## 3 Results
### Pelagic Part of the Ecosystem
#### 3.2.2 Zooplankton  
The multivariate CAP analysis showed that the zooplankton community structure was influenced by: warming (F1,31 = 4.91, \(p\) = 0.002), HBCDD addition (F1,31 = 2.65, \(p\) = 0.035), PO4 concentrations (F1,31 = 7.88, \(p\) = 0.001), chlorophyll a concentrations (F1,31 = 4.09, \(p\) = 0.009), and the abundance of _Melosira_ sp. (F1,31 = 3.72, \(p\) = 0.008; Figure 6). Overall, the warm treatments were characterized by bivalve larvae, copep nauplii, and _Acartia bifilosa_ (Figures 6 and 7b,d,e), and differences between the warm and ambient treatments were driven mainly by higher chlorophyll a values, while the main driving factors in ambient treatments were total N and _Melosira_ sp. abundance (Figure 6). However, the relative abundance of these taxa varied with time point (Figure 7, Tables S6-S9). Overall, across all time and temperature treatments, HBCDD treatments were characterized by higher numbers of rotifers, bivalve larvae, gastropod larvae, and _A. bifilosa_, and lower numbers of copep nauplii (Figure 7, Table S5).  
Figure 3: (**a**) Total N (sum of NO2\({}^{-}\), NO3\({}^{-}\), and NH4\({}^{+}\)); (**b**) PO4 concentration in the water at t1, t6, and t13. Values are means and SE of each treatment; \(n\) = 5, except for t6 W\(-\) where \(n\) = 4.  
Figure 4: CAP (constrained analysis of principle coordinates) biplot, based on the phytoplankton community matrix, and constrained by time, where each symbol represents each cosm with the individual treatment. The centroids are ambient (A) and warm (W) temperature treatments, also indicated by different colors. The arrows represent the different predictor variables and point into the direction of increasing value. The species shown represent the taxa that contribute 70% to the dissimilarity identified in the similarity percentages (SIMPER) analysis (Tables S1–S3).  
Figure 5: Time series of (**a**) average chlorophyll a concentrations in \(\mu\)g L\({}^{-1}\) (\(\pm\) standard error (SE)) (\(n=5\), except t6 A\(-\) where \(n=4\)); (**b**) average density of _Dolichosperm_ heterocysts (\(\pm\)SE); (**c**) average cell density of _Pyamimonas_ species (\(\pm\)SE); (**d**) average density of _Dolichosperm_ filaments (\(\pm\)SE); (**e**) average cell density of centric diatom species (\(\pm\)SE); (**f**) average cell density of _Melosira_ species (\(\pm\)SE). For phytoplankton graphs: \(n=5\), except for t6 W\(-\) where \(n=6\) and t6 W+ where \(n=3\). The taxa shown are those identified in the SIMPER analysis as together contributing to 70% of the dissimilarity between treatments/times (Tables S1–S3).  
Figure 6: CAP biplot based on the zooplankton community matrix, and constrained by time, where each symbol represents each cosm with the individual treatment. The arrows represent the different predictor variables and point in the direction of increasing value of each variable and their lengths indicate their relative importance. The centroids displayed are ambient (A) and warm (W) temperature treatments, which were based on a higher significance of the temperature effect compared to the HBCDD effect. The species shown represent the taxa that contribute 70% to the dissimilarity identified in the SIMPER analysis (Tables S4–S9).  
Figure 7: Time series of individuals per L (**a**) Rotifera (\(\pm\)SE); **(b)** Bivalvia larvae (\(\pm\)SE); **(c)** Gastropoda larvae (\(\pm\)SE); **(d)** Copepoda naupli (\(\pm\)SE); **(e)**_Acartia bifilosa_ (\(\pm\)SE); **(f)**_Eurytemora affinis_ (\(\pm\)SE). \(n\) = 5, except for t13 W+ where \(n\) = 3. The taxa shown are those identified in the SIMPER analysis as together contributing to 70% of the dissimilarity between treatments/times (Tables S4–S9).