Oligotrophic phytoplankton community response to changes in N substrates and the resulting impact on genetic, taxonomic and functional diversity

Jonathan P. Zehr, Zbigniew Kolber, University of California Santa Cruz (NSF 1241221); Kevin R. Arrigo, Stanford University (NSF 1241093); Matthew Church, University of Hawaii (NSF 1241263)

Marine phytoplankton, unicellular photosynthetic microorganisms suspended in the dilute waters of the surface ocean, are responsible for about half of the carbon dioxide fixation on Earth. They play a primary role in Earth’s biogeochemical cycle of carbon, of significance in maintaining productivity, but also affecting the concentrations of atmospheric greenhouse gases.  The microalgae comprising phytoplankton are taxonomically and physiologically diverse, and growth is dependent on their ability to acquire the resources they need for growth. Nitrogen (N), an essential nutrient for all organisms, is found at extremely low concentrations throughout vast regions of the subtropical ocean, where N availability generally limits phytoplankton growth and productivity. N exists in different chemical compounds, and phytoplankton have different affinities for different forms. Thus, the fluxes and concentrations of different N compounds may affect phytoplankton communities because of the diverse genetic and physiological characteristics of phytoplankton species. Understanding the effects of different N compounds on marine phytoplankton communities is important since the chemical forms and rates of supply of N to phytoplankton have already been altered by anthropogenic activities, and are likely to be further affected in the future. 

The aims of this project were to determine the links between the forms and fluxes of nitrogen compounds in the ocean and the diversity of phytoplankton species. Using new technologies for genomics, molecular biology, and isotope tracers, this project investigated the effects nitrogen forms and supply have on the taxonomic, genetic, and functional diversity of marine phytoplankton communities in the N-depleted Pacific Ocean, one of the largest biomes on Earth. We investigated community-to-single-cell level microbial metabolic activities and strain-specific gene expression patterns to see how different N compounds affect the growth and activity of different phytoplankton species and strains and thus how different N compounds affect phytoplankton community structure. 

Experiments were performed in the open waters of the North Pacific Ocean in summer of 2014 to test the effect of additions of nitrate, ammonium, and urea on the phytoplankton community composition and their activities. In order to fully understand how different nutrient sources affected the community, the effects on phylogenetic (e.g. species), genetic (genome encoded capabilities) and functional (biological activities such as growth and metabolism) were assayed using a suite of state-of-the-art approaches. The comprehensive results of these experiments showed that each N compound had distinct effects on different phytoplankton groups, along with effects on primary productivity (carbon dioxide fixation) and photosynthetic efficiency. An unexpected result was that urea is likely to be an important N source for the most abundant cyanobacteria in the oceans, Prochlorococcus. The application of new bioinformatics approaches developed in this study, showed that distinct populations of phytoplankton respond differently to individual N substrates. The results of this study show that changes in N availability including differences in availability of different compounds, such as those affected by anthropogenic activities, may favor distinct populations of phytoplankton in different oceanic regions, which has implications for ecosystem function. 

This project represented a novel approach for understanding a complex environmental problem, that had significant impacts on both scientific understanding and training and educating the next generation. Because of the multipronged approach examining genetics, function and phylogeny, a comprehensive understanding of the effects of nutrient composition on phytoplankton community structure was obtained, of significance to ocean food webs and carbon cycling. This project also developed and applied new molecular biology tools to environmental problems. High school students, undergraduate students, graduate students, postdoctoral researchers and junior scientists received training in state-of-the-art analytical methods, molecular biology applications and training in bioinformatics, as well as training in oceanographic research expedition preparation and execution. The project also provided opportunities to several female undergraduates to participate in oceanographic field research, conduct research and present results at an international scientific conference. Analytical products were developed in the project and include the MicroTOOLs microarray and an R package for microarray analysis. Finally, we participated in public outreach activities with the San Francisco Exploratorium geared towards engaging youth in scientific pursuits.