Some of most used indicators in marine ecology are nucleic acid-derived indices. They can be divided by target levels in three groups: 1) at the organism level as ecophysiologic indicators, indicators such as RNA:DNA ratios, DNA:dry weight and RNA:protein, 2) at the population level, indicators such as growth rate, starvation incidence or fisheries impact indicators, and 3) at the community level, indicators such as trophic interactions, exergy indices and prey identification. The nucleic acids derived indices, especially RNA:DNA ratio, have been applied with success as indicators of nutritional condition, well been and growth in marine organisms. They are also useful as indicators of natural or anthropogenic impacts in marine population and communities, such as upwelling or dredge fisheries, respectively. They can help in understanding important issues of marine ecology such as trophic interactions in marine environment, fish and invertebrate recruitment failure and biodiversity changes, without laborious work of counting, measuring and identification of small marine organisms. Besides the objective of integrate nucleic acid derived indices across levels of organization, the paper will also include a general characterization of most used nucleic acid derived indices in marine ecology and also advantages and limitations of them. We can conclude that using indicators, such RNA:DNA ratios and other nucleic acids derived indices concomitantly with organism and ecosystems measures of responses to climate change (distribution, abundance, activity, metabolic rate, survival) will allow for the development of more rigorous and realistic predictions of the effects of anthropogenic climate change on marine systems.

SUMMARY: This study describes sea urchin spatial distribution in relation to environmental factors, and the relationship between Diadema antillarum density and algal abundance. Twenty-three transects around Madeira Island were surveyed by scuba divers, and sea urchin density and algal cover were determined in situ. Sampling sites along these transects were characterised in terms of distance from the tide line, water depth, substratum type, bottom declivity and water turbulence. Diadema antillarum was the dominant sea urchin species. Paracentrotus lividus and Arbacia lixula occurred at shallower depths (2-6 m), contrasting with the distribution of Sphaerechinus granularis, which occurs among D. antillarum (4-20 m). Surveys found two alternative types of communities on rocky shores: 1) a community with high algal cover and low numbers of sea urchins, along the north and south-west coasts and; 2) a community with little algal cover and high densities of sea urchins, along the south-east coast. Macroalgal cover and D. antillarum densities were inversely correlated (adjusted R 2 =75.6%; n = 429; p<0.05). The results showed that water turbulence was the most important factor limiting the distribution of D. antillarum on rocky substrates. We propose a multiple non-linear regression model (using backward stepwise analysis) to explain D. antillarum abundance on the rocky shores: D. antillarum/m 2 (√√)= 0.121 -0.209 distance from shore (in m) (√√) + 2.052 water depth (in m) (√√) -1.778 water turbulence level (√√) -0.007 water turbulence level 4 (√√); where √√ indicates data are square-root transformed (adjusted R 2 = 60.99%; n = 454; p<0.05).

Throughout the world, estuaries and coastal waters have experienced degradation. Present proposed remedial measures based on engineering and technological fix are not likely to restore the ecological processes of a healthy, robust estuary and, as such, will not reinstate the full beneficial functions of the estuary ecosystem. The successful management of estuaries and coastal waters requires an ecohydrologybased, basin-wide approach. This necessitates changing present practices by official institutions based on municipalities or counties as an administrative unit, or the narrowly focused approaches of managers of specific activities (e.g., farming and fisheries, water resources, urban and economic developments, wetlands management and nature conservationists). Without this change in thinking and management concept, estuaries and coastal waters will continue to degrade, whatever integrated coastal management plans are implemented. To help in this process of change there is a need to (1) develop a profound understanding of the effects of biota and biotic processes on mediating estuary response to changing hydrology, sediment and nutrient flux and of the biota on hydrology at the river basin scale, and (2) to develop science-based remediation measures at the river basin scale, with elements of ecohydrology and phytotechnology at their core, to strengthen the ability of the biota to sustain and adapt to human-induced stresses.

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