Structure and function of benthic microbial community in highly variable freshwater systems

In the semi-arid Mediterranean regions, extended reaches of rivers and streams show a recurrent dry phases of varying duration and spatial extent. It is important to study the effects of water stress on riverine ecological processes since freshwater systems are crucial in linking terrestrial and marine environments, My Doctorate thesis research, supported by the European TempQsim project (EVK1-CT2002-00112), was aimed to investigate the dynamics of microbial communities associated to sediments in temporary rivers. In particular, I have been investigating the effects of water stress on the structure and function of benthic bacterial communities and their role in the carbon cycle of rivers characterized by a seasonal hydrologic regime. Bacterial abundance and phylogenetic composition were assessed by molecular techniques, while bacterial activity was estimated by measuring the incorporation rates of radioactive tracers and by immunofluorescence. From a methodological point of view, all applied techniques required a specific optimization phase in order to increase their analytical efficiency. In particular, a detachment procedure to extract and purify bacterial cells from freshwater sediments was optimized by the combined use of different chemical and physical treatments, followed by high-speed density gradient centrifugation using the medium Nycodenz. This procedure was initially applied to analyze the benthic bacterial communities in rivers with stable water flow conditions (Rivers Albegna, Ente, Fiora – Tuscany, Italy; River Cremera – Lazio, Italy). In addition, the efficiency of specific in situ hybridization techniques (Fluorescence In Situ Hybridization with fluorescently monolabeled probes – FISH; Fluorescence In Situ Hybridization with signal amplification by Catalyzed Reporter Deposition – CARD-FISH) was tested with regards to the different physicochemical characteristics of selected sediments (i.e. sediment organic matter and moisture content). In this respect, CARD-FISH protocol was improved to better estimate the occurrence of specific phylogenetic clusters in dry sediments. For the field study, sediments were regularly collected at the river outlet section of the River Mulargia (Sardinia, Italy). A seasonal in-depth study was performed for benthic bacterial composition and activity analyses. Additional tests were performed in artificial microcosms to experimentally describe benthic bacterial responses to drying and rewetting processes, by simulating desiccation and re-inundation of sediments collected from four European temporary rivers (River Mulargia and Tagliamento - Italy; River Krathis - Greece; River Pardiela - Portugal). In a further laboratory experiment, the composition and activity of the bacterial community that primary colonized the water phase was followed in microcosms set up with Mulargia sediments. This study could contribute to better understand the ecological role of those benthic microbes that reside in a state of low-activity in dry sediments and promptly colonize the new incoming water at the end of the dry period. In synthesis, my Doctorate research contributed to a better understanding of the functional role of bacterial community in river sediments. The results could help to elucidate the mechanisms involved in the sediment transformation processes during drought periods, which are attended to increase in length and frequency as a possible effect of climatic changes.