Seagrass and associated benthic community data derived from field surveys at Low Isles, Great Barrier Reef, conducted July-August, 1997

The distribution of seagrass and associated benthic communities on the reef and lagoon of Low Isles, Great Barrier Reef, was mapped between the 29 July and 29 August 1997. For this survey, observers walked or free-dived at survey points positioned approximately 50 m apart along a series of transects. Visual estimates of above-ground seagrass biomass and % cover of each benthos and substrate type were recorded at each survey point. A differential handheld global positioning system (GPS) was used to locate each survey point (accuracy ±3m). A total of 349 benthic survey points were examined. To assist with mapping meadow/habitat type boundaries, an additional 177 field points were assessed and a georeferenced 1:12,000 aerial photograph (26th August 1997) was used as a secondary source of information. Bathymetric data (elevation below Mean Sea Level) measured at each point assessed and from Ellison (1997) supplemented information used to determine boundaries, particularly in the subtidal lagoon. 127.8 ±29.6 hectares was mapped. Seagrass and associated benthic community data was derived by haphazardly placing 3 quadrats (0.25m**2) at each survey point. Seagrass above ground biomass (standing crop, grams dry weight (g DW m**-2)) was determined within each quadrat using a non-destructive visual estimates of biomass technique and the seagrass species present identified. In addition, the cover of all benthos was measured within each of the 3 quadrats using a systematic 5 point method. For each quadrat, frequency of occurrence for each benthic category was converted to a percentage of the total number of points (5 per quadrat). Data are presented as the average of the 3 quadrats at each point. Polygons of discrete seagrass meadow/habitat type boundaries were created using the on-screen digitising functions of ArcGIS (ESRI Inc.), differentiated on the basis of colour, texture, and the geomorphic and geographical context. The resulting seagrass and benthic cover data of each survey point and for each seagrass meadow/habitat type was linked to GPS coordinates, saved as an ArcMap point and polygon shapefile, respectively, and projected to Universal Transverse Mercator WGS84 Zone 55 South.

Thalassiosira weissflogii attachment assay and phylogenetic affiliation of bacterial isolates from samples of the German Wadden Sea

Aggregation of algae, mainly diatoms, is an important process in marine systems leading to the settling of particulate organic carbon predominantly in the form of marine snow. Exudation products of phytoplankton form transparent exopolymer particles (TEP), which acts as the glue for particle aggregation. Heterotrophic bacteria interacting with phytoplankton may influence TEP formation and phytoplankton aggregation. This bacterial impact has not been explored in detail. We hypothesized that bacteria attaching to Thalassiosira weissflogii might interact in a yet-to-be determined manner, which could impact TEP formation and aggregate abundance. The role of individual T. weissflogii-attaching and free-living new bacterial isolates for TEP production and diatom aggregation was investigated in vitro. T. weissflogii did not aggregate in axenic culture, and striking differences in aggregation dynamics and TEP abundance were observed when diatom cultures were inoculated with either diatom-attaching or free-living bacteria. The data indicated that free-living bacteria might not influence aggregation whereas bacteria attaching to diatom cells may increase aggregate formation. Interestingly, photosynthetically inactivated T. weissflogii cells did not aggregate regardless of the presence of bacteria. Comparison of aggregate formation, TEP production, aggregate sinking velocity and solid hydrated density revealed remarkable differences. Both, photosynthetically active T. weissflogii and specific diatom-attaching bacteria were required for aggregation. It was concluded that interactions between heterotrophic bacteria and diatoms increased aggregate formation and particle sinking and thus may enhance the efficiency of the biological pump.

Phosphorus components and barite in untreated and in carbonate-free sediments of ODP Hole 199-1221C

We determined changes in equatorial Pacific phosphorus (µmol P/g) and barite (BaSO4; wt%) concentrations at high resolution (2 cm) across the Paleocene/Eocene (P/E) boundary in sediments from Ocean Drilling Program (ODP) Leg 199 Site 1221 (153.40 to 154.80 meters below seafloor [mbsf]). Oxide-associated, authigenic, and organic P sequentially extracted from bulk sediment were used to distinguish reactive P from detrital P. We separated barite from bulk sediment and compared its morphology with that of modern unaltered biogenic barite to check for diagenesis. On a CaCO3-free basis, reactive P concentrations are relatively constant and high (323 µmol P/g or ~1 wt%). Barite concentrations range from 0.05 to 5.6 wt%, calculated on a CaCO3-free basis, and show significant variability over this time interval. Shipboard measurements of P and Ba in bulk sediments are systematically lower (by ~25%) than shore-based concentrations and likely indicate problems with shipboard standard calibrations. The presence of Mn oxides and the size, crystal morphology, and sulfur isotopes of barite imply deposition in sulfate-rich pore fluids. Relatively constant reactive P, organic C, and biogenic silica concentrations calculated on a CaCO3-free basis indicate generally little variation in organic C, reactive P, and biogenic opal burial across the P/E boundary, whereas variable barite concentrations indicate significant changes in export productivity. Low barite Ba/reactive P ratios before and immediately after the Benthic Extinction Event (BEE) may indicate efficient nutrient burial, and, if nutrient burial and organic C burial are linked, high relative organic C burial that could temporarily drawdown CO2 at this site. This interpretation requires postdepositional oxidation of organic C because organic C to reactive P ratios are low throughout the section. After the BEE, higher barite Ba/reactive P ratios combined with higher barite Ba concentrations may imply that higher export productivity was coupled with unchanged reactive P burial, indicating efficient nutrient and possibly also organic C recycling in the water column. If the nutrient recycling is decoupled from organic C, the high export production could be indicative of drawdown of CO2. However, the observation that organic C burial is not high where barite burial is high may imply that either C sequestration was restricted to the deep ocean and thus occurred only on timescales of the deep ocean mixing or that postdepositional oxidation (burn down) of organic matter affected the sediments. The decoupling of barite and opal may result from low opal preservation or production that is not diatom based.

Percentage of cultured cell-populations that stained positively and/or negatively for apoptotic markers cleaved caspase-3 and cleaved PARP, following DNA damage treatments induced by doxorubicin and TNF-alpha co-treatments

The present dataset contains the source data for Figure 2B of Tentner et al. (2012). The data shows the percentage of cultured cell-populations that stained positively and/or negatively for apoptotic markers cleaved caspase-3 and cleaved PARP, following DNA damage treatments induced by various doses of doxorubicin (0, 2 and 10 µmole/L) in the presence (100 ng/mL) or absence (0 ng/mL) of TNF-alpha co-treatment. For the six treatment conditions investigated, cell counts were made by flow cytometry at times 6, 12, 24, and 48 h following treatment; CULTURE DETAILS: U2OS cells were obtained from ATCC were maintained at 21% oxygen and 5% CO2 in Dulbecco's modified Eagle medium supplemented with 10% fetal bovine serum, penicillin, streptomycin, 2mM L-glutamine, and used within 15-20 passages. The first thymidine block was released by washing the plates three times with PBS, and incubating them in fresh thymidine-free media for 12 h. A second thymidine block was then performed by re-addition of thymidine to 2.5 mM followed by incubation for an additional 18 h. Media was aspirated, plates were washed 3 with PBS, and replaced with fresh media in the presence or absence of 10 mM aphidicolin; ANALYSIS DETAILS: See supplementary journal publication; RESULT: The authors of the supplementary journal publication conclude that TNF enhances dose-dependent cell death following doxorubicin-induced DNA damage with minimal affect on dose-dependent cell-cycle arrest.