(Table S1) Boron isotope and trace element data and reconstructed carbonate system parameters, ODP Holes 122-761B and 154-926A

The middle Miocene Climatic Optimum (17-15 Ma; MCO) is a period of global warmth and relatively high CO2 and is thought to be associated with a significant retreat of the Antarctic Ice Sheet (AIS). We present here a new planktic foraminiferal d11B record from 16.6 to 11.8 Ma from two deep ocean sites currently in equilibrium with the atmosphere with respect to CO2. These new data demonstrate that the evolution of global climate during the middle Miocene (as reflected by changes in the cyrosphere) was well correlated to variations in the concentration of atmospheric CO2. What is more, within our sampling resolution (~1 sample per 300 kyr) there is no evidence of hysteresis in the response of ice volume to CO2 forcing during the middle Miocene, contrary to what is understood about the Antarctic Ice Sheet from ice sheet modelling studies. In agreement with previous data, we show that absolute levels of CO2 during the MCO were relatively modest (350-400 ppm) and levels either side of the MCO are similar or lower than the pre-industrial (200-260 ppm). These new data imply the presence of either a very dynamic AIS at relatively low CO2 during the middle Miocene or the advance and retreat of significant northern hemisphere ice. Recent drilling on the Antarctic margin and shore based studies indicate significant retreat and advance beyond the modern limits of the AIS did occur during the middle Miocene, but the complete loss of the AIS was unlikely. Consequently, it seems that ice volume and climate variations during the middle Miocene probably involved a more dynamic AIS than the modern but also some component of land-based ice in the northern hemisphere.

Figure 2. Downcore variations of total diatom concentration in core MD02-2529

The modern eastern equatorial Pacific (EEP) is a major natural source for atmospheric carbon dioxide and is thought to be connected to high-latitude ocean dynamics by oceanic teleconnections on glacial-interglacial timescales. A wealth of sedimentary records aiming at reconstructing last Quaternary changes in primary productivity and nutrient utilization have been devoted to understanding those linkages between the EEP and other distant oceanic areas. Most of these records are, however, clustered in the pelagic EEP cold tongue, with comparatively little attention devoted to coastal areas. Here we present downcore measurements of the composition and concentration of the diatom assemblage together with opal (biogenic silica) concentration at site MD02-2529 recovered in the coastal Panama Basin. Piston core MD02-2529, collected in an area affected by a multitude of processes, provides evidence for strong variations in diatom production at the millennial timescale during the last glacial cycle. The maxima in total diatom concentration occurred during the early marine isotopic stage (MIS) 4 as well as during the MIS 4/3 transition and MIS 3. Rapid changes in diatom concentrations during the MIS 3 mimics Bond cycles as independently recorded by the SSS estimation derived from planktonic foraminifera from the same core. Such patterns indicate a clear linkage between diatom production in the coastal EEP and rapid climate changes in the high-latitude North Atlantic. In parallel, the long-term succession of the diatom community from coastal diatoms, predominantly thriving during MIS 5 and 4, towards pelagic diatoms, dominant during MIS 3 and 2, points to a long-term change in the surface hydrology. During Heinrich Events, diatoms strongly reduced their production, probably due to enhanced stratification in the upper water column. After the last glacial maximum, diatom production and valve preservation strongly decreased in response to the advection of nutrient (H2SiO4)-depleted, warmer water masses. Our high-resolution record highlights how regional climatic processes can modulate rapid changes in siliceous primary production as triggered by wind-induced local upwelling, indicating that millennial climatic variability can overtake other prominent hydrological processes such as those related to silicic acid leakage.

Seawater carbonate chemistry and photosynthetic response of Emiliania huxleyi (CS-369) to UV radiation and elevated temperature duirng experiments, 2011

Changes in calcification of coccolithophores may affect their photosynthetic responses to both, ultraviolet radiation (UVR, 280-400 nm) and temperature. We operated semi-continuous cultures of Emiliania huxleyi (strain CS-369) at reduced (0.1 mM, LCa) and ambient (10 mM, HCa) Ca2+ concentrations and, after 148 generations, we exposed cells to six radiation treatments (>280, >295, >305, >320, >350 and >395 nm by using Schott filters) and two temperatures (20 and 25 °C) to examine photosynthesis and calcification responses. Overall, our study demonstrated that: (1) decreased calcification resulted in a down regulation of photoprotective mechanisms (i.e., as estimated via non-photochemical quenching, NPQ), pigments contents and photosynthetic carbon fixation; (2) calcification (C) and photosynthesis (P) (as well as their ratio) have different responses related to UVR with cells grown under the high Ca2+ concentration being more resistant to UVR than those grown under the low Ca2+ level; (3) elevated temperature increased photosynthesis and calcification of E. huxleyi grown at high Ca2+concentrations whereas decreased both processes in low Ca2+ grown cells. Therefore, a decrease in calcification rates in E. huxleyi is expected to decrease photosynthesis rates, resulting in a negative feedback that further reduces calcification.

Physiological response measures (respiration, clearance, byssus production, survival) of Perna viridis during a 91 day exposure experiment to microplastics in Bogor, Indonesia, 2014

Perna viridis from the Bay of Jakarta was exposed to different concentrations (0, 21.6, 216 and 2160 mg/l) of PVC microplastic particles for 91 days in a controlled laboratory experiment. Particles were negatively buoyant, but were regularly resuspended from the sediment, mimicking tidal events. The particles were contaminated with the organic pollutant fluoranthene, except for one control group, which was exposed to the highest plastic concentration (2160 mg/l) but with clean particles. Within the 91 days survival was monitored. After 40 - 44 days of the exposure, physiological responses of all mussel individuals were measured. Respiration rates were measured as the decrease of oxygen in a sealed container in 20 minutes. Clearance rates were determined by measuring the depletion of algal cells in the water in 30 minutes. Byssus production was assessed by counting the number of newly formed byssus discs within 24 hours.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Downwelling spectral irradiance as measured in different depths, remote sensing reflectance and phytoplankton pigment concentration during POLARSTERN cruises ANT-XXIV/1, ANT-XXIV/4, ANT-XXVI/4 and Maria S. Merian cruise MSM18/3

The composition and abundance of algal pigments provide information on phytoplankton community characteristics such as photoacclimation, overall biomass and taxonomic composition. In particular, pigments play a major role in photoprotection and in the light-driven part of photosynthesis. Most phytoplankton pigments can be measured by high-performance liquid chromatography (HPLC) techniques applied to filtered water samples. This method, as well as other laboratory analyses, is time consuming and therefore limits the number of samples that can be processed in a given time. In order to receive information on phytoplankton pigment composition with a higher temporal and spatial resolution, we have developed a method to assess pigment concentrations from continuous optical measurements. The method applies an empirical orthogonal function (EOF) analysis to remote-sensing reflectance data derived from ship-based hyperspectral underwater radiometry and from multispectral satellite data (using the Medium Resolution Imaging Spectrometer - MERIS - Polymer product developed by Steinmetz et al., 2011, doi:10.1364/OE.19.009783) measured in the Atlantic Ocean. Subsequently we developed multiple linear regression models with measured (collocated) pigment concentrations as the response variable and EOF loadings as predictor variables. The model results show that surface concentrations of a suite of pigments and pigment groups can be well predicted from the ship-based reflectance measurements, even when only a multispectral resolution is chosen (i.e., eight bands, similar to those used by MERIS). Based on the MERIS reflectance data, concentrations of total and monovinyl chlorophyll a and the groups of photoprotective and photosynthetic carotenoids can be predicted with high quality. As a demonstration of the utility of the approach, the fitted model based on satellite reflectance data as input was applied to 1 month of MERIS Polymer data to predict the concentration of those pigment groups for the whole eastern tropical Atlantic area. Bootstrapping explorations of cross-validation error indicate that the method can produce reliable predictions with relatively small data sets (e.g., < 50 collocated values of reflectance and pigment concentration). The method allows for the derivation of time series from continuous reflectance data of various pigment groups at various regions, which can be used to study variability and change of phytoplankton composition and photophysiology.

The morphological response of Emiliania huxleyi to seawater carbonate chemistry changes: an inter-strain comparison

Four strains of the coccolithophore Emiliania huxleyi (RCC1212, RCC1216, RCC1238, RCC1256) were grown in dilute batch culture at four CO2 levels ranging from ~200 µatm to ~1200 µatm. Coccolith morphology was analyzed based on scanning electron micrographs. Three of the four strains did not exhibit a change in morphology over the CO2 range tested. One strain (RCC1256) displayed an increase in the percentage of malformed coccoliths with increasing CO2 concentration. We conclude that the sensitivity of the coccolith-shaping machinery to carbonate chemistry changes is strain-specific. Although it has been shown before that carbonate chemistry related changes in growth- and calcification rate are strain-specific, there seems to be no consistent correlation between coccolith morphology and growth or calcification rate. We did not observe an increase in the percentage of incomplete coccoliths in RCC1256, indicating that the coccolith-shaping machinery per se is affected by acidification and not the signalling pathway that produces the stop-signal for coccolith growth.

Under-ice fauna, sea-ice concentration, sea-ice thickness and under-ice water parameters from the Eurasian central Arctic Ocean during POLARSTERN cruise ARK-XXVII/3 (PS80) in August-September 2012

Arctic sea-ice decline is expected to have a significant impact on Arctic marine ecosystems. Ice-associated fauna play a key role in this context because they constitute a unique part of Arctic biodiversity and transmit carbon from sea-ice algae into pelagic and benthic food webs. Our study presents the first regional-scale record of under-ice faunal distribution and the environmental characteristics of under-ice habitats throughout the Eurasian Basin. Sampling was conducted with a Surface and Under-Ice Trawl, equipped with a sensor array recording ice thickness and other physical parameters during trawling. We identified 2 environmental regimes, broadly coherent with the Nansen and Amundsen Basins. The Nansen Basin regime was distinguished from the Amundsen Basin regime by heavier sea-ice conditions, higher surface salinities and higher nitrate + nitrite concentrations. We found a diverse (28 species) under-ice community throughout the Eurasian Basin. Change in community structure reflected differences in the relative contribution of abundant species. Copepods (Calanus hyperboreus and C. glacialis) dominated in the Nansen Basin regime. In the Amundsen Basin regime, amphipods (Apherusa glacialis, Themisto libellula) dominated. Polar cod Boreogadus saida was present throughout the sampling area. Abrupt changes from a dominance of ice-associated amphipods at ice-covered stations to a dominance of pelagic amphipods (T. libellula) at nearby ice-free stations emphasised the decisive influence of sea ice on small-scale patterns in the surface-layer community. The observed response in community composition to different environmental regimes indicates potential long-term alterations in Arctic marine ecosystems as the Arctic Ocean continues to change.

(Table 1) Average sea surface temperature, average sea surface salinity, C37 concentration, palmitic acid concentration, Uk'37, C37/C38 ratio, dD of water, dD of C37 and dD of palmitic acid of water samples from a transect across the Amazon Plume

The stable hydrogen isotope composition of lipid biomarkers, such as alkenones, is a promising new tool for the improvement of palaeosalinity reconstructions. Laboratory studies confirmed the correlation between lipid biomarker dD composition (dDLipid), water dD composition (dDH2O) and salinity; yet there is limited insight into the applicability of this proxy in oceanic environments. To fill this gap, we test the use of the dD composition of alkenones (dDC37) and palmitic acid (dDPA) as salinity proxies using samples of surface suspended material along the distinct salinity gradient induced by the Amazon Plume. Our results indicate a positive correlation between salinity and dDH2O, while the relationship between dDH2O and dDLipid is more complex: dDPAM correlates strongly with dDH2O (r2 = 0.81) and shows a salinity-dependent isotopic fractionation factor. dDC37 only correlates with dDH2O in a small number (n = 8) of samples with alkenone concentrations > 10 ng L**-1, while there is no correlation if all samples are taken into account. These findings are mirrored by alkenone-based temperature reconstructions, which are inaccurate for samples with low alkenone concentrations. Deviations in dDC37 and temperature are likely to be caused by limited haptophyte algae growth due to low salinity and light limitation imposed by the Amazon Plume. Our study confirms the applicability of dDLipid as a salinity proxy in oceanic environments. But it raises a note of caution concerning regions where low alkenone production can be expected due to low salinity and light limitation, for instance, under strong riverine discharge.