Supplementary Material: Adaptation strategies of iron-oxidizing bacteria Gallionella and Zetaproteobacteria crossing the marine–freshwater barrier

This repository contains supplementary material related to the manuscript "Adaptation strategies of iron-oxidizing bacteria Gallionella and Zetaproteobacteria crossing the marine–freshwater barrier".

1) SupplementaryMaterial1_SupplementaryTables.xlsx

Supplementary Material 1. Supplementary Tables.

Supplementary Table S1. Sampling locations at Fåvne and Troll Wall vent fields.
Supplementary Table S2. Gallionella MAGs used in this study.

Supplementary Table S3. Zetaproteobacteria MAGs used in this study.
Supplementary Table S4. Coverage and relative abundances of FeOB Gallionellaceae and Zetaproteobacteria MAGs from this study.
Supplementary Table S5. Gallionellaceae MAGs recovered in this study.

Supplementary Table S6. List of single-copy marker genes used for concatenated phylogeny of Gallionella.

Supplementary Table S7. Functional enrichment of genes in Gallionella MAGs based on the environment.

Supplementary Table S8. Functional enrichment of genes in Zetaproteobacteria MAGs based on the environment.
Supplementary Table S9. Functional enrichment of genes in Mariprofundus MAGs based on the environment.

Supplementary Table S10. Average MAG statistics of Gallionella and Zetaproteobacteria genomes.

Supplementary Table S11. Isoelectric point (pI) relative frequencies of the predicted proteomes.

2) SupplementaryMaterial2_Methods.pdf

Supplementary Material 2. Material and Methods.

3) FigS1.pdf

Fig S1. Phylogeny of typically freshwater Betaproteobacteria genus Gallionella. The phylogenomics tree is based on a concatenated alignment of a manually curated set of 15 single copy gene markers (Table SX) using MAGs from this study and references. Sfz1-4/Sfb1-4: potential stalk formation genes in Zetaproteobacteria/Betaproteobacteria. Environment specified is based on NCBI metadata. Blue genomes have been reconstructed from the Fåvne vent field and Jan Mayen vent field. The maximum likelihood tree with substitution model GTR20+F+R6. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations. The root of the tree is based on non-Gallionella Gallionellaceae MAG sequences as an outgroup.

4) FigS2.pdf

Fig S2. Phylogeny of typically freshwater Betaproteobacteria genus Gallionella. The phylogenomics tree is based on a concatenated alignment of a manually curated set of 17 single copy gene markers using MAGs from this study and references. Environment specified is based on NCBI metadata. Blue genomes have been reconstructed from the Fåvne vent field and Troll Wall vent field. The maximum likelihood tree with substitution model GTR20+F+R6. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations. The root of the tree is based on non-Gallionella Gallionellaceae MAG sequences as an outgroup.

5) FigS3.pdf

Fig S3. Phylogeny of typically freshwater Betaproteobacteria genus Gallionella. The phylogenomics tree is based on a concatenated alignment of a manually curated set of 19 single copy gene markers using MAGs from this study and references. Environment specified is based on NCBI metadata. Blue genomes have been reconstructed from the Fåvne vent field and Troll Wall vent field. The maximum likelihood tree with substitution model GTR20+F+R6. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations. The root of the tree is based on non-Gallionella Gallionellaceae MAG sequences as an outgroup.

6) FigS4.pdf

Fig S4. Phylogeny of class Zetaproteobacteria. The phylogenomics tree is based on a concatenated alignment of a manually curated set of 12 single copy gene markers (Hribovšek et al., 2023) using MAGs from this study and references. Sfz1-6: potential stalk formation genes in Zetaproteobacteria. The environment specified is based on NCBI metadata. Blue genomes have been reconstructed from the Fåvne vent field and Troll Wall vent field. The maximum likelihood tree with substitution model LG+F+R9. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations.

7) FigS5.pdf

Fig S5. Phylogeny of ectoine synthase genes. Ectoine synthase genes were extracted from MAGs from this study and references. Metadata on isolation source were collected from NCBI for genes closely related to ectoine synthase genes of Gallionella. Blue-marked sequences were extracted from MAGs reconstructed from Fåvne and Troll Wall vent field. The phylogenomics tree is based on an alignment of 177 sequences of comparable length at 130 positions using IQ-TREE v2.0.3. The maximum likelihood tree with substitution model LG+I+I+R4. Black node circles mark branches with support values higher than 80% with SH-like approximate likelihood ratio test and 95% with ultrafast bootstrapping, both including 1000 iterations.

8) FigS6.pdf

Fig S6. Relative frequencies of predicted isoelectric points (pI) in Gallionella MAGs. MAGs over 50% completeness and lower than 10% contamination. Average across environment groups with error bars standing for standard deviation.

9) FigS7.png

Fig S7. Relative frequencies of predicted isoelectric points (pI) in Mariprofundus MAGs. MAGs over 50% completeness and lower than 10% contamination. Average across environment groups with error bars standing for standard deviation.

10) FigS8.png

Fig S8. Relative frequencies of predicted isoelectric points (pI) in Zetaproteobacteria MAGs. MAGs over 50% completeness and lower than 10% contamination. Average across environment groups with error bars standing for standard deviation.

References

Hribovšek, P., Olesin Denny, E., Dahle, H., Mall, A., Øfstegaard Viflot, T., Boonnawa, C., et al. (2023). Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field. mSystems 8, 2023.06.20.545787. doi:10.1128/msystems.00543-23.