In this study, we compared three methods for extraction and quantification of RNA and DNA from marine sediments: (i) a spectrophotometric method using the diphenylamine assay; (ii) a fluorometric method utilizing selective fluorochromes (thiazole orange for total nucleic acids and Hoechst 33258 for DNA); and (iii) a high-pressure liquid chromatography (HPLC) method which uses a specific column to separate RNA and DNA and UV absorption of the nucleic acids for quantification. Sediment samples were collected in the oligotrophic Cretan Sea (eastern Mediterranean, from 40 to 1,540 m in depth) and compared to the distribution and composition of the benthic microbial assemblages (i.e., bacteria and microprotozoa). DNA concentrations measured spectrophotometrically and by HPLC were not significantly different, while fluorometric yields were significantly lower. Such differences appear mainly due to fact that the stain-DNA complex is strongly dependent on the DNA composition and structure. RNA concentrations determined by the three methods displayed some differences; fluorometric and spectrophotometric methods obtain RNA concentration by difference and therefore may be biased by DNA estimates. By contrast, the HPLC method provides independent assessments of RNA and DNA concentrations. We tentatively estimated the contribution of the detrital DNA to the total DNA pools in two ways. The two calculations provided quite similar results indicating that the majority of the DNA pool in the deep-sea sediments was detrital. Microbial RNA generally accounted for almost the entire sedimentary RNA pools below 100-m depth. RNA concentrations were found to decrease along the Cretan shelf and slope. The RNA/DNA ratio calculated by using fluorometric DNA concentrations was significantly correlated with values of sediment community oxygen consumption only below 100-m depth (dominated by the microbial biomass). These data suggest that the RNA/DNA ratio, based on fluorometric estimates of DNA, can be used as an indicator of benthic metabolic activity, but only when metazoan contribution to the microbial DNA is negligible.

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In-situ and shipboard measurements of sediment community oxygen consumption (SCOC), in conjunction with a study of, the distributions of macro and megafauna and phytopigments, were used to determine and, where possible, explain the distribution of labile particulate organic matter (POM) on the NE Atlantic continental slope (Goban Spur, SW Ireland). A specific issue concerned the existence of depocentres of labile POM on the slope caused by lateral transport. a phenomenon that has been found previously in ,the' NW Atlantic. The SCOC data from October 1993 and May 1994 showed a steady decrease with increasing water depth. SCOC values ranged from 5.4 mmol m-? d-' at the shelfbreak to 0.3 mmol m-' d-' at 4,500 m depth. No evidence was found for seasonal variation in SCOC. A clear seasonal signal was observed with regard to sediment phytopigments and phytopigment fluxes into sediment traps attached to the benthic lander. The upper-and mid-slope values of both parameters were much higher in May 1994 than in October 1993 and August 1995. This is consistent with the normal spring bloom pattern; but because of the degraded state of the May phytodetritus in the nearbottom water, reflected in the lack of a response in SCOC and the low chlorophyll-o concentrations, it was concluded that the material was not derived from the overlying photic zone, but instead transported from elsewhere in the benthic nepheloid layer (BNL). In August 1995, the lower slope (>3,000 m) had received a strong and fresh phytodetritus pulse (3 g C m-') forming a mucous layer on top of the sediment. Using phytopigments and sterols as molecular markers, it was shown that the pulse was derived from an offshore bloom with an important contribution by dinoflagellates. By contrast, no mucous layer was found on the upper slope stations in August 1995. Macrofauna biomass showed a distinct decline from the upper slope down to the lower slope conforming to the diminishing supply of labile POM. The total wet biomass of megafauna reached relatively high values at the lower slope (>3,500 m) owing to large motile sea cucumbers. The presence of these "vacuum-cleaner" sea cucumbers is considered indicative of the occurrence of phytodetritus pulses. In spite of their assumed adaptation to periodic pulses, the estimated contribution by the sea cucumbers to the total benthic mineralization is minor, When combining data from different yeardseasons we observed decoupling between the food supply to the lower slope and the upper and mid slopes. The major pulse to the former comes from an offshore summer bloom. The upper and mid slope appear to be fuelled by spring bloom material which is subsequently redistributed on the upper slope in a BNL. The quality of the seston in the BNL diminished in the offshore direction as indicated by the phytopigment concentrations.

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RNA/DNA ratios are used in many organisms as an indicator of growth, biomass or metabolic functioning. We hypothesised that hermatypic corals, as they depend for growth largely on energy transferred from their algal symbionts, may show an effect in the RNA/DNA ratio with factors influencing irradiance. This was tested along 2 environmental gradients: in relation to depth (decreasing irradiance) and in relation to environmental degradation (increased turbidity). RNA/DNA ratios were determined by HPLC in coral samples collected over depth gradients in 3 islands off the coast of north-west Java, Indonesia. The reefs range from shallow reefs (depth < 3 m) in very turbid water, which are close to eroded shores, to intermediate reefs (depth < 6 m) further from the shore with less turbid water, to offshore clear water control reefs (depth < 20 m). RNA/DNA ratio was shown to be negatively correlated with depth in all but the most turbid conditions, suggesting it is an expression of metabolic acclimatisation of the coral host-symbiont community with decreasing irradiance (i.e. photoadaptation). Comparing the RNA/DNA ratio in clear and turbid waters, the decrease with depth tended to be steeper over a shorter depth range under turbid conditions, analogous with the more rapid extinction of light in these conditions. The relationship between the RNA/DNA ratio and light was consistently higher under turbid conditions (p = 0.0037), indicating that RNA/DNA ratio had shifted to a higher level, possibly indicating a genetic adaptation in the metabolic functioning of corals in the turbid environment. The positive relation between light and RNA/DNA ratio would suggest the opposite, i.e. lower ratio under turbid conditions. The RNA/DNA ratio may provide a relatively reliable method to determine the metabolic functioning (health) of individual coral colonies.

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