Alpha and beta diversity
Here we studied three microeukaryotic groups: Nematoda ,Foraminifera , and Ciliophora and rarefaction analyses showed that the majority of the genera had been detected in the samples (Supplementary Figure 1). The species richness Chao1 index was lower forNematoda and Foraminifera at the High OC stations compared to Low OC (One-Way ANOVA test for each group; Nematoda ,F (1,19) = 32.7, P = 0.000016;Foraminifera , F (1,19) = 57.0, P = 0.0000004; Figure 2a-b). No difference in species richness was observed for Ciliophora (Figure 2c). Shannon’s H alpha diversity index was also significantly lower for Nematoda and Foraminifera at the High OC stations when compared to Low OC (One-Way ANOVA test for each group; Nematoda , F (1,19) = 24.8,P = 0.000083; Foraminifera , F (1,19)= 48.2, P = 0.000001; Figure 2d-e). No difference in Shannon’s H alpha diversity index was observed for Ciliophora (Figure 2f). A full list of Shannon’s H values is available in Supplementary Data 3.
Beta diversity was also significantly different between stations for all three groups, with the presence/absence Sørensen index test (PERMANOVA (9999 permutations) test for each group, Nematoda , pseudoF = 4.9, P = 0.0001; Foraminifera , pseudo F= 10.5, P = 0.0001; Ciliophora , pseudo F = 3.1,P = 0.0001; Figure 3). Similarly, there was a difference in beta diversity when testing the stations grouped as Low OC against High OC (PERMANOVA (9999 permutations) test for each group, Nematoda , pseudo F = 11.4, P = 0.0001; Foraminifera , pseudoF = 25.5, P = 0.0001; Ciliophora , pseudo F = 5.1, P = 0.0001; Figure 3).
CCAs based on the relative abundance of genera showed that the measured abiotic variables (water depth, sediment % C and % N, plus pore water NH4+ and PO43-) were associated with the High OC stations for all of the three studied taxonomic groups, i.e.Nematoda , Foraminifera , and Ciliophora (Figure 4). The CCA analysis showed that 67 %, 77 % and 66 % of the total constrained inertia for nematodes, foraminifera and ciliophoran, respectively, was explained with the five environmental variables here studied. There was also a significant association between all five abiotic variables and the community composition for each studied group (PERMANOVA test (9999 permutations), Nematoda ,R2 = 0.76–0.83, P < 0.001;Foraminifera , R2 = 0.52–0.94, P< 0.05; Ciliophora , R2 = 0.53–0.85, P < 0.01; Supplementary Data 4).