Picoeukaryotes (< 2 to 3 µm) are important components of aquatic ecosystems. The genetic diversity and seasonal variability of marine picoeukaryotes were compared between a semienclosed harbour and the adjacent open sea off the subtropical coast in the western Pacific Ocean based on 18S rRNA clone library analysis. Examination of 733 clones revealed 186 different restriction fragment length polymorphism (RFLP) patterns, representing 186 operational taxonomic units (OTUs). At least 19 high-level taxonomic groups of picoeukaryotes were recorded. Alveolates group II, ciliates and stramenopiles comprising 37, 17 and 11% of the picoeukaryotes, respectively, were the most dominant groups. Phototrophs such as prasinophytes, cryptophytes and haptophytes were retrieved occasionally. Members from the 2 newly defined phyla, picobiliphytes and Telonemia, were also obtained. A differential spatial distribution of OTUs was observed between samples collected from the 2 sampling sites. Seasonal variations in picoeukaryote composition were more pronounced in the open sea libraries than in the semi-enclosed harbour libraries.
MATERIALS AND METHODSSample collection. Surface seawater samples (~2.5 l) were collected from stations in Tolo Harbour (22°26' N, 114°13' E) and Mirs Bay (22°30' N, 114°21' E) in January, April, July and October 2006 (Fig. 1). Immediately after collection, the water samples were filtered through a 200 µm mesh sieve to remove most of the mesozooplankton and large particles. Water temperatures, salinities and dissolved oxygen (DO) levels were measured on board ship using a HydroLab sensor. In the laboratory, chlorophyll a (chl a) concentrations were determined using a Turner Designs 10-AU fluorometer as described in Wong & Wong (2003). Diatom and dinoflagellate concentrations were determined by counting them under an inverted microscope. Two litres of water were prefiltered through 3 µm pore size Nuclepore ® membranes (Whatman) and the microbial biomass was then collected onto a GF/F filter (Whatman). A gentle vacuum (< 20 cm Hg) created by a hand pump was used to facilitate the filtration processes. The filter was then immersed in DNA lysis buffer (0.75 M sucrose, 40 mM EDTA, 50 mM Tris-HCl, pH 8), immediately frozen in liquid nitrogen and stored at -80°C until DNA extraction.DNA extraction and PCR. DNA was extracted using a cetyltrimethylammonium bromide (CTAB) extraction procedure (Doyle & Doyle 1990). Extracts were purified with the Geneclean ® II Kit (Q-BIOgene) and then stored at -20°C until use. The 18S rRNA gene was amplified by PCR using the eukaryotic primers Euk328f (5'-ACC TGG TTG ATC CTG CCA G-3') and Euk329r (5'-TGA TCC TTC YGC AGG TTC AC-3') complementary to regions of conserved sequences proximal to the 5' and 3' termini of the 18S rRNA gene (Moon-van der Staay et al. 2000, Romari & Vaulot 2004. Each PCR mixture (50 µl) contained 2 µl of DNA template, 5 µl of 10× PCR buffer (50 mM KCl, 10 mM Tris-HCl and 1.5 mM MgCl 2 ), 200 µM of dNTP, 0.2 µM of each primer and 2.5 U Taq polymerase ...