Additional file 1 of CO-driven electron and carbon flux fuels synergistic microbial reductive dechlorination
Creators: name: Wang, Jingjing
name: Li, Xiuying
name: Jin, Huijuan
name: Yang, Shujing
name: Yu, Lian
name: Wang, Hongyan
name: Huang, Siqi
name: Liao, Hengyi
name: Wang, Xuhao
name: Yan, Jun
name: Yang, Yi
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Microcosm setup and transferred enrichment cultures. Trichloroethylene (TCE) was dechlorinated in enrichment cultures fed with acetate and CO (represented by the royal blue bottles). Similarly, TCE dechlorination occurred in CO-fed enrichment cultures with bicarbonate-buffered medium (represented by the green bottles) and HEPES-buffered medium (represented by the orange bottles). Conversely, in acetate-fed enrichment cultures without CO or H2 supplementation (represented by the yellow bottles), the TCE dechlorination process did not occur, denoted by the symbol “X”, signifying the inability to dechlorinate. Figure S2. Reductive dechlorination of TCE in CO plus acetate enrichment cultures from transfer 1 to transfer 3. Approximately 33 μmol of TCE was dechlorinated to ethene over 100 days in transfer 1 cultures fed with acetate and CO (A). In transfer 2 cultures, 33 μmol of TCE was dechlorinated to ethene within 30 days, and an additional 33 μmol of TCE was dechlorinated within 25 days (B). In transfer 3 cultures, 33 μmol of TCE was dechlorinated to ethene over 50 days (C). Red arrows indicate CO additions, with each dose amounting to 2 mL. Figure S3. Reductive dechlorination of TCE in CO-fed enrichment cultures from transfer 2 to transfer 4. Approximately 33 μmol of TCE was dechlorinated to VC over 120 days in transfer 2 cultures (A). In transfer 3 cultures, 33 μmol of TCE was dechlorinated to VC with a small amount of ethene in 80 days (B). In transfer 4 cultures, 33 μmol of TCE was dechlorinated to ethene over 160 days (C). Red arrows indicate CO additions, with each dose amounting to 2 mL. Figure S4. Phylogenetic tree constructed based on the amino acid sequences of 43 RDases, with branches calculated from 500 bootstrap iterations. Functional assignments of these RDases were determined through biochemical characterization, expression analysis, or phylogenetic inference, representing a diverse array of OHRB. The tree also includes 20 RDases annotated from the draft genome of strain CO, highlighted in blue branches. Figure S5. Phylogeny of Acetobacterium based on genome sequences. The tree was constructed using the maximum-likelihood method, with GenBank accession numbers provided in parentheses. Bootstrap values, derived from 1,000 resamplings, are indicated at branching points. Figure S6. Phylogenetic tree based on protein sequences of 63 carbon monoxide dehydrogenases (CODHs) from diverse bacteria and methanogens (archaea). CODHs from methanogens are indicated with a blue background, those from Acetobacterium with a green background, and CODHs identified in CO enrichment cultures are highlighted in blue. Figure S7. Proposed model for interspecies interactions supporting TCE-to-ethene dechlorination by Dehalococcoides with CO as electron donor and carbon source. Hydrogenogenic carboxydotrophs (e.g., Methanosarcina) oxidize CO, generating H2. This H2 is then transferred to Acetobacterium, which in turn produces acetate. Both acetate and H2 are subsequently utilized by Dehalococcoides for reductive dechlorination of TCE to ethene. Additionally, Methanosarcina can use acetate and H2 to produce methane. Table S1. The average nucleotide identity (%) and digital DNA-DNA hybridization (%) of strain CO with other strains in the genus of Dehalococcoides. Table S2. RDases with assigned functions and their host OHRB used in Figure S4. Table S3. The average nucleotide identity (%) and digital DNA-DNA hybridization (%) of strain Z1 with other strains in the genus of Acetobacterium. Table S4 Metagenome-assembled genomes recovered from CO-fed TCE-dechlorinating enrichment cultures.