AQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS Aquatic Conserv: Mar. Freshw. Ecosyst. 18: S27–S44 (2008) Published online in Wiley InterScience (www.interscience.wiley.com) DOI: 10.1002/aqc.953 Sediment biogeochemical differences in two pristine Mediterranean coastal lagoons (in Italy) characterized by different phanerogam dominance–A comparative approach A. SIGNORINI*, G. MASSINI, G. MIGLIORE, M. TOSONI, C. VARRONE and G. IZZO ENEA Cre Casaccia BIOTEC, Via Anguillarese 301, 00123 Rome, Italy ABSTRACT 1. The aim of this study was to investigate functional differences in two Italian coastal lagoons (Caprolace and Fogliano, Tyrrhenian Sea) characterized by the dominance of two different seagrass species: Cymodocea nodosa (Ucria) Ascherson in the Caprolace lagoon and Ruppia cirrhosa (Petagna) Grande in the Fogliano lagoon. 2. A monitoring system was set up in both lagoons in order to (i) map the distribution of macrophytes, (ii) measure spatio–temporal changes in the biological parameters of the seagrasses, and (iii) measure spatio– temporal changes in biological and chemical–physical parameters in the water column and sediments. 3. The results showed that the relationships between macrophytes and aquatic and sediment compartments entail functional differences described by buffering systems that counteract the accumulation of free sulphide. 4. This study also suggests that R. cirrhosa and C. nodosa are indicators of different levels of ecological stability. Copyright # 2008 John Wiley & Sons, Ltd. Received 31 August 2007; Accepted 4 January 2008 KEY WORDS: coastal lagoon; R. cirrhosa; C. nodosa; dominant seagrasses; biogeochemical parameters INTRODUCTION Transitional ecosystems, such as lagoons and coastal lakes, are highly vulnerable to eutrophication, as a consequence of their position between land and sea, their shallowness and their relatively limited exchange with the open sea. These ecosystems are characterized by alternative stable ecological states (dynamic regimes) with structural and functional changes on short-, medium- and long-term scales. In particular, displacement of long life-cycle species such as phanerogams by species with short life cycles, such as Chlorophyceae, is a process that affects coastal areas and has been related to increasing eutrophication (Duarte, 1995; Nixon, 1995; Cloern, 2001). These shifts typically occur in a sudden and drastic way, and early-warning signals are difficult to obtain (Scheffer et al., 2001). In shallow water ecosystems, the mineralization of organic matter (OM) occurs in sediments and at the water–sediment *Correspondence to: A. Signorini, ENEA Cre Casaccia BIOTEC, Via Anguillarese 301, 00123 Rome, Italy. E-mail: antonella.signorini@casaccia.enea.it Copyright # 2008 John Wiley & Sons, Ltd.