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###Rationale and Significance  Seagrasses are the only group of fully-submerged marine angiosperms, and are globally distributed along coastlines of every continent except Antarctica \cite{Costanza_1997}. They form dense meadows in shallow coastal waters, providing critical habitat for many marine species \cite{Harborne_2006}. These meadows harbor tremendous amounts of biodiversity, providing homes to many rare/endemic macroogramisms macroorganisms  and are critical in biogeochemical cycling in the ocean system \cite{Orth_2006}. Although they occupy only a small percentage of area on Earth \cite{Costanza_1997} they are one of the most important carbon sinks, sequestering carbon 35X faster than Tropical Rainforests \cite{Mcleod_2011} and storing this carbon for millennia if left undisturbed \cite{Macreadie_2012} \cite{Mateo_1997} \cite{Serrano_2012}. The levels of biodiversity in seagrass beds and their importance in biogeochemical cycling and carbon sequestration makes them excellent candidates for investigating unexplored microbial eukaryotic diversity. Microeukaryotes themselves play important roles in marine ecosystems; they are primary producers, predators/prey, decomposers, involved in biogeochemical cycling, untapped sources of natural products, potential pathogens and symbionts \cite{Whitman_1998}\cite{Imhoff_2016}\cite{Caron_1999}\cite{Li_1994}. It is likely that microeukaryotes contribute to seagrass bed biodiversity and to biogeochemical cycling and carbon sequestration.