Assessing marine plankton community structure from long-term monitoring data with multivariate autoregressive (MAR) models: a comparison of fixed station versus spatially distributed sampling data

We examined how marine plankton interaction networks, as inferred by multivariate autoregressive (MAR) analysis of time-series, differ based on data collected at a fixed sampling location (L4 station in the Western English Channel) and four similar time-series prepared by averaging Continuous Plankton Recorder (CPR) datapoints in the region surrounding the fixed station. None of the plankton community structures suggested by the MAR models generated from the CPR datasets were well correlated with the MAR model for L4, but of the four CPR models, the one most closely resembling the L4 model was that for the CPR region nearest to L4. We infer that observation error and spatial variation in plankton community dynamics influenced the model performance for the CPR datasets. A modified MAR framework in which observation error and spatial variation are explicitly incorporated could allow the analysis to better handle the diverse time-series data collected in marine environments.

Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers to efficiently identify parental species and hybrids. Using next-generation sequencing analysis of both the genome and transcriptome from two sibling species, Calanus finmarchicus and Calanus glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species-specific amplicon length. Furthermore, most of the markers were successfully amplified in other Calanus species, allowing the molecular identification of Calanus helgolandicus, Calanus hyperboreus and Calanus marshallae.

Abundance of phytoplankton, heterotrophic nanoflagellates and bacteria through the water column at time series station L4 in the Western English Channel, 2007-2013

short doi:10/rf8 full doi:10.5285/f014becf-d6d6-3bb9-e044-000b5de50f38

Feeding selectivity of bivalve larvae on natural plankton assemblages in the Western English Channel

Meroplankton, including bivalve larvae, are an important and yet understudied component of coastal marine food webs. Understanding the baseline of meroplankton ecology is imperative to establish and predict their sensitivity to local and global marine stressors. Over an annual cycle (October 2009–September 2010), bivalve larvae were collected from the Western Channel Observatory time series station L4 (50°15.00′N, 4°13.02′W). The morphologically similar larvae were identified by analysis of the 18S nuclear small subunit ribosomal RNA gene, and a series of incubation experiments were conducted to determine larval ingestion rates on natural plankton assemblages. Complementary gut content analysis was performed using a PCR-based method for detecting prey DNA both from field-collected larvae and those from the feeding experiments. Molecular identification of bivalve larvae showed the community composition to change over the course of the sampling period with domination by Phaxas in winter and higher diversity in autumn. The larvae selected for nanoeukaryotes (2–20 µm) including coccolithophores (<20 µm) which together comprised >75 % of the bivalve larvae diet. Additionally, a small percentage of carbon ingested originated from heterotrophic ciliates (<30 µm). The molecular analysis of bivalve larvae gut content provided increased resolution of identification of prey consumed and demonstrated that the composition of prey consumed established through bottle incubations conferred with that established from in situ larvae. Despite changes in bivalve larvae community structure, clearance rates of each prey type did not change significantly over the course of the experiment, suggesting different bivalve larvae species may consume similar prey.

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.