ECIMMEE Project: Forging the Missing Link: A Protein-Level View of Marine Microbial Ecology
Proteomic analysis — the identification of proteins in complex biological samples, and the quantification of protein-level gene expression — can enable quantitative, mechanistic connections between large-scale measurements of the chemical state of the oceans and of the genomic diversity in marine microbial ecosystems. In this project, we will use proteomics to gain new insights into two key aspects of marine microbial biogeochemistry: nitrogen limitation and anoxygenic phototrophy. Nitrogen availability is one of the most globally significant ecological pressures shaping the physiology and evolution of marine microbes, limiting primary production throughout much of the tropical and subtropical surface ocean. Since typically more than 80% of a cell’s nitrogen is in protein, N limitation is fundamentally a constraint on protein production, yet many questions remain about the molecular basis of this phenomenon in protein-level gene expression. Proteomic analysis can lend new insight into marine N limitation by quantification of community proteome abundance scales across spatial and temporal biogeochemical gradients. And while significant contributions of anoxygenic phototrophy to the metabolic energy budget of marine microbial communities (e.g., ATP production by proteorhodopsin-based phototrophy) have been hypothesized based on the abundance and diversity of sequences for these genes in marine metagenomic and metatranscriptomic datasets, testing this hypothesis has proven challenging. Measurement of the protein machinery that enables these metabolisms is a direct means to quantify their role in energy transduction. High-resolution proteomic measurements can also identify the primary organisms responsible for different modes of anoxygenic phototrophy in a range of oceanic habitats.
Jacob Waldbauer is a Neubauer Family assistant professor in the Department of the Geophysical Sciences at the University of Chicago. His research combines field observations and laboratory experiments to explore the metabolic basis of biogeochemical fluxes, how microbial community response to environmental perturbations shapes biogeochemical feedbacks, and the molecular fossil record of past life and environments. His laboratory develops novel molecular analytical techniques, particularly using high-resolution mass spectrometry, to address outstanding questions in biogeoscience. He received a B.A. in Physics and Astronomy from Dartmouth College and a Ph.D. in Chemical Oceanography from the MIT/WHOI Joint Program, and was a Stanback/Beckman Postdoctoral Fellow at Caltech. He is the recipient of an Alfred P. Sloan Foundation Research Fellowship in Ocean Sciences and of the Cozzarelli Prize from the National Academy of Sciences.