Description: Suspensions of small fibres are known to produce clusters of particles during sedimentation, independently of fluid shear and Brownian motion. This phenomenon, which is due to hydrodynamic interactions at low Reynolds number, has been predicted theoretically and observed in experiments and numerical simulations. We hypothesize that this mechanism may be at least partially responsible for the encounter and aggregation of marine diatoms.

Description: Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed.

Description: Ocean iron fertilization experiments enable the quantitative study of processes shaping the structure and functioning of pelagic ecosystems following perturbation under in situ conditions. EIFEX was conducted within a stationary eddy adjacent to the Antarctic Polar Front over 38 days in February/March 2004 and induced a massive diatom bloom. Here, we present the responses in abundance and biomass of all identifiable protozooplankton taxa (heterotrophic protists ranging from 2 to 500 µm) during the bloom. Acantharia, dinoflagellates and ciliates together contributed 〉90% of protozooplankton biomass in the upper 100 m throughout the experiment with heterotrophic nanoflagellates, nassellaria, spumellaria, phaeodaria, foraminifera and the taxopodidean Sticholonche zanclea providing the remainder. Total protozooplankton biomass increased slightly from 1.0 to 1.3 g C m –2 within the fertilized patch and remained at 0.7+0.04 g C m –2 outside it. However, distinct trends in population build-up or decline were observed within the dominant taxa in each group. In general, smaller less-defended groups such as aloricate ciliates and athecate dinoflagellates declined, whereas the biomass of large, spiny and armoured groups, in particular acantharia, large tintinnids and thecate dinoflagellates increased inside the patch. We attribute the higher accumulation rates of defended taxa to selective, heavy grazing pressure by the large stocks of copepods. Of the defended taxa, acantharia had the lowest mortality rates and the highest biomass. Large stocks of tintinnid loricae in the deep water column identify this group as a relevant contributor to deep organic carbon export. Highest accumulation rates (0.11 day –1 ) were recorded in S. zanclea .

Description: The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR 2 , http://ssu-rrna.org/ ) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists.

Description: We tracked temporal changes in protist diversity at the Long Term Ecological Research (LTER) station MareChiara in the Gulf of Naples (Mediterranean Sea) on eight dates in 2011 using a metabarcoding approach. Illumina analysis of the V4 and V9 fragments of the 18S rDNA produced 869 522 and 1 410 071 sequences resulting in 6517 and 6519 OTUs, respectively. Marked compositional variations were recorded across the year, with less than 2% of OTUs shared among all samples and similar patterns for the two marker tags. Alveolata, Stramenopiles and Rhizaria were the most represented groups. A comparison with light microscopy data indicated an over-representation of Dinophyta in the sequence dataset, whereas Bacillariophyta showed comparable taxonomic patterns between sequence and light microscopy data. Shannon diversity values were stable from February to September, increasing thereafter with a peak in December. Community variance was mainly explained by seasonality (as temperature), trophic status (as chlorophyll a ), and influence of coastal waters (as salinity). Overall, the background knowledge of the system provided a sound context for the result interpretation, showing that LTER sites provide an ideal setting for high-throughput sequencing (HTS) metabarcoding characterisation of protist assemblages and their relationships with environmental variations.

Description: eddy located along the Antarctic Polar Front in the Atlantic sector of the Southern Ocean. Mixed layer (ML) waters were characterized by high nitrate (~20 μM), low dissolved iron (DFe ~0.2 nM) and low silicate concentrations (below 1 μM) restricting diatom growth. Upon initial fertilization, chlorophyll-a doubled during the first two weeks and stabilized thereafter, despite a second fertilization on day 21, due to an increase in grazing pressure. Biomass at the different trophic levels was mostly comprised of small autotrophic flagellates, the large copepod Calanus simillimus and the amphipod Themisto gaudichaudii. The downward flux of particulate material comprised mainly copepod fecal pellets that were remineralized in the upper 150 m of the water column with no significant deeper export. showed a greater variability (ranging from 0.3 to 1.3 nM) without a clear vertical pattern. Particulate iron concentrations (measured after 2 months at pH 1.4) decreased with time and showed a vertical pattern that indicated an important non-biogenic component at the bottom of the mixed layer. In order to assess the contribution of copepod grazing to iron cycling we used two different approaches: first, we measured for the first time in a field experiment copepod fecal pellet concentrations in the water column together with the iron content per pellet, and second, we devised a novel analytical scheme based on a two-step leaching protocol to estimate the contribution of copepod fecal pellets to particulate iron in the water column. Analysis of the iron content of isolated fecal pellets from C. simillimus showed that after the second fertilization, the iron content per fecal pellet was ~5 fold higher if the copepod had been captured in fertilized waters. We defined a new fraction termed leachable iron (pH 2.0) in 48 h (LFe48h) that, for the conditions during LOHAFEX, was shown to be an excellent proxy for the concentration of iron contained in copepod fecal pellets. We observed that, as a result of the second fertilization, iron accumulated in copepod fecal pellets and remained high at one third of the total iron stock in the upper 80 m. We hypothesize that our observations are due to a combination of two biological processes. First, phagotrophy of iron colloids freshly formed after the second fertilization by the predominant flagellate community resulted in higher Fe:C ratios per cell that, via grazing, lead to iron enrichment in copepod fecal pellets in fertilized waters. Second, copepod coprophagy could explain the rapid recycling of particulate iron in the upper 100–150 m, the accumulation of LFe48h in the upper 80 m after the second fertilization and provided the iron required for the maintenance of the LOHAFEX bloom for many weeks. Our results provide the first quantitative evidence of the major ecological relevance of copepods and their fecal products in the cycling of iron in silicate depleted areas of the Southern Ocean.