Diversity of zooplankton assemblages at Station L4, Western English Channel, measured using next generation DNA sequencing

Background: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel Next Generation Sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify the richness and diversity of a mixed zooplankton assemblage from a productive monitoring site in the Western English Channel. Methodology/Principle Findings: Plankton WP2 replicate net hauls (200 µm) were taken at the Western Channel Observatory long-term monitoring station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,042 sequences were obtained for all samples. The sequences clustered in to 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 138 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 75 taxonomic groups. Conclusions: The percentage of OTUs assigned to major eukaryotic taxonomic groups broadly aligns between the metagenetic and morphological analysis and are dominated by Copepoda. However, the metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for estimating diversity and species richness of zooplankton communities.

Calcareous nannofossils and planktic foraminiferal assemblages of ODP Hole 198-1210A

Calcareous nannofossil and planktic foraminiferal assemblages from ODP Hole 1210A in the northwestern Pacific Ocean were used to reconstruct surface-water conditions for the past 500 kyr. Stratigraphic control was provided by calcareous nannofossil events that are thought to be synchronous over a broad range of latitudes. Calcareous nannofossil and planktic foraminiferal assemblages and abundance patterns indicate the unlikelihood of long term (Milankovitch-scale) latitudinal shifts of the Kuroshio Extension over the last 500 kyr and illustrate two successive surface water-mass states, one that prevailed prior to 300 ka and one that existed after 300 ka. The relative abundance of very small placoliths and the absolute abundance of the upper photic zone (UPZ) coccolith species decrease abruptly at approximately 300 ka. The relative abundance of the lower photic zone (LPZ) species Florisphaera profunda greatly increases at the same time, although intervals during which the relative abundance of this taxon is very low or absent also occur prior to 300 ka. The absolute abundance of planktic foraminifera gradually increased after the 300-ka boundary, including peaks of Globoconella inflata. These assemblage and abundance changes suggest significant modifications to the surface water-mass structure. Surface water was weakly stratified prior to 300 ka, but alternated between intensely stratified and vertically mixed after 300 ka. Changes in the surface water-mass structure suggest an intensification of the East Asian summer and winter monsoon after 300 ka.