Culture-independent molecular analyses of open-sea microorganisms have revealed the existence and apparent abundance of novel eukaryotic lineages, opening new avenues for phylogenetic, evolutionary, and ecological research. Novel marine stramenopiles, identified by 18S ribosomal DNA sequences within the basal part of the stramenopile radiation but unrelated to any previously known group, constituted one of the most important novel lineages in these open-sea samples. Here we carry out a comparative analysis of novel stramenopiles, including new sequences from coastal genetic libraries presented here and sequences from recent reports from the open ocean and marine anoxic sites. Novel stramenopiles were found in all major habitats, generally accounting for a significant proportion of clones in genetic libraries. Phylogenetic analyses indicated the existence of 12 independent clusters. Some of these were restricted to anoxic or deep-sea environments, but the majority were typical components of coastal and open-sea waters. We specifically identified four clusters that were well represented in most marine surface waters (together they accounted for 74% of the novel stramenopile clones) and are the obvious targets for future research. Many sequences were retrieved from geographically distant regions, indicating that some organisms were cosmopolitan. Our study expands our knowledge on the phylogenetic diversity and distribution of novel marine stramenopiles and confirms that they are fundamental members of the marine eukaryotic picoplankton.Genetic libraries of small subunit (SSU) ribosomal DNA (rDNA) genes constructed from environmental DNA have proven very valuable to study the taxonomic composition of marine prokaryotic plankton (8,16). Prokaryotic assemblages in the sea appeared to be dominated by novel bacterial and archaeal lineages (17), and this was an important breakthrough for understanding the structure and function of natural assemblages (37). Picoeukaryotes (eukaryotic microbes less than 2 to 3 m in diameter) are also recognized as fundamental components of marine ecosystems. Phototrophic picoeukaryotes contribute significantly to phytoplankton biomass and primary production (26), and heterotrophic picoeukaryotes, generally small flagellates (5), are the main grazers of bacteria and play key roles within the microbial food web (41). Despite the ecological importance of marine picoeukaryotes, the use of molecular tools to investigate their taxonomic composition, in particular by 18S rDNA libraries, is very recent (9, 28, 34). The most remarkable finding of these studies was the recovery of novel lineages within the stramenopile and alveolate phylogenetic divisions that accounted for a significant fraction of clones in the libraries. These novel lineages represent organisms that must contribute to marine processes but have not been investigated before and thus deserve further detailed phylogenetic and ecological studies.The stramenopiles (Heterokonta) form one of the eight major phylogenetic groups of eukaryo...

Planktonic picoeukaryotes are important players in coastal marine food webs but little is known about their diversity. Here we report the picoeukaryotic diversity in Blanes Bay (NW Mediterranean) by retrieving environmental 18S rDNA sequences and by obtaining stable cultures. Four genetic libraries (one per season) were constructed and 383 clones analyzed, yielding 176 distinct sequences. The diversity of picoeukaryotes was very large, both at higher and lower phylogenetic levels. Novel alveolates‐I (36% of clones), dinoflagellates (17%), novel stramenopiles (10%), prasinophytes (5%) novel alveolates‐II (5%), and cryptophytes (4%) were the better represented phylogenetic groups. Nineteen additional groups were found at <3% clonal abundance. The four genetic libraries were dominated by the above‐mentioned groups, implying a relative stability at high taxonomic level, but identical sequences were seldom found in consecutive dates, suggesting fast temporal changes of picoeukaryotic populations. Coastal and open sea picoeukaryotes were similar, but the representation of groups varied between habitats. The culturing effort revealed that some groups were well represented in clone libraries and in cultures (prasinophytes), others were found by both approaches but often with different sequences (cryptophytes), and others were found only in cultures (bicosoecids) or in clone libraries (novel alveolates and stramenopiles). Our data confirm that molecular approaches, such as cloning and sequencing 18S rRNA genes, are a necessary first step to study picoeukaryotic diversity. These results will aid to focus future research, most likely based on new and imaginative culturing efforts and the design and application of specific molecular probes.