Phylogenetic and ecological analysis of novel marine stramenopiles

Abstract

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.

FIG. 1.

Maximum-likelihood phylogenetic tree constructed with complete 18S rDNA sequences of stramenopiles and of two dinoflagellates as an outgroup. Novel marine stramenopile clusters (MAST-1 to MAST-12) are boxed and appear among known heterotrophic basal groups. The scale bar indicates 0.1 substitution per position. Bayesian posterior probabilities (mean of four separate analyses) and neighbor-joining and maximum-parsimony bootstrap values are shown (in that order) to the right of MAST clusters (boxed) and to the left of some other relevant nodes.

FIG. 2.

Phylogenetic trees constructed with partial 18S rDNA sequences of novel marine stramenopiles from clusters MAST-1 (A); MAST-2 (B); MAST-3 (C); MAST-12 (D); and MAST-4, -6, -7, -8, -9, -10, and -11 (E). We used a closely related sequence as an outgroup (later removed from the tree for clarity). The scale bar indicates 0.1 substitution per position in all trees. Clones are coded according to their origin: North Atlantic (NA), Mediterranean (ME1), Pacific (OLI), Antarctica (ANT and DH), Orkney (OR), Helgoland (HE), Roscoff (RA and RD), Blanes Bay (BL), shallow sediments (BAQA and BAQD), and hydrothermal vents (C1, C2, and C3).