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ABSTRACT1. Transitional waters, described as critical transition zones because of their position at terrestrial, freshwater and marine interfaces, provide essential goods and services to the biosphere including human populations. These ecotones face increasing human influence mainly due to population density increase in coastal areas.2. Transitional water bodies have, to date, received little attention in the development of ecological status indicators; this is a critical deficiency when trying to meet the Water Framework Directive objective of all significant water bodies achieving good ecological status by the year 2015.3. In order to assess changes in transitional water communities many taxonomic-based indicators have already been proposed but there are a number of concerns for their use such as taxonomic classification difficulties, their unsuitability for multi-site comparisons and their inconsistent relationships with disturbance or stress.4. Alternative methods based on body size, abundance distribution among functional groups, functional diversity and productivity descriptors are proposed. These methods offer the opportunity to compare sites with different taxonomic compositions and allow derivation of indicators related to ecological status of communities under scrutiny.5. Finally, the suitability of these taxonomic-free descriptors to provide relevant information for each of the four main biotic compartments in coastal lagoons is discussed. The use of biomass distribution among functional groups for fish, benthos and macrophyte and to use body-size distribution for benthos and plankton is proposed.

SignificanceExplaining why there are more species than limiting resources in natural systems constitutes a long-standing challenge among ecologists. Recently, this apparent paradox was resolved theoretically by showing that species can coexist in clumps along niche gradients. However, models demonstrating this effect have failed to account for a ubiquitous feature of nature, namely variability in environmental conditions. This leaves open the question of whether the proposed mechanisms underpinning “lumpy coexistence” apply in nature or arise as a coincidence of modeling frameworks. Here, we demonstrate the emergence of lumpy coexistence in assemblages self-organizing under fluctuating resource supplies. We show that clumps form predictably as the result of the dynamic pattern in ambient resources driven by the most competitive species in the assemblage.

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