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Whereas much is known about the biodiversity of prokaryotes and macroorganisms in the deep sea, knowledge on the biodiversity of protists remains very limited. Molecular studies have changed our view of marine environments and have revealed an astonishing number of previously unknown eukaryotic organisms. Morphological findings have shown that at least some widely dis- tributed nanoflagellates can also be found in the deep sea. Whether these flagellates have contact with populations from other habitats is still uncertain. We performed a molecular comparison of strains isolated from deep-sea sediments (>5000 m depth) and surface waters on the basis of their small subunit ribosomal DNA (SSU rDNA). Sequences of Rhynchomonas nasuta, Amastigomonas debruynei, Ancyromonas sigmoides, Cafeteria roenbergensis and Caecitellus parvulus were analysed, and 2 contrasting results obtained. Firstly, we found nearly identical genotypes within 1 morphospecies (C. roenbergensis), and secondly, quite different genotypes within certain morpho- species (R. nasuta, A. sigmoides and C. parvulus). In addition, high genetic distances between the dif- ferent strains of A. sigmoides and C. parvulus indicate that these morphospecies should be divided into different at least genetically distinguishable species. In contrast, some heterotrophic nanoflagel- lates must indeed be regarded as being cosmopolitan. According to the low genetic distances between isolates of R. nasuta, A. debruynei and C. roenbergensis as well as between our isolates of A. sigmoides from deep-sea and surface waters, exchanges between these habitats and also on a global scale might be possible. In summary, our results show that 3 morphospecies obviously contain several cryptic species, while some of the investigated genotypes occur in both deep-sea as well as in surface waters.

Molecular identity of strains of heterotrophic flagellates isolated from surface waters and deep-sea sediments of the South Atlantic based on SSU rDNA