Table S1. 10μM_rfp_B1 2,074, ohr 10μM_rfp_C2 2,074, ohr
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1 Table S1 Selection without RpoD Insert Start Position Insert End Position Potential Tolerance Gene Candidates 0μM_rfp_A1 2,076, ohr 0μM_rfp_B1 2,082, ohr 0μM_rfp_C1 2,076, ohr 1μM_rfp_A1 2,040,459 2,045,404 pyrf: COG284 (PyrF) Orotidine-5'-phosphate decarboxylase [F] Pp_1816: COG2130 Putative NADP-dependent oxidoreductases [R] Pp_1817: COG1028 (FabG) Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [IQR] Pp_1818: hypothetical protein 1μM_rfp_C1 2,076, ohr 10μM_rfp_B1 2,074, ohr 10μM_rfp_C2 2,074, ohr 100μM_rfp_A1 2,084, ohr 100μM_rfp_C2 5,479,207 5,481,748 prma: COG2264 (PrmA) Ribosomal protein L11 methylase [J] Pp_4819: hypothetical protein Selection with RpoD Insert Start Position Insert End Position Potential Tolerance Gene Candidates 0μM_rpoD_A1 2,078, ohr 0μM_rpoD_B1 2,075, ohr 0μM_rpoD_C1 2,074, ohr 1μM_rpoD_A2 4,908,095 4,994,115 bkdb: COG508 (AceF) Pyruvate/2-oxoglutarate dehydrogenase complex, lpdv: COG1249 (Lpd) Pyruvate/2-oxoglutarate dehydrogenase complex,
2 dihydrolipoamide dehydrogenase (E3) component, and related enzymes [C] Pp_4405: COG2199 FOG: GGDEF domain [T] Pp_4312: hypothetical protein Pp_4313: hypothetical protein Pp_4314: COG3791 Uncharacterized conserved protein [S] Pp_4315: COG384 Predicted epimerase, PhzC/PhzF homolog [R] Pp_4316: COG1052 (LdhA) Lactate dehydrogenase and related dehydrogenases [CHR] Pp_4317: hypothetical protein Pp_4318: hypothetical protein Pp_4319: hypothetical protein Pp_4320: hypothetical protein (Approximate insert size: 4kb) 1μM_rpoD_B1 2,076, ohr 1μM_rpoD_C1 2,074, ohr 10μM_rpoD_A1 (referred to as 10µM_rpoD_A in the main text) 10μM_rpoD_B1 (referred to as 10µM_rpoD_B in the main text) 1,400,873 3,611,923 tola: biopolymer transport protein TolA tolb: COG823 (TolB) Periplasmic component of the Tol biopolymer transport system [U] oprl: COG2885 (OmpA) Outer membrane protein and related peptidoglycanassociated (lipo)proteins[m] Pp_1224: COG1729 Uncharacterized protein conserved in bacteria [S] Pp_1225: COG602 (NrdG) Organic radical activating enzymes [O] Pp_1226: COG603 Predicted PP-loop superfamily ATPase [R] Pp_1227: COG3965 Predicted Co/Zn/Cd cation transporters [P] Pp_3143: COG583 (LysR) Transcriptional regulator [K] Pp_3144: COG1760 (SdaA) L-serine deaminase [E] Pp_3145: conserved hypothetical protein Pp_3146: COG665 (DadA) Glycine/D-amino acid oxidases (deaminating) [E] Pp_3147: COG687 (PotD) Spermidine/putrescine-binding periplasmic protein [E] (Approximate insert size: 3kb) 264,579 3,325,971 Pp_0219: COG2011 (AbcD) ABC-type metal ion transport system, permease component [P] Pp_0220: COG1135 (AbcC) ABC-type metal ion transport system, ATPase component [P]
3 Pp_0221: COG1464 (NlpA) ABC-type metal ion transport system, periplasmic component/surface antigen [P] Pp_0222: COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases [C] Pp_0223: COG1960 (CaiA) Acyl-CoA dehydrogenases [I] Pp_0224: COG1960 (CaiA) Acyl-CoA dehydrogenases [I] (Approximate insert size: 2.5kb) 10μM_rpoD_C1 254, ,579 Pp_0204: COG2188 (PhnF) Transcriptional regulators [K] Pp_0205: COG1053 (SdhA) Succinate dehydrogenase/fumarate reductase, flavoprotein subunit [C] Pp_0206: COG1146 Ferredoxin [C] Pp_0207: COG715 (TauA) ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [P] Pp_0208: COG600 (TauC) ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [P] Pp_0209: COG1116 (TauB) ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [P] Pp_0210: COG1413 FOG: HEAT repeat [C] Pp_0211: COG3536 Uncharacterized protein conserved in bacteria [S] Pp_0212: hypothetical protein gabd: COG1012 (PutA) NAD-dependent aldehyde dehydrogenases [C] 10μM_rpoD_B2 2,074, ohr 10μM_rpoD_C3 405, ,791 Pp_0337: COG5001 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [T] acef: COG508 (AceF) Pyruvate/2-oxoglutarate dehydrogenase complex, 100μM_rpoD_B1 1,554,529 3,769,293 Pp_1362: COG469 (PykF) Pyruvate kinase [G] Pp_1363: conserved hypothetical protein Pp_1364: conserved hypothetical protein Pp_1365: COG2925 (SbcB) Exonuclease I [L] Pp_1366: transcriptional regulator Pp_1367: COG788 (PurU) Formyltetrahydrofolate hydrolase [F] Pp_1368: COG392 Predicted integral membrane protein [S]
4 Pp_3329: COG4325 Predicted membrane protein [S] Pp_3330: COG1629 (CirA) Outer membrane receptor proteins, mostly Fe transport [P] Pp_3331: conserved hypothetical protein (Approximate insert size: 3kb) 100μM_rpoD_A1 2,078, ohr 100μM_rpoD_B3 4,994,115 4,998,562 bkdb: COG508 (AceF) Pyruvate/2-oxoglutarate dehydrogenase complex, lpdv: COG1249 (Lpd) Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3) component, and related enzymes [C] Pp_4405: COG2199 FOG: GGDEF domain [T] 100μM_rpoD_C3 2,693,079 2,696,334 csuc: COG3121 (FimC) P pilus assembly protein, chaperone PapD [NU] csud: COG3188 (FimD) P pilus assembly protein, porin PapC [NU] 100μM_rpoD_A5 5,182,053 5,188,548 Pp_4561: conserved hypothetical protein Pp_4562: conserved hypothetical protein Pp_4563: COG2996 Uncharacterized protein conserved in bacteria [S] Pp_4564: conserved hypothetical protein acek: COG4579 Isocitrate dehydrogenase kinase/phosphatase [T] Pp_4566: membrane protein Pp_4567: hypothetical protein Pp_4568: membrane protein 1000μM_rpoD_A1 2,082, ohr 1000μM_rpoD_B1 2,086, ohr 1000μM_rpoD_C1 2,086, ohr
5 Table S2 Selection without RpoD Insert Start Position Insert End Position Known Tolerance Gene Candidates FosA1 2,041,821 2,082,192 ohr FosA2 2,041,821 2,082,192 ohr FosB1 3,594,543 2,096,380 ohr FosB2 3,594,543 2,096,594 ohr FosC1 2,069,717 2,111,474 ohr Sample with RpoD Insert Start Position Insert End Position rpod_fosa1 3,912,065 3,945,734 Pp_3456 rpod_fosa2 2,057,403 2,539,218 rpod_fosa3 1,584,206 1,544,143 ttgabc rpod_fosb1 2,438,045 2,399,033 rpod_fosb2 2,438,045 2,399,033 rpod_fosb3 2,438, rpod_fosc1 1,469,748 1,431,620 Pp_1271 rpod_fosc2 3,912,042 3,945,729 rpod_fosc3 2,075,733 2,040,789
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COG1487 Predicted nucleic acid binding protein, contains PIN domain R General function prediction only
COG Function Functional Category COG2258 Uncharacterized protein conserved in bacteria S Function unknown COG4251 Bacteriophytochrome (light regulated signal transduction histidine kinase) T Signal transduction
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