(Table S1) Diatom abundance in coastal upwelling systems

Coastal upwelling systems account for approximately half of global ocean primary production and contribute disproportionately to biologically driven carbon sequestration. Diatoms, silica-precipitating microalgae, constitute the dominant phytoplankton in these productive regions, and their abundance and assemblage composition in the sedimentary record is considered one of the best proxies for primary production. The study of the sedimentary diatom abundance (SDA) and total organic carbon content (TOC) in the five most important coastal upwelling systems of the modern ocean (Iberia-Canary, Benguela, Peru-Humboldt, California and Somalia-Oman) reveals a global-scale positive relationship between diatom production and organic carbon burial. The analysis of SDA in conjunction with environmental variables of coastal upwelling systems such as upwelling strength, satellite-derived net primary production and surface water nutrient concentrations shows different relations between SDA and primary production on the regional scale. At the global-scale, SDA appears modulated by the capacity of diatoms to take up silicic acid, which ultimately sets an upper limit to global export production in these ocean regions.

Nitrogen cycling driven by organic matter export in the South Pacific oxygen minimum zone

Oxygen minimum zones are expanding globally, and at present account for around 20-40% of oceanic nitrogen loss. Heterotrophic denitrification and anammox-anaerobic ammonium oxidation with nitrite-are responsible for most nitrogen loss in these low-oxygen waters. Anammox is particularly significant in the eastern tropical South Pacific, one of the largest oxygen minimum zones globally. However, the factors that regulate anammox-driven nitrogen loss have remained unclear. Here, we present a comprehensive nitrogen budget for the eastern tropical South Pacific oxygen minimum zone, using measurements of nutrient concentrations, experimentally determined rates of nitrogen transformation and a numerical model of export production. Anammox was the dominant mode of nitrogen loss at the time of sampling. Rates of anammox, and related nitrogen transformations, were greatest in the productive shelf waters, and tailed off with distance from the coast. Within the shelf region, anammox activity peaked in both upper and bottom waters. Overall, rates of nitrogen transformation, including anammox, were strongly correlated with the export of organic matter. We suggest that the sinking of organic matter, and thus the release of ammonium into the water column, together with benthic ammonium release, fuel nitrogen loss from oxygen minimum zones.

Tidal and spatial variations of DI13C and aquatic chemistry in a temperate tidal basin during winter time

Here, the pelagic carbonate system and the ?13C signature of dissolved inorganic carbonate (DIC) were investigated in a tidal basin of the southern North Sea, the Jade Bay, with respect to tidal cycles and a transect towards the North Sea in winter time (January and November, 2010). Physical parameters, major and trace elements, and nutrient concentrations were considered, too. Primary production and pelagic organic matter respiration were negligible during winter time. Both, the compositional variations on the transects as well as during the tidal cycles indicate the mixing of North Sea with fresh water. The combined spatial co-variations of different parameters indicate an introduction of fresh water that was enriched in DI12C, metabolites (e.g., ammonia), protons, and dissolved redox-sensitive elements (e.g., Mn2+). During the January campaign, the discharge via the flood gates was limited due to ice cover of the hinterland drainage ditches, allowing for an observation of tidal variations without significant mixing contributions from surface water discharges. Considering a binary mixing model with North Sea and fresh water as end-members, the extrapolated fresh water end-member composition for this campaign is estimated to contain about 3.8 mmol/kg DIC , and enhanced concentrations of NH4+, Mn2+, and protons compared to North Sea water. The fast temporal response of dissolved geochemical tracers on tidal variations in the Jade Bay indicates a continuous supply of a fresh water component. The measured composition of fresh waters entering the Jade Bay via flood gates (end of October, 2010) did not match the values estimated by the binary mixing model. Therefore, the overall fresh water component likely is a mixture between sources originating from flood gates and (in January) dominating submarine groundwater discharge entering the Jade Bay. This model is consistent with the results obtained during the November campaign, when a more important contribution from flood gates is expected and a more variable fresh water end-member is estimated. The co-variations of the concentrations and the stable carbon isotope composition of DIC are applied to evaluate possible superimposed sink-source-transformation processes in the coastal waters and a general co-variation scheme is suggested.

Dinoflagellate cysts in surface sediment samples of METEOR cruises M20/2, M23/1, M34/1, M34/2, M34/3 and M34/4

To enhance the limited information available about the palaeo-ecological significance of calcareous dinoflagellates, we have studied their lateral distribution in surface sediments of the equatorial and south Atlantic between 13°N and 36°S. Calcareous dinoflagellate cysts appear to be widely distributed throughout the studied area. In the surface sediments, concentrations (cyst per gram dry sediment) of the vegetative stage Thoracosphaera heimii are generally higher than that of the (presumably) calcareous resting cysts. Distribution patterns in surface sediments of Orthopithonella granifera (Fütterer) Keupp and Versteegh, Rhabdothorax spp. Kamptner., Sphaerodinella albatrosiana (Kamptner) Keupp and Versteegh S. albatrosiana praratabulated, Sphaerodinella tuberosa var. 1 (Kamptner) Keupp and Versteegh and S. tuberosa var. 2 and the ratios between these species have been compared with temperature, salinity, density and stratification gradients in the upper water column. Rhabdothorax spp. is characteristically present in sediments of more temperate regions characterized by high seasonality. Dinoflagellates producing these cysts are able to tolerate high nutrient concentrations, and mixing of the water column. S. albatrosiana is abundant in regions characterized by high sea surface temperatures and oligotrophic surface water conditions. In contrast, the distribution of S. tuberosa var. 2 is negatively related to temperature. The other cyst species did not show a characteristic pattern in relation to the studied environmental gradients. The ratio of Sphaerodinella tuberosa var. 2 to Orthopithonella granifera can be used for reconstructing the presence of stratification in the upper 50 m of the water column, whereas the ratios of S. tuberosa var. 2 to Sphaerodinella albatrosiana and of O. granifera to Rhabdothorax spp. might be used for palaeotemperature reconstructions. Calcareous dinoflagellate cysts are abundant in oligotrophic areas and may be useful for the reconstruction of palaeoenvironmental conditions.

Silicon isotope ratios of ODP Site 177-1089 and sediment core E33-22

Reconstruction of nutrient concentrations in the deep Southern Ocean has produced conflicting results. The cadmium/calcium (Cd/Ca) data set suggests little change in nutrient concentrations during the last glacial period, whereas the carbon isotope data set suggests that nutrient concentrations were higher. We determined the silicon isotope composition of sponge spicules from the Atlantic and Pacific sectors of the Southern Ocean and found higher silicic acid concentrations in the Pacific sector during the last glacial period. We propose that this increase results from changes in the stoichiometric uptake of silicic acid relative to nitrate and phosphate by diatoms, thus facilitating a redistribution of nutrients across the Pacific and Southern Oceans. Our results are consistent with the global Cd/Ca data set and support the silicic acid leakage hypothesis.

(Table 1) Sea surface temperature reconstruction for eastern equatorial Pacific surface sediment samples

Significant uncertainties persist in the reconstruction of past sea surface temperatures in the eastern equatorial Pacific, especially regarding the amplitude of the glacial cooling and the details of the post-glacial warming. Here we present the first regional calibration of alkenone unsaturation in surface sediments versus mean annual sea surface temperatures (maSST). Based on 81 new and 48 previously published data points, it is shown that open ocean samples conform to established global regressions of Uk'37 versus maSST and that there is no systematic bias from seasonality in the production or export of alkenones, or from surface ocean nutrient concentrations or salinity. The flattening of the regression at the highest maSSTs is found to be statistically insignificant. For the near-coastal Peru upwelling zone between 11-15°S and 76-79°W, however, we corroborate earlier observations that Uk'37 SST estimates significantly over-estimate maSSTs at many sites. We posit that this is caused either by uncertainties in the determination of maSSTs in this highly dynamic environment, or by biasing of the alkenone paleothermometer toward El Niño events as postulated by Rein et al. (2005).

Dinoflagellates of multicorer surface sediments

Only very few studies focus on recent calcareous dinoflagellate cyst diversity, geographic distribution and ecology, so that information on the distribution patterns and environmental affinities of individual cyst species is extremely limited. This information is, however, essential if we want to use calcareous dinoflagellate cysts for palaeoenvironmental reconstruction. Surface sediment samples from the generally oligotrophic western equatorial Atlantic Ocean, offshore northeast Brazil, were therefore quantitatively analysed for their calcareous dinoflagellate cyst content, including the calcareous vegetative coccoid Thoracosphaera heimii. Seven calcareous dinoflagellate cyst species/morphotypes and T. heimii were encountered in high concentrations throughout the area. Substantial differences in the distribution patterns were observed. The highest concentrations of cysts are found in sediments of the more oligotrophic, oceanic regions, beyond the influence of Amazon River discharge waters. Dinoflagellates producing calcareous cysts thus appear to be capable of surviving low nutrient concentrations and produce large numbers of cysts in relatively stable and predictable environments affected by minimal seasonality. To test for the environmental affinities of individual species, distribution patterns in surface sediments were compared with temperature, salinity, density and stratification gradients within the upper water column (0-100 m) over different times of the year, using principal components analysis and redundancy analysis. T. heimii and four of the seven encountered cyst species (Sphaerodinella? albatrosiana, two morphotypes of Sphaerodinella? tuberosa and Scrippsiella regalis) relate to these parameters significantly and the variations in the cyst associations appear to be associated with the different surface water currents characterising the area. The results imply that calcareous dinoflagellate cyst distributions can potentially be used to distinguish between different open oceanic environments and they could, therefore, be useful in tracing water mass movements throughout the late Quaternary.

(Table 2) Age determination of Aegean Sea sediments

The modern Aegean Sea is an important source of deep water for the eastern Mediterranean. Its contribution to deep water ventilation is known to fluctuate in response to climatic variation on a decadal timescale. This study uses marine micropalaeontological and stable isotope data to investigate longer-term variability during the late glacial and Holocene, in particular that associated with the deposition of the early Holocene dysoxic/anoxic sapropel S1. Concentrating on the onset of sapropel-forming conditions, we identify the start of 'seasonal' stratification and highlight a lag in d18O response of the planktonic foraminifer N. pachyderma to termination T1b as identified in the d18O record of G. ruber. By use of a simple model we determine that this offset cannot be a function of bioturbation effects. The lag is of the order of 1 kyr and suggests that isolation of intermediate/deep water preceded the start of sapropel formation by up to 1.5 kyr. Using this discovery, we propose an explanation for the major unresolved problem in sapropel studies, namely, the source of nutrient supply required for export productivity to reach levels needed for sustained sapropel deposition. We suggest that nutrients had been accumulating in a stagnant basin for 1-1.5 kyr and that these accumulated resources were utilized during the deposition of S1. In addition, we provide a first quantitative estimate of the diffusive (1/e) mixing timescale for the eastern Mediterranean in its "stratified" sapropel mode, which is of the order of 450 years.

Seawater carbonate chemistry, and Lithophyllum sp. and Feldmannia spp. coverage and dry weight during experiments, 2009

Climate-driven change represents the cumulative effect of global through local-scale conditions, and understanding their manifestation at local scales can empower local management. Change in the dominance of habitats is often the product of local nutrient pollution that occurs at relatively local scales (i.e. catchment scale), a critical scale of management at which global impacts will manifest. We tested whether forecasted global-scale change [elevated carbon dioxide (CO2) and subsequent ocean acidification] and local stressors (elevated nutrients) can combine to accelerate the expansion of filamentous turfs at the expense of calcifying algae (kelp understorey). Our results not only support this model of future change, but also highlight the synergistic effects of future CO2 and nutrient concentrations on the abundance of turfs. These results suggest that global and local stressors need to be assessed in meaningful combinations so that the anticipated effects of climate change do not create the false impression that, however complex, climate change will produce smaller effects than reality. These findings empower local managers because they show that policies of reducing local stressors (e.g. nutrient pollution) can reduce the effects of global stressors not under their governance (e.g. ocean acidification). The connection between research and government policy provides an example whereby knowledge (and decision making) across local through global scales provides solutions to some of the most vexing challenges for attaining social goals of sustainability, biological conservation and economic development.

Cadmium analytical results from sediment and foraminifera shells

There has been a major contradiction between benthic foraminiferal Cd/Ca and d13C data concerning the labile nutrient chemistry of the Southern Ocean during the Last Glacial Maximum (LGM). Cd data indicates that LGM South Atlantic nutrient concentrations were as low as they are today, indicative of a persistent influx of nutrient-depleted North Atlantic Deep Water (NADW). d13C data indicates that LGM South Atlantic nutrient concentrations were much higher than at present (even higher than anywhere else in the ocean at that time), and these data have been interpreted as signifying the complete shutdown ofthe export of NADW into the global ocean. This paper examines both true geochemical differences and various confounding foraminiferal artifacts for both tracers. While many different processes and artifacts affect both tracers in the margin, we conclude the discrepancy is mainly due to the "Mackensen Effect" of low foraminiferal d13C as a result of high carbon flux to the sediments, and that LGM Atlantic Sector Southern Ocean nutrient concentrations remained similar to the levels encountered today.

Benthic cyanobacterial mat (BCM) abundance on samples from the coast of Curacao

Benthic cyanobacterial mats (BCMs) are impacting coral reefs worldwide. However, the factors and mechanisms driving their proliferation are unclear. We conducted a multi-year survey around the Caribbean island of Curaçao, which revealed highest BCM abundance on sheltered reefs close to urbanised areas. Reefs with high BCM abundance were also characterised by high benthic cover of macroalgae and low cover of corals. Nutrient concentrations in the water-column were consistently low, but markedly increased just above substrata (both sandy and hard) covered with BCMs. This was true for sites with both high and low BCM coverage, suggesting that BCM growth is stimulated by a localised, substrate-linked release of nutrients from the microbial degradation of organic matter. This hypothesis was supported by a higher organic content in sediments on reefs with high BCM coverage, and by an in situ experiment which showed that BCMs grew within days on sediments enriched with organic matter (Spirulina). We propose that nutrient runoff from urbanised areas stimulates phototrophic blooms and enhances organic matter concentrations on the reef. This organic matter is transported by currents and settles on the seabed at sites with low hydrodynamics. Subsequently, nutrients released from the organic matter degradation fuel the growth of BCMs. Improved management of nutrients generated on land should lower organic loading of sediments and other benthos (e.g. turf and macroalgae) to reduce BCM proliferation on coral reefs.

The effect of a reduction of nitrogen and phosphorus to eutrophic and mesotrophic conditions towards silver nanoparticle (AgNP) on freshwater green algae species

We investigated the sensitivity of algae towards silver nanoparticles with OECD test medium and lower nutrient concentrations under standard test conditions to improve comparability and to exclude any other confounding factor aside nutrient levels. Two unicellular freshwater microalgae Desmodesmus subspicatus and Raphidocelis subcapitata were chosen due to their status as standard test organisms for the algae growth inhibition test and the response to changes in nutrient supply was compared. The original medium was used as the reference (standard). For the other four media, the amount of either nitrogen or phosphorus in the medium was lowered from half (50%) to one-fourth (25 %) of that of the OECD guideline, resulting in the following media: 50% N, 25% N, 50% P and 25% P medium. As test substance, the OECD reference material NM-300K was used. For this reason, the characterization of AgNP was done using DLS and Absorption spectra (UV/vis). Actual silver concentrations and ionic silver concentrations were measured at the highest test concentration used (100 µg Ag L-1) in R. subcapitata treatments only to reduce the number of samples. All tests were run according to the OECD guideline 201 with sterilized 50 mL cell culture flask. Each medium was tested using the test conditions for culturing with 3 replicates. Test concentrations for both algae species were 0, 25, 50 and 100 µg Ag L-1 for OECD, 50% P and 25% P while for both N reductions, the silver concentrations were 0, 10, 25 and 100 µg Ag L-1. Samples for determining the algal density were taken at every 24 h.

(Table 1) Stable carbon isotope ratios of methane and carbon dioxide from ODP Leg 169S holes

Sites 1033 and 1034 of ODP Leg 169S in Saanich Inlet have an unusual diagenetic system, that has the appearance of being depth reversed, i.e. a bacterial methane accumulation zone underlain by a sulphate reduction zone. During the late Pleistocene grey, undifferentiated, glacio-marine clays were deposited with low Corg contents (<0.4 wt.%), and interstitial fluids replete in SO4 (ca. 27 mM), devoid of CH4 and low in nutrients. This indicates oxic conditions are present, reflecting the open exchange of waters with Haro Strait during the Pleistocene before the Saanich Peninsula emerged. In the earliest Holocene (ca. 11,000 years BP) the inlet was formed, severely restricting water circulation, and leading to the presence of anoxic bottom waters. The sediments are laminated and show a dramatic rise to high Corg, Norg and Stot contents (up to 2.5, 0.4, 1.4 wt.%, respectively) over a period of ca. 1000 years. The nutrient concentrations are especially high (TA, NH4, PO4 up to 115 meq/l, 20 mM and 400 µM, respectively), SO4 is exhausted and CH4 is prolific. Stable carbon isotope ratio measurements of CH4 and co-existing CO2 indicate that methanogenesis is via carbonate reduction (delta13C-CH4 ca. -60 to - 70 per mil, delta13C-CO2 ca. +10 per mil). At the sulphate-methane interfaces, both at the near-surface and at 50 mbsf (Site 1033) and 80 mbsf (Site 1034) methane consumption by sulphate reducing bacteria is intensive.

Delta 13C measured on alkenones of surface sediment samples GeoB1008-6 to GeoB3603-1 from the South Atlantic

We have analyzed the stable carbon isotopic composition of the diunsaturated C37 alkenone in 29 surface sediments from the equatorial and South Atlantic Ocean. Our study area covers different oceanographic settings, including sediments from the major upwelling regions off South Africa, the equatorial upwelling, and the oligotrophic western South Atlantic. In order to examine the environmental influences on the sedimentary record the alkenone-based carbon isotopic fractionation (Ep) values were correlated with the overlying surface water concentrations of aqueous CO2 ([CO2(aq)]), phosphate, and nitrate. We found Ep positively correlated with 1/[CO2(aq)] and negatively correlated with [PO43-] and [NO3-]. However, the relationship between Ep and 1/[CO2(aq)] is opposite of what is expected from a [CO2(aq)] controlled, diffusive uptake model. Instead, our findings support the theory of Bidigare et al. (1997, doi:10.1029/96GB03939) that the isotopic fractionation in haptophytes is related to nutrient-limited growth rates. The relatively high variability of the Ep-[PO4] relationship in regions with low surface water nutrient concentrations indicates that here other environmental factors also affect the isotopic signal. These factors might be variations in other growth-limiting resources such as light intensity or micronutrient concentrations.

Trace elements in benthic foraminifera of sediment core V30-49

Eastern tropical Atlantic benthic foraminiferal Ba/Ca and Cd/Ca data from core V30-949 (3093 m) reveal large inferred changes in nutrient concentrations of deep Atlantic waters during the last 250 kyr. Relative changes in North Atlantic Deep Water contribution to this site are estimated by scaling the V30-49 Cd/Ca record to values of modern end-member water masses; these estimates agree well with the relative structure and timing of circulation changes in the eastern tropical Atlantic reconstructed from a d13C record-based mixing model (Raymo et al., 1997, doi:10.1029/97PA01019). Temporal differences between V30-49 Cd/Ca and Ba/Ca records suggest that the Ba/Ca record reflects changes in circulation with an additional increase in the Ba composition of deep Atlantic water masses during glacial episodes, possibly resulting from increased productivity. Similarity between the d13C and Ba/Ca records suggests that carbon isotopes in the deep glacial Atlantic also reflect productivity increases.