153 Physiological stress response to sulfide exposure of freshwater anaerobic methanotrophic archaea Table 2. The sulfide:quinone oxidoreductase (sqr) [EC: 1.8.5.4] gene transcript expression across all conditions in MAGs that showed a significant change of Padj<0.05 (in bold) and log2FC of 2 up or downregulated for at least one condition. MAGs have been ordered from highest to lowest level of expression based on T0-T1 condition. Asterisks indicate genes belonging to the unbinned fraction that were later taxonomically classified. Condition differences (T0-T1, T0-T2 and T0-T3) indicate log2 fold chain (FC) values. “NA” (Not Available). MAGs (contig) T0-T1 T0-T2 T0-T3 Bacteroidota_g_SpSt_333 (1645_23) NA NA -6.28 Nordella_1 (315_163) 8.33 -2.69 -7.73 Hyphomicrobium_1 (1674_16) 7.78 NA -8.72 Burkholderiales_g_SHXO01 (3712_1) 6.72 NA -7.17 Rubrivivax (2134_20) 6.07 2.22 -7.26 Xanthobacteraceae (1849_8) 5.84 -1.16 -6.27 Dokdonella_A (573_81) 5.74 1.17 -7.38 Gammaproteobacteria_g_QUBU01 (121_124) 5.72 NA -6.46 Albidovulum_1 (6517_5) 5.59 -0.74 -6.69 *Rhizobiaceae (2807_18) 5.55 NA -6.01 Dongiaceae_2 (2981_11) 5.21 -4.12 -9.64 Zeimonas_2 (4346_13) 5.11 -1.30 -1.71 Albidovulum_2 (201_90) 4.93 1.42 -5.78 *Bauldia (54474_2) 4.78 NA -4.78 Rhizobiaceae_g_DUSC01_1 (1071_34) 3.84 -2.42 -5.77 Aquamicrobium_A (7_319) 3.52 -0.50 -7.00 Rubrivivax (758_16) 2.68 -0.76 -4.69 Rhizobiaceae_g_DUSC01 (526_102) 2.41 -1.19 -3.74 Ferrovibrionaceae_1 (2199_17) 2.12 -4.80 -4.01 Desulfobacillus (39810_2) 1.89 -0.77 -3.25 *Patescibacteria (27434_2) -0.16 0.62 -3.57 Hyphomicrobiaceae_g_AWTP1_13 (32_23) -0.84 -2.25 1.01 We also considered sulfide detoxification/oxidation by the contiguous cytochrome subunit of sulfide dehydrogenase (fccA) and sulfide dehydrogenase [flavocytochrome c] flavoprotein chain (fccB) [EC:1.8.2.3] gene presence and 5
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