Project: EAGER: Novel genome-based method to measure taxon-specific phytoplankton growth rates in natural communities

NSF award abstract:
Phytoplankton are the main primary producers in the ocean, i.e., the basis of the marine food chain. They contribute about half of the global oxygen production, and thereby sustain all life on earth. Thus, the rate at which phytoplankton grow and produce biomass is a key variable in determining the fertility of the seas (the distribution and magnitude of fish production) and the role of phytoplankton in biogeochemical cycles (e.g., oxygen production, nutrient consumption). The importance of phytoplankton growth rate is evident in the plethora of methods that have been suggested and applied to the problem. Many of the existing methods work well for phytoplankton cultures in the lab, but none of them are capable of measuring the growth rate of an individual species in its natural environment, as a member of a very complex diverse natural community. The investigators on this project will develop a new method, which is free of many of the artifacts associated with existing methods. It will allow the determination of growth rates of individual species as components of natural assemblages. This method will enable the study of phytoplankton response to environmental conditions -- changing temperature or nutrient availability -- independently of cell loss from grazing by herbivorous zooplankton. Improved growth rate information will be useful in just about every aspect of phytoplankton field research and in translating that field research into models and theory. As part of the project, two globally important phytoplankton genera will be grown in the laboratory, and growth rate experiments will be incorporated into the teaching laboratory for the introductory Oceanography course at Princeton University. Student research will thus contribute fundamental knowledge on phytoplankton physiological traits, producing data that are crucial to understanding what determines growth rate in natural assemblages.

The ability to obtain DNA sequence information from natural seawater samples, i.e., the development of culture-independent methods, has increased our understanding of the diversity and metabolic potential of phytoplankton. It is generally not possible, however, to link biogeochemical activities, such as nutrient assimilation and growth, to individual taxa in natural assemblages. It is also difficult to distinguish the importance of phytoplankton instantaneous growth rate vs. losses to e.g., grazing pressure, in controlling biomass accumulation rates because even the best methods for quantifying cell loss are very time-consuming and subject to large uncertainties. This distinction is crucial because biomass accumulation is the basis of most assays for growth rate. All these methods require incubations and or cannot account for grazing, and often have limited taxonomic resolution, which limits understanding of ecosystem functioning. This project will develop a novel method for taxon-specific growth rate measurement, called iRep, that is based on genome sequence analysis. The method does not require incubations or time series sampling, and has been applied by others to evaluate complex bacterial communities such as the human gut microbiome. It will be tested and validated using cultures of Synechococcus (cyanobacteria that dominate the biomass and production in vast expanses of the subtropical ocean). In addition, the first steps towards applying iRep to eukaryotic phytoplankton will be undertaken by characterizing turnover of chloroplast DNA (cpDNA) and determining the origins of cpDNA replication in Chaetoceros (diatoms that often dominate the biomass of upwelling regions). This EAGER proposal focuses on two sets of experiments to establish the potential of the method:
1. Application of the iRep method to Synechococcus in culture and artificial mixed assemblages.
2. Determination of the relationship between cpDNA turnover and diatom specific growth rate.
Very little is known about the mode of cpDNA replication in eukaryotic algae, and controversy still exists over the question of cpDNA replication in higher plants. The goal of taxon-specific determination of growth rate has been a long term quest in oceanography. Thus this exploratory proposal is a good fit for the EAGER program.