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Additional file 1: Table S1. Investigated sites and selected geographic features. Table S2a. Parameters thresholds and scores assigned for LIMeco calculation (Buffagni et al., 2008; DM 260/2010). Table S2b. Thresholds for LIMeco classification. Table S3. Summary statistics for the selection of the AP solution and number of groups. Material S4. Association between environmental, physicochemical and anthropogenic variables and PCoA axes. Material S5. Complete results of BDM and Dunn’s tests. Table S6. Mean values of selected variables in exemplar sites of Affinity Propagation (AP) clusters . Material S7. Variability of atmospheric deposition rates of inorganic nitrogen ordered by increasing yearly rain amount 200.

Despite the enormous efforts made in recent years to face the problems relating to the alteration of nutrient cycles, both in scientific and management terms, we are still far from effective resolutions and fluxes of nitrogen (N) and phosphorus (P) through river basins continue to be very high. In Europe, the achievement of good ecological status, required by the WFD before 2015, necessitates rapid uptake of effective and verifiable measures to reduce nutrient loading to surface waters and groundwater. Over the last decade there has been increasing evidence that biogeochemical processes occurring naturally in portions of the river ecosystem (buffer strips) and / or in the riverbed where are able to modulate the concentrations of nutrients exported downstream. For these reasons, within INHABIT project, we performed an investigation aimed to deepen the knowledge of the factors controlling the transformations of nutrients in river systems, with particular attention to the hydro-morphological features and habitats. Some nutrient retention metrics have been estimated through experiments of nutrient additions in some selected river sites in Sardinia and Piedmont (Italy).The results highlight the importance of the areas of "transient storage" (As) in regulating the efficiency of NH4 and PO4 retention, expressed by the values of "uptake length" in both regions. Moreover we observed a highly significant relationship between As (normalized for the river section) and the ratio between the width and the depth (w/d) of the channel, after having separated the river stretches in natural and resectioned channels.

We analysed a large number of concurrent samples of macroinvertebrate communities and chemical indicators of eutrophication and organic pollution [total-P, total-N, NH4-N, biological oxygen demand (BOD5)] from 594 Danish stream sites. Samples were taken over an 11-year time span as part of the Danish monitoring programme on the aquatic environment. Macroinvertebrate communities were sampled in spring using a standardised kick-sampling procedure whereas chemical variables were sampled six to 24 times per year per site. Habitat variables were assessed once when macroinvertebrates were sampled. The plecopteran Leuctra showed a significant negative exponential relationship (r2 = 0.90) with BOD5 and occurred at only 16% of the sites with BOD5 above 1.6 mg L-1. Sharp declines with increasing BOD5 levels were found for the trichopteran families Sericostomatidae and Glossosomatidae although they appeared to be slightly less sensitive than Leuctra. Other plecopterans such as Isoperla showed a similar type of response curve to Leuctra (negative exponential) but occurred at sites with relatively high concentrations of BOD5 up to 3-4 mg L-1. In contrast, the response curve of the isopod Asellus aquaticus followed a saturation function reaching a plateau above 3-4 mg L-1 BOD5 and the dipteran Chironomus showed an exponential increase in occurrence with increasing BOD5 concentration. Macroinvertebrate occurrence appeared to be related primarily to concentrations of BOD5, NH4-N and total-P whereas there were almost no relationships to total-N. Occurrence of a number of taxa showed a stronger relationship to habitat conditions (width and substrate) than chemical variables. Important macroinvertebrate taxa are reduced at concentrations of BOD5 that are normally perceived as indicating unimpacted stream site conditions. Our results confirmed sensitivity/tolerance patterns used by existing bioassessment systems only to some degree.