Additional file 1 of Carbon-wise utilization of lignin-related compounds by synergistically employing anaerobic and aerobic bacteria
Creators: name: Meriläinen, Ella
name: Efimova, Elena
name: Santala, Ville
name: Santala, Suvi
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Supplementary Material 1. Cultivating A. woodii on vanillate as a sole organic carbon source. Cultivating A. woodii on ferulate and coumarate as a sole organic carbon source. Cultivating A. woodii on guaiacol. Sequence of the knock-out cassette. Table S1: Stoichiometric equations of vanillate, syringate, and ferulate utilization by A. woodii according to Bache and Pfennig. Table S2: The production of PCA and acetate by A. woodii when cultivated on vanillate as a sole organic carbon source. Standard deviations describe the differences between the duplicates. Table S3: The production of caffeate, dihydrocaffeate, and acetate by A. woodii when cultivated on ferulate as a sole organic carbon source. Standard deviations describe the differences between the duplicates. Table S4: The production of phloretate and acetate by A. woodii when cultivated on coumarate as a sole organic carbon source. Standard deviations describe the differences between the duplicates. Table S5: The production of catechol and acetate by A. woodii when cultivated on guaiacol as a sole organic carbon source. The standard deviations describe the differences between the duplicates. Table S6: List of the used primers and their names. Figure S1: A correlation curve between OD600 and CDW in ADP1. Figure S2: A A. woodii cultivated in acetobacterium medium with A ferulate or B coumarate as a sole organic carbon source. The fructose present at the beginning of the cultivation is a carry-over substrate coming from the inoculation. Error bars in both graphs are describing the differences between the duplicates. The error bars indicate the standard deviations from the average values of the biologically independent duplicates. In some cases, the error bars are smaller than the size of the marker. Figure S3: The growth of ADP1 on ferulate or caffeate and dihydrocaffeate modeling the aromatic metabolites obtained when A. woodii is cultivated on ferulate. Used concentrations are A 5 mM, B 7.5 mM, and C 10 mM. The error bars indicate the standard deviations from the average values of the biologically independent triplicates. In some cases, the error bars are smaller than the size of the marker. Figure S4: The growth of ADP1 on coumarate or phloretate modeling the aromatic metabolites obtained when A. woodii is cultivated on coumarate. Used concentrations are A 5 mM, B 7.5 mM, and C 10 mM. The error bars indicate the standard deviations from the average values of the biologically independent triplicates. In some cases, the error bars are smaller than the size of the marker. Figure S5: The growth of ADP1 in MSM with catechol as a sole carbon source. The cultivation volume was 200 µl. The linear increase of OD600 in 10 mM cultivations was caused by the color change of catechol in the medium, and therefore, it is not representing the accumulation of biomass. The error bars indicate the standard deviations from the average values of the biologically independent triplicates. In some cases, the error bars are smaller than the size of the marker. Figure S6: Experimental data of the three-phase one-pot coculture of A. woodii and ADP1ΔcatBC. In this graph, only the utilization and production of sugars and organic acids are presented. Glucose is supplemented in the medium at the beginning of the cultivation. Fructose and acetate peaks at the first dashed lined are caused by the inoculation of A. woodii. Please notice that compared to Fig. 5, the presented acetate concentration here describes the overall concentration of acetate, not only the acetate produced by A. woodii. In these growth conditions, ADP1 consumed acetate faster than glucose during the aerobic phase, which is potentially related to the complex medium composition and a long oxygen-depletion period; previously, ADP1 has been reported to consume acetate and glucose simultaneously (5). DO = deoxygenation phase. Figure S7: Consumption of catechol and acetate by ADP1 WT. The cultivation volume was 30 mL. The error bars indicate the standard deviations from the average values of the biologically independent duplicates. In some cases, the error bars are smaller than the size of the marker. One of the duplicate cultivations was lost after 7 h, and thus, the rest of the data points are describing values obtained from single cultivation.