecedented geobiological response: the evolutionary novelty of animal biomineralization.
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Affiliation(s)
- H Cui
- Department of Geology, University of Maryland, College Park, MD, USA
- Department of Geoscience and NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - A J Kaufman
- Department of Geology, University of Maryland, College Park, MD, USA
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD, USA
| | - S Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
| | - S Peek
- Department of Geology, University of Maryland, College Park, MD, USA
| | - H Cao
- Department of Geology, University of Maryland, College Park, MD, USA
| | - X Min
- Department of Geology, Northwest University, Xi'an, China
| | - Y Cai
- Department of Geology, Northwest University, Xi'an, China
| | - Z Siegel
- Bethesda-Chevy Chase High School, Bethesda, MD, USA
| | - X-M Liu
- Department of Geological Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Y Peng
- Department of Geology and Geophysics, Louisiana State University, Baton Rouge, LA, USA
| | - J D Schiffbauer
- Department of Geological Sciences, University of Missouri, Columbia, MO, USA
| | - A J Martin
- División de Geociencias Aplicadas, IPICYT, San Luis Potosí, Mexico
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