Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing

Abstract

Information on genetic diversity of picoeukaryotes (o2-3 lm) comes mainly from traditional gene cloning and sequencing, but this method suffers from cloning biases and limited throughput. In this study, we explored the feasibility of using the cloning-independent and massively parallel 454 pyrosequencing technology to study the composition and genetic diversity of picoeukaryotes in the coastal waters of the subtropical western Pacific using the hypervariable V4 region of the 18S rRNA gene. Picoeukaryote assemblages between two sites with different hydrography and trophic status were also compared. The approach gave a high coverage of the community at genetic difference X5% but still underestimated the total diversity at a genetic difference p2%. Diversity of picoeukaryotes was higher in an oligomesotrophic bay than in a eutrophic bay. Stramenopiles, dinoflagellates, ciliates and prasinophytes were the dominant groups comprising approximately 27, 19, 11 and 11%, respectively, of the picoeukaryotes. Water samples collected from the two bays contained different high-level taxonomic groups and phylotype operational taxonomic units of picoeukaryotes. Our study represents one of the first and most comprehensive examinations of marine picoeukaryotic diversity using the 454 sequencing-by-synthesis technology.

Phylogeny and Molecular Evolution of the Green Algae

“…Beside portals dedicated to the annotation of each of the different genomes, web sites focused on comparative analysis between the different organisms belonging to the green lineage, as PLAZA (bioinformatics.psb.ugent.be/plaza/) (Proost et al, 2009) and its derivative Pico-PLAZA (bioinformatics.psb.ugent.be/pico-plaza/) are now available. Such tools for comparative approaches, coupled to the development of new sequencing possibilities for both new genomes and metagenomes (Cheung et al, 2010;Marie et al, 2010) from various environments open the door to a better understanding of the adaptations of the organisms to their environment.…”

The efficient long-term inhibition of forsterite dissolution by common soil bacteria and fungi at Earth surface conditions

“…18S rRNA genes were amplified using the eukaryotic primers 528F (5′-GCGGTAATTCCAGCTCCAA) and 706R (5'-AATCCRAGAATTTCACCTCT) (Cheung et al, 2010) Sequence processing and analyses were carried out in Qiime (Caporaso et al, 2010).…”

Reproducibility and quantitation of amplicon sequencing-based detection

“…At present, the 454 pyrosequencing technology has been widely used to reveal microbial diversity and ecology in different natural environments, such as the deep sea (Sogin et al, 2006;Huber et al, 2007), extreme hydrogeological conditions (Edwards et al, 2006) and soil (Leininger et al, 2006;Roesch et al, 2007). In addition, multiplexed high-throughput pyrosequencing of individual genes (for example, 16S rRNA) by tagging or bar coding with short nucleotides (also called pyrotag sequencing ) Parameswaran et al, 2007;Roesch et al, 2007;Hamady et al, 2008) has been developed to process many samples simultaneously and has been widely used in microbial community studies (Youssef et al, 2009;Cheung et al, 2010;Chun et al, 2010;He et al, 2010a, b;Koopman et al, 2010;Schutte et al, 2010;Teixeira et al, 2010;Uroz et al, 2010). A similar strategy has also been used for sequencing functional genes (Iwai et al, 2010).…”