Ecological Indicators 29 (2013) 390–397 Contents lists available at SciVerse ScienceDirect Ecological Indicators jo ur n al homep ag e: www.elsevier.com/locate/ecolind New multi-metric Salt Marsh Sediment Microbial Index (SSMI) application to salt marsh sediments ecological status assessment B. Duarte a,∗ , J. Freitas a , T. Couto b , J. Valentim c , J.M. Dias c , H. Silva c , J.C. Marques b , I. Cac ¸ ador a a Centre of Oceanography of the Faculty of Sciences of the University of Lisbon (CO), Campo Grande, 1749-016 Lisbon, Portugal b Institute of Marine Research – Marine and Environment Research Centre (IMAR-CMA), c/o Department of Zoology, Faculty of Sciences and Technology, University of Coimbra, 3000 Coimbra, Portugal c Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal a r t i c l e i n f o Article history: Received 29 June 2012 Received in revised form 7 January 2013 Accepted 10 January 2013 Keywords: Salt marsh Ecological Status Sediment SSMI Microbial Activities a b s t r a c t Salt marshes are very important areas for biogeochemical cycling, sediment accretion, pollution filtra- tion and retention and erosion and stabilization of the river margins. The high organic matter content in the salt marsh plant sediments along with the radial oxygen diffusion provided by these halophyte root systems gather the ideal conditions for the development of a microbial rhizosphere community. Due to the quick feedback of the microbial communities to an environmental change, these organisms become important monitors for environmental impact assessment. A Salt marsh Sediment Microbial Index (SSMI) that reflected physical–chemical and microbial parameters was applied to plant rhizosphere sediments of five salt marshes from three important water bodies from Portugal. The SSMI revealed to be plant-independent evaluating efficiently the different marshes according to their maturity degree and disturbance influence. Mature salt marshes SSMI classification grouped all the systems at this develop- ment stage, while the younger salt marshes are classified in different groups according to their evolution degree. Also the impact degree is reflected at this level discriminating also the more adversely impacted salt marshes. Being a multi-metric index, the SSMI sub-metrics are also susceptible of ecological interpre- tation, giving important backstage information about the underlying biogeochemical cycling processes. © 2013 Elsevier Ltd. All rights reserved. 1. Introduction Salt marshes are very important areas in terms of estuarine biodiversity, with elevated primary production, supporting a large number of habitats as feeding areas, shelters, nurseries, matting and reproduction sites and as migration points (Williams et al., 1994; Doyle and Otte, 1997; Vinagre et al., 2008; Cac ¸ ador et al., 2009). About 2/3 of the world population lives near rivers, estuar- ies and coastal zones, with consequent and inevitable impacts on the aquatic environment. Today only a very small part of the world wetlands remain undisturbed, as consequence of years of nearby industrialization and urbanization. In the last years, several of these industrial areas were abandoned and their industries shutdown, although their effects can still be detected in nowadays (Duarte and Cac ¸ ador, 2012). Among the estuarine ecosystems, salt marshes appear as key zones for the estuarine biogeochemical cycling, sed- iment deposition, thus promoting river margin stabilization and contaminant filtration and retention (Mitsch and Gosselink, 2007). ∗ Corresponding author. Fax: +351 21 75 00009. E-mail address: baduarte@fc.ul.pt (B. Duarte). As key players of biogeochemical cycling, are the microorgan- isms inhabiting the halophytic species rhizosphere (Duarte et al., 2008). Both these two biotic compartments (plant roots and micror- ganisms) comprising the rhizosphere are key players in such an important processes like nitrification and denitrification (Sousa et al., 2012), or iron and sulphide oxidation and the coupled phos- phorous cycling (Zak et al., 2008). Although the adverse haline environment and potentially anoxic salt marsh sediments, these microbial communities are stimulated by the aerobic environment created in the halophyte rhizosphere, throughout radial oxygen loss by the halophyte root system (Duarte et al., 2008, 2009; Garthwaite et al., 2008). These communities have a fundamental role in the ecosys- tems functions, as they are essential for nutrient regeneration and organic matter decomposition. Salt marshes located at estuaries frequently receive large inputs of nutrients (Tobias et al., 2001), and also of particulate and dissolved organic matter. The large amounts of particulate organic matter that enter in the salt marsh, during tidal flooding, settles in the sediments, where it may be buried and serve as substrate to the decomposition processes. Microbial-mediated processes play a key role in these mineral- ization processes (Rauch and Denis, 2008). This large spectrum 1470-160X/$ – see front matter © 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.ecolind.2013.01.008