Ecological insights through single-cell measurements of marine bacteria

Abstract

Bacteria in the ocean, though invisible to the naked eye, play an indispensable role in facilitating life on Earth by driving chemical reactions that are essential to the planet's habitability. Some marine bacteria, however, cause disease outbreaks that are capable of rapid and massive destruction of ecosystems. Although individual bacterial cells are ~1 [mu]m in size, their collective action enables large-scale nutrient fluxes throughout the marine food web, as well as wreak havoc in marine systems with major socioeconomic consequences for humans. In this Thesis, I seek to connect single-cell measurements of behavior and metabolism of marine bacteria to ecological processes that shape global biogeochemical cycles and influence ecosystem health.

In particular, I focus on the impact of microbial activities on two globally-relevant contexts: (1) the biogeochemical cycling of sulfur, a chemical element that is essential to life, and (2) coral disease, which threatens the reef ecosystems that support marine biodiversity and provide food security for many human coastal communities. In Chapter 1, I describe the development of synthetic biology tools for the construction of fluorescent reporters in a marine bacterium (Ruegeria pomeroyi). These engineered reporter strains enabled the investigations in Chapter 2, which presents the first single-cell measurements of the transcriptional response of R. pomeroyi to different concentrations of dimethylsulfoniopropionate (DMSP), a pivotal compound in the oceans' carbon and sulfur cycles and a key chemical currency in marine microbial interactions. These measurements revealed the importance of microscale DMSP hotspots in marine sulfur cycling.

In Chapter 3, I describe the simultaneous measurements of behavior (through microscopy) and gene expression (through RNA sequencing) of a coral pathogen, Vibrio coralliilyticus, to investigate the sequence of microscopic events preceding infection. The Appendix describes the methodology of tracking single cells over time through quantitative microscopy and high-throughput image analysis. The application of new tools from biological engineering to marine microbial ecology presents an unprecedented opportunity to understand the connections between single-cell behaviors, and ecosystem- and global-scale processes.