From tiny cells to large drifting animals, planktonic organisms shape oceanic ecosystems and biogeochemical fluxes. Their interactions and behaviors determine how much carbon dioxide is fixed - and how much is transferred into the food web or exported into the deep sea. Most of our studies in this area are on the diversity and interactions of surface ocean microbes – including algae and their predators as well as other entities, such predators and their symbionts and viruses. We use multiple approaches, including Stable Isotope Probing (SIP) and at sea single-eukaryote cell sorting to tease apart interactions between protists and other biological entities in the sea. Sorting is followed by DNA sequencing and, from there, characterization of genomes, protein functions and transcriptional activities in the field. Understanding interactions is essential for predicting the fate of organic carbon – does it end up being exported into the deep sea, or is it respired while still in the surface ocean?

Our interest in the forces of mortality that act on microbial cells in the ocean has led to pursue viruses, who they infect, and the factors that influence infection – which are still poorly understood (see our review article with colleagues ranging from trace metal chemists to phage biologists: Zimmerman et al. Nature Reviews Microbiology 2020)! We use several different approaches to try to understand host-virus interactions. The first is culture experiments (Fig. 1) – where we have explored infection kinetics and how they are shaped by the nutrient status of the host cell. Our models here are widespread picoeukaryotic marine green algae, specifically Bathycoccus, Micromonas, and Ostreococcus. Also, we know that some viruses carry auxiliary metabolic genes – like the cross-domain ones we captured in viruses of bacteria and eukaryotes alike in our early metagenomic and targeted metagenomics work. One approach we use is to study responses of both the host and virus at the molecular level using transcriptomics.

In addition to laboratory studies, we use targeted metagenomics to recover novel viruses directly from the ocean and yet uncultured hosts. We perform single cell sorting at sea to isolate individual cells or populations of algae (e.g. Bathycoccus, Synechococcus) or Choanoflagellates. This allows us to isolate one part of the microbial community, which we then analyze using different bioinformatic tools to identify its viral pathogens and interactions at microscale rather than recovering metagenomes from bulk water filtrations. For example, using this approach, we were able to characterize several giant viruses in the uncultured unicellular predator Bicosta minor, and other hosts, expressing a rhodopsin photosystem. Some of these recently discovered eukaryote-infecting marine viruses approach, or even exceed, the genome size of small bacteria. Some of their genes challenge our definition of what viruses are and about half of their proteins have unknown functions leaving room for speculation about what secrets are still to be uncovered.

We also use other observational methods in the field, including in situ optical systems. With these, we determine how planktonic organisms are distributed in the ocean in relation to environmental drivers. In this fast-developing area of our research, we estimate impacts on elemental cycling in the water column, both in the sunlit surface and in the twilight and dark zones. For this research theme we are involved in field campaigns and diverse time-series around the globe! We focus on regions that are considered climate sensitive – and regions where large populations rely on the ocean.