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Lindsay MR, D’Angelo T, Munson-McGee JH, Saidi-Mehrabad A, Devlin M, McGonigle J, Goodell E, Herring M, Lubelczyk LC, Mascena C, Brown JM, Gavelis G, Liu J, Yousavich DJ, Hamilton-Brehm SD, Hedlund BP, Lang S, Treude T, Poulton NJ, Stepanauskas R, Moser DP, Emerson D, Orcutt BN. Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem. Proc Natl Acad Sci U S A 2024; 121:e2309636121. [PMID: 38573964 PMCID: PMC11009646 DOI: 10.1073/pnas.2309636121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024] Open
Abstract
Rates of microbial processes are fundamental to understanding the significance of microbial impacts on environmental chemical cycling. However, it is often difficult to quantify rates or to link processes to specific taxa or individual cells, especially in environments where there are few cultured representatives with known physiology. Here, we describe the use of the redox-enzyme-sensitive molecular probe RedoxSensor™ Green to measure rates of anaerobic electron transfer physiology (i.e., sulfate reduction and methanogenesis) in individual cells and link those measurements to genomic sequencing of the same single cells. We used this method to investigate microbial activity in hot, anoxic, low-biomass (~103 cells mL-1) groundwater of the Death Valley Regional Flow System, California. Combining this method with electron donor amendment experiments and metatranscriptomics confirmed that the abundant spore formers including Candidatus Desulforudis audaxviator were actively reducing sulfate in this environment, most likely with acetate and hydrogen as electron donors. Using this approach, we measured environmental sulfate reduction rates at 0.14 to 26.9 fmol cell-1 h-1. Scaled to volume, this equates to a bulk environmental rate of ~103 pmol sulfate L-1 d-1, similar to potential rates determined with radiotracer methods. Despite methane in the system, there was no evidence for active microbial methanogenesis at the time of sampling. Overall, this method is a powerful tool for estimating species-resolved, single-cell rates of anaerobic metabolism in low-biomass environments while simultaneously linking genomes to phenomes at the single-cell level. We reveal active elemental cycling conducted by several species, with a large portion attributable to Ca. Desulforudis audaxviator.
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Affiliation(s)
| | | | | | | | - Molly Devlin
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Julia McGonigle
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Elizabeth Goodell
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Geology, Oberlin College, Oberlin, OH44074
| | - Melissa Herring
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA02115
| | | | | | - Julia M. Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Greg Gavelis
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Jiarui Liu
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | - D. J. Yousavich
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | - Brian P. Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Susan Lang
- School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC29208
| | - Tina Treude
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
- Department of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | | | - Duane P. Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
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