## S1-3 Zooplankton

<figure><img src="image_15.png" /><figcaption>Figure S1-8: Percentage of variance explained by each eigenvector of the PCA of the zooplankton composition.</figcaption></figure>

<table><caption>Table S1-4: Contributions of zooplankton taxa (%) to the main eigenvectors.</caption><thead><tr><th></th><th>Dim 1</th><th>Dim 2</th><th>Dim 3</th><th>Dim 4</th></tr></thead><tbody><tr><td>Small clado.</td><td>41</td><td>12.4</td><td>10.3</td><td>36.3</td></tr><tr><td>Copepods</td><td>5.5</td><td>49.3</td><td>26.3</td><td>18.9</td></tr><tr><td>Chaoborus</td><td>36.3</td><td>17.3</td><td>12.3</td><td>34.1</td></tr><tr><td>Rotifers</td><td>17.2</td><td>21</td><td>51.1</td><td>10.7</td></tr></tbody></table>

<figure><img src="image_16.png" /><figcaption>Figure S1-9: Response of the three main aggregated groups of zooplankton. A) Cladocera (Chydoridae and Bosminiae), B) Copepods (adults and nauplii), C) Chaoborus (large Diptera larvae) and D) rotifers (Lecanes, Lepadella, Bdelloid, Polyarthra, Brachionus, Hexarthra and Anuraepsis), Keratella were not included because of their strong variance.</figcaption></figure>
<table><caption>Table S1-8: Significance (p-values) of treatments on zooplankton taxa abundance. Each subpart corresponds respectively to data at the genus level aggregated for dates, data at the genus level analysed independently for the two dates and aggregated genus analysed independently for the two dates.</caption><thead><tr><th></th><th>Taxa</th><th>Fish (F)</th><th>Light (L)</th><th>OM</th><th>F:L</th><th>F:OM</th><th>L:OM</th><th>F:L:OM</th></tr></thead><tbody><tr><td rowspan="4">global</td><td>Copepoda</td><td>0.34</td><td><strong>0.037</strong></td><td>0.68</td><td>0.81</td><td>0.28</td><td>0.95</td><td>0.28</td></tr><tr><td>Cladocera</td><td><strong>10<sup>-8</sup></strong></td><td>0.072</td><td>0.078</td><td>0.52</td><td>0.39</td><td><strong>0.039</strong></td><td>0.80</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Rotifer</td><td>0.98</td><td>0.85</td><td>0.18</td><td>0.83</td><td>0.87</td><td>0.39</td><td>0.51</td></tr><tr><td rowspan="4">19/08</td><td>Copepods</td><td><strong>0.0009</strong></td><td>0.26</td><td>0.67</td><td>0.81</td><td>0.80</td><td>0.46</td><td>0.92</td></tr><tr><td>Chladocerans</td><td><strong>10<sup>-5</sup></strong></td><td>0.36</td><td>0.76</td><td>0.56</td><td>0.77</td><td>0.022</td><td>0.93</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Rotifers</td><td>0.81</td><td>0.89</td><td>0.97</td><td>0.36</td><td>0.51</td><td>0.37</td><td>0.50</td></tr><tr><td rowspan="4">25/09</td><td>Copepoda</td><td>0.41</td><td>0.11</td><td>0.7</td><td>0.72</td><td>0.22</td><td>0.50</td><td>0.093</td></tr><tr><td>Chladocera</td><td><strong>10<sup>-5</sup></strong></td><td>0.11</td><td><strong>0.05</strong></td><td>0.70</td><td>0.48</td><td>0.41</td><td>0.78</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Rotifers</td><td>0.74</td><td>0.70</td><td><strong>0.046</strong></td><td>0.24</td><td>0.44</td><td>0.89</td><td>0.38</td></tr><tr><td rowspan="10">global</td><td>Cyclopidae</td><td><strong>0.014</strong></td><td>0.053</td><td>0.79</td><td>0.69</td><td>0.13</td><td>0.25</td><td>0.51</td></tr><tr><td>Nauplii</td><td>0.60</td><td>0.052</td><td>0.61</td><td>0.75</td><td>0.11</td><td>0.84</td><td>0.32</td></tr><tr><td>Chydoridae</td><td><strong>10<sup>-8</sup></strong></td><td>0.11</td><td>0.11</td><td>0.51</td><td>0.42</td><td>0.055</td><td>0.83</td></tr><tr><td>Lecane</td><td><strong>0.033</strong></td><td>0.73</td><td>0.20</td><td>0.75</td><td>0.79</td><td>0.64</td><td>0.77</td></tr><tr><td>Lepadella</td><td>0.28</td><td>0.62</td><td>0.84</td><td>0.22</td><td>0.25</td><td><strong>0.030</strong></td><td><strong>0.0051</strong></td></tr><tr><td>Bdelloide</td><td><strong>0.0083</strong></td><td>0.40</td><td><strong>0.011</strong></td><td>0.59</td><td>0.55</td><td>0.12</td><td>0.38</td></tr><tr><td>Polyarthra</td><td><strong>0.0055</strong></td><td>0.50</td><td>0.80</td><td>0.79</td><td>0.76</td><td><strong>0.023</strong></td><td>0.25</td></tr><tr><td>Keratella</td><td><strong>10<sup>-8</sup></strong></td><td>0.19</td><td><strong>0.015</strong></td><td>0.98</td><td>0.91</td><td>0.36</td><td>0.90</td></tr><tr><td>Brachionus</td><td>0.47</td><td>0.076</td><td><strong>0.0038</strong></td><td><strong>0.045</strong></td><td>0.38</td><td>0.60</td><td>0.10</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td rowspan="10">19/08</td><td>Cyclopidae</td><td><strong>0.0012</strong></td><td>0.16</td><td>0.13</td><td>0.69</td><td>0.36</td><td>0.43</td><td>0.58</td></tr><tr><td>Nauplii</td><td><strong>0.0021</strong></td><td>0.34</td><td>0.41</td><td>0.86</td><td>0.93</td><td>0.52</td><td>0.82</td></tr><tr><td>Chydoridae</td><td><strong>10<sup>-5</sup></strong></td><td>0.36</td><td>0.76</td><td>0.56</td><td>0.77</td><td><strong>0.022</strong></td><td>0.93</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Lecane</td><td>0.054</td><td>0.15</td><td>0.33</td><td>0.97</td><td>0.81</td><td>0.67</td><td>0.93</td></tr><tr><td>Lepadella</td><td>0.29</td><td>0.91</td><td>0.93</td><td>0.36</td><td>0.43</td><td>0.066</td><td><strong>0.034</strong></td></tr><tr><td>Bdelloide</td><td><strong>0.033</strong></td><td>0.72</td><td>0.85</td><td>0.79</td><td>0.55</td><td>0.45</td><td>0.062</td></tr><tr><td>Polyarthra</td><td><strong>0.017</strong></td><td>0.087</td><td>0.23</td><td>0.82</td><td>0.76</td><td>0.32</td><td>0.23</td></tr><tr><td>Keratella</td><td><strong>0.0005</strong></td><td>0.68</td><td>0.16</td><td>0.99</td><td>0.43</td><td>0.061</td><td>0.12</td></tr><tr><td>Brachionus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td rowspan="10">25/09</td><td>Cyclopidae</td><td>0.40</td><td>0.20</td><td>0.56</td><td>0.74</td><td>0.35</td><td>0.070</td><td>0.41</td></tr><tr><td>Nauplii</td><td>0.28</td><td>0.12</td><td>0.77</td><td>0.57</td><td>0.094</td><td>0.78</td><td>0.098</td></tr><tr><td>Chydoridae</td><td><strong>10<sup>-5</sup></strong></td><td>0.18</td><td>0.085</td><td>0.69</td><td>0.53</td><td>0.50</td><td>0.81</td></tr><tr><td>Bosmine</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Lecane</td><td><strong>0.0001</strong></td><td>0.30</td><td>0.81</td><td>0.26</td><td>0.64</td><td>0.17</td><td>0.42</td></tr><tr><td>Lepadella</td><td>0.66</td><td>0.055</td><td>0.51</td><td>0.81</td><td>0.30</td><td>0.70</td><td>0.11</td></tr><tr><td>Bdelloide</td><td><strong>0.044</strong></td><td>0.42</td><td><strong>0.029</strong></td><td>0.66</td><td>0.64</td><td>0.26</td><td>0.52</td></tr><tr><td>Polyarthra</td><td>0.12</td><td><strong>0.0050</strong></td><td><strong>0.0046</strong></td><td>0.89</td><td>0.66</td><td>0.59</td><td>0.95</td></tr><tr><td>Keratella</td><td><strong>10<sup>-5</sup></strong></td><td>0.36</td><td>0.087</td><td>0.99</td><td>0.93</td><td>0.53</td><td>0.93</td></tr><tr><td>Brachionus</td><td>0.61</td><td>0.21</td><td><strong>0.042</strong></td><td>0.17</td><td>0.55</td><td>0.72</td><td>0.26</td></tr><tr><td>Anuraeopsis</td><td><strong>0.037</strong></td><td>0.65</td><td>0.66</td><td>0.10</td><td>0.25</td><td>0.19</td><td>0.85</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr></tbody></table>
<figure><img src="image_17.png" /><figcaption>Figure S1-10: Zooplankton numeration of large zooplankton from 24 L samples. A) Cyclopidea (large Copepoda) B) Nauplii (Copepoda juveniles) and C) Chydoridae (small Cladocera).</figcaption></figure>

<figure><img src="image_18.png" /><figcaption>Figure S1-11: Zooplankton numeration of small rotifers from 24 L samples. A) Lecane B) Lepadella and C) Bdelloide.</figcaption></figure>

<figure><img src="image_19.png" /><figcaption>Figure S1-12: Zooplankton numeration of large rotifers from 24 L samples. A) Polyarthra, B) Keratella, C) Brachionus and D) Anuraeopsis.</figcaption></figure>
<figure><img src="image_17.png" /><figcaption>Figure S1-11: Zooplankton numeration of small rotifers from 24 L samples A) Lecane B) Lepadella and C) Bdelloid.</figcaption></figure>

<figure><img src="image_18.png" /><figcaption>Figure S1-12: Zooplankton numeration of large rotifers from 24 L samples A) Polyarthra, B) Keratella, C) Brachionus and D) Anuraeopsis.</figcaption></figure>
<table><caption>Table S1-5: Significance (p-values) of treatments on zooplankton taxa abundance. Each subpart corresponds to data aggregated for dates (global vs specific dates) and/or genius (e.g. Cyclopidae, Nauplii vs Copepoda).</caption><thead><tr><th></th><th>Taxa</th><th>Fish (F)</th><th>Light (L)</th><th>OM</th><th>F:L</th><th>F:OM</th><th>L:OM</th><th>F:L:OM</th></tr></thead><tbody><tr><td rowspan="4">global</td><td>Copepoda</td><td>0.34</td><td><strong>0.037</strong></td><td>0.68</td><td>0.81</td><td>0.28</td><td>0.95</td><td>0.28</td></tr><tr><td>Cladocera</td><td><strong>10<sup>-8</sup></strong></td><td>0.072</td><td>0.078</td><td>0.52</td><td>0.39</td><td><strong>0.039</strong></td><td>0.80</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Rotifer</td><td>0.98</td><td>0.85</td><td>0.18</td><td>0.83</td><td>0.87</td><td>0.39</td><td>0.51</td></tr><tr><td rowspan="4">19/08</td><td>Copepods</td><td><strong>0.0009</strong></td><td>0.26</td><td>0.67</td><td>0.81</td><td>0.80</td><td>0.46</td><td>0.92</td></tr><tr><td>Chladocerans</td><td><strong>10<sup>-5</sup></strong></td><td>0.36</td><td>0.76</td><td>0.56</td><td>0.77</td><td>0.022</td><td>0.93</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Rotifers</td><td>0.81</td><td>0.89</td><td>0.97</td><td>0.36</td><td>0.51</td><td>0.37</td><td>0.50</td></tr><tr><td rowspan="4">25/09</td><td>Copepoda</td><td>0.41</td><td>0.11</td><td>0.7</td><td>0.72</td><td>0.22</td><td>0.50</td><td>0.093</td></tr><tr><td>Chladocera</td><td><strong>10<sup>-5</sup></strong></td><td>0.11</td><td><strong>0.05</strong></td><td>0.70</td><td>0.48</td><td>0.41</td><td>0.78</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Rotifers</td><td>0.74</td><td>0.70</td><td><strong>0.046</strong></td><td>0.24</td><td>0.44</td><td>0.89</td><td>0.38</td></tr><tr><td rowspan="14">global</td><td>Cyclopidae</td><td><strong>0.014</strong></td><td>0.053</td><td>0.79</td><td>0.69</td><td>0.13</td><td>0.25</td><td>0.51</td></tr><tr><td>Nauplii</td><td>0.60</td><td>0.052</td><td>0.61</td><td>0.75</td><td>0.11</td><td>0.84</td><td>0.32</td></tr><tr><td>Chydoridae</td><td><strong>10<sup>-8</sup></strong></td><td>0.11</td><td>0.11</td><td>0.51</td><td>0.42</td><td>0.055</td><td>0.83</td></tr><tr><td>Lecane</td><td><strong>0.033</strong></td><td>0.73</td><td>0.20</td><td>0.75</td><td>0.79</td><td>0.64</td><td>0.77</td></tr><tr><td>Lepadella</td><td>0.28</td><td>0.62</td><td>0.84</td><td>0.22</td><td>0.25</td><td><strong>0.030</strong></td><td><strong>0.0051</strong></td></tr><tr><td>Bdelloide</td><td><strong>0.0083</strong></td><td>0.40</td><td><strong>0.011</strong></td><td>0.59</td><td>0.55</td><td>0.12</td><td>0.38</td></tr><tr><td>Polyarthra</td><td><strong>0.0055</strong></td><td>0.50</td><td>0.80</td><td>0.79</td><td>0.76</td><td><strong>0.023</strong></td><td>0.25</td></tr><tr><td>Keratella</td><td><strong>10<sup>-8</sup></strong></td><td>0.19</td><td><strong>0.015</strong></td><td>0.98</td><td>0.91</td><td>0.36</td><td>0.90</td></tr><tr><td>Brachionus</td><td>0.47</td><td>0.076</td><td><strong>0.0038</strong></td><td><strong>0.045</strong></td><td>0.38</td><td>0.60</td><td>0.10</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td rowspan="10">19/08</td><td>Cyclopidae</td><td><strong>0.0012</strong></td><td>0.16</td><td>0.13</td><td>0.69</td><td>0.36</td><td>0.43</td><td>0.58</td></tr><tr><td>Nauplii</td><td><strong>0.0021</strong></td><td>0.34</td><td>0.41</td><td>0.86</td><td>0.93</td><td>0.52</td><td>0.82</td></tr><tr><td>Chydoridae</td><td><strong>10<sup>-5</sup></strong></td><td>0.36</td><td>0.76</td><td>0.56</td><td>0.77</td><td><strong>0.022</strong></td><td>0.93</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Lecane</td><td>0.054</td><td>0.15</td><td>0.33</td><td>0.97</td><td>0.81</td><td>0.67</td><td>0.93</td></tr><tr><td>Lepadella</td><td>0.29</td><td>0.91</td><td>0.93</td><td>0.36</td><td>0.43</td><td>0.066</td><td><strong>0.034</strong></td></tr><tr><td>Bdelloide</td><td><strong>0.033</strong></td><td>0.72</td><td>0.85</td><td>0.79</td><td>0.55</td><td>0.45</td><td>0.062</td></tr><tr><td>Polyarthra</td><td><strong>0.017</strong></td><td>0.087</td><td>0.23</td><td>0.82</td><td>0.76</td><td>0.32</td><td>0.23</td></tr><tr><td>Keratella</td><td><strong>0.0005</strong></td><td>0.68</td><td>0.16</td><td>0.99</td><td>0.43</td><td>0.061</td><td>0.12</td></tr><tr><td>Brachionus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td rowspan="10">25/09</td><td>Cyclopidae</td><td>0.40</td><td>0.20</td><td>0.56</td><td>0.74</td><td>0.35</td><td>0.070</td><td>0.41</td></tr><tr><td>Nauplii</td><td>0.28</td><td>0.12</td><td>0.77</td><td>0.57</td><td>0.094</td><td>0.78</td><td>0.098</td></tr><tr><td>Chydoridae</td><td><strong>10<sup>-5</sup></strong></td><td>0.18</td><td>0.085</td><td>0.69</td><td>0.53</td><td>0.50</td><td>0.81</td></tr><tr><td>Bosmine</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr><tr><td>Lecane</td><td><strong>0.0001</strong></td><td>0.30</td><td>0.81</td><td>0.26</td><td>0.64</td><td>0.17</td><td>0.42</td></tr><tr><td>Lepadella</td><td>0.66</td><td>0.055</td><td>0.51</td><td>0.81</td><td>0.30</td><td>0.70</td><td>0.11</td></tr><tr><td>Bdelloide</td><td><strong>0.044</strong></td><td>0.42</td><td><strong>0.029</strong></td><td>0.66</td><td>0.64</td><td>0.26</td><td>0.52</td></tr><tr><td>Polyarthra</td><td>0.12</td><td><strong>0.0050</strong></td><td><strong>0.0046</strong></td><td>0.89</td><td>0.66</td><td>0.59</td><td>0.95</td></tr><tr><td>Keratella</td><td><strong>10<sup>-5</sup></strong></td><td>0.36</td><td>0.087</td><td>0.99</td><td>0.93</td><td>0.53</td><td>0.93</td></tr><tr><td>Brachionus</td><td>0.61</td><td>0.21</td><td><strong>0.042</strong></td><td>0.17</td><td>0.55</td><td>0.72</td><td>0.26</td></tr><tr><td>Anuraeopsis</td><td><strong>0.037</strong></td><td>0.65</td><td>0.66</td><td>0.10</td><td>0.25</td><td>0.19</td><td>0.85</td></tr><tr><td>Chaoborus</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td><td>-</td></tr></tbody></table>

In the following, we present zooplankton counting at the genus level. We aggregated the two dates or treated them as independent data sets to test the robustness of the effects of our treatments over time. When dates were aggregated, sampling date was included in the model.

Copepods were positively affected by light exposure when Cyclopidae and nauplii were aggregated over the two sampling dates (+0.55 ± 0.27 (Log individuals per 24L), Table S1-5). However, we only see a positive effect of fish in August sampling (Fig. S1-9A and Fig. S1-10A and B) for aggregated and non-aggregated data and the light effect is not significant. Thus, fish had a positive effect on Copepoda at the beginning of the experiment but this effect vanished later, while the positive effect of fish on
S1-4 Functional diversity of heterotrophic prokaryotes, Ecoplates™

<table><caption>Table S1-9: Significance (p-values) of treatments on the degradation capacity by heterotrophic prokaryotes of substrate families present in the EcoPlates™ Biolog.</caption><thead><tr><th>Variable</th><th></th><th>Fish (F)</th><th>Light (L)</th><th>OM</th><th>F:L</th><th>F:OM</th><th>L:OM</th><th>F:L:OM</th></tr></thead><tbody><tr><td rowspan="3">Amine</td><td>p-value</td><td>0.623</td><td>0.342</td><td>0.545</td><td>0.801</td><td>0.299</td><td>0.078</td><td>0.847</td></tr><tr><td>F</td><td>0.242</td><td>0.91</td><td>0.368</td><td>0.064</td><td>1.086</td><td>3.161</td><td>0.037</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Amino acids</td><td>p-value</td><td>0.158</td><td>0.134</td><td><strong>0.041</strong></td><td>0.8</td><td>0.184</td><td>0.896</td><td>0.733</td></tr><tr><td>F</td><td>2.005</td><td>2.259</td><td>4.211</td><td>0.064</td><td>1.771</td><td>0.017</td><td>0.117</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Carbohydrates</td><td>p-value</td><td>0.666</td><td>0.794</td><td>0.208</td><td>0.32</td><td>0.426</td><td>0.178</td><td>0.324</td></tr><tr><td>F</td><td>0.187</td><td>0.068</td><td>1.591</td><td>0.992</td><td>0.635</td><td>1.819</td><td>0.976</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Carboxylic acids</td><td>p-value</td><td>0.5</td><td><strong>0.012</strong></td><td>0.184</td><td>0.308</td><td>0.805</td><td>0.951</td><td>0.98</td></tr><tr><td>F</td><td>0.456</td><td>6.385</td><td>1.767</td><td>1.041</td><td>0.061</td><td>0.004</td><td>0.001</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Phenolic acids</td><td>p-value</td><td>0.75</td><td>0.394</td><td>0.788</td><td>0.862</td><td>0.997</td><td>0.511</td><td>0.821</td></tr><tr><td>F</td><td>0.102</td><td>0.731</td><td>0.072</td><td>0.03</td><td>0</td><td>0.434</td><td>0.051</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Polymer</td><td>p-value</td><td>0.58</td><td>0.174</td><td>0.17</td><td>0.558</td><td>0.248</td><td>0.213</td><td>0.169</td></tr><tr><td>F</td><td>0.307</td><td>1.855</td><td>1.89</td><td>0.345</td><td>1.342</td><td>1.557</td><td>1.905</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Amine</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.344</td><td>0.833</td><td>0.437</td><td><strong>0.05</strong></td><td>0.304</td><td>0.408</td></tr><tr><td>F</td><td>57.12</td><td>0.9</td><td>0.044</td><td>0.608</td><td>3.907</td><td>1.066</td><td>0.69</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Amino acids</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.367</td><td>0.089</td><td>0.303</td><td>0.102</td><td>0.539</td><td>0.581</td></tr><tr><td>F</td><td>76.61</td><td>0.815</td><td>2.903</td><td>1.064</td><td>2.688</td><td>0.378</td><td>0.305</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Carbohydrates</td><td>p-value</td><td><strong>&lt;.001</strong></td><td><strong>0.008</strong></td><td>0.41</td><td>0.156</td><td><strong>0.015</strong></td><td>0.977</td><td>0.243</td></tr><tr><td>F</td><td>13.94</td><td>7.096</td><td>0.679</td><td>2.014</td><td>5.988</td><td>0.001</td><td>1.363</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Carboxylic acids</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.564</td><td><strong>0.011</strong></td><td>0.552</td><td><strong>&lt;.001</strong></td><td>0.627</td><td>0.206</td></tr><tr><td>F</td><td>75.24</td><td>0.333</td><td>6.495</td><td>0.355</td><td>16.56</td><td>0.236</td><td>1.602</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Phenolic acids</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.125</td><td>0.176</td><td>0.706</td><td>0.073</td><td>0.579</td><td>0.207</td></tr><tr><td>F</td><td>41.06</td><td>2.379</td><td>1.853</td><td>0.143</td><td>3.274</td><td>0.31</td><td>1.605</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Polymer</td><td>p-value</td><td>0.401</td><td>0.205</td><td>0.2</td><td>0.526</td><td>0.053</td><td>0.631</td><td><strong>0.011</strong></td></tr><tr><td>F</td><td>0.707</td><td>1.613</td><td>1.653</td><td>0.403</td><td>3.774</td><td>0.231</td><td>6.624</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr></tbody></table>
Chydoridae (the only Cladocera in our experiments, except in one mesocosm) held at the two sampling dates (+2.26 ± 0.7 (Log individuals per 24L) Fig. S1-9B and Fig. S1-10C). Chaoborus (large Diptera larvae) were only present in enclosures without fish (Fig. S1-9C).

Rotifers were not affected by our treatments when the two sampling dates were aggregated (Fig. S1-9D). However, a significant effect of the addition of organic matter was observed in September. This effect was observed in September for Bdelloid (positive effect, Fig. S1-11C), Polyarthra (negative effect, Fig. S1-12A) and Brachionus (positive effect, Fig. S1-12C). Polyarthra were negatively affected by organic matter addition while full light exposure had a positive effect. Thus, Bdelloid and Brachionus can be associated to the brown food web while Polyarthra would be assimilated to the green food web. Fish had a negative effect on Bdelloid (Fig. S1-11C) and Polyarthra (Fig. S1-12A) and a positive effect on Keratella (Fig. S1-12B) in August. In September, the effect of fish on Bdelloid (Fig. S1-11C) and Keratella (Fig. S1-12B) was still visible. Anuraeopsis (Fig. S1-12D) and Lecane (Fig. S1-11A) were negatively affected by fish. Thus, except for Keratella, fish had a negative effect on many rotifer species.

## S1-4 Functional diversity of heterotrophic prokaryotes, Ecoplates™

<figure><img src="image_20.png" /></figure>

Figure S1-13: Optical density (OD) after 7 days for the different families of substrates after incubation of heterotrophic prokaryote samples from the pelagic or benthic compartments.

<figure><img src="image_21.png" /></figure>

Figure S1-14: Optical density after 7 days for: A) α-cyclodextrin, B) D-cellobiose and C) L-asparagine.
<figure><img src="image_19.png" /><figcaption>Figure S1-13: Optical density (OD) after 7 days for the different families of substrates after incubation of heterotrophic prokaryote samples from the pelagic or benthic compartments.</figcaption></figure>

<table><caption>Table S1-10: Significance (p-values) of treatments on the degradation capacity of α-cyclodextrine, D-cellobiose (two of the molecules used in the organic carbon addition treatment (OM)) and L-asparagine by heterotrophic prokaryotes.</caption><thead><tr><th>Variable</th><th></th><th>Fish (F)</th><th>Light (L)</th><th>OM</th><th>F:L</th><th>F:OM</th><th>L:OM</th><th>F:L:OM</th></tr></thead><tbody><tr><td rowspan="12">pelagic</td><td rowspan="3">α-cyclodextrine</td><td>p-value</td><td>0.055</td><td>0.323</td><td>0.924</td><td><strong>0.007</strong></td><td>0.886</td><td>0.654</td><td>0.125</td></tr><tr><td>F</td><td>3.807</td><td>0.992</td><td>0.009</td><td>7.714</td><td>0.021</td><td>0.203</td><td>2.419</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">D-cellobiose</td><td>p-value</td><td>0.633</td><td>0.789</td><td>0.764</td><td>0.031</td><td>0.278</td><td>0.373</td><td>0.137</td></tr><tr><td>F</td><td>0.23</td><td>0.072</td><td>0.091</td><td>4.859</td><td>1.198</td><td>0.806</td><td>2.273</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">L-asparagine</td><td>p-value</td><td>0.189</td><td>0.234</td><td>0.126</td><td><strong>&lt;.001</strong></td><td>0.846</td><td>0.79</td><td>0.95</td></tr><tr><td>F</td><td>1.759</td><td>1.447</td><td>2.404</td><td>32.48</td><td>0.038</td><td>0.071</td><td>0.004</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="12">benthic</td><td rowspan="3">α-cyclodextrine</td><td>p-value</td><td>0.294</td><td>0.777</td><td>0.959</td><td>0.475</td><td>0.444</td><td>0.492</td><td>0.096</td></tr><tr><td>F</td><td>1.122</td><td>0.081</td><td>0.003</td><td>0.517</td><td>0.594</td><td>0.477</td><td>2.852</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">D-cellobiose</td><td>p-value</td><td>0.477</td><td>0.251</td><td>0.751</td><td>0.243</td><td>0.236</td><td><strong>0.009</strong></td><td>0.303</td></tr><tr><td>F</td><td>0.512</td><td>1.341</td><td>0.102</td><td>1.388</td><td>1.428</td><td>7.36</td><td>1.077</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">L-asparagine</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.477</td><td>0.084</td><td>0.762</td><td>0.19</td><td>0.883</td><td>0.864</td></tr><tr><td>F</td><td>27.37</td><td>0.511</td><td>3.083</td><td>0.093</td><td>1.751</td><td>0.022</td><td>0.03</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr></tbody></table>
<table><caption>Table S1-6: Significance (p-values) of treatments on the degradation capacity by heterotrophic prokaryotes of substrate families present in the EcoPlates™ Biolog.</caption><thead><tr><th>Variable</th><th></th><th>Fish (F)</th><th>Light (L)</th><th>OM</th><th>F:L</th><th>F:OM</th><th>L:OM</th><th>F:L:OM</th></tr></thead><tbody><tr><td rowspan="3">Amine</td><td>p-value</td><td>0.623</td><td>0.342</td><td>0.545</td><td>0.801</td><td>0.299</td><td>0.078</td><td>0.847</td></tr><tr><td>F</td><td>0.242</td><td>0.91</td><td>0.368</td><td>0.064</td><td>1.086</td><td>3.161</td><td>0.037</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Amino acids</td><td>p-value</td><td>0.158</td><td>0.134</td><td><strong>0.041</strong></td><td>0.8</td><td>0.184</td><td>0.896</td><td>0.733</td></tr><tr><td>F</td><td>2.005</td><td>2.259</td><td>4.211</td><td>0.064</td><td>1.771</td><td>0.017</td><td>0.117</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Carbohydrates</td><td>p-value</td><td>0.666</td><td>0.794</td><td>0.208</td><td>0.32</td><td>0.426</td><td>0.178</td><td>0.324</td></tr><tr><td>F</td><td>0.187</td><td>0.068</td><td>1.591</td><td>0.992</td><td>0.635</td><td>1.819</td><td>0.976</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Carboxylic acids</td><td>p-value</td><td>0.5</td><td><strong>0.012</strong></td><td>0.184</td><td>0.308</td><td>0.805</td><td>0.951</td><td>0.98</td></tr><tr><td>F</td><td>0.456</td><td>6.385</td><td>1.767</td><td>1.041</td><td>0.061</td><td>0.004</td><td>0.001</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Phenolic acids</td><td>p-value</td><td>0.75</td><td>0.394</td><td>0.788</td><td>0.862</td><td>0.997</td><td>0.511</td><td>0.821</td></tr><tr><td>F</td><td>0.102</td><td>0.731</td><td>0.072</td><td>0.03</td><td>0</td><td>0.434</td><td>0.051</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Polymer</td><td>p-value</td><td>0.58</td><td>0.174</td><td>0.17</td><td>0.558</td><td>0.248</td><td>0.213</td><td>0.169</td></tr><tr><td>F</td><td>0.307</td><td>1.855</td><td>1.89</td><td>0.345</td><td>1.342</td><td>1.557</td><td>1.905</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Amine</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.344</td><td>0.833</td><td>0.437</td><td><strong>0.05</strong></td><td>0.304</td><td>0.408</td></tr><tr><td>F</td><td>57.12</td><td>0.9</td><td>0.044</td><td>0.608</td><td>3.907</td><td>1.066</td><td>0.69</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Amino acids</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.367</td><td>0.089</td><td>0.303</td><td>0.102</td><td>0.539</td><td>0.581</td></tr><tr><td>F</td><td>76.61</td><td>0.815</td><td>2.903</td><td>1.064</td><td>2.688</td><td>0.378</td><td>0.305</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Carbohydrates</td><td>p-value</td><td><strong>&lt;.001</strong></td><td><strong>0.008</strong></td><td>0.41</td><td>0.156</td><td><strong>0.015</strong></td><td>0.977</td><td>0.243</td></tr><tr><td>F</td><td>13.94</td><td>7.096</td><td>0.679</td><td>2.014</td><td>5.988</td><td>0.001</td><td>1.363</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Carboxylic acids</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.564</td><td><strong>0.011</strong></td><td>0.552</td><td><strong>&lt;.001</strong></td><td>0.627</td><td>0.206</td></tr><tr><td>F</td><td>75.24</td><td>0.333</td><td>6.495</td><td>0.355</td><td>16.56</td><td>0.236</td><td>1.602</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Phenolic acids</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.125</td><td>0.176</td><td>0.706</td><td>0.073</td><td>0.579</td><td>0.207</td></tr><tr><td>F</td><td>41.06</td><td>2.379</td><td>1.853</td><td>0.143</td><td>3.274</td><td>0.31</td><td>1.605</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">Polymer</td><td>p-value</td><td>0.401</td><td>0.205</td><td>0.2</td><td>0.526</td><td>0.053</td><td>0.631</td><td><strong>0.011</strong></td></tr><tr><td>F</td><td>0.707</td><td>1.613</td><td>1.653</td><td>0.403</td><td>3.774</td><td>0.231</td><td>6.624</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr></tbody></table>

As presented in Fig. 3C, fish had a strong negative effect on the degradation capacity of the substrates of the EcoPlates™ (Fig. S1-13). In addition, heterotrophic prokaryotes had a poor degradation capacity of the two recalcitrant molecules of our organic matter addition: α-cyclodextrin (Fig. S1-14A) and cellobiose (Fig. S1-14B), compared to asparagine (Fig. S1-14C) for instance. The degradability capacity for both molecules was not significantly affected by our organic matter addition treatment (Table S1-7), which might explain the weak general effects of our organic matter addition compared to previous studies (Faithfull et al., 2011; Degerman et al., 2018).
<figure><img src="image_20.png" /><figcaption>Figure S1-14: Optical density after 7 days for: A) α-cyclodextrin, B) D-cellobiose and C) L-asparagine.</figcaption></figure>

As presented in Fig. 3C, fish had a strong negative effect on the degradation capacity of the substrates of the EcoPlates™ (Fig. S1-13). In addition, heterotrophic prokaryotes had a poor degradation capacity of the two recalcitrant molecules of our organic matter addition: α-cyclodextrin (Fig. S1-14A) and cellobiose (Fig. S1-14B), compared to asparagine (Fig. S1-14C) for instance. The degradability capacity for both molecules was not significantly affected by our organic matter addition treatment (Table S1-10, which might explain the weak general effects of our organic matter addition compared to previous studies (Faithfull et al., 2011; Degerman et al., 2018).

## References

Degerman, R., Lefébure, R., Byström, P., Båmstedt, U., Larsson, S., & Andersson, A. (2018). Food web interactions determine energy transfer efficiency and top consumer responses to inputs of dissolved organic carbon. *Hydrobiologia*, *805*(1), 131–146. https://doi.org/10.1007/s10750-017-3298-9

Faithfull, C. L., Huss, M., Vrede, T., & Bergström, A.-K. (2011). Bottom-up carbon subsidies and top-down predation pressure interact to affect aquatic food web structure. *Oikos*, *120*(2), 311–320. https://doi.org/10.1111/j.1600-0706.2010.18683.x

Rock, A. M., Hall, M. R., Vanni, M. J., & González, M. J. (2016). Carnivore identity mediates the effects of light and nutrients on aquatic food-chain efficiency. *Freshwater Biology*, *61*(9), 1492–1508. https://doi.org/10.1111/fwb.12790

## S2 Supplementary methods

<figure><img src="image_21.png" /><figcaption>Figure S2-1: Experimental design consisting of three crossed treatments: light filtration (Light+ = no light filtration), soluble organic carbon addition (OM+ = carbon addition) and fish addition (Fish+ = fish addition). Each category of treatment combination is represented by a different colour and has four replicates, except for combinations with Fish+ that have five replicates.</figcaption></figure>
<table><caption>Table S1-7: Significance (p-values) of treatments on the degradation capacity of α-cyclodextrine, D-cellobiose (two of the molecules used in the organic carbon addition treatment (OM)) and L-asparagine by heterotrophic prokaryotes.</caption><thead><tr><th>Variable</th><th></th><th>Fish (F)</th><th>Light (L)</th><th>OM</th><th>F:L</th><th>F:OM</th><th>L:OM</th><th>F:L:OM</th></tr></thead><tbody><tr><td rowspan="12">pelagic</td><td rowspan="3">α-cyclodextrine</td><td>p-value</td><td>0.055</td><td>0.323</td><td>0.924</td><td><strong>0.007</strong></td><td>0.886</td><td>0.654</td><td>0.125</td></tr><tr><td>F</td><td>3.807</td><td>0.992</td><td>0.009</td><td>7.714</td><td>0.021</td><td>0.203</td><td>2.419</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">D-cellobiose</td><td>p-value</td><td>0.633</td><td>0.789</td><td>0.764</td><td>0.031</td><td>0.278</td><td>0.373</td><td>0.137</td></tr><tr><td>F</td><td>0.23</td><td>0.072</td><td>0.091</td><td>4.859</td><td>1.198</td><td>0.806</td><td>2.273</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">L-asparagine</td><td>p-value</td><td>0.189</td><td>0.234</td><td>0.126</td><td><strong>&lt;.001</strong></td><td>0.846</td><td>0.79</td><td>0.95</td></tr><tr><td>F</td><td>1.759</td><td>1.447</td><td>2.404</td><td>32.48</td><td>0.038</td><td>0.071</td><td>0.004</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="12">benthic</td><td rowspan="3">α-cyclodextrine</td><td>p-value</td><td>0.294</td><td>0.777</td><td>0.959</td><td>0.475</td><td>0.444</td><td>0.492</td><td>0.096</td></tr><tr><td>F</td><td>1.122</td><td>0.081</td><td>0.003</td><td>0.517</td><td>0.594</td><td>0.477</td><td>2.852</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">D-cellobiose</td><td>p-value</td><td>0.477</td><td>0.251</td><td>0.751</td><td>0.243</td><td>0.236</td><td><strong>0.009</strong></td><td>0.303</td></tr><tr><td>F</td><td>0.512</td><td>1.341</td><td>0.102</td><td>1.388</td><td>1.428</td><td>7.36</td><td>1.077</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr><tr><td rowspan="3">L-asparagine</td><td>p-value</td><td><strong>&lt;.001</strong></td><td>0.477</td><td>0.084</td><td>0.762</td><td>0.19</td><td>0.883</td><td>0.864</td></tr><tr><td>F</td><td>27.37</td><td>0.511</td><td>3.083</td><td>0.093</td><td>1.751</td><td>0.022</td><td>0.03</td></tr><tr><td>Df</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td><td>1</td></tr></tbody></table>

## References

Degerman, R., Lefébure, R., Byström, P., Båmstedt, U., Larsson, S., & Andersson, A. (2018). Food web interactions determine energy transfer efficiency and top consumer responses to inputs of dissolved organic carbon. *Hydrobiologia*, *805*(1), 131–146. https://doi.org/10.1007/s10750-017-3298-9

Faithfull, C. L., Huss, M., Vrede, T., & Bergström, A.-K. (2011). Bottom-up carbon subsidies and top-down predation pressure interact to affect aquatic food web structure. *Oikos*, *120*(2), 311–320. https://doi.org/10.1111/j.1600-0706.2010.18683.x

Rock, A. M., Hall, M. R., Vanni, M. J., & González, M. J. (2016). Carnivore identity mediates the effects of light and nutrients on aquatic food-chain efficiency. *Freshwater Biology*, *61*(9), 1492–1508. https://doi.org/10.1111/fwb.12790

# S2 Supplementary methods

<figure><img src="image_22.png" /><figcaption>Figure S2-1: Experimental design consisting of three crossed treatments: light filtering (Light+ = no light filtering), soluble organic carbon addition (OM+ = carbon addition) and fish addition (Fish+ = fish addition). Each category of treatment combination is represented by a different colour and has four replicates, except for combinations with Fish+ that have five replicates.</figcaption></figure>
<table><caption>Table S2-11: Taxonomy and mixotrophic ability of identified phytoplankton species.</caption><thead><tr><th>Species</th><th>Class</th><th>Division</th><th>Mixotrophic</th></tr></thead><tbody><tr><td>Chlamydomonas</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Crucigeniella</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Dictyosphaerium</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Dictyosphaerium subsolitarium</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Kirchneriella</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>cf. Neochloris</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Oocystis</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Oocystis cf. marssonii</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Oocystis cf. parva</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Pediastrum boryanum</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Pediastrum tetras</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Scenedesmus (2 cells)</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>yes</td></tr><tr><td>Scenedesmus ecornis var. concavus</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>yes</td></tr><tr><td>Scenedesmus gr. Abundantes/ Spinosi</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>yes</td></tr><tr><td>Scenedesmus gr. Acutodesmus</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>yes</td></tr><tr><td>Tetraedron minimum</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Tetraedron minimum "Kivu form"</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Tetraedron triangulare</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Cosmarium inconspicuum</td><td>Zygnematophyceae</td><td>Streptophyta</td><td>no</td></tr><tr><td>Cosmarium laeve</td><td>Zygnematophyceae</td><td>Streptophyta</td><td>no</td></tr><tr><td>Mallomonas</td><td>Synurophyceae</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Ochromonas</td><td>Chrysophyceae</td><td>Stramenopiles</td><td>yes</td></tr><tr><td>Synura</td><td>Synurophyceae</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Undetermined Chrysophyceae</td><td>Chrysophyceae</td><td>Stramenopiles</td><td>unknown</td></tr><tr><td>Chrysophyceae kyst</td><td>Chrysophyceae</td><td>Stramenopiles</td><td>unknown</td></tr><tr><td>Trachydiscus sexangulatus</td><td>Eustigmatophyceae</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Achnanthidium</td><td>Bacillariophyta</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Fragilaria</td><td>Bacillariophyta</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Cryptomonas</td><td>Cryptomonadales</td><td>Cryptophyta</td><td>yes</td></tr><tr><td>Plagioselmis nannoplanctica</td><td>Cryptomonadales</td><td>Cryptophyta</td><td>yes</td></tr><tr><td>Gymnodinium</td><td>Dinophyceae</td><td>Alveolata</td><td>yes</td></tr><tr><td>Peridiniopsis cf. penadiforme</td><td>Dinophyceae</td><td>Alveolata</td><td>yes</td></tr><tr><td>Peridinien</td><td>Dinophyceae</td><td>Alveolata</td><td>yes</td></tr><tr><td>Aphanocapsa</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Aphanothece</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Chroococcus</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Cyanogranis ferruginea</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Cyanogranis libera</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Merismopedia tenuissima</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Pseudanabaena</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr></tbody></table>
<table><caption>Table S2-1: Taxonomy and mixotrophic ability of identified phytoplankton species.</caption><thead><tr><th>Species</th><th>Class</th><th>Division</th><th>Mixotrophic</th></tr></thead><tbody><tr><td>Chlamydomonas</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Crucigeniella</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Dictyosphaerium</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Dictyosphaerium subsolitarium</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Kirchneriella</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>cf. Neochloris</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Oocystis</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Oocystis cf. marssonii</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Oocystis cf. parva</td><td>Trebouxiophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Pediastrum boryanum</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Pediastrum tetras</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Scenedesmus (2 cells)</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>yes</td></tr><tr><td>Scenedesmus ecornis var. concavus</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>yes</td></tr><tr><td>Scenedesmus gr. Abundantes/ Spinosi</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>yes</td></tr><tr><td>Scenedesmus gr. Acutodesmus</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>yes</td></tr><tr><td>Tetraedron minimum</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Tetraedron minimum "Kivu form"</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Tetraedron triangulare</td><td>Chlorophyceae</td><td>Chlorophyta</td><td>no</td></tr><tr><td>Cosmarium inconspicuum</td><td>Zygnematophyceae</td><td>Streptophyta</td><td>no</td></tr><tr><td>Cosmarium laeve</td><td>Zygnematophyceae</td><td>Streptophyta</td><td>no</td></tr><tr><td>Mallomonas</td><td>Synurophyceae</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Ochromonas</td><td>Chrysophyceae</td><td>Stramenopiles</td><td>yes</td></tr><tr><td>Synura</td><td>Synurophyceae</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Undetermined Chrysophyceae</td><td>Chrysophyceae</td><td>Stramenopiles</td><td>unknown</td></tr><tr><td>Chrysophyceae kyst</td><td>Chrysophyceae</td><td>Stramenopiles</td><td>unknown</td></tr><tr><td>Trachydiscus sexangulatus</td><td>Eustigmatophyceae</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Achnanthidium</td><td>Bacillariophyta</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Fragilaria</td><td>Bacillariophyta</td><td>Stramenopiles</td><td>no</td></tr><tr><td>Cryptomonas</td><td>Cryptomonadales</td><td>Cryptophyta</td><td>yes</td></tr><tr><td>Plagioselmis nannoplanctica</td><td>Cryptomonadales</td><td>Cryptophyta</td><td>yes</td></tr><tr><td>Gymnodinium</td><td>Dinophyceae</td><td>Alveolata</td><td>yes</td></tr><tr><td>Peridiniopsis cf. penadiforme</td><td>Dinophyceae</td><td>Alveolata</td><td>yes</td></tr><tr><td>Peridinien</td><td>Dinophyceae</td><td>Alveolata</td><td>yes</td></tr><tr><td>Aphanocapsa</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Aphanothece</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Chroococcus</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Cyanogranis ferruginea</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Cyanogranis libera</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Merismopedia tenuissima</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr><tr><td>Pseudanabaena</td><td>Cyanobacteria</td><td>Terrabacteria</td><td>no</td></tr></tbody></table>