Phylogenetic information from ribosomal RNA genes directly amplified from t
he environment changed our view of the biosphere, revealing an extraordinar
y diversity of previously undetected prokaryotic lineages. Using ribosomal
RNA genes from marine picoplankton, several new groups of bacteria and arch
aea have been identified, some of which are abundant2-4. Little is known, h
owever, about the diversity of the smallest planktonic eukaryotes, and avai
lable information in general concerns the phytoplankton of the euphotic reg
ion. Here we recover eukaryotes in the size fraction 0.2-5 mum from the aph
otic zone (250-3,000 m deep) in the Antarctic polar front. The most diverse
and relatively abundant were two new groups of alveolate sequences, relate
d to dinoflagellates that are found at all studied depths. These may be imp
ortant components of the microbial community in the deep ocean. Their phylo
genetic position suggests a radiation early in the evolution of alveolates.