(Table S2) Cell concentrations of individual and combined Alexandrium spp. and phylogenetic groups as obtained by qPCR assay and Utermöhl counts, as well as particulate PSP toxin concentrations from discrete water depths

Molecular methods provide promising tools for routine detection and quantification of toxic microalgae in plankton samples. To this end, novel TaqMan minor groove binding probes and primers targeting the small (SSU) or large (LSU) ribosomal subunit (rRNA) were developed for two species of the marine dinoflagellate genus Alexandrium (A. minutum, A. tamutum) and for three groups/ribotypes of the A. tamarense species complex: Group I/North American (NA), Group II/Mediterranean (ME) and Group III/Western European (WE). Primers and probes for real-time quantitative PCR (qPCR) were species-specific and highly efficient when tested in qPCR assays for cross-validation with pure DNA from cultured Alexandrium strains. Suitability of the qPCR assays as molecular tools for the detection and estimation of relative cell abundances of Alexandrium species and groups was evaluated from samples of natural plankton assemblages along the Scottish east coast. The results were compared with inverted microscope cell counts (Utermöhl technique) of Alexandrium spp. and associated paralytic shellfish poisoning (PSP) toxin concentrations. The qPCR assays indicated that A. tamarense (Group I) and A. tamutum were the most abundant Alexandrium taxa and both were highly positively correlated with PSP toxin content of plankton samples. Cells of A. tamarense (Group III) were present at nearly all stations but in low abundance. Alexandrium minutum and A. tamarense (Group II) cells were not detected in any of the samples, thereby arguing for their absence from the specific North Sea region, at least at the time of the survey. The sympatric occurrence of A. tamarense Group I and Group III gives further support to the hypothesis that the groups/ribotypes of the A. tamarense species complex are cryptic species rather than variants belonging to the same species.

Acoustic multi-frequency indicator of four major groups on a spatial grid in the Bay of Biscay

The first data set contains the mean and cofficient of variation (standard deviation divided by mean) of a multi-frequency indicator I derived from ER60 acoustic information collected at five frequencies (18, 38, 70, 120, and 200 kHz) in the Bay of Biscay in May of the years 2006, 2008, 2009 and 2010 (Pelgas surveys). The multi-frequency indicator was first calculated per voxel (20 m long × 5 m deep sampling unit) and then averaged on a spatial grid (approx. 20 nm × 20 nm) for five 5-m depth layers in the surface waters (10-15m, 15-20m, 20-25m, 25-30m below sea surface); there are missing values in particular in the shallowest layer. The second data set provides for each grid cell and depth layer the proportion of voxels for which the multi-frequency indicator I was indicative of a certain group of organisms. For this the following interpretation was used: I < 0.39 swim bladder fish or large gas bubbles, I = 0.39-0.58 small resonant bubbles present in gas bearing organisms such as larval fish and phytoplankton, I = 0.7-0.8 fluidlike zooplankton such as copepods and euphausiids, and I > 0.8 mackerel. These proportions can be interpreted as a relative abundance index for each of the four organism groups.

Small Changes in pH Have Direct Effects on Marine Bacterial Community Composition: A Microcosm Approach

As the atmospheric CO2 concentration rises, more CO2 will dissolve in the oceans, leading to a reduction in pH. Effects of ocean acidification on bacterial communities have mainly been studied in biologically complex systems, in which indirect effects, mediated through food web interactions, come into play. These approaches come close to nature but suffer from low replication and neglect seasonality. To comprehensively investigate direct pH effects, we conducted highly-replicated laboratory acidification experiments with the natural bacterial community from Helgoland Roads (North Sea). Seasonal variability was accounted for by repeating the experiment four times (spring, summer, autumn, winter). Three dilution approaches were used to select for different ecological strategies, i.e. fast-growing or low-nutrient adapted bacteria. The pH levels investigated were in situ seawater pH (8.15-8.22), pH 7.82 and pH 7.67, representing the present-day situation and two acidification scenarios projected for the North Sea for the year 2100. In all seasons, both automated ribosomal intergenic spacer analysis and 16S ribosomal amplicon pyrosequencing revealed pH-dependent community shifts for two of the dilution approaches. Bacteria susceptible to changes in pH were different members of Gammaproteobacteria, Flavobacteriaceae, Rhodobacteraceae, Campylobacteraceae and further less abundant groups. Their specific response to reduced pH was often context-dependent. Bacterial abundance was not influenced by pH. Our findings suggest that already moderate changes in pH have the potential to cause compositional shifts, depending on the community assembly and environmental factors. By identifying pH-susceptible groups, this study provides insights for more directed, in-depth community analyses in large-scale and long-term experiments.

Benthic foraminifera groups of ODP Site 162-982

The pulsed decline and eventual extinction of 51 species of elongate, cylindrical deep-sea benthic foraminifera (Stilostomellidae, Pleurostomellidae, and some Nodosariidae) occurred at intermediate water depths (1145-2168 m, Sites 980 and 982) in the northern North Atlantic during the mid-Pleistocene transition (MPT, 1.2-0.6 Ma). In the early Pleistocene, prior to their disappearance, these species comprised up to 20% of the total abundance of the benthic foraminiferal assemblage at 2168 m, but up to only 2% at 1145 m. The MPT extinction of 51 species represents ?20% of the total benthic foraminiferal diversity at bathyal depths in the North Atlantic (excluding the myriad of small unilocular forms). The extinction rate during the MPT was approximately 10 species per 0.1 myr, being one or two orders of magnitude greater than normal background turnover rates of deep-sea benthic foraminifera. Comparison of the precise timings of declines and disappearances (= highest occurrences) of each species shows that they were often diachronous between the two depths. The last of these species to disappear in the North Atlantic was Pleurostomella alternans at ~0.679 and ~0.694 Ma in Sites 980 and 982, respectively, which is in good agreement with the previously documented global "Stilostomella extinction" datum within the period 0.7-0.58 Ma. Comparison with similar studies in intermediate depth waters in the Southwest Pacific Gateway indicates that ~61% of the extinct species were common to both regions, and that although the pattern of pulsed decline was similar, the precise order and timing of the extinction of individual species were mostly different on opposite sides of the world. Previous studies have indicated that this extinct group of elongate, cylindrical foraminifera lived infaunally and had their greatest abundances in poorly ventilated, lower oxygen environments. This is supported by our study where there is a strong positive correlation (r = ~+ 0.8) between the flux of the extinction group and low-oxygen/high organic input species (such as Uvigerina, Bulimina and Bolivina) during the MPT, suggesting a close relationship with lower oxygen levels and high food supply to the sea floor. The absolute abundance, flux, and number of the extinction group of species show a progressive withdrawal pattern with major decreases occurring in cold periods with high d13C values. This might be related to increasing chemical ventilation of glacial intermediate water.