Linking amino acid sequences to sources and fates of organic matter in aquatic systems

Abstract

Proteins enact life’s intent. These macromolecules, directed by genes and informed by the environment, are the engines that power the cells of all biological entities on Earth. From viruses and bacteria to humans and blue whales, proteins serve a vast range of metabolic, transport, communication, and structural purposes. Along with geological and chemical drivers, protein-driven biological processes modulate planetary cycles of carbon, oxygen, and nitrogen. By unlocking the information stored in peptide and protein sequences, we can learn the biological origins and functions of cells within a community. For organic geochemists, there is useful information here as well: proteins make up a large proportion of organic carbon and nitrogen in aquatic systems. Thus, the cycling and degradation dynamic of proteins is of great importance when thinking about global organic carbon preservation and sequestration. The dissertation I present here addresses the cycling of proteins and protein-derived organic matter in both laboratory settings and environmental systems. Chapter 2, my M.S. project, describes the usefulness of integrating a different kind of peptide sequencing, de novo sequencing, into the traditional environmental proteomics workflow to access degraded and unanticipated sequences. This is described in “Protein cycling in the eastern tropical North Pacific oxygen deficient zone: a de novo-assisted peptidomic approach”, (Duffy et al., in press). The three subsequent projects utilize this technique to ask questions about proteins and peptide cycling in complex environmental systems. Chapter 3 uses the de novo-assisted peptidomic technique to follow the peptides of a diatom through a simulated bloom and subsequent degradation by a natural microbial community (Duffy et al., 2022). Chapter 4 is a comparison of organic matter flux across time and space in an ODZ. Chapter 5 moves out of the purely marine realm and bridges the span between terrestrial and marine systems in the Amazon River tidal reach, probing how proteinaceous organic matter is transformed in the final stretch of the Amazon River mouth before it empties into the Atlantic and characterizing the community composition and function of microbes working to alter its reactivity and character.