Project: Linking Single-Cell Growth Rates and Genomics

Description from NSF award abstract:
Marine ecosystems are primarily microbial in nature. Microscopic organisms represent over 90% of biomass, including the major primary producers, and drive biogeochemical processes. Although this insight is merely 30 years old, it has led to concerted efforts in studying the structure and functioning of microbial communities in the ocean. Techniques are now available to estimate many key ecological parameters of microbial life; however, one fundamental gap is that estimates of microbial growth rates in the wild remain poorly constrained. Questions, which have largely remained unsolved, are:

What does the growth rate distribution look like for free-living microbes?
Which species grow at what rates?
How do environmental changes (e.g., nutrients, light) affect growth rates of different microbes?

To begin to address these questions, this project will develop a single-cell based system that allows coupled measurement of in situ growth rates and genomic characteristics. The suspended microchannel resonator (SMR) is a well-developed microfluidics-based mass-sensor that has sufficient resolution for measuring the natural range in size and growth rate of ocean microbes; here, this system will be adapted to enable: (i) capture and growth measurement of individual microbial cells in their native seawater microenvironment, (ii) genomic analysis of the same cells for which growth rates have been determined, and (iii) direct analysis of bacterioplankton communities obtained from mesocosm and natural ocean samples. This system is unique in that it couples quantitative growth rate determination and genomic identification of individual microbial cells in their natural microenvironment, and therefore promises to be applicable to the above questions.

Understanding what regulates bacterial growth on the single cell and population level is of fundamental importance in linking microbial diversity to function, and to model and predict carbon fluxes in the ocean. This project establishes a prototype system to couple determination of growth and genomics on the single cell level, for which no data currently exist. Future directions will include design of a system with increased throughput and capability of running onboard ship or autonomous sampling devices.