RNASeq ofALE_H2O2_0nM_Rep1
Bacterial strains, both utilized and generated for this study, are listed in Supplementary Table S2. Vibrio natriegens ATCC 14048 (Vn) was used as the wild-type strain in this study. Routine aerobic cultivation of Vn was conducted at 30C in LBv2 media (25 g/L LB Miller broth, 200 mM NaCl, 4.2 mM KCl, and 23.14 mM MgCl2), agitated at 180 rpm, or on LBv2 agar plates (LBv2 plus 1.5% wt/vol agar). Brain Heart Infusion broth with added NaCl (BHIN: 37 g/L [#53286], 1.5% wt/vol) served as a comparative medium to LBv2. For the construction of 44 RNA-Seq data, Vn strains were cultivated at 30C with agitation at 180 rpm. Unless stated otherwise, chemical reagents used for cell culture were sourced from Sigma-Aldrich (Burlington, MA). For additional RNA-Seq carbon samples, a range of carbon sources was added into M9Na medium (M9 minimal medium enriched with NaCl [42 mM Na2HPO4, 22 mM KH2PO4, 258.5 mM NaCl, 18.6 mM NH4Cl, 2 mM MgSO4, 0.1 mM CaCl2]) at a uniform concentration of 1.0% wt/vol, including sodium acetate, cellobiose, glycogen, and rhamnose, consistent with previous data (Shin et al. 2023). Oxidative stress conditions in M9Na were induced by adding H2O2 (0 mM, 0.1 mM, 0.2 mM, and 0.4 mM) to WT and VN-ALE-1 strains, the latter being an evolved strain from adaptive laboratory evolution experiments under oxidative stress [Anand2020-bt]. Low- and high-temperature stress conditions were set in M9Na at 25C and 40C, respectively. Osmolarity stress conditions were established by varying NaCl concentrations (0, 200, 500, and 800 mM) in M9woNa (M9 medium without NaCl [42 mM Na2HPO4, 22 mM KH2PO4, 18.6 mM NH4Cl, 2 mM MgSO4, 0.1 mM CaCl2]). When an antibiotic selection of Vn was required, the antibiotics were used at specified concentrations: 50 g/mL carbenicillin (Carb), 10 g/mL chloramphenicol (Cm), or 360 g/mL spectinomycin (Spec). For plasmid cloning, NEB 10-beta Competent Escherichia coli (New England BioLabs, Ipswich, MA) was cultivated aerobically at 37C in LB Miller broth (LB, #71753-6) with shaking at 180 rpm or on LB agar (LB with 1.5% wt/vol agar). When E. coli harbored a plasmid, appropriate antibiotics were used: 100 g/mL ampicillin/carbenicillin, 25 g/mL chloramphenicol, or 120 g/mL spectinomycin.