High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal for the prokaryotic or eukaryotic groups of interest. Full primer universality is difficult or impossible to achieve and studies using different primer sets make biodiversity comparisons problematic. The aim of this study was to design and optimize universal eukaryotic primers that could be used as a standard in future biodiversity studies. Using the alignment of all eukaryotic sequences from the publicly available SILVA database, we generated a full characterization of variable versus conserved regions in the 18S rRNA gene. All variable regions within this gene were analyzed and our results suggested that the V2, V4 and V9 regions were best suited for biodiversity assessments. Previously published universal eukaryotic primers as well as a number of self-designed primers were mapped to the alignment. Primer selection will depend on sequencing technology used, and this study focused on the 454 pyrosequencing GS FLX Titanium platform. The results generated a primer pair yielding theoretical matches to 80% of the eukaryotic and 0% of the prokaryotic sequences in the SILVA database. An empirical test of marine sediments using the AmpliconNoise pipeline for analysis of the high throughput sequencing data yielded amplification of sequences for 71% of all eukaryotic phyla with no isolation of prokaryotic sequences. To our knowledge this is the first characterization of the complete 18S rRNA gene using all eukaryotes present in the SILVA database, providing a robust test for universal eukaryotic primers. Since both in silico and empirical tests using high throughput sequencing retained high inclusion of eukaryotic phyla and exclusion of prokaryotes, we conclude that these primers are well suited for assessing eukaryote diversity, and can be used as a standard in biodiversity studies.

The pan-global marine appendicularian, Oikopleura dioica, shows considerable promise as a candidate model organism for cross-disciplinary research ranging from chordate genetics and evolution to molecular ecology research. This urochordate, has a simplified anatomical organization, remains transparent throughout an exceptionally short life cycle of less than 1 week and exhibits high fecundity. At 70 Mb, the compact, sequenced genome ranks among the smallest known metazoan genomes, with both gene regulatory and intronic regions highly reduced in size. The organism occupies an important trophic role in marine ecosystems and is a significant contributor to global vertical carbon flux. Among the short list of bona fide biological model organisms, all share the property that they are amenable to long-term maintenance in laboratory cultures. Here, we tested diet regimes, spawn densities and dilutions and seawater treatment, leading to optimization of a detailed culture protocol that permits sustainable long-term maintenance of O. dioica, allowing continuous, uninterrupted production of source material for experimentation. The culture protocol can be quickly adapted in both coastal and inland laboratories and should promote rapid development of the many original research perspectives the animal offers.

Pelagic urochordate appendicularians are a vital component of marine zooplankton communities, second in abundance only to copepods. Found in all major ocean systems, they are capable of rapid blooms, attaining densities exceeding 53 000 ind. m . We maintained a widely distributed species, Oikopleura dioica, under controlled laboratory conditions, and examined some key life history parameters, including growth rates, fecundity, and generation time, in response to varying temperature and food regimes. The results allowed us to divide the life cycle into 4 distinct phases, during which somatic growth of the animal appeared highly programmed as a function of temperature, but non-responsive to food concentrations exceeding a minimum level necessary for survival. All resources above this level were directed to the reproductive organ, yielding clear differences in fecundity as a function of food regime. Generation times and spawning windows were also independent of food concentration, but dependent on temperature. The generation time, which is extremely short for a complex metazoan, combined with high fecundity, yielded a relationship between animal size and maximal intrinsic rate of natural increase that considerably exceeded values recorded for other poikilothermic metazoans. Intrinsic rates of natural increase were similar to those determined for some algal species reproducing by binary fission, explaining the capacity of O. dioica to respond quickly and opportunistically to algal blooms. KEY WORDS: Appendicularia · Life history · Zooplankton · Filter feeding · SemelparousResale or republication not permitted without written consent of the publisher

As global exploitation of available resources increases, operations extend towards sensitive and previously protected ecosystems. It is important to monitor such areas in order to detect, understand and remediate environmental responses to stressors. The natural heterogeneity and complexity of communities means that accurate monitoring requires high resolution, both temporally and spatially, as well as more complete assessments of taxa. Increased resolution and taxonomic coverage is economically challenging using current microscopy-based monitoring practices. Alternatively, DNA sequencing-based methods have been suggested for cost-efficient monitoring, offering additional insights into ecosystem function and disturbance. Here, we applied DNA metabarcoding of eukaryotic communities in marine sediments, in areas of offshore drilling on the Norwegian continental shelf. Forty-five samples, collected from seven drilling sites in the Troll/Oseberg region, were assessed, using the small subunit ribosomal RNA gene as a taxonomic marker. In agreement with results based on classical morphology-based monitoring, we were able to identify changes in sediment communities surrounding oil platforms. In addition to overall changes in community structure, we identified several potential indicator taxa, responding to pollutants associated with drilling fluids. These included the metazoan orders Macrodasyida, Macrostomida and Ceriantharia, as well as several ciliates and other protist taxa, typically not targeted by environmental monitoring programmes. Analysis of a co-occurrence network to study the distribution of taxa across samples provided a framework for better understanding the impact of anthropogenic activities on the benthic food web, generating novel, testable hypotheses of trophic interactions structuring benthic communities.

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