Microbial pathways when passing from lotic to lentic environments

Carbon and energy budgets in inland waters (i.e. rivers, lakes and reservoirs) are dominated by processes associated with detrital organic matter, and mediated by microbes. Microbial degradation of dissolved and particulate organic matter and the ensuing detritus based food webs are critical to ecosystem functioning and affect the overall ecology of freshwater systems. In flowing waters, microbial attached communities (biofilms) constitute the major component for the uptake, storage and cycling of carbon, nutrients and anthropogenic contaminants. When passing from lotic to lentic environment (i.e., lakes inflow, river hydrological fragmentation by drought; river segmentation and disruption by dams) the altered hydrological and biogeochemical conditions and the changes in the suspended particle and bedload transport, lead to the accumulation of sediments in absence of dissolved O2, with the possible depletion of oxidized solutes. While microbial degradation of organic matter in sediments at aerobic conditions mainly produces CO2, anaerobic pathways, e.g. in freshwater sediments, also produce CH4. The challenge is to understand the destiny of these greenhouse gases (GHG) and to provide an analysis of the factors regulating CH4 emissions and emission pathways in these systems. In this context, here we present results from different Mediterranean catchments and we discuss how the biogeochemical vertical structure renders a meromictic lake a trap for geogenic CO2. Volcanic lakes are characterized by physicochemical favourable conditions for the development of reservoirs of C-bearing GHG and can be considered as model system to picture the destiny of greenhouse gases in lentic waters. By combining a microbiological and geochemical approach, we showed that the chemical and isotopic features of the CO2- and CH4-rich gas reservoir hosted within the meromictic Lake Averno are strictly related to the microbial niche differentiation along the vertical water column. The simultaneous occurrence of diverse functional groups of microbes operating under different conditions suggests that these habitats harbour complex microbial consortia that strongly impact on the production and consumption of GHG. In the epilimnion, the activity of aerobic methanotrophic bacteria and photosynthetic biota, together with CO2 dissolution at relatively high pH, enhanced CO2- and CH4 consumption. Overall the lake acts as a sink for the CO2, displaying a significant influence on the local carbon budget.