Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences

Abstract

We analyzed picoeukaryote assemblages at a French coastal site of the English Channel by sequencing cloned eukaryotic 18S rRNA genes in eight genetic libraries constructed from environmental samples (seven coastal, one estuarine) collected at different periods of the year. Eight hundred clones were examined by amplified restriction fragment length polymorphism (RFLP) using the restriction enzyme HaeIII. The coverage value calculated from the relative distribution of RFLP types was low, indicating that the library diversity was not entirely recovered. A variable region of the rRNA gene was partially sequenced (550 bases) and analyzed for 397 clones. Thirty-two clones were affiliated with metazoans. Of the remaining clones, 132 were affiliated to algal classes (especially Prasinophyceae, Cryptophyceae, Dinophyceae, and Prymnesiophyceae) and 107 to known heterotrophic groups (Cercozoa, choanoflagellates, stramenopiles, and ciliates). One hundred three sequences fell into uncultivated groups of stramenopiles (43 clones) and alveolates (60 clones). We also found two potentially novel eukaryotic lineages, represented by 9 and 14 clones, respectively, not belonging to any known eukaryotic group. The overall composition of the picoeukaryote community remained fairly stable at the class/division level except during the early summer diatom bloom, when groups such as the Cryptophyceae and the ciliates completely disappeared. However, at a finer taxonomic level (corresponding to 98% sequence identity), the majority of the operational taxonomic units (OTU) were only observed once.

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

“…could lead to the slight underestimation of prasinophytes here, and especially of this latter genus. While pelagophytes appear to be widely distributed in these environments, though generally found at lower abundance than in this study (Bidigare and Ondrusek, 1996;Díez et al, 2001;Moon-van der Staay et al, 2001;Wilmotte et al, 2002;Romari and Vaulot, 2004;Fuller et al, 2006b;McDonald et al, 2007), there are few reports of members of the class Chrysophyceae in marine systems. While some 'photosynthetic' chrysophytes have been observed by microscopy, these are not abundant and usually refer to cells larger than 5 mm (Throndsen, 1996;Novarino et al, 1997).…”

“…Moreover, studies based on size-fractionated pigment analysis also suggest a wide distribution of these small photosynthetic eukaryotes (Latasa and Bidigare, 1998;Wright et al, 2009). Recent progress using molecular approaches has begun to reveal their diversity (Moon-van der Staay et al, 2000;Díez et al, 2001;Vaulot et al, 2008;Worden and Not, 2008) showing a dominance of prymnesiophytes, pelagophytes and prasinophytes in marine environments (for example, see Moon-van der Staay et al, 2001;Romari and Vaulot, 2004;Not et al, 2004;Fuller et al, 2006a, b;Viprey et al, 2008;Liu et al, 2009) and lately of chrysophytes (Fuller et al, 2006b;McDonald et al, 2007;Lepère et al, 2009). However, we still have a poor understanding of the phylogenetic affiliation of the smallest cells (for example, see Liu et al, 2010), and particularly in directly linking taxonomic identity with 14 C primary production measurements.…”

Ecology and Diversity of Picoeukaryotes

“…Therefore, it is possible that some of these sequences are derived from larger organisms, which could have broken during the prefiltration step (Massana et al 2004;Romari and Vaulot 2004;Worden 2006). For example, choanoflagellate-related sequences are occasionally found in picosize-fractionated clone libraries, although composing a minor fraction of the total (Diez et al 2001;Lovejoy et al 2006;Not et al 2007a;Romari and Vaulot 2004). Another possibility is that certain life-stages of larger organisms (e.g., swarmers) could be small enough to pass through the prefilter, but because of their minute size, simply are not yet recognized as belonging to a larger species.…”

“…Cryptophytes have a unique orange color derived from their phycobiliproteins (photosynthetic pigments; Table 6.1. Other picocryptophytes have been shown in envPCR surveys (Fuller et al 2006b;Not et al 2007a;Romari and Vaulot 2004). The paucity of cultured picophytoeukaryotes from this and other divisions is a major restriction on physiological and ecological research on photosynthetic picoeukaryotes.…”

Culture-independent assessment of planktonic ciliate diversity in coastal northwest Atlantic waters

“…Such studies revealed considerable microbial diversity not captured by culture-dependent methods. With these new methods, it is possible to sample from a broader range of microbial habitats (Dawson & Pace 2002, Edgcomb et al 2002, Zettler et al 2002, Lopez-Garcia et al 2003, to sample previously undetected microbes (Diez et al 2001, Moon-van der Staay et al 2001, and to determine the spatial and temporal scales of microbial diversity (Romari & Vaulot 2004, Behnke et al 2006, Cordova-Kreylos et al 2006, Ley et al 2006. Although ciliates are often captured in studies of eukaryotic diversity, we know of no published reports focusing specifically on ciliate diversity using cultureindependent molecular methods.…”