A laboratory-scale experiment and a numerical simulation of unusual spiral plumes in a High-Prandtl-number fluid, links supplementary material

We experimentally and numerically investigated the generation of plumes from a local heat source (LHS) and studied the interaction of these plumes with cellular convective motion (CCM) in a rectangular cavity filled with silicon oil at a Prandtl number (Pr) of approximately two thousand. The LHS is generated using a 0.2-W green laser beam. A roll-type CCM is generated by vertically heating one side of the cavity. The CCM may lead to the formation of an unusual spiral convective plume that resembles a vertical Archimedes spiral. A similar plume is obtained in a direct numerical simulation. We discuss the physical mechanism for the formation of a spiral plume and the application of the results to mantle convection problems. We also estimate the Reynolds (Re) and Rayleigh (Ra) numbers and apply self-similarity theory to convection in the Earth's mantle. Spiral plumes can be used to interpret mantle tomography results over the last decade.

Simultaneous high-resolution pH and spectrophotometric recordings of oxygen binding in native blood microvolumes, link to supplementary material

Oxygen equilibrium curves have been widely used to understand oxygen transport in numerous organisms. A major challenge has been to monitor oxygen binding characteristics and concomitant pH changes as they occur in vivo, in limited sample volumes. Here we report a technique allowing highly resolved and simultaneous monitoring of pH and blood pigment saturation in minute blood volumes. We equipped a gas diffusion chamber with a broad range fibre optic spectrophotometer and a micro-pH optode and recorded changes of pigment oxygenation along PO2 and pH gradients to test the setup. Oxygen binding parameters derived from measurements in only 15 µl of haemolymph from the cephalopod Octopus vulgaris showed low instrumental error (0.93%) and good agreement with published data. Broad range spectra, each resolving 2048 data points, provided detailed insight into the complex absorbance characteristics of diverse blood types. After consideration of photobleaching and intrinsic fluorescence, pH optodes yielded accurate recordings and resolved a sigmoidal shift of 0.03 pH units in response to changing PO2 from 0-21 kPa. Highly resolved continuous recordings along pH gradients conformed to stepwise measurements at low rates of pH changes. In this study we showed that a diffusion chamber upgraded with a broad range spectrophotometer and an optical pH sensor accurately characterizes oxygen binding with minimal sample consumption and manipulation. We conclude that the modified diffusion chamber is highly suitable for experimental biologists who demand high flexibility, detailed insight into oxygen binding as well as experimental and biological accuracy combined in a single set up.

Age analysis, aragonite and high magnesium calcite content from different IODP Holes from Exp 310

The widespread occurrence of microbialites in the last deglacial reef frameworks (16-6 Ka BP) implies that the accurate study of their development patterns is of prime importance to unravel the evolution of reef architecture through time and to reconstruct the reef response to sea-level variations and environmental changes. The present study is based on the sedimentological and chronological analysis (14C AMS dating) of drill cores obtained during the IODP Expedition #310 "Tahiti Sea Level" on the successive terraces which typify the modern reef slopes from Tahiti. It provides a comprehensive data base to investigate the microbialite growth patterns (i.e. growth rates and habitats), to analyze their roles in reef frameworks and to reconstruct the evolution of the reef framework architecture during sea-level rise. The last deglacial reefs from Tahiti are composed of two distinctive biological communities: (1) the coralgal communities including seven assemblages characterized by various growth forms (branching, robust branching, massive, tabular and encrusting) that form the initial frameworks and (2) the microbial communities developed in the primary cavities of those frameworks, a few meters (1.5 to 6 m) below the living coral reef surface, where they heavily encrusted the coralgal assemblages to form microbialite crusts. The dating results demonstrate the occurrence of two distinctive generations of microbialites: the "reefal microbialites" which developed a few hundred years after coralgal communities in shallow-water environments, whereas the "slope microbialites" grew a few thousands of years later in significantly deeper water conditions after the demise of coralgal communities. The development of microbialites was controlled by the volume and the shape of the primary cavities of the initial reef frameworks determined by the morphology and the packing of coral colonies. The most widespread microbialite development occurred in frameworks dominated by branching, thin encrusting, tabular and robust branching coral colonies which built loose and open frameworks typified by a high porosity (> 50%). In contrast, their growth was minimal in compact coral frameworks formed by massive and thick encrusting corals where primary cavities yielded a low porosity (~ 30%) and could not host a significant microbialite expansion.

High-resolution marine record of sediment core MD99-2343 in the Balearic Sea

The IMAGES core MD99-2343, recovered from a sediment drift north of the island of Minorca, in the north-western Mediterranean Sea, holds a high-resolution sequence that is perfectly suited to study the oscillations of the overturning system of the Western Mediterranean Deep Water (WMDW). Detailed analysis of grain-size and bulk geochemical composition reveals the sensitivity of this region to climate changes at both orbital and centennial-millennial temporal scales during the last 50 kyr. The dominant orbital pattern in the K/Al record indicates that sediment supply to the basin was controlled by the insolation evolution at 40°N, which forced changes in the fluvial regime, with more efficient sediment transport during insolation maxima. This orbital control also modulated the long-term pattern of the WMDW intensity as illustrated by the silt/clay ratio. However, deep convection was particularly sensitive to climatic changes at shorter time-scales, i.e. to centennial-millennial glacial and Holocene oscillations that are well documented by all the paleocurrent intensity proxies (Si/Al, Ti/Al and silt/clay ratios). Benthic isotopic records (d13C and d18O) show a Dansgaard-Oeschger (D-O) pattern of variability of WMDW properties, which can be associated with changing intensities of the deep currents system. The most prominent reduction on the WMDW overturning was caused by the post-glacial sea level rise. Three main scenarios of WMDW overturning are revealed: a strong mode during D-O Stadials, a weak mode during D-O Interstadials and an intermediate mode during cooling transitions. In addition, D-O Stadials associated with Heinrich events (HEs) have a very distinct signature as the strong mode of circulation, typical for the other D-O Stadials, was never reached during HE due to the surface freshening induced by the inflowing polar waters. Consequently, the WMDW overturning system oscillated around the intermediate mode of circulation during HE. Though surface conditions were more stable during the Holocene, the WMDW overturning cell still reacted synchronously to short-lived events, as shown by increments in the planktonic d18O record, triggering quick reinforcements of the deep water circulation. Overall, these results highlight the sensitivity of the WMDW to rapid climate change which in the recent past were likely induced by oceanographic and atmospheric reorganizations in the North Atlantic region.

Siliceous fossils in sediments of the Ibero-Moroccan shelf and adjacent deep sea plains

Siliceous skeletons were investigated in two core profiles (9 cores), one off Cap de Sines, Portugal and the other off Cap de Mazagan, Morocco. Total number of skeletons was determined per gram of dried sediment at different core depths of the fraction >21 µ. Results are compared with a core profile from the Arabian Sea. Diatoms are of four groups: (A) marine-planktonic, B) marine-benthic, (C) freshwater and (D) Tertiary species (Trinacria e.g.). Species from groups (B), (C) and (D) are redeposited in all cores taken at a water depth of greater than 100 m. Small numbers of Silicoflagellates and Radiolarians were found throughout the cores from the Ibero-Moroccan shelf. In the Arabian Sea core, Radiolarians were concentrated in distinct horizons in which Tertiary material was redeposited (40-50, 140-150, 250-260 cm). The number of siliceous skeletons per gram of dried sediment decreases more or less rapidly with increasing depth in all cores. Whereas about 2500 skeletons were found in sediments close to the surface, approximately 100 skeletons only were found in deeper (>40 cm) layers. Deeper horizons with more than 100 specimens were interpreted as redeposited material. This sediment contained robust skeletons, resistant against dissolution, as well as benthic and Tertiary material. The decrease of siliceous skeletons relative to core depth depends upon the sedimentation rate. Where the sedimentation rate is high, the opal dissolution zone extends down to 30-60 cm, where the sedimentation rate is low, it is located at 10-30 cm. Below these depths opals disappears. These zones also have approximately the same age (4000 years) everywhere. Siliceous skeletons dissolve differentially, first the Silicoflagellates disappear, second the Diatoms, third the Radiolarians, and fourth the Sponge Spicules. Surface structure of skeletons from near the opal dissolution zones are similar to those of skeletons treated with NaOH. Tertiary diatoms (Trinacria e. g.) and benthic diatoms (Campylodiscus e.g.) dissolve less rapidly than skeletons of modern planktonic diatoms (Coscinodiscus e.g.). The time control of the opal dissolution zones appeared rather independent of various oceanic influences. No evidence was found for effects from upwelling either off Portugal or off Morocco. No difference in dissolution rates was recorded between the abyssal plains lying off these two areas. Likewise, there was no change in solution rates from Pleistocene to Holocene within either one of the abyssal plains. The Mediterranean outflow, which is enriched in dissolved silica, apparently had no effect on dissolution rates of siliceous skeletons in the sediment.

Composition and fluxes of sinking particulate material and bottom sediments in the northeast Black Sea in 1998-1999

For the first time deep-sea mooring stations with sediment traps were deployed in the northeast Black Sea. One sediment trap for long-term studies was located at Station 1 (44°15'N, 37°43'E, deployment depth 1800 m, depth 1900 m). The trap collected sinking sedimentary material from January to May 1998. Material collectors were changed every 15 days. Other stations with sediment traps for short-term studies (September-October 1999) were located on the shelf: Station 2 (44°16'N, 38°37'E, deployment depth 45 m, depth 50 m) and on the bottom of the canyon: Station 3 (44°16'N, 38°22'E, deployment depth 1145 m, depth 1150 m), Station 4 (44°11'N, 38°21'E, deployment depths 200, 1550, 1650 m, depth 1670 m). Collected material indicates that vertical particle fluxes are controlled by seasonal changes of in situ production and by dynamics of terrigenous matter input. Higher vertical particle flux of carbonate and biogenic silica was in spring due to bloom of plankton organisms. Maximum of coccolith bloom is in April-May. Bloom of diatoms begins in March. In winter and autumn lithogenic material dominates in total flux. Its amount strongly depends on storms and river run-off. Suspended particle material differs from surface shelf sediments by finer particles (mainly clay fraction) and high content of clay minerals and biogenic silica. This material may form lateral fluxes with higher concentration of particles transported along the bottom of deep-sea canyons from the shelf to the deep basin within the nepheloid layer. In winter such transportation of sedimentary material is more intensive due to active vertical circulation of water masses.

Intraspecific facilitation by allelochemical mediated grazing protection within a toxigenic dinoflagellate population, link to supplementary material

Dinoflagellates are a major cause of harmful algal blooms, with consequences for coastal marine ecosystem functioning and services. Alexandrium tamarense is one of the most abundant and widespread toxigenic species in the temperate northern and southern hemisphere, and produces paralytic shellfish poisoning toxins as well as lytic allelochemical substances. These bioactive compounds may support the success of A. tamarense and its ability to form blooms. Here we investigate the impact of grazing on monoclonal and mixed set-ups of highly (Alex2) and moderately (Alex4) allelochemically active A. tamarense strains and on a non-allelochemically active conspecific (Alex5) by the heterotrophic dinoflagellate Polykrikos kofoidii. While Alex4 and particularly Alex5 were strongly grazed by P. kofoidii when offered alone, both strains grew well in the mixed assemblages (Alex4+Alex5 and Alex2+Alex5). Hence, the allelochemical active strains facilitated growth of the non-active strain by protecting the population as a whole against grazing. Based on our results, we argue that facilitation among clonal lineages within a species may partly explain the high genotypic and phenotypic diversity of Alexandrium populations. Populations of Alexandrium may comprise multiple cooperative traits that act in concert with intraspecific facilitation, and hence promote the success of this notorious harmful algal bloom species.

Spatial compartmentalization of free radical formation and mitochondrial heterogeneity in bivalve gills revealed by live-imaging techniques, supplementary material

Live-imaging techniques (LIT) utilize target-specific fluorescent dyes to visualize biochemical processes using confocal and multiphoton scanning microscopy, which are increasingly employed as non-invasive approach to physiological in-vivo and ex-vivo studies. Here we report application of LIT to bivalve gills for ex-vivo analysis of gill physiology and mapping of reactive oxygen (ROS) and nitrogen (RNS) species formation in the living tissue. Our results indicate that H2O2, HOO. and ONOO- radicals (assessed through C-H2DFFDA staining) are mainly formed within the blood sinus of the filaments and are likely to be produced by hemocytes as defense against invading pathogens. The oxidative damage in these areas is controlled by enhanced CAT (catalase) activities recorded within the filaments. The outermost areas of the ciliated epithelial cells composing the filaments, concentrated the highest mitochondrial densities (MTK Deep Red 633 staining) and the most acidic pH values (as observed with ageladine-a). These mitochondria have low (depolarized) membrane potentials (D psi m) (JC-1 staining), suggesting that the high amounts of ATP required for ciliary beating may be in part produced by non-mitochondrial mechanisms, such as the enzymatic activity of an ATP-regenerating kinase. Nitric oxide (NO, DAF-2DA staining) produced in the region of the peripheral mitochondria may have an effect on mitochondrial electron transport and possibly cause the low membrane potential. High DAF-2DA staining was moreover observed in the muscle cells composing the wall of the blood vessels where NO may be involved in regulating blood vessel diameter. On the ventral bend of the gills, subepithelial mucus glands (SMG) contain large mucous vacuoles showing higher fluorescence intensities for O2.- (DHE staining) than the rest of the tissue. Given the antimicrobial properties of superoxide, release of O2.- into the mucus may help to avoid the development of microbial biofilms on the gill surface. However, cells of the ventral bends are paying a price for this antimicrobial protection, since they show significantly higher oxidative damage, according to the antioxidant enzyme activities and the carbonyl levels, than the rest of the gill tissue. This study provides the first evidence that one single epithelial cell may contain mitochondria with significantly different membrane potentials. Furthermore, we provide new insight into ROS and RNS formation in ex-vivo gill tissues which opens new perspectives for unraveling the different ecophysiological roles of ROS and RNS in multifunctional organs such as gills.

Impact of thermal stress on evolutionary trajectories of pathogen resistance in three-spined stickleback (Gasterosteus aculeatus), supplementary material

Background: Pathogens are a major regulatory force for host populations, especially under stressful conditions. Elevated temperatures may enhance the development of pathogens, increase the number of transmission stages, and can negatively influence host susceptibility depending on host thermal tolerance. As a net result, this can lead to a higher prevalence of epidemics during summer months. These conditions also apply to marine ecosystems, where possible ecological impacts and the population-specific potential for evolutionary responses to changing environments and increasing disease prevalence are, however, less known. Therefore, we investigated the influence of thermal stress on the evolutionary trajectories of disease resistance in three marine populations of three-spined sticklebacks Gasterosteus aculeatus by combining the effects of elevated temperature and infection with a bacterial strain of Vibrio sp. using a common garden experiment. Results: We found that thermal stress had an impact on fish weight and especially on survival after infection after only short periods of thermal acclimation. Environmental stress reduced genetic differentiation (QST) between populations by releasing cryptic within-population variation. While life history traits displayed positive genetic correlations across environments with relatively weak genotype by environment interactions (GxE), environmental stress led to negative genetic correlations across environments in pathogen resistance. This reversal of genetic effects governing resistance is probably attributable to changing environment-dependent virulence mechanisms of the pathogen interacting differently with host genotypes, i.e. GPathogenxGHostxE or (GPathogenxE)x(GHostxE) interactions, rather than to pure host genetic effects, i.e. GHostxE interactions. Conclusion: To cope with climatic changes and the associated increase in pathogen virulence, host species require wide thermal tolerances and pathogen-resistant genotypes. The higher resistance we found for some families at elevated temperatures showed that there is evolutionary potential for resistance to Vibrio sp. in both thermal environments. The negative genetic correlation of pathogen resistance between thermal environments, on the other hand, indicates that adaptation to current conditions can be a weak predictor for performance in changing environments. The observed feedback on selective gradients exerted on life history traits may exacerbate this effect, as it can also modify the response to selection for other vital components of fitness.

Mg/Ca ratios in planktonic foraminifera

The primary Mg/Ca ratio of foraminiferal shells is a potentially valuable paleoproxy for sea surface temperature (SST) reconstructions. However, the reliable extraction of this ratio from sedimentary calcite assumes that we can overcome artifacts related to foraminiferal ecology and partial dissolution, as well as contamination by secondary calcite and clay. The standard batch method for Mg/Ca analysis involves cracking, sonicating, and rinsing the tests to remove clay, followed by chemical cleaning, and finally acid-digestion and single-point measurement. This laborious procedure often results in substantial loss of sample (typically 30-60%). We find that even the earliest steps of this procedure can fractionate Mg from Ca, thus biasing the result toward a more variable and often anomalously low Mg/Ca ratio. Moreover, the more rigorous the cleaning, the more calcite is lost, and the more likely it becomes that any residual clay that has not been removed by physical cleaning will increase the ratio. These potentially significant sources of error can be overcome with a flow-through (FT) sequential leaching method that makes time- and labor-intensive pretreatments unnecessary. When combined with time-resolved analysis (FT-TRA) flow-through, performed with a gradually increasing and highly regulated acid strength, produces continuous records of Mg, Sr, Al, and Ca concentrations in the leachate sorted by dissolution susceptibility of the reacting material. Flow-through separates secondary calcite from less susceptible biogenic calcite and clay, and further resolves the biogenic component into primary and more resistant fractions. FT-TRA reliably separates secondary calcite (which is not representative of original life habitats) from the more resistant biogenic calcite (the desired signal) and clay (a contaminant of high Mg/Ca, which also contains Al), and further resolves the biogenic component into primary and more resistant fractions that may reflect habitat or other changes during ontogeny. We find that the most susceptible fraction of biogenic calcite in surface dwelling foraminifera gives the most accurate value for SST and therefore best represents primary calcite. Sequential dissolution curves can be used to correct the primary Mg/Ca ratio for clay, if necessary. However, the temporal separation of calcite from clay in FT-TRA is so complete that this correction is typically <=2%, even in clay-rich sediments. Unlike hands-on batch methods, that are difficult to reproduce exactly, flow-through lends itself to automation, providing precise replication of treatment for every sample. Our automated flow-through system can process 22 samples, two system blanks, and 48 mixed standards in <12 hours of unattended operation. FT-TRA thus represents a faster, cheaper, and better way to determine Mg/Ca ratios in foraminiferal calcite.

Cenozoic oxygen isotopic values for benthic foraminifera from DSDP and ODP low and high latitude marine sediment cores

The climate during the Cenozoic era changed in several steps from ice-free poles and warm conditions to ice-covered poles and cold conditions. Since the 1950s, a body of information on ice volume and temperature changes has been built up predominantly on the basis of measurements of the oxygen isotopic composition of shells of benthic foraminifera collected from marine sediment cores. The statistical methodology of time series analysis has also evolved, allowing more information to be extracted from these records. Here we provide a comprehensive view of Cenozoic climate evolution by means of a coherent and systematic application of time series analytical tools to each record from a compilation spanning the interval from 4 to 61 Myr ago. We quantitatively describe several prominent features of the oxygen isotope record, taking into account the various sources of uncertainty (including measurement, proxy noise, and dating errors). The estimated transition times and amplitudes allow us to assess causal climatological-tectonic influences on the following known features of the Cenozoic oxygen isotopic record: Paleocene-Eocene Thermal Maximum, Eocene-Oligocene Transition, Oligocene-Miocene Boundary, and the Middle Miocene Climate Optimum. We further describe and causally interpret the following features: Paleocene-Eocene warming trend, the two-step, long-term Eocene cooling, and the changes within the most recent interval (Miocene-Pliocene). We review the scope and methods of constructing Cenozoic stacks of benthic oxygen isotope records and present two new latitudinal stacks, which capture besides global ice volume also bottom water temperatures at low (less than 30°) and high latitudes. This review concludes with an identification of future directions for data collection, statistical method development, and climate modeling.

High-resolution sedimentological and paleontological record of ODP Site 167-1019

Holocene and latest Pleistocene oceanographic conditions and the coastal climate of northern California have varied greatly, based upon high-resolution studies (ca. every 100 years) of diatoms, alkenones, pollen, CaCO3%, and total organic carbon at Ocean Drilling Program (ODP) Site 1019 (41.682°N, 124.930°W, 980 m water depth). Marine climate proxies (alkenone sea surface temperatures [SSTs] and CaCO3%) behaved remarkably like the Greenland Ice Sheet Project (GISP)-2 oxygen isotope record during the Bølling-Allerod, Younger Dryas (YD), and early part of the Holocene. During the YD, alkenone SSTs decreased by >3°C below mean Bølling-Allerod and Holocene SSTs. The early Holocene (ca. 11.6 to 8.2 ka) was a time of generally warm conditions and moderate CaCO3 content (generally >4%). The middle part of the Holocene (ca. 8.2 to 3.2 ka) was marked by alkenone SSTs that were consistently 1-2°C cooler than either the earlier or later parts of the Holocene, by greatly reduced numbers of the gyre-diatom Pseudoeunotia doliolus (<10%), and by a permanent drop in CaCO3% to <3%. Starting at ca. 5.2 ka, coastal redwood and alder began a steady rise, arguing for increasing effective moisture and the development of the north coast temperate rain forest. At ca. 3.2 ka, a permanent ca. 1°C increase in alkenone SST and a threefold increase in P. doliolus signaled a warming of fall and winter SSTs. Intensified (higher amplitude and more frequent) cycles of pine pollen alternating with increased alder and redwood pollen are evidence that rapid changes in effective moisture and seasonal temperature (enhanced El Niño-Southern Oscillation [ENSO] cycles) have characterized the Site 1019 record since about 3.5 ka.

Geochemistry of terrigenous material in deep-sea sediments of the equatorial Pacific

Biological productivity in the modern equatorial Pacific Ocean, a region with high nutrients and low chlorophyll, is currently limited by the micronutrient Fe. In order to test whether Fe was limiting in the past and to identify potential pathways of Fe delivery that could drive Fe fertilization (i.e., dust delivery from eolian inputs vs. Fe supplied by the Equatorial Undercurrent), we chemically isolated the terrigenous material from sediment along a cross-equatorial transect in the central equatorial Pacific at 140°W and at Ocean Drilling Program Site 850 in the eastern equatorial Pacific. We quantified the contribution from each potential Fe-bearing terrigenous source using a suite of chemical- and isotopic discrimination strategies as well as multivariate statistical techniques. We find that the distribution of the terrigenous sources (i.e., Asian loess, South American ash, Papua New Guinea, and ocean island basalt) varies through time, latitude, and climate. Regardless of which method is used to determine accumulation rate, there also is no relationship between flux of any particular Fe source and climate. Moreover, there is no connection between a particular Fe source or pathway (eolian vs. Undercurrent) to total productivity during the Last Glacial Maximum, Pleistocene glacial episodes, and the Miocene "Biogenic Bloom". This would suggest an alternative process, such as an interoceanic reorganization of nutrient inventories, may be responsible for past changes in total export in the open ocean, rather than simply Fe supply from dust and/or Equatorial Undercurrent processes. Additionally, perhaps a change in Fe source or flux is related to a change in a particular component of the total productivity (e.g., the production of organic matter, calcium carbonate, or biogenic opal).

Sedimentation rate, bulk density, accumulation rate of terrigenous material and grain sizes of ODP Leg 167 sites

The terrigenous mineral fraction of sediments recovered by drilling during Ocean Drilling Program Leg 167 at Sites 1018 and 1020 is used to evaluate changes in the source and transport of fine-grained terrigenous sediment and its relation to regional climates and the paleoceanographic evolution of the California Current system during the late Pleistocene. Preliminary time scales developed by correlation of oxygen isotope stratigraphies with the global SPECMAP record show average linear sedimentation rates in excess of 100 m/m.y., which provide an opportunity for high-resolution studies of terrigenous flux, grain size, and mineralogy. The mass flux of terrigenous minerals at Site 1018 varies from 5 to 30 g/(cm**2 x k.y.) and displays a general trend toward increased flux during glacials. The terrigenous record at Site 1020 shows a similar pattern of increased glacial input, but overall accumulation rates are significantly lower. Spectral analysis demonstrates that most of this variability is concentrated in frequency bands related to orbital cycles of eccentricity, tilt, and precession. Detailed grain-size analysis performed on the isolated terrigenous mineral fraction shows that sediments from Site 1018 are associated with higher energy transport and depositional regimes than those found at Site 1020. Grain-size data are remarkably uniform throughout the last 500 k.y., with no discernible difference observed between glacial and interglacial size distributions within each site. X-ray diffraction analysis of the <2-µm clay component suggests that the deposition of minerals found at Site 1020 is consistent with transport from a southern source during intervals of increased terrigenous input.