Using Isotope Probing of Microbe-to-Microbe Interactions to Determine the Fate of Carbon and Impacts on Climate Change

Ty Samo | 19-LW-044

Project Overview

Microbes control carbon (C) cycling on Earth. In particular, marine bacteria play an outsized role since the oceans are the primary conduit through which the greenhouse gas carbon dioxide is absorbed and stored. However, we lack a refined understanding of carbon fate, and this precludes our ability to link microbial metabolism with geochemical predictions. Such knowledge is especially necessary to compare current conditions versus future climate impacts that are warming and acidifying the oceans. Through a collaboration with California Polytechnic State University, we have developed a saltwater chemistry manipulation system to adjust the carbon dioxide, oxygen, and temperature conditions of microbial cultures to mimic conditions in the year 2100. Experimental work has addressed the inherent complexity of microbial communities and chemical makeup of marine ecosystems by applying a simplified experimental system that examined the abilities of a library of 16 diverse bacterial isolates to incorporate and metabolize glycolate, a concentrated and ubiquitous marine organic compound, using genomic analyses and isotope tracing at the single-cell and bulk levels. Nanoscale secondary ion mass spectrometry (NanoSIMS) performed on over 500 cells revealed that 11 of the isolates incorporated large quantities of 13C-glycolate to reveal high affinity for the compound. Comparative genomics of the bacteria confirmed these uptake patterns in some, but not all, cases, which highlighted how differences in gene content can significantly influence the magnitude to which individual bacteria can impact marine chemistry. In the final stage of the project, we added complexity to this investigation of carbon fate by performing experiments in which bacterial isolates were grown with 13C-glycolate side-by-side but separated by a membrane that only allowed water, chemicals, and salt exchange. A glycolate incorporator was grown on one side and non-incorporator was grown on the other. As expected, the glycolate incorporator became 13C-labeled, and, interestingly, the non-incorporator became significantly labeled as well. This '€˜cross-feeding' phenomenon was dependent on the species of incorporator and non-incorporator being examined, suggesting that bacterially excreted secondary products are, in themselves, significant sources of carbon that can be further metabolized by different bacterial species, thereby influencing carbon cycling ad infinitum.

Mission Impact

This research contributes to Lawrence Livermore National Laboratory's mission of characterizing planetary carbon by aligning with and strengthening the Director's initiative "Engineering the Carbon Economy." New isotope tracing and culturing methods have been introduced, and new interactions with academia have been fostered to provide a new research tool available for the Laboratory's growing aquatic research program. Our comprehensive analyses of microbial metabolism to characterize complex biological systems and their transport of carbon supports the DOE goal of delivering the scientific discoveries and tools that transform our understanding of nature and strengthen the connection between advances in fundamental science and technology innovation. This project supports the NNSA goal to advance the science, technology, and engineering competencies that are the foundation of the NNSA mission. This project also supports the Laboratory's core competencies in energy and climate security, nuclear, chemical, and isotopic sciences, bioscience and bioengineering, and earth and atmospheric science.

Publications, Presentations, and Patents

Samo, T.J., et al. 2019. "Insights on algal-bacterial symbioses mediated by metabolite exchange and organic matter remineralization." Gordon Research Conference - Environmental Microbiology, South Hadley, MA, July 2019. LLNL-POST-791481.

Samo, T.J., et al. 2020. "Determining bacterially mediated fate of carbon: A stable isotope approach with a selection of cultivated marine bacteria." Ocean Sciences Meeting, San Diego, CA, February 2020. LLNL-PRES-805478.