Description: In May 2016, the remote-controlledAutomatedFiltration System forMarine Microbes (AUTOFIM) was implemented in parallel to the Long Term Ecological Research (LTER) observatory Helgoland Roads in the German Bight. We collected samples for characterization of dynamics within the eukaryotic microbial communities at the end of a phytoplankton bloom via 18S meta-barcoding. Understanding consequences of environmental change for key marine ecosystem processes, such as phytoplankton bloom dynamics requires information on biodiversity and species occurrences with adequate temporal and taxonomic resolution via time series observations. Sampling automation and molecular high throughput methods can serve these needs by improving the resolution of current conventional marine time series observations. A technical evaluation based on an investigation of eukaryotic microbes using the partial 18S rRNA gene suggests that automated filtration with the AUTOFIM device and preservation of the plankton samples leads to highly similar 18S community profiles, compared to manual filtration and snap freezing. The molecular data were correlated with conventional microscopic counts. Overall, we observed substantial change in the eukaryotic microbial community structure during the observation period. A simultaneous decline of diatom and ciliate sequences succeeded a peak ofMiracula helgolandica, suggesting a potential impact of these oomycete parasites on diatom bloom dynamics and phenology in the North Sea. As oomycetes are not routinely counted at Helgoland Roads LTER, our findings illustrate the benefits of combining automated filtration with metabarcodingto augment classical time series observations, particularly for taxa currently neglected due to methodological constraints.

Description: Knowledge about the protist diversity of the Pacific sector of the Southern Ocean is scarce. We tested the hypothesis that distinct protist community assemblages characterize large-scale water masses. Therefore, we determined the composition and biogeography of late summer protist assemblages along a transect from the coast of New Zealand to the eastern Ross Sea. We used state of the art molecular approaches, such as automated ribosomal intergenic spacer analysis and 454-pyrosequencing, combined with high-performance liquid chromatography pigment analysis to study the protist assemblage. We found distinct biogeographic patterns defined by the environmental conditions in the particular region. Different water masses harbored different microbial communities. In contrast to the Arctic Ocean, picoeukaryotes had minor importance throughout the investigated transect and showed very low contribution south of the Polar Front. Dinoflagellates, Syndiniales, and small stramenopiles were dominating the sequence assemblage in the Subantarctic Zone, whereas the relative abundance of diatoms increased southwards, in the Polar Frontal Zone and Antarctic Zone. South of the Polar Front, most sequences belonged to haptophytes. This study delivers a comprehensive and taxon detailed overview of the protist composition in the investigated area during the austral summer 2010.

Description: The iron fertilization experiment LOHAFEX was conducted in a cold-core eddy in the Southern Atlantic Ocean during austral summer. Within a few days after fertilization, a phytoplankton bloom developed dominated by nano- and picoplankton groups. Unlike previously reported for other iron fertilization experiments, a diatom bloom was prevented by iron and silicate co-limitation. We used 18S rRNA gene tag pyrosequencing to investigate the diversity of these morphologically similar cell types within the nano- and picoplankton and microscopically enumerated dominant clades after catalyzed reported deposition fluorescence in situ hybridization (CARD-FISH) with specific oligonucleotide probes. In addition to Phaeocystis, members of Syndiniales group II, clade 10–11, and the Micromonas clades ABC and E made up a major fraction of the tag sequences of the nano- and picoplankton community within the fertilized patch. However, the same clades were also dominant before the bloom and outside the fertilized patch. Furthermore, only little changes in diversity could be observed over the course of the experiment. These results were corroborated by CARD-FISH analysis which confirmed the presence of a stable nano- and picoplankton community dominated by Phaeocystis and Micromonas during the entire course of the experiment. Interestingly, although Syndiniales dominated the tag sequences, they could hardly be detected by CARD-FISH, possibly due to the intracellular parasitic life style of this clade. The remarkable stability of the nano- and picoplankton community points to a tight coupling of the different trophic levels within the microbial food web during LOHAFEX.

Description: In the Arctic Ocean, sea-ice decline will significantly change the structure of biological communities. At the same time, changing nutrient dynamics can have similarly strong and potentially interacting effects. To investigate the response of the taxonomic and trophic structure of planktonic and ice-associated communities to varying sea-ice properties and nutrient concentrations, we analysed four different communities sampled in the Eurasian Basin in summer 2012: (1) protists and (2) metazoans from the under-ice habitat, and (3) protists and (4) metazoans from the epipelagic habitat. The taxonomic composition of protist communities was characterised with 18S meta-barcoding. The taxonomic composition of metazoan communities was determined based on morphology. The analysis of environmental parameters identified (i) a ‘shelf-influenced’ regime with melting sea ice, high-silicate concentrations and low NOx (nitrate + nitrite) concentrations; (ii) a ‘Polar’ regime with low silicate concentrations and low NOx concentrations; and (iii) an ‘Atlantic’ regime with low silicate concentrations and high NOx concentrations. Multivariate analyses of combined bio-environmental datasets showed that taxonomic community structure primarily responded to the variability of sea-ice properties and hydrography across all four communities. Trophic community structure, however, responded significantly to NOx concentrations. In three of the four communities, the most heterotrophic trophic group significantly dominated in the NOx-poor shelf-influenced and Polar regimes compared to the NOx-rich Atlantic regime. The more heterotrophic, NOx-poor regimes were associated with lower productivity and carbon export than the NOx-rich Atlantic regime. For modelling future Arctic ecosystems, it is important to consider that taxonomic diversity can respond to different drivers than trophic diversity.