1) Food quality issues and functional responses of microbial predators. Within the last 7 years tremendous diversity of marine protozoa has been revealed based on environmental SSU rDNA gene sequencing. Many of these protozoa are novel, not yet cultured and of unknown functional roles. Some are likely to be predators, while others are photosynthetic or mixotrophic. We are characterizing both novel and ubiquitous protozoa. Furthermore, we are studying interactions between predator and prey populations. In combination with other studies our research shows that protozoan grazers can exhibit prey specificity, as well as functional responses, and that assimilation efficiencies differ dramatically between prey groups (e.g. Prochlorococcus is assimilated more efficiently than Synechococcus). Thus, different prey can be consumed at different rates and a greater proportion of carbon from some prey groups is transferred to higher trophic levels than from others. This impacts not only the complexity of trophic linkages amongst the smaller size fractions but also the diversity and distribution of microbial populations (via selective protozoan grazing). To accurately model food webs, protozoan grazing strategies and prey digestibility (some are of better food quality than others) must be accounted for. We are developing biochemical and proteomic approaches as well as ‘species’-specific probes to target and study specific interactions in natural systems, including analysis of protozoan food vacuoles and food particle processing. Cues employed in prey selectivity, prey switching and the influence of food quality on these interactions are under study. These studies also address parasitism by novel protozoa, one group of which has already been found to parasitize dinoflagellates (which can cause red and brown tides). The regulatory role of parasitism in marine systems is largely unknown.

2) Biochemical and molecular mechanisms of microbe-algae interactions and conditions specifically influencing interaction type. Although we know that bacteria attach to algae (even to picophytoplankton), the relationship between these organisms has not yet been characterized despite its potential influence on population dynamics and biogeochemical cycles. The relationship could be mutualistic, or range from mutualistic to parasitic or pathogenic as environmental conditions or colonizing bacterial populations change.

3) Competition processes and population dynamics. Elucidating the underpinnings of niche differentiation and competition is essential to understanding food webs. It is now recognized that resource utilization capabilities of heterotrophic and autotrophic microorganisms overlap. My group is currently sequencing the genomes of two phylogenetically distinct strains of Micromonas pusilla in collaboration with the Joint Genome Institute of the U.S. Department of Energy. These organisms fall at the base of the green lineage and hence shed light on the evolution of higher plants, in addition to being important marine primary producers. We are also members of a team of collaborators from Ghent University, the Station Biologique du Roscoff, and Laboratoire Arago at Banyuls sur Mer who sequenced and annotated the genome of Ostreococcus tauri, a tiny, but important marine photosynthetic eukaryote discovered in 1994. A second Ostreococcus genome from a strain isolated from waters off the Scripps Institution of Oceanography's Pier (coastal Pacific Ocean USA) has just been released. This strain, Ostreococcus CCE9901 was the focus of my NSF Postdoctoral fellowship research, for which I identifed and characterized CCE9901 in addition to exploring its ecology, after which we (successfully) proposed it as a genome sequencing candidate relevant to the DOE mission. Taken together, these genomes are being used to develop hypothesis driven studies on niche differentiation. For example, we are using a combination of genomic (in silico), micro-array, quantitative-PCR and biochemical approaches to understand the photobiology of Micromonas and Ostreococcus and their relative success in high-light/high-ultraviolet radiation environments. Using gene and protein expression to detect real-time cell response to environmental changes (e.g. mitigating negative effects and capitalizing on favorable conditions) will help identify conditions of immediate relevance to survival or success. We are currently focusing on photoautotrophs but plan to apply similar approaches to predator populations. By avoiding the use of heavy-handed field manipulations that may be of little ecological relevance, this approach will help researchers define conditions contributing to the relative success of individual microbial populations. You can read more about the prasinophyte genomes on PrasinoSite.

Mechanisms of interactions amongst microorganisms are key to modeling system dynamics accurately. Our goal is to conduct a series of innovative field studies with a suite of new, sensitive tools to probe the strength and direction of these linkages/interactions and quantify carbon flow to other trophic compartments. Our work will allow development of mechanistically based ecosystem models for prediction of primary production, carbon cycling and marine food web dynamics.