From Pure Cultures to Particles: Tracing Microbial Metabolism Through Amino Acid ²H/¹H Ratios

Author: Silverman, Shaelyn Nicole

Year: 2025

Degree: Dissertation (Ph.D.)

Advisors: Sessions, Alex L.; Orphan, Victoria J.

Committee Members: Orphan, Victoria J.; Sessions, Alex L.; Newman, Dianne K.; Leadbetter, Jared R.

Option: Geobiology

DOI: 10.7907/5v12-1149

Abstract

Microbial metabolisms exert profound impact on our planet’s atmosphere and surface geochemistry. Most available tools to study microbial metabolism in the environment provide only snapshots of activity at the time of sampling. However, holistic understanding of microbial function requires the ability to quantitatively reconstruct their activities prior to sampling, for which tools are currently limited. The overarching research presented in this thesis addresses this challenge through development of a new isotopic tool, amino acid hydrogen isotope (δ2HAA) analysis, into a useful tracer of microbial metabolism in the environment. We begin by solving a major analytical challenge: correcting for contributions of exchangeable amine-bound hydrogen in derivatized amino acids, which unlocks the ability to accurately measure δ2HAA values in organisms via gas chromatography-pyrolysis-isotope ratio mass spectrometry. We demonstrate in aerobic heterotrophic bacteria and phytoplankton that δ2HAA values are controlled by metabolism (specifically, carbon flow in cells), and we apply this isotopic tool to natural samples of marine particulate organic matter (POM), demonstrating substantial potential turnover of photoautotrophic proteins into heterotrophic proteins (up to 57 ± 18%) in POM with depth at different ocean sites. We further explore the microscale dynamics of marine bacteria on diatom aggregates to contextualize our understanding of controls on marine POM degradation. In particular, we find that both intra- and interspecies interactions profoundly shape microbial colonization dynamics, which in turn likely affect bulk particle degradation rates. Together, this body of work demonstrates the profound utility of δ2HAA analysis as a tracer of microbial metabolism—a timely development given the need to trace and quantify the metabolic responses of microbial communities to ongoing environmental perturbations.

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