117 Unraveling nitrogen, sulfur and carbon microbial bioreactor responses to stress MAG 39 Nitrobium versatile MAG 60 Thermoanaerobaculia 1 MAG 37 Methylomirabilis lanthanidiphila MAG 44 Plantomycetes 1 MAG 56 Sulfuricella MAG 22 Desulfobacterota MAG 32 Kuenenia stuttgartiensis MAG 65 Thiohalobacteraceae MAG 23 Dokdonella MAG 55 Scalindua rubra MAG 57 Sulfuricella denitrificans MAG 25 Flavobacteriales MAG 02 Altibacter MAG 50 Rhodocyclaceae 1 MAG 03 Anaerolineae 1 MAG 49 Rhodobacteraceae MAG 40 Notoacmeibacter MAG 35 Melioribacteraceae 2 MAG 18 Comamonas MAG 63 Thermomonas MAG 20 Cyclobacteriaceae MAG 19 Cutibacterium acnes MAG 05 Anaerolineae 3 MAG 64 Thiobacillus MAG 27 Hyphomicrobium MAG 13 Bacteria FEN 1099 MAG 52 Rhodocyclaceae 3 MAG 14 Bacteria OBL16 MAG 06 Anaerolineae 4 MAG 11 Bacteria ARS69 MAG 58 Sulfuricellaceae MAG 26 Haliangiaceae MAG 12 Bacteria BMS3BBIN04 MAG 29 Ignavibacteriaceae 1 MAG 34 Melioribacteraceae 1 MAG 45 Plantomycetes 2 MAG 31 Kapabacteriaceae MAG 04 Anaerolineae 2 MAG 17 Burkholderiales MAG 38 Methylomirabilis tolerans MAG 36 Methanoperedens nitroreducens 0 100 200 300 400 G0 G1 G2 G3 G4 G5 Normalized Genome Coverage NH4+ starvation B A pre B A NO and H2S toxicity R Figure 3. Heat map displaying normalized genome coverage for the most abundant MAGs across experimental conditions. Abbreviations are as follows: B, before; A, after; R, recovery; pre, preparatory phase. Experiments are indicated in bold on top. MAGs are ordered based on normalized genome coverage values and abundance change patterns. Between 91-95% of the reads were assembled and mapped to the MAGs across all experimental time points. 4
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