Bacterial abundance in the eastern Mediteranean Sea in August and September 2008 during SES_GR2

The SES_GR2_MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the Ionian, Libyan and Aegean Sea during August-September 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column. Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 ?m (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson).

Bacterial production in the eastern Mediteranean Sea in August and September 2008 during SES_GR2

The SES_GR2_MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the Ionian, Libyan and Aegean Sea during August-September 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column. Bacterial production was estimated by the 3H-leucine method (Kirchman et al. 1986, Kirchman 1993). At each depth, duplicate samples and a control were incubated with 20 nM L-[4,5 3H]-leucine. Samples were incubated in the dark, at in situ temperature.

Chemical composition of sediment core GeoB12309-5 from the northern Arabian Sea, its pore water profile and age depth relationship as well as CTD data obtained during cruise M74/3

The Arabian Sea off the Pakistan continental margin is characterized by one of the world's largest oxygen minimum zones (OMZ). The lithology and geochemistry of a 5.3 m long gravity core retrieved from the lower boundary of the modern OMZ (956 m water depth) were used to identify late Holocene changes in oceanographic conditions and the vertical extent of the OMZ. While the lower part of the core (535 - 465 cm, 5.04 - 4.45 cal kyr BP, Unit 3) is strongly bioturbated indicating oxic bottom water conditions, the upper part of the core (284 - 0 cm, 2.87 cal kyr BP to present, Unit 1) shows distinct and well-preserved lamination, suggesting anoxic bottom waters. The transitional interval from 465 to 284 cm (4.45 - 2.87 cal kyr BP, Unit 2) contains relicts of lamination which are in part intensely bioturbated. These fluctuations in bioturbation intensity suggest repetitive changes between anoxic and oxic/suboxic bottom-water conditions between 4.45 - 2.87 cal kyr BP. Barium excess (Baex) and total organic carbon (TOC) contents do not explain whether the increased TOC contents found in Unit 1 are the result of better preservation due to low BWO concentrations or if the decreased BWO concentration is a result of increased productivity. Changes in salinity and temperature of the outflowing water from the Red Sea during the Holocene influenced the water column stratification and probably affected the depth of the lower boundary of the OMZ in the northern Arabian Sea. Even if we cannot prove certain scenarios, we propose that the observed downward shift of the lower boundary of the OMZ was also impacted by a weakened Somali Current and a reduced transport of oxygen-rich Indian Central Water into the Arabian Sea, both as a response to decreased summer insolation and the continuous southward shift of the Intertropical Convergence Zone during the late Holocene.

Tintinnids of the western Arabian Sea

The results of an investigation of tintinnids from the western Arabian Sea are described. A total of 134 closing-net samples was obtained from 22 stations of the German "Meteor" expedition 1964/1965. Distribution charts of the dominant species of tintinnids from the study area are presented as well as a list of the world-wide distribution of these species as derived from the literature. Tintinnids were most abundant in the surface waters. The layer from 0 - 25 m yielded a maximum 94.3% and a minimum of 61.3% of the tintinnids present from 0 - 175 m; the mean was 80%. There was no significant difference in the vertical distribution between day and night stations nor was there any indication of the influence of the thermocline upon vertical distribution of tintinnids. TS-diagrams show different water types in the western Arabian Sea. Temperatur-salinity-tintinnid -diagrams indicate regional patterns in the distribution of various species of tintinnids. Some tintinnids can be used as indicator species: Climacocylis scalaria, Parundella lohmanni and Amphorella amphora were typical for the Somali Current whereas Rhabdonella apophysata and Branditella palliata indicated the presence of East African Coastal Current water. The concentration of tintinnids in the upper 25 m raged between 4,800 and 39,300 individuals/m**3 (mean 19,000/m**3). Plasma volume of tintinnids was calculated to permit comparison of different links in the food chain. There was a mean of 51 mm**3/m**2 in the upper layer, equivalent to a concentration of 2 mm**3/m**3. Carbon values were computed from the plasma volume of tintinnids, phytoplankton and larger zooplankton. The ratio of phytoplankton plus microzooplankton carbon to large zooplankton carbon was 1 : 0.8 in the Somali Current, 1 : 0.4 in the East African Coastal Current and 1 : 1.2 in the mixing zone of these current systems. Tintinnids are one of the first links in the food chain. It is very likely that a part of the organic detritus and of the nanoplankton is transfered to large herbivores or omnivores via tintinnids and other protozoans. This mechanism might be especially effective during seasons when large phytoplankters are not available in the ocean.

Late Cretaceous-Early Neogene oxygen and carbon isotope record of the Indian Ocean

Stable isotopic data of calcareous nannofossil, monogeneric and monospecific planktic and benthic foraminifera from five Indian Ocean DSDP sites (212, 217, 220, 237, and 253), leads to the following paleoclimatic and paleoceanographic conclusions: - The latest Cretaceous oxygen isotopic record implies a cooling (3-4°C) during the Maastrichtian. At the Cretaceous/Tertiary boundary only a minor warming (about 2°C) has been recorded. The parallel delta13C decrease of more than 1? indicates a significant decrease in productivity. - During the latest Paleocene a positive delta13C excursion was detected in Sites 217 and 237. This transient enrichment in delta13C may be due to productivity changes on continents and/or a change in the storage rate of organic matter in marginal basins or shelf areas. - The most striking feature in the oxygen isotopic record is noted at the Early/Middle Eocene transition. The shift towards more positive values (which were probably enhanced to a certain extent by a preceding diagenetic alteration) delineates a dramatic climatic deterioration at high and mid latitudes during the earlier Tertiary. - Near the Eocene/Oligocene boundary a cooling is evident within the latest Eocene interval. During the earliest Oligocene time a hiatus at Sites 217 and 253 partially obscures the climatic record. - Several climatic fluctuations have been noted during the Oligocene: a cooling at the base of Zone NP 23, a warming at the top of Zone NP 23 through NP 24, and a cooling during Zone NP 25. - The Miocene oxygen isotopic record is dominated by changes in surface and bottom water environments during Zone NN5. The decreasing and then increasing delta18O values, together with the subsequent steepening of the vertical delta18O gradient, point towards major climatic instabilities. These events coincide with the Mid-Miocene build-up of Antarctic ice-sheets. During the latest Miocene to the earliest Pliocene the delta18O record of planktic foraminifera indicates a significant warming of the Indian Ocean at mid-latitudes. - The delta13C record during the Oligocene and Miocene reveals several cycles (delta13C enrichments: NP 24, NN2, NN5, NN9, and base NN 11) which are most likely related to changes in storage rates of organic matter and biological productivity due to climatic changes and transgression/regression cycles. In addition, changes in the circulation patterns may also have influenced the carbon isotopic record.

Abundance of large protists from the Infrakingdom Rhizaria in the global ocean

The present data set is a worldwide compilation from 11 oceanographic expeditions during which an underwater vision profiler (UVP) was deployed in situ to determine the vertical distribution (abundance) of 10 taxonomic/morphological groups of plankton larger than 600 µm, belonging to the Infrakingdom Rhizaria, including Phaeodaria, Radiolaria, Collodaria and Acantharia.

Environmental context of a compilation about the distribution of large protists from the Infrakingdom Rhizaria in the global ocean

The present data set provides environmental context to a worldwide compilation from 11 oceanographic expeditions during which an underwater vision profiler (UVP) was deployed in situ to determine the vertical distribution plankton larger than 600 µm, belonging to the Infrakingdom Rhizaria.

Abundance and Biomass from heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus in the eastern Mediteranean Sea in October 2008 during SES_GR2

The HCMR_SES_LAGRANGIAN_GR2_ MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the North Aegean Sea during October 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column as influenced by the BSW. Heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus abundance: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Heterotrophic Nanoflagellate abundance: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6?m and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Ciliate abundance: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Heterotrophic bacteria, Synechococcus, Prochlorococcus bacteria: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Abundance data were converted into C biomass using 250 fgC cell-1 (Kana & Glibert 1987) for Synechococcus, 50 fgC cell-1 (Campbell et al. 1994) for Prochlorococcus and 20fgC cell-1 (Lee & Fuhrman 1987) for heterotrophic bacteria. Heterotrophic Nanoflagellate biomass: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6µm and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Abundance data were converted into C biomass using 183 fgC µm**3 (Caron et al. 1995). Ciliate biomass: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Ciliate cell sizes were measured and converted into cell volumes using appropriate geometric formulae using image analysis. For biomass estimation, the conversion factor 190 fgC µm**3 was used (Putt and Stoecker 1989).

Effects of Ocean Acidification on the Ballast of Surface Aggregates Sinking through the Twilight Zone

The dissolution of CaCO3 is one of the ways ocean acidification can, potentially, greatly affect the ballast of aggregates. A diminution of the ballast could reduce the settling speed of aggregates, resulting in a change in the carbon flux to the deep sea. This would mean lower amounts of more refractory organic matter reaching the ocean floor. This work aimed to determine the effect of ocean acidification on the ballast of sinking surface aggregates. Our hypothesis was that the decrease of pH will increase the dissolution of particulate inorganic carbon ballasting the aggregates, consequently reducing their settling velocity and increasing their residence time in the upper twilight zone. Using a new methodology for simulation of aggregate settling, our results suggest that future pCO2 conditions can significantly change the ballast composition of sinking aggregates. The change in aggregate composition had an effect on the size distribution of the aggregates, with a shift to smaller aggregates. A change also occurred in the settling velocity of the particles, which would lead to a higher residence time in the water column, where they could be continuously degraded. In the environment, such an effect would result in a reduction of the carbon flux to the deep-sea. This reduction would impact those benthic communities, which rely on the vertical flow of carbon as primary source of energy.

Physical oceanography and current meter measurements on the Gulf of Lion continental margin between June 1993 and July 1996

Nine hydrographic cruises were performed on the Gulf of Lion continental margin between June 1993 and July 1996. These observations are analysed to quantify the fluxes of particulate matter and organic carbon transported along the slope by the Northern Current and to characterise their seasonal variability. Concentration of particulate matter and organic carbon are derived from light-transmission data and water sample analyses. The circulation is estimated from the geostrophic current field. The uncertainty on the transport estimate, related to the error on the prediction of particle concentrations from light-transmission data and the error on velocities, is assessed. The particulate matter inflow entering the Gulf of Lion off Marseille is comparable to the Rhône River input and varies seasonally with a maximum transport between autumn and spring. These modifications result from variations of the water flux rather than variations of the particulate matter concentration. Residual transports of particulate matter and organic carbon across the entire Gulf of Lion are calculated for two cruises enclosing the domain that were performed in February 1995 and July 1996. The particulate matter budgets indicate a larger export from the shelf to deep ocean in February 1995 (110 ± 20 kg/s) than in July 1996 (25 ± 18 kg/s). Likewise, the mean particulate organic carbon export is 12.8 ± 0.5 kg/s in February 1995 and 0.8 ± 0.2 kg/s in July 1996. This winter increase is due to larger allochthonous and autochthonous inputs and also to enhanced shelf-slope exchange processes, in particular the cascading of cold water from the shelf. The export of particulate matter by the horizontal currents is moreover two orders of magnitude larger than the vertical particulate fluxes measured at the same time with sediment traps on the continental slope.

Bulk properties and isotopic data of sediment cores from the Bounty Trough and Tasman Sea off New Zealand

Glacial/interglacial changes in Southern Ocean's air-sea gas exchange have been considered as important mechanisms contributing to the glacial/interglacial variability in atmospheric CO2. Hence, understanding past variability in Southern Ocean intermediate- to deep-water chemistry and circulation is fundamental to constrain the role of these processes on modulating glacial/interglacial changes in the global carbon cycle. Our study focused on the glacial/interglacial variability in the vertical extent of southwest Pacific Antarctic Intermediate Water (AAIW). We compared carbon and oxygen isotope records from epibenthic foraminifera of sediment cores bathed in modern AAIW and Upper Circumpolar Deep Water (UCDW; 943 - 2066 m water depth) to monitor changes in water mass circulation spanning the past 350,000 years. We propose that pronounced freshwater input by melting sea ice into the glacial AAIW significantly hampered the downward expansion of southwest Pacific AAIW, consistent with climate model results for the Last Glacial Maximum. This process led to a pronounced upward displacement of the AAIW-UCDW interface during colder climate conditions and therefore to an expansion of the glacial carbon pool.

Zooplankton and chlorophyll in upper water layers within research polygons in the Atlantic Ocean, June-September 2001

During Cruise 46 of R/V Akademik Mstislav Keldysh (from June to September 2001), vertical distributions of Radiolaria (Acantharia - Bac and Euradiolaria - Beur), mesozooplankton (from 0.2 to 3.0 mm size, Bm), and chlorophyll a (Cchl) in the epipelagic zone of the North Atlantic were studied. To examine the above-listed characteristics, samples were taken by Niskin 30 l bottles from 12-16 depth levels within the upper 100 to 200 m layer in the subarctic (48°11'N, 16°06'W) and subtropical (27°31'N, 75°51'W) waters, as well as in the transitional zone (41°44'N, 49°57'W). The latter proved to be characterized by the highest values of all averaged parameters examined by us within the upper 100 m layer (Bm - 365mg/m**3, Bac - 140 mg/m**3, Beur - 0.37 mg/m**3, and Cchl - 0.32 mg/m**3). For subarctic and subtropical waters corresponding characteristics were as follows: Bm - 123 and 53 mg/m**3, Bac - 0 and 0.06 mg/m**3, Beur - 0.17 and 0.19 mg/m**3, and Cchl - 0.27 and 0.05 mg/m**3, respectively. Percentage of Acantharia in total biomass of Radiolaria and zooplankton ranged from 0 to 39%, whereas that of Euradiolaria varied from 0.01 to 0.36%. Depth levels with maximum abundance of Acantharia were located above maxima of zooplankton and chlorophyll a or coincided with them. As for Euradiolaria, vertical profiles of their biomass were more diverse as compared with Acantharia. The latter group preferred more illuminated depth levels for its maximum development (10-100% of surface irradiance, E0) with respect to Euradiolaria (1-60% of E0). Possible reasons for this difference are discussed.

Bacterial production in the Aegean Sea in April 2008 during SES_GR1

The HCMR_SES_LAGRANGIAN_GR1_ MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the North Aegean Sea during April 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column as influenced by the BSW. Bacterial production was estimated by the 3H-leucine method (Kirchman et al. 1986, Kirchman 1993). At each depth, duplicate samples and a control were incubated with 20 nM L-[4,5 3H]-leucine. Samples were incubated in the dark, at in situ temperature.

Abundance and Biomass from heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus in the Aegean Sea in April 2008 during SES_GR1

The HCMR_SES_LAGRANGIAN_GR1_ MICROBIAL PARAMETERS dataset is based on samples collected in the framework of the project SESAME, in the North Aegean Sea during April 2008. The objectives were to measure the standing stocks and calculate the production of the microbial compartment of the food web, describe the vertical distribution pattern and characterize its structure and function through the water column as influenced by the BSW. Heterotrophic bacteria, Synechococcus, Prochlorococcus and Virus abundance: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Heterotrophic Nanoflagellate abundance: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6µm and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Ciliate abundance: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Heterotrophic bacteria, Synechococcus, Prochlorococcus biomass: Subsamples for virus, heterotrophic bacteria and cyanobacteria (Synechococcus spp. and Prochlorococcus spp.) counting were analyzed using a FACSCalibur (Becton Dickinson) flow cytometer equipped with a standard laser (488 nm) and filter set and using deionized water as sheath fluid. Fluorescent beads with a diameter of 0.97 µm (Polysciences) were added to each sample as an internal standard, and all parameters were normalized to the beads and expressed as relative units. SYBRGreen I stain (Molecular Probe) was used to stain viral and heterotrophic bacterial DNA. Viruses were counted according to (Brussaard 1984). In order to avoid bulk consentrations of viruses samples we dilluted to Tris-EDTA (pH=8,0) buffer to a final sollution of 1/5 to 1/100. Total abundance and nucleid content classes were calculated using the Paint-A-Gate software (Becton Dickinson). Abundance data were converted into C biomass using 250 fgC cell-1 (Kana & Glibert 1987) for Synechococcus, 50 fgC cell-1 (Campbell et al. 1994) for Prochlorococcus and 20fgC cell-1 (Lee & Fuhrman 1987) for heterotrophic bacteria. Heterotrophic Nanoflagellate biomass: Subsamples (30-150 ml) were concentrated on 25mm black polycarbonate filters of porosity 0.6µm and stained with DAPI for 10 min (Porter and Feig 1980). Under epifluorescence microscopy heterotrophic nanoflagellates (HNAN) were distinguished using UV and blue excitation and enumerated. Nanoflagellates were classified in size categories and the biovolume was calculated. Abundance data were converted into C biomass using 183 fgC µm**3 (Caron et al. 1995). Ciliate biomass: For ciliate identification and enumeration, 100-3000 ml samples were left for 24h-4d for sedimentation and then observed under an inverted microscope. Ciliates were counted, distinguished into size-classes and major taxonomic groups and identified down to genus or species level where possible (Pitta et al. 2005). Ciliate cell sizes were measured and converted into cell volumes using appropriate geometric formulae using image analysis. For biomass estimation, the conversion factor 190 fgC µm**3 was used (Putt and Stoecker 1989).