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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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Magnuson E, Mykytczuk NC, Pellerin A, Goordial J, Twine SM, Wing B, Foote SJ, Fulton K, Whyte LG. Thiomicrorhabdus
streamers and sulfur cycling in perennial hypersaline cold springs in the Canadian high Arctic. Environ Microbiol 2020; 23:3384-3400. [DOI: 10.1111/1462-2920.14916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 12/10/2019] [Accepted: 01/08/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Elisse Magnuson
- Natural Resource Sciences McGill University Montreal QC Canada
| | | | - Andre Pellerin
- Centre for Geomicrobiology Aarhus University Aarhus Denmark
| | - Jacqueline Goordial
- Natural Resource Sciences McGill University Montreal QC Canada
- School of Environmental Sciences University of Guelph Guelph, ON Canada
| | - Susan M. Twine
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Boswell Wing
- Earth and Planetary Sciences McGill University Montreal QC Canada
| | - Simon J. Foote
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Kelly Fulton
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Lyle G. Whyte
- Natural Resource Sciences McGill University Montreal QC Canada
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3
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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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4
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Perrot V, Landing WM, Grubbs RD, Salters VJM. Mercury bioaccumulation in tilefish from the northeastern Gulf of Mexico 2 years after the Deepwater Horizon oil spill: Insights from Hg, C, N and S stable isotopes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:828-838. [PMID: 30818207 DOI: 10.1016/j.scitotenv.2019.02.295] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/18/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Mercury (Hg) concentration in fish of the Gulf of the Mexico (GoM) is a major concern due to the importance of the GoM for U.S. fisheries. The Deepwater Horizon (DWH) oil spill in April 2010 in the northern GoM resulted in large amounts of oil and dispersant released to the water column, which potentially modified Hg bioaccumulation patterns in affected areas. We measured Hg species (methylmercury (MMHg) and inorganic Hg (IHg)) concentrations, and light (C, N and S) and Hg stable isotopes in muscle and liver tissues from tilefish (Lopholatilus chamaleonticeps) sampled in 2012 and 2013 along the shelf break of the northeastern GoM. Fish located close to the mouth of the Mississippi River (MR) and northwest of the DWH well-head (47 km) showed significantly lower Hg levels in muscle and liver than fish located further northeast of the DWH (>109 km), where 98% of tilefish had Hg levels in the muscle above US consumption advisory thresholds (50% for tilefish close to the DWH). Differences in light and Hg stable isotopes signatures were observed between these two areas, showing higher δ15N, and lower δ202Hg, Δ199Hg and δ34S in fish close to the DWH/MR. This suggests that suspended particles from the MR reduces Hg bioavailability at the base of the GoM food chains. This phenomenon can be locally enhanced by the DWH that resulted in increased particles in the water column as evidenced by the marine snow layer in the sediments. On the other hand, freshly deposited Hg associated with organic matter in more oligotrophic marine waters enhanced Hg bioaccumulation in local food webs. Comparing Hg isotopic composition in liver and muscle of fish indicates specific metabolic response in fish having accumulated high levels of MMHg.
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Affiliation(s)
- Vincent Perrot
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA.
| | - William M Landing
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, 117 N. Woodward Ave, Tallahassee, FL 32306, USA
| | - R Dean Grubbs
- Coastal and Marine Laboratory, Florida State University, 3618 Coastal Highway 98, St. Teresa, FL 32358-2702, USA
| | - Vincent J M Salters
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
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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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6
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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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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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8
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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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