Award: OCE-1129734

Our project aimed to understand the distribution of ciliate communities spatially (e.g. by distance and with depth). We use ciliates as model organisms given their presence everywhere there is water (e.g. ocean, ponds, soils). The ciliates are an ancient clade, ~1 billion years old, and have evolved numerous innovations. Previous studies have described ciliates based on their morphology (e.g. presence of a shell named lorica, arrangement of cilia) and around 8,000 morphospecies have been described. Ciliates are one of the major clades of microbial eukaryotes in the planktonic food web in term of diversity and importance – they link bacteria to higher trophic levels such as copepods and fish. As the ocean plays an important role in Carbon sequestration through the planktonic food web, it is critical to understand who are the main players. Methods: For our project we mostly used two DNA-based methods: a fingerprinting technique, which allows us to observe the composition of the abundant ciliates and generates a set of easily exploitable data, and high throughput sequencing (HTS), which allow us to assess the whole community -- abundant and rare members of the community – but is much more complicated to analyze (i.e. millions of DNA sequences). Reults: During the first year, we carried out some pilot studies. First, we sampled in the Long Island Sound to test our sampling methods and observed the variation of the community at small scale (spatial and temporal). Secondly, we tested methods to analyze HTS data that had been primarily designed for studies of bacteria. We observed that these methods donÆt allow us to assess at the diversity of ciliates so we designed our own pipeline to analyze the HTS data. In our second and third years, we carried out a research cruise from the Narragansett Bay to the shelf break. From inshore to the open ocean, we sampled every 6 Km resulting in 23 stations. On our way back we sampled at smaller scale (2km and 1km) for some representative locations (open ocean, middle shore, inshore), resulting in 16 supplementary stations. For each station, the water column varied from 40 to more than 1,000m depth. In order to have a representative sampling, we analyzed the deepest water we could access (from above 5m of the sea floor to 850m depth) through to the surface. We also took samples where the chlorophyll was the highest (i.e. chlorophyll maximum depth or CMD) and another one where the temperature and salinity presenting the strongest variation (i.e. pycnocline). These four layers (surface, pycnocline, CMD and deep) were selected given their strong difference in term of environmental conditions (temperature, salinity, chlorophyll, etc.). We observed the presence of a ciliate assemblage almost everywhere from inshore to offshore and from surface to deep, suggesting that this ciliate assemblage is not affect by environmental conditions given the strong variation observed during our cruise. We also expected to observe the highests diversity from the surface to the CMD, where the ciliates prey on phytoplankton, and a decrease within our deep samples. However, we found the highest diversity within our deepest samples. We conclude that (1) the phytoplankton is not the main driver for ciliate diversity, (2) the deep ocean is a seed bank for ciliates – when the environmental conditions are suitable, and (3) the observed diversity in the deep may also be related to sinking material (i.e. sea or marine snow). We also carried out a microcosm experiment to have a better understanding of the environmental conditions that affect ciliate communities. For example, we incubated a wild ciliates community with (1) no predator (here we used copepods), (2) few predators and (3) many predators. We observed that the ciliates with a shell seemed to be less suitable as food as they grew even with many predators, while the ciliates without shell were eat first. Summary: Overall, our work yielded importa...