Faecal pellet production of copepoda collected in water depth up to 30 meters in the eastern Mediterranean Sea in Oktober 2008 during SES_GR2

Mesozooplankton is collected by vertical tows within the Black sea water body mass layer in the NE Aegean, using a WP-2 200 µm net equipped with a large non-filtering cod-end (10 l). Macrozooplankton organisms are removed using a 2000 µm net. A few unsorted animals (approximately 100) are placed inside several glass beaker of 250 ml filled with GF/F or 0.2 µm Nucleopore filtered seawater and with a 100 µm net placed 1 cm above the beaker bottom. Beakers are then placed in an incubator at natural light and maintaining the in situ temperature. After 1 hour pellets are separated from animals and placed in separated flasks and preserved with formalin. Pellets are counted and measured using an inverted microscope. Animals are scanned and counted using an image analysis system. Carbon- Specific faecal pellet production is calculated from a) faecal pellet production, b) individual carbon: Animals are scanned and their body area is measured using an image analysis system. Body volume is then calculated as an ellipsoid using the major and minor axis of an ellipse of same area as the body. Individual carbon is calculated from a carbon- total body volume of organisms (relationship obtained for the Mediterranean Sea by Alcaraz et al. (2003) divided by the total number of individuals scanned and c) faecal pellet carbon: Faecal pellet length and width is measured using an inverted microscope. Faecal pellet volume is calculated from length and width assuming cylindrical shape. Conversion of faecal pellet volume to carbon is done using values obtained in the Mediterranean from: a) faecal pellet density 1,29 g cm**3 (or pg µm**3) from Komar et al. (1981); b) faecal pellet DW/WW=0,23 from Elder and Fowler (1977) and c) faecal pellet C%DW=25,5 Marty et al. (1994).

Abundance and biomass of mesozooplankton in the eastern Mediterranean Sea in March and April 2008 during SES_GR1

The dataset is based on samples taken during March-April 2008 in Libyan Sea, in Southern Aegean Sea and in Northern Aegean Sea. Sampling volume was estimated by the net mouth surface and the towing distance for WP-2. Taxon-specific mesozooplankton abundance and total abundance: The sample was split on board in two halves by using the beaker approach. The first sub-sample was immediately fixed and preserved in a seawater formalin solution containing about 4% buffered formaldehyde to allow the determination of species composition abundance. Pipette for the subsamples used in the taxonomic analysis of zooplankton under binocular microscope.

Ingestion rate and egg production of copepods collected in the upper 20m in the eastern Mediterranean Sea in April 2008 during SES_GR2

The ingestion on ciliates and phytoplankton dataset is based on samples taken during October 2008 in Northern Aegean Sea, the area influenced by the Black Sea water outflow. A Lagrangian experiment was established and copepod ingestion was estimated from experiments performed at stations according to the different positions of drifters during the cruise. Copepods for the experiments were obtained with slow non-quantitative tows from the upper 20 m layer of the water column using 200 µm mesh size nets fitted with a large non-filtering cod end. For the grazing experiments we used the following copepod species: Clausocalanus furcatus, and Temoraa stylifera according to the relevant reference (Bamstedt et al. 2000). Copepod clearance rates on ciliates were calculated according to Frost equations (Frost 1972). Ingestion rates were calculated by multiplying clearance rates by the initial standing stocks (Bamstedt et al. 2000). The egg production dataset is based on samples taken during October 2008 in Northern Aegean Sea, the area influenced by the Black Sea water outflow. A Lagrangian experiment was established and copepod egg production was estimated from experiments performed at stations according to the different positions of drifters during the cruise. Egg production rates of the dominant calanoid copepods were determined by incubation of fertilised females (eggs female/day) collected in the 0-20m layer. Copepod egg production was measured for the copepods Clausocalanus furcatus, Temora stylifera. On board experiments for the estimation of copepod egg production were taken place. For the estimation of copepod production (mgC/m**2/day), lengths (copepods and eggs) were converted to body carbon (Hopcroft et al., 1998) and production was estimated from biomass and weight-specific egg production rates, by assuming that those rates are representative for juvenile specific growth rates (Berggreen et al., 1988).

Sedimentary lipids and palynomorphs of sediment core ABC26 from the Eastern Mediterranean

Selective degradation of organic matter in sediments is important for reconstructing past environments and understanding the carbon cycle. Here, we report on compositional changes between and within lipid classes and kerogen types (represented by palynomorph groups) in relation to the organic matter flux to the sea floor and oxidation state of the sediments since the early Holocene for central Eastern Mediterranean site ABC26. This includes the initially oxic but nowadays anoxic presapropelic interval, the still unoxidised lower part of the organic rich S1 sapropel, its postdepositionally oxidised and nowadays organic-poor upper part as well as the overlying postsapropelic sediments which have always been oxic. A general ~ 2.3 times increase in terrestrial and marine input during sapropel formation is estimated on the basis of the total organic carbon (TOC), pollen, spore, dinoflagellate cyst, n-alkane, n-alkanol and n-alkanoic acid concentration changes in the unoxidised part of the sapropel. The long-chain alkenones, 1,15 diols and keto-ols, loliolides and sterols indicate that some plankton groups, notably dinoflagellates, may have increased much more. Apart from the terrestrial and surface water contributions to the sedimentary organic matter, anomalous distributions and preservation of some C23-C27 alkanes, alkanols and alkanoic acids have been observed, which are interpreted as a contribution by organisms living in situ. Comparison of the unoxidised S1 sapropel with the overlying oxidised sapropel and the organic matter concentration profiles in the oxidised postsapropelic sediments demonstrates strong and highly selective aerobic degradation of lipids and palynomorphs. There seems to be a fundamental difference in degradation kinetics between lipids and pollen which may be possibly related with the absence of sorptive preservation as a protective mechanism for palynomorph degradation. The n-alkanes, Impagidinium, and Nematosphaeropsis are clearly more resistant than TOC. The n-alkanols and n-carboxylic acids are about equally resistant whereas the pollen, all other dinoflagellate cysts and other lipids appear to degrade considerably faster, which questions the practice of normalising to TOC without taking diagenesis into account. Selective degradation also modifies the relative distributions within lipid classes, whereby the longer-chain alkanes, alcohols and fatty acids disappear faster than their shorter-chain equivalents. Accordingly, interpretation of lipid and palynomorph assemblages in terms of pre- or syndepositional environmental change should be done carefully when proper knowledge of the postdepositional preservation history is absent. Two lipid-based preservation proxies are tested the diol-keto-ol oxidation index based on the 1,15C30 diol and keto-ols (DOXI) and the alcohol preservation index (API) whereby the former seems to be the most promising.

(Table 1) Position and astronomical ages of sedimentary cycles in the eastern Mediterranean Sea

An astronomically calibrated timescale has recently been established [Hilgen, 1991, doi:10.1016/0012-821X(91)90082-S; doi:10.1016/0012-821X(91)90206-W] for the Pliocene and earliest Pleistocene based on the correlation of dominantly precession controlled sedimentary cycles (sapropels and carbonate cycles) in Mediterranean marine sequences to the precession time series of the astronomical solution of Berger and Loutre [1991, doi:10.1016/0277-3791(91)90033-Q ] (hereinafter referred to as Ber90). Here we evaluate the accuracy of this timescale by (1) comparing the sedimentary cycle patterns with 65°N summer insolation time series of different astronomical solutions and (2) a cross-spectral comparison between the obliquity-related components in the 65°N summer insolation curves and high-resolution paleoclimatic records derived from the same sections used to construct the timescale. Our results show that the carbonate cycles older than 3.5 m.y. should be calibrated to one precession cycle older than previously proposed. Application of the astronomical solution of Laskar [1990, doi:10.1016/0019-1035(90)90084-M], (hereinafter referred to as La90) with present-day values for the dynamical ellipticity of the Earth and tidal dissipation by the Sun and Moon results in the best fit with the geological record, indicating that this solution is the most accurate from a geological point of view. Application of Ber90, or La90 solutions with dynamical ellipticity values smaller or larger than the present-day value, results in a less obvious fit with the geological record. This implies that the change in the planetary shape of the Earth associated with ice loading and unloading near the poles during the last 5.3 million years was too small to drive the precession into resonance with the perturbation term, s6-g6+g5, of Jupiter and Saturn. Our new timescale results in a slight but significant modification of all ages of the sedimentary cycles, bioevents, reversal boundaries, chronostratigraphic boundaries, and glacial cycles. Moreover, a comparison of this timescale with the astronomical timescales of ODP site 846 [Shackleton et al., 1995, doi:10.2973/odp.proc.sr.138.106.1995; doi:10.2973/odp.proc.sr.138.117.1995] and ODP site 659 [Tiedemann et al., 1994, doi:10.1029/94PA00208] indicates that all obliquity-related glacial cycles prior to ~4.7 Ma in ODP sites 659 and 846 should be correlated with one obliquity cycle older than previously proposed.

Faecal pellet production of copepoda collected in water depth up to 100 meters in the eastern Mediterranean Sea in March and April 2008 during SES_GR1

The SES_UNLUATA_GR1-Mesozooplankton faecal pellet production rates dataset is based on samples taken during March and April 2008 in the Northern Libyan Sea, Southern Aegean Sea and in the North-Eastern Aegean Sea. Mesozooplankton is collected by vertical tows within the 0-100 m layer or within the Black sea water body mass layer in the case of the NE Aegean, using a WP-2 200 µm net equipped with a large non-filtering cod-end (10 l). Macrozooplankton organisms are removed using a 2000 µm net. A few unsorted animals (approximately 100) are placed inside several glass beaker of 250 ml filled with GF/F or 0.2 µm Nucleopore filtered seawater and with a 100 µm net placed 1 cm above the beaker bottom. Beakers are then placed in an incubator at natural light and maintaining the in situ temperature. After 1 hour pellets are separated from animals and placed in separated flasks and preserved with formalin. Pellets and are counted and measured using an inverted microscope. Animals are scanned and counted using an image analysis system. Carbon- Specific faecal pellet production is calculated from a) faecal pellet production, b) individual carbon: Animals are scanned and their body area is measured using an image analysis system. Body volume is then calculated as an ellipsoid using the major and minor axis of an ellipse of same area as the body. Individual carbon is calculated from a carbon- total body volume of organisms (relationship obtained for the Mediterranean Sea by Alcaraz et al. (2003) divided by the total number of individuals scanned and c) faecal pellet carbon: Faecal pellet length and width is measured using an inverted microscope. Faecal pellet volume is calculated from length and width assuming cylindrical shape. Conversion of faecal pellet volume to carbon is done using values obtained in the Mediterranean from: a) faecal pellet density 1,29 g cm**3 (or pg µm**3) from Komar et al. (1981); b) faecal pellet DW/WW=0,23 from Elder and Fowler (1977) and c) faecal pellet C%DW=25,5 Marty et al. (1994).

Faecal pellet production of copepoda collected at different water depth in the eastern Mediterranean Sea during SES_GR2

The SES_GR2-Mesozooplankton faecal pellet production rates dataset is based on samples taken during August and September 2008 in the Northern Libyan Sea, Southern Aegean Sea and the North-Eastern Aegean Sea. Mesozooplankton is collected by vertical tows within the 0-100 m layer or within the Black sea water body mass layer in the case of the NE Aegean, using a WP-2 200 µm net equipped with a large non-filtering cod-end (10 l). Macrozooplankton organisms are removed using a 2000 µm net. A few unsorted animals (approximately 100) are placed inside several glass beaker of 250 ml filled with GF/F or 0.2 µm Nucleopore filtered seawater and with a 100 µm net placed 1 cm above the beaker bottom. Beakers are then placed in an incubator at natural light and maintaining the in situ temperature. After 1 hour pellets are separated from animals and placed in separated flasks and preserved with formalin. Pellets are counted and measured using an inverted microscope. Animals are scanned and counted using an image analysis system. Carbon- Specific faecal pellet production is calculated from a) faecal pellet production, b) individual carbon: Animals are scanned and their body area is measured using an image analysis system. Body volume is then calculated as an ellipsoid using the major and minor axis of an ellipse of same area as the body. Individual carbon is calculated from a carbon- total body volume of organisms (relationship obtained for the Mediterranean Sea by Alcaraz et al. (2003) divided by the total number of individuals scanned and c) faecal pellet carbon: Faecal pellet length and width is measured using an inverted microscope. Faecal pellet volume is calculated from length and width assuming cylindrical shape. Conversion of faecal pellet volume to carbon is done using values obtained in the Mediterranean from: a) faecal pellet density 1,29 g cm**3 (or pg µm**3) from Komar et al. (1981); b) faecal pellet DW/WW=0,23 from Elder and Fowler (1977) and c) faecal pellet C%DW=25,5 Marty et al. (1994).

Faecal pellet production of copepoda collected in water depth up to 20 meters in the eastern Mediterranean Sea in March and April 2008 during SES_GR1

The SES_GR1-Mesozooplankton faecal pellet production rates dataset is based on samples taken during April 2008 in the North-Eastern Aegean Sea. Mesozooplankton is collected by vertical tows within the Black sea water body mass layer in the NE Aegean, using a WP-2 200 µm net equipped with a large non-filtering cod-end (10 l). Macrozooplankton organisms are removed using a 2000 µm net. A few unsorted animals (approximately 100) are placed inside several glass beaker of 250 ml filled with GF/F or 0.2 µm Nucleopore filtered seawater and with a 100 µm net placed 1 cm above the beaker bottom. Beakers are then placed in an incubator at natural light and maintaining the in situ temperature. After 1 hour pellets are separated from animals and placed in separated flasks and preserved with formalin. Pellets are counted and measured using an inverted microscope. Animals are scanned and counted using an image analysis system. Carbon- Specific faecal pellet production is calculated from a) faecal pellet production, b) individual carbon: Animals are scanned and their body area is measured using an image analysis system. Body volume is then calculated as an ellipsoid using the major and minor axis of an ellipse of same area as the body. Individual carbon is calculated from a carbon- total body volume of organisms (relationship obtained for the Mediterranean Sea by Alcaraz et al. (2003) divided by the total number of individuals scanned and c) faecal pellet carbon: Faecal pellet length and width is measured using an inverted microscope. Faecal pellet volume is calculated from length and width assuming cylindrical shape. Conversion of faecal pellet volume to carbon is done using values obtained in the Mediterranean from: a) faecal pellet density 1,29 g cm**3 (or pg µm**3) from Komar et al. (1981); b) faecal pellet DW/WW=0,23 from Elder and Fowler (1977) and c) faecal pellet C%DW=25,5 Marty et al. (1994).

Niche differentiation among mat-forming, sulfide-oxidizing bacteria in chemosynthetic ecosystems of the Nile Deep Sea Fan (Eastern Mediterranean Sea)

Sulfidic muds of cold seeps on the Nile Deep Sea Fan are populated by different types of mat-forming sulfide-oxidizing bacteria. The predominant sulfide oxidizers of three different mats were identified by microscopic and phylogenetic analyses as (i) Arcobacter species producing cotton-ball-like sulfur precipitates, (ii) large filamentous sulfur bacteria including Beggiatoa species, or (iii) single, spherical cells resembling Thiomargarita species. High resolution in situ microprofiles revealed different geochemical settings selecting for different mat types. Arcobacter mats occurred where oxygen and sulfide overlapped at the bottom water interface. Filamentous sulfide oxidizers were associated with non-overlapping, steep gradients of oxygen and sulfide. A dense population of Thiomargarita was favored by temporarily changing supplies of oxygen and sulfide. These results indicate that the decisive factors in selecting for different mat-forming bacteria within one deep-sea province are spatial or temporal variations in energy supply. Furthermore, the occurrence of Arcobacter spp.-related 16S rRNA genes in the sediments below all three types of mats, as well as on top of brine lakes of the Nile Deep Sea Fan, indicates that this group of sulfide oxidizers can switch between different life modes depending on the geobiochemical habitat setting.

Abundance and biomass of ciliates in the eastern Mediterranean Sea in April 2008

The dataset was obtained on samples taken from 6 stations in the Dardanelles Straits, Marmara Sea and Bosporus Straits. These experiments were set up according to DoW of SESAME project. Ciliate abundance: Borax-buffered formalin (final concentration 2% formaldehyde). Samples for ciliate counting were stored at 4°C in the dark until observation. For ciliate identification and enumeration, 100 ml samples were left for 24 h in sedimentation cylinders and then observed under an inverted epifluorescence microscope. Ciliate biomass: Ciliate cell sizes were measured and converted into cell volumes using appropriate geometric formulae (Peuto-Moreau 1991). For biomass estimation, the conversion factor 140 fgC µm**3 was used (Putt and Stoecker (1989), doi:10.4319/lo.1989.34.6.1097)).

Biogeochemical investigation of cold seep sediments in the Eastern Mediterranean Sea

Cold seep ecosystems are highly productive, fragmented ecosystems of the deep-sea floor. They form worldwide where methane reaches the surface seafloor, and are characterized by rich chemosynthetic communities fueled by the microbial utilization of hydrocarbons. Here we investigated with in situ (benthic chamber, microprofiler) and ex situ (pore water constituents, turnover rates of sulfate and methane, prokaryote abundance) techniques reduced sites from three different seep ecosystems in the Eastern Mediterranean deep-sea. At all three cold seep systems, the Amon Mud Volcano, Amsterdam Mud Volcano and the Nile Deep Sea Fan Pockmark area, we observed and sampled patches of highly reduced, methane-seeping sulfidic sediments which were separated by tens to hundreds of (kilo)meters with non-reduced oxygenated seafloor areas. All investigated seep sites were characterized by gassy, sulfidic sediments of blackish color, of which some were overgrown with thiotrophic bacterial mats. Fluxes of methane and oxygen, as well as sulfate reduction rates varied between the different sites.

Nanoflagellates (mixotrophs, heterotrophs and autotrophs) in the oligotrophic eastern Mediterranean

The vertical distribution (0 to 100 m) and abundance of nanoflagellates were examined in the oligotrophic Aegean Sea (east Mediterranean) in early spring (south basin) and late summer (north and south basins) of 1997 in the framework of the MATER project (Mass Transfer and Ecosystem Response). Different trophic types of nanoflagellates (mixotrophic, heterotrophic, and phototrophic) were identified based on the possession of chloroplasts and the consumption of Fluorescently Labelled Minicells (FLM). Bacterial production (leucine method) was compared with bacterivory estimated from FLM consumption. We found that mixotrophic nanoflagellates played a small role as bacterivores relative to heterotrophic nanoflagellates and total bacterivory roughly balanced bacterial production. In early spring with cool (14.2°C) well-mixed water columns, flagellate concentrations were lowest, phototrophic flagellates were the dominant group and concentrations varied little with depth. Average concentrations of mixotrophs, heterotrophs and autotrophs were 0.07, 0.34, and 0.64 x 103 cells/ml, respectively. Bacterial production in the 0 to 100 m layer averaged about 0.74 µg C/l/d. Estimated nanoflagellate bacterivory from FLM ingestion accounted for 40% of bacterial production with mixotrophic nanoflagellates consuming 5% of bacterial production. In late summer, total nanoflagellate concentrations were higher. Average concentrations of mixotrophs, heterotrophs and autotrophs were 0.09, 1.14, and 0.66 x 103 cells/ml, respectively, in the southern basin and 0.09, 1.1, and 0.98 x 103 cells/ml, respectively, in the northern basin. In September, bacterial production for both basins roughly balanced estimated nanoflagellate consumption. Similar to the March estimates, mixotrophic nanoflagellates accounted for about 5% of nanoflagellate bacterivory. In a nutrient enrichment experiment in March, treatments including phosphorus resulted in increased bacterial production and reductions in identifiable mixotrophs.

Stable carbon and oxygen isotopes from samples of the Anaximander seamounts in the eastern Mediterranean Sea

Porous seep-carbonates are exposed at mud volcanoes in the eastern Mediterranean Sea. The 13C-depleted aragonitic carbonates formed as a consequence of the anaerobic oxidation of methane in a shallow sub-surface environment. Besides the macroscopically visible cavernous fabric, extensive carbonate corrosion was revealed by detailed analysis. After erosion of the background sediments, the carbonates became exposed to oxygenated bottom waters that are periodically influenced by the release of methane and upward diffusion of hydrogen sulphide. We suggest that carbonate corrosion resulted from acidity locally produced by aerobic oxidation of methane and hydrogen sulphide in the otherwise, with respect to aragonite, oversaturated bottom waters. Although it remains to be tested whether the mechanisms of carbonate dissolution suggested herein are valid, this study reveals that a better estimate of the significance of corrosion is required to assess the amount of methane-derived carbon that is permanently fixed in seep-carbonates.