(Data S1) Palynological analysis of IODP and ODP sediment cores around the Antarctic margin

The circum-Antarctic Southern Ocean is an important region for global marine food webs and carbon cycling because of sea-ice formation and its unique plankton ecosystem. However, the mechanisms underlying the installation of this distinct ecosystem and the geological timing of its development remain unknown. Here, we show, on the basis of fossil marine dinoflagellate cyst records, that a major restructuring of the Southern Ocean plankton ecosystem occurred abruptly and concomitant with the first major Antarctic glaciation in the earliest Oligocene (~33.6 million years ago). This turnover marks a regime shift in zooplankton-phytoplankton interactions and community structure, which indicates the appearance of eutrophic and seasonally productive environments on the Antarctic margin. We conclude that earliest Oligocene cooling, ice-sheet expansion, and subsequent sea-ice formation were important drivers of biotic evolution in the Southern Ocean.

Geochemical analysis of sediments and interstitial water in sediment cores from the North-West African continental margin and from the Central Pacific

A. Continental slope sediments off Spanish-Sahara and Senegal contain up to 4% organic carbon and up to 0.4% total nitrogen. The highest concentrations were found in sediments from water depths between 1000 and 2000 m. The regional and vertical distribution of organic matter differs significantly. Off Spanish-Sahara the organic matter content of sediment deposited during glacial times (Wuerm, Late Riss) is high whereas sediments deposited during interglacial times (Recent, Eem) are low in organic matter. Opposite distribution was found in sediments off Senegal. The sediments contain 30 to 130 ppm of fixed nitrogen. In most sediments this corresponds to 2-8 % of the total nitrogen. Only in sediments deposited during interglacial times off Spanish-Sahara up to 20 % of the total nitrogen is contained as inorganically bound nitrogen. Positive correlations of the fixed nitrogen concentrations to the amounts of clay, alumina, and potassium suggest that it is primarily fixed to illites. The amino acid nitrogen and hexosamine nitrogen account for 17 to 26 % and 1.3 to 2.4 %, respectively of the total nitrogen content of the sediments. The concentrations vary between 200 and 850 ppm amino acid nitrogen and 20 to 70 ppm hexosamine nitrogen, both parallel the fluctiations of organic matter in the sediment. Fulvic acids, humic acids, and the total organic matter of the sediments may be clearly differentiated from one another and their amino acid and hexosamine contents and their amino acid composition: a) Fulvic acids contain only half as much amino acids as humic acids b) The molar amino acid/hexosamine ratios of the fulvic acids are half those of the humic acids and the total organic matter of the sediment c) The amino acid spectra of fulvic acids are characterized by an enrichment of aspartic acid, alanine, and methionine sulfoxide and a depletion of glycine, valine, isoleucine, leucine, tyrosine, phenylalanine, lysine, and arginine compared to the spectra of the humic acids and those of the total organic matter fraction of the sediment. d) The amino acid spectra of the humic acids and those of the total organic matter fraction of the sediments are about the same with the exception that arginine is clearly enriched in the total organic matter. In general, as indicated by the amino compounds humic acids resemble closer the total organic matter composition than the low molecular fulvic acids do. This supports the general idea that during the course of diagenesis in reducing sediments organic matter stabilizes from a fulvic-like structure to humic-like structure and finally to kerogen. The decomposition rates of single aminio acids differ significantly from one another. Generally amino acids which are preferentially contained in humic acids and the total organic matter fraction show a smaller loss with time than those preferably well documented in case of the basic amino acids lysine and arginine which- although thermally unstable- are the most stable amino acids in the sediments. A favoured incorporation of these compounds into high molecular substances as well as into clay minerals may explain their relatively high "stability" in the sediment. The nitrogen loss from the sediments due to the activity of sulphate-reducing bacteria amounts to 20-40 % of the total organic nitrogen now present. At least 40 % of the organic nitrogen which is liberated by sulphate-reducing bacteria can be explained ny decomposition of amino acids alone. B. Deep-sea sediments from the Central Pacific The deep-seas sediments contain 1 to 2 orders of magnitude less organic matter than the continental slope sediments off NW Africa, i.e. 0.04 to 0.3 % organic carbon. The fixed nitrogen content of the deep-sea sediments ranges from 60 to 270 ppm or from 20 to 45 % of the total nitrogen content. While ammonia is the prevailing inorganic nitrogen compound in anoxic pore waters, nitrate predominates in the oxic environment of the deep-sea sediments. Near the sediment/water interface interstital nitrate concentrations of around 30 µg-at. N/l were recorded. These generally increase with sediment depth by 10 to 15 µg-at. NO3- N/l. This suggests the presence of free oxygen and the activity of nitrifying bacteria in the interstitial waters. The ammonia content of the interstitial water of the oxic deep-sea sediments ranges from 2 to 60 µg-at. N/l and thus is several orders of magnitude less than in anoxic sediments. In contrast to recorded nitrate gradients towards the sediments/water interface, there are no ammonia concentration gradients. However, ammonia concentrations appear to be characteristic for certain regional areas. It is suggested that this regional differentiation is caused by ion exchange reactions involving potassium and ammonium ions rather than by different decomposition rates of organic matter. C. C/N ratios All estimated C/N ratios of surface sediments vary between 3 and 9 in the deep-sea and the continental margin, respectively. Whereas the C/N ratios generally increase with depth in the sediment cores off NW Africa they decrease in the deep-sea cores. The lowest values of around 1.3 were found in the deeper sections of the deep-sea cores, the highest of around 10 in the sediments off NW Africa. The wide range of the C/N ratios as well as their opposite behaviour with increasing sediment depth in both the deep-sea and continental margin sediment cores, can be attributed mainly to the combination of the following three factors: 1. Inorganic and organic substances bound within the latticed of clay minerals tend to decrease the C/N ratios. 2. Organic matter not protected by absorption on the clay minerals tends to increase C/N ratios 3. Diagenetic alteration of organic matter by micro-organisms tends to increase C/N ratios through preferential loss of nitrogen The diagenetic changes of the microbially decomposable organic matter results in both oxic and anoxic environments in a preferential loss of nitrogen and hence in higher C/N ratios of the organic fraction. This holds true for most of the continental margin sediments off NW Africa which contain relatively high amounts of organic matter so that factors 2 and 3 predominate there. The relative low C/N ratios of the sediments deposited during interglacial times off Spanish-Sahara, which are low in organic carbon, show the increasing influence of factor 1 - the nitrogen-rich organic substances bound to clay minerals. In the deep-sea sediments from the Central Pacific this factor completely predominates so that the C/N rations of the sediments approach that of the substance absorbed to clay minerals with decreasing organic matter content. In the deeper core sections the unprotected organic matter has been completely destroyed so that the C/N ratios of the total sediments eventually fall into the same range as those of the pure clay mineral fraction.

Metadata und statistic analysis of archael and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (Z1-Z3, all habitats)

DNA extraction was carried out as described on the MICROBIS project pages (http://icomm.mbl.edu/microbis ) using a commercially available extraction kit. We amplified the hypervariable regions V4-V6 of archaeal and bacterial 16S rRNA genes using PCR and several sets of forward and reverse primers (http://vamps.mbl.edu/resources/primers.php). Massively parallel tag sequencing of the PCR products was carried out on a 454 Life Sciences GS FLX sequencer at Marine Biological Laboratory, Woods Hole, MA, following the same experimental conditions for all samples. Sequence reads were submitted to a rigorous quality control procedure based on mothur v30 (doi:10.1128/AEM.01541-09) including denoising of the flow grams using an algorithm based on PyroNoise (doi:10.1038/nmeth.1361), removal of PCR errors and a chimera check using uchime (doi:10.1093/bioinformatics/btr381). The reads were taxonomically assigned according to the SILVA taxonomy (SSURef v119, 07-2014; doi:10.1093/nar/gks1219) implemented in mothur and clustered at 98% ribosomal RNA gene V4-V6 sequence identity. V4-V6 amplicon sequence abundance tables were standardized to account for unequal sampling effort using 1000 (Archaea) and 2300 (Bacteria) randomly chosen sequences without replacement using mothur and then used to calculate inverse Simpson diversity indices and Chao1 richness (doi:10.2307/4615964). Bray-Curtis dissimilarities (doi:10.2307/1942268) between all samples were calculated and used for 2-dimensional non metric multidimensional scaling (NMDS) ordinations with 20 random starts (doi:10.1007/BF02289694). Stress values below 0.2 indicated that the multidimensional dataset was well represented by the 2D ordination. NMDS ordinations were compared and tested using Procrustes correlation analysis (doi:10.1007/BF02291478). All analyses were carried out with the R statistical environment and the packages vegan (available at: http://cran.r-project.org/package=vegan), labdsv (available at: http://cran.r-project.org/package=labdsv), as well as with custom R scripts. Operational taxonomic units at 98% sequence identity (OTU0.03) that occurred only once in the whole dataset were termed absolute single sequence OTUs (SSOabs; doi:10.1038/ismej.2011.132). OTU0.03 sequences that occurred only once in at least one sample, but may occur more often in other samples were termed relative single sequence OTUs (SSOrel). SSOrel are particularly interesting for community ecology, since they comprise rare organisms that might become abundant when conditions change.16S rRNA amplicons and metagenomic reads have been stored in the sequence read archive under SRA project accession number SRP042162.

Strontium isotope analysis of seawater and at a mixture of planktic foraminifera during the Paleocene and Early Eocene from different holes of ODP Leg 2008

We refined the strontium isotope seawater curve for the Paleocene and early Eocene by analysis of samples recovered from the Walvis Ridge during Ocean Drilling Project (ODP) Leg 208. The highest 87Sr/86Sr values occurred in the earliest Paleocene at 65 Ma and generally decreased throughout the Paleocene, reaching minimum values between 53 and 51 Ma in the early Eocene before beginning to increase again at 50 Ma. A plausible explanation for the 87Sr/86Sr decrease between 65 and 51 Ma is increased rates of hydrothermal activity and/or the eruption and weathering of large igneous provinces (e.g., Deccan Traps and North Atlantic). Strontium isotope variations closely parallel sea level and benthic d18O changes during the late Paleocene and early Eocene, supporting previous studies linking tectonic reorganization and increased volcanism to high sea level, high CO2, and warm global temperatures.

Combined metabolome and proteome analysis of the mantle tissue from Pacific oyster Crassostrea gigas exposed to elevated pCO2

Ocean acidification (OA) has been found to affect an array of normal physiological processes in mollusks, especially posing a significant threat to the fabrication process of mollusk shell. In the current study, the impact of exposure to elevated pCO2 condition was investigated in mantle tissue of Crassostrea gigas by an integrated metabolomic and proteomic approach. Analysis of metabolome and proteome revealed that elevated pCO2 could affect energy metabolism in oyster C. gigas, marked by differentially altered ATP, succinate, MDH, PEPCK and ALDH levels. Moreover, the up-regulated calponin-2, tropomyosins and myosin light chains indicated that elevated pCO2 probably caused disturbances in cytoskeleton structure in mantle tissue of oyster C. gigas. This work demonstrated that a combination of proteomics and metabolomics could provide important insights into the effects of OA at molecular levels.