Comparing present (DNA) and active (RNA) marine ciliate communities across depth gradients

Despite their important role in the marine food web, marine ciliate biogeography and ecology remains underexplored. Traditionally, marine ciliate diversity and abundance was believed to be greatest at the chlorophyll maximum, where there is an abundance of autotrophic prey, and then declines dramatically with depth. However, recent studies using high-throughput sequencing of ciliate communities showed that the diversity did not decline with depth (Grattepanche et al submitted). Instead Grattepanche et al (submitted) suggests there is a highly diverse ciliate community present in deep waters. In this study we compared the abundant (DNA) and the active (RNA) marine ciliate communities of the New England coast (Northwest Atlantic) across depth gradients in a transect crossing the continental shelf. We compared estimates of ciliate communities from SSU-rDNA (abundant) and SSU-rRNA (active) on a Denaturing Gradient Gel Electrophoresis (DGGE), which reveals abundant community members based on band brightness. Our findings 1) confirm that ciliate communities are diverse far below the chlorophyll maximum, 2) show that at all depths some ciliate members are abundant but not active (perhaps encysted) and 3) suggests that rare members of the ciliate community are sometimes extremely active. Our study provides a novel approach to understanding marine ciliate ecology and characterizes rare and active ciliates throughout the water column, with a focus on communities below the photic zone.