Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

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 richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings Plankton net hauls (200 µm) were taken at the Western Channel Observatory 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 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 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 58 taxonomic groups. Conclusions Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify 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 elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.

Hidden Gems: systematically searching electronic databases for research publications for social work and social care.

Context: Electronic bibliographic databases are a key source for professional publications about social work and community care more generally. This article describes and evaluates a method of identifying relevant articles as part of a systematic review of research evidence. Decision making about institutional and home care services for older people is used as an example. Method: Four databases (Social Science Citation Index, Medline, CINAHL, and Caredata) that abstract publications relevant to health and social services were searched systematically to identify relevant research studies. The items retrieved were appraised independently using a standard form developed for the purpose. The searches were compared in terms of sensitivity, precision, overlap between databases, and inter-rater reliability. Results: The search retrieved 525 articles, of which 276 were relevant. The four databases retrieved 55%, 41%, 19%, and 1% of the relevant articles respectively, achieving these sensitivities with precision levels of 54%, 48%, 84% and 94%. The databases retrieved 116, 73, 24 and 15 unique relevant articles respectively, showing the need to use a range of databases. Discussion: A general approach to creating a search to retrieve relevant research has been developed. The development of an international, indexed database dedicated to literature relevant to social services is a priority to enable progress in evidence-based policy and practice in social work. Editors and researchers should consider using structured abstracts in order to improve the retrieval and dissemination of research.