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.

Svalbard 2010 mesocosm experiment: Protistan diversity

Hierarchical clustering. Taxonomic assignment of reads was performed using a preexisting database of SSU rDNA sequences from including XXX reference sequences generated by Sanger sequencing. Experimental amplicons (reads), sorted by abundance, were then concatenated with the reference extracted sequences sorted by decreasing length. All sequences, experimental and referential, were then clustered to 85% identity using the global alignment clustering option of the uclust module from the usearch v4.0 software (Edgar, 2010). Each 85% cluster was then reclustered at a higher stringency level (86%) and so on (87%, 88%,.) in a hierarchical manner up to 100% similarity. Each experimental sequence was then identified by the list of clusters to which it belonged at 85% to 100% levels. This information can be viewed as a matrix with the lines corresponding to different sequences and the columns corresponding to the cluster membership at each clustering level. Taxonomic assignment for a given read was performed by first looking if reference sequences clustered with the experimental sequence at the 100% clustering level. If this was the case, the last common taxonomic name of the reference sequence(s) within the cluster was used to assign the environmental read. If not, the same procedure was applied to clusters from 99% to 85% similarity if necessary, until a cluster was found containing both the experimental read and reference sequence(s), in which case sequences were taxonomically assigned as described above.

Diversity of benthic foraminiferal faunas in Tertiary and Quaternary sediments of DSDP Hole 33-317_Site from the Manihiki Plateau, Pacific Ocean (Table 1)

A study is made of the benthic foraminifers (size fraction > 63 µm) recovered from 59 upper Eocene through Quaternary sediment samples at DSDP Site 317 (Leg 33), located at a depth of 2598 m in the central part of the Manihiki Plateau (South Pacific). The sediments cored are disturbed in only two samples. The stratigraphic assignements used are based on previous studies of planktic foraminifers and other microfossils. In total, 216 taxa are identified. A cluster analysis based on the 77 species which comprised 5% or more of the entire foraminiferal assemblage in at least one sample suggests the presence of 3 major biostratigraphic zones corresponding approximately to the following ages, zone A: middle Miocene-Quaternary; zones B-C: early Miocene-Oligocene; and zone D: Eocene. The most important faunal turnover occurred between the Eocene and the Oligocene; a less pronounced break took place between the early and the middle Miocene, and an additional minor turnover between the Oligocene and the early Miocene. Eighteen taxa are long-ranging, being recorded from the middle Eocene through the Pliocene-Quaternary. It is concluded that, in general, benthic foraminifers of the bathyal zone are poor worldwide stratigraphic guide fossils; the following taxa are conditionally considered as the most suitable in the Eocene-Quaternary sequence: Aragonia aragonensis, Quadrimorphina profunda, Nuttallides truempyi, Abyssamina poagi, Buliminella grata, Bulimina jarvisi, B. macilenta, Turrilina alsatica, Cibicides notocenicus, C. wuellerstorfi, Pyrgo murrhina. However, most of these species are relatively rare.