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.

Abundance of phytoplankton, heterotrophic nanoflagellates and bacteria through the water column at time series station L4 in the Western English Channel. 2007-2011

The marine laboratories in Plymouth have sampled at two principle sites in the Western English Channel for over a century in open-shelf (station E1; 50° 02'N, 4° 22'W) and coastal (station L4; 50° 15'N, 4° 13'W) waters. These stations are seasonally stratified from late-April until September, and the variable biological response is regulated by subtle variations in temperature, light, nutrients and meteorology. Station L4 is characterized by summer nutrient depletion, although intense summer precipitation, increasing riverine input to the system, results in pulses of increased nitrate concentration and surface freshening. The winter nutrient concentrations at E1 are consistent with an open-shelf site. Both stations have a spring and autumn phytoplankton bloom; at station E1, the autumn bloom tends to dominate in terms of chlorophyll concentration. The last two decades have seen a warming of around 0.6°C per decade, and this is superimposed on several periods of warming and cooling over the past century. In general, over the Western English Channel domain, the end of the 20th century was around 0.5°C warmer than the first half of the century. The warming magnitude and trend is consistent with other stations across the north-west European Shelf and occurred during a period of reduced wind stress and increased levels of insolation (+20%); these are both correlated with the larger scale climatic forcing of the North Atlantic Oscillation.

Radiolarian biostratigraphy in sediments of ODP Site 202-1237

Site 1237 is located on Nazca Ridge ~140 km off the coast of Peru and thus within the offshore region of the Peru-Chile Current. A total of 83 samples were used to provide an initial radiolarian biostratigraphic framework for Site 1237; radiolarians are present to Sample 202-1237B-19H-2, 58-60 cm (186.45 meters composite depth [mcd]) and are of good to fair abundance and preservation. Site 1237 is influenced by both subtropical and northward-transported southern latitude waters, has 55 ash layers within the uppermost 166 m, and has minimal to gross reworking. Shipboard paleomagnetic results showed that the upper 200 m spanned the last 12 m.y., and in the upper 100 mcd, the paleomagnetic inclination pattern could be directly correlated to the geomagnetic polarity timescale (GPTS). Tropical biostratigraphy was used to establish the zonal boundaries for Site 1237, and the paleomagnetic and radiolarian stratigraphy were well correlated.

Determination of ages and fossil Coleoptera fauna from eight sites in the London region

These data sets report the fossil beetle assemblages identified from the Mesolithic to Late Bronze Age at eight sites in the London region. All but one of the study sites are within 2 km of the modern course of the Thames. The sites produced 128 faunal assemblages that yielded 218 identified species in 41 families of Coleoptera (beetles).  Beetle faunas of Mesolithic age indicate extensive wetlands near the Thames, bordered by rich deciduous woodlands. The proportion of woodland species declined in the Neolithic, apparently because of the expansion of wetlands, rather than because of human activities. The Early Bronze Age faunas contained a greater proportion of coniferous woodland and aquatic (standing water) species. An increase in the dung beetle fauna indicates the presence of sheep, cattle and horses, and various beetles associated with crop lands demonstrate the local rise of agriculture, albeit several centuries after the beginnings of farming in other regions of Britain. Late Bronze Age faunas show the continued development of agriculture and animal husbandry along the lower Thames. About 33% of the total identified beetle fauna from the London area sites have limited modern distributions or are extinct in the U.K. Some of these species are associated with the dead wood found in primeval forests; others are wetland species whose habitat has been severely reduced in recent centuries. The third group is stream-dwelling beetles that require clean, clear waters and river bottoms.