Unexpected biodiversity of ciliates in marine samples from below the photic zone.

Marine microbial eukaryotes play critical roles in planktonic food webs and have been described as most diverse in the photic zone where productivity is high. We used high-throughput sequencing (HTS) to analyze the spatial distribution of planktonic ciliate diversity from shallow waters (<30m depth) to beyond the continental shelf (>800m depth) along a 163Km transect off the coast of New England, USA. Using HTS and specific primers, we observed that the most abundant OTUs correspond to those previously-reported elsewhere. However, we did not find the expected decrease of diversity below the photic zone and instead saw an increase of diversity with depth. This highly diversity within samples taken below the photic zone also reveals the prevalence of two ‘new’ clades (i.e. lacking sequenced morphospecies) defined by two deletions within the region of the SSU-rDNA analyzed here. Further, the ciliate communities cluster by layer (e.g. surface, pycnocline) and degree of water column stratification, suggesting that community assembly is driven by environmental factors such as temperature, salinity, phytoplankton and mesozooplankton. Together, these data reinforce that we still have much to learn about microbial diversity in marine ecosystems, especially in deeper waters that may be a reservoir for rare species.