*3.3. Prokaryotic Abundance, Biomass, and Diversity*

The prokaryotic abundance, biomass, richness of OTU, and OTU composition are illustrated in Figure 3A–D. The results of PERMANOVA tests reveal a significant effect of theinteractionStation × Season on the prokaryotic abundance, biomass, and OTU composition (Table S2A). Both in summer and winter, the prokaryotic abundance and biomass were the highest at the lagoon (Gorino and Giralda) and sea (Cesenatico) stations. At all stations, with exceptions for the Delta and sea stations, the prokaryotic abundance and biomass were higher in winter than in summer. The richness of prokaryotic OTU was highest at the Po River station in summer and at the Gorino Lagoon station in winter. At all stations, except for the Oglio and Po River and lagoon Delta stations, the richness of prokaryotic OTU was higher in winter than in summer (Figure 3C). The bi-plot produced after the CAP confirms the presence of strong spatial and temporal variations in the OTU composition of prokaryotic assemblages (Figure 3D).

#### *3.4. Meiofaunal Abundance, Richness of Taxa, and Community Structure*

The meiofaunal abundance, biomass, richness of taxa, and taxonomic composition are reported in Figure 4A–D. The results of two-way PERMANOVA tests reveal a significant effect of the interaction Station × Season on the meiofaunal abundance, biomass, and taxonomic composition (Table S2B). The results of the pair wise tests (Table S2B) reveal that both the meiofaunal abundance and biomass varied significantly among stations in both seasons and between seasons at almost all sampling stations. Specifically, the highest meiofaunal abundance and biomass occurred at lagoon stations in both seasons (Giralda in summer and Gorino and Giralda in winter). At the Po River and Delta lagoon stations, the meiofaunal abundance was higher in summer than in winter, whereas at the Gorino Lagoon (Gorino) and marine (Cesenatico) stations, values were the highest in winter. At the Delta lagoon station, the meiofaunal biomass was higher in summer than in winter, whereas at sea (Cesenatico), the highest values occurred in winter.

The richness of meiofaunal taxa did not display significant differences among sampling stations, or between seasons (Table S2B). At all stations and in both seasons, the meiofaunal community was dominated by nematodes (51–98%), followed by copepods (1–22%). "Other" taxa included Bivalvia, Kinorhyncha, Cumacea, Isopoda, Nemertea, Platelminta, Tunicata, and Gnatostomulida, each accounting for <1% of the total meiofaunal abundance.

The results of the multivariate PERMANOVA tests reveal a significant effect of the factors Station and Station × Season on the meiofaunal taxonomic composition (Table S2B). Specifically, the results of the pair wise tests show that the meiofaunal taxonomic composition varied significantly among sampling stations in both seasons and between seasons at four of six sampling stations (Po, Gorino, Delta, and Cesenatico). The bi-plot produced after the CAP analysis confirms the presence of strong spatial and temporal variations in the meiofaunal taxonomic composition (Figure 4D).

SIMPER analysis (Table 2) revealed that the % dissimilarity among different systems was 50–76% in summer and 64–80% in winter, and that the observed % was mainly due to the higher contribution of nematodes in the lagoon community structure and to the absence/reduction of the other taxa, in both seasons.


**Table 2.** Output of SIMPER analysis (cut off 90%), testing for % dissimilarity among systems in each season and between seasons in each system.

The % dissimilarity between summer and winter was lowest at sea (31%) and highest in river (38%) systems, and such differences were driven by different sets of taxa, depending on the system.
