Supplementary Material for Doctoral Thesis: Ecology and genomic diversity of iron-oxidizing bacteria at Arctic deep-sea hydrothermal vents: Lessons from genome-resolved metagenomics and microscopy

This repository contains supplementary material related to the doctoral thesis “Ecology and genomic diversity of iron-oxidizing bacteria at Arctic deep-sea hydrothermal vents: Lessons from genome-resolved metagenomics and microscopy”.

Doctoral Thesis for philosophiae doctor (Phd) at University of Bergen. 2024.

Thesis Figures in higher resolution:

Figure 8. Phylogeny of Zetaproteobacteria from Aurora vent field.

Figure 9. Phylogeny of the large subunit of uptake NiFe hydrogenase (hya; 1d).

Figure 10. Phylogeny of the large subunit of sensing NiFe hydrogenase (hup; 2b).

Figure 11. Phylogeny of Zetaproteobacteria.

Supplementary Figures

1) FigureS1.pdf

Figure S1. Phylogeny of Zetaproteobacteria from Aurora vent field. The 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. Blue genomes have been reconstructed from the Aurora 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.

2) FigureS2.pdf

Figure S2. Phylogeny of the large subunit of uptake NiFe hydrogenase (hya; 1d). Phylogenetic tree of the large subunit of uptake NiFe hydrogenase (hya; 1d) present in MAGs from Aurora vent field and in all publicly available Zetaproteobacteria genomes, with closest relative reference using BLAST. Blue MAGs have been reconstructed from the Aurora vent field. 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. Maximum likelihood tree with substitution model LG+I+I+R8.

3) FigureS3.pdf

Figure S3. Phylogeny of the large subunit of sensing NiFe hydrogenase (hup; 2b). Phylogenetic tree of the large subunit of H2-sensing hydrogenase histidine kinase-linked (hup; 2b) present in MAGs from Aurora vent field and in all publicly available Zetaproteobacteria genomes, with closest relative reference using BLAST. Blue MAGs have been reconstructed from the Aurora vent field. 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. Maximum likelihood tree with substitution model LG+I+I+R9.

4) FigureS4.pdf

Figure S4. Phylogeny of Zetaproteobacteria. Genomes shown in blue have been reconstructed and analyzed in this thesis. The 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. MAGs above 0.5 coverage were selected. Sfz1-6: potential stalk formation genes in Zetaproteobacteria. The maximum likelihood tree was constructed using IQTREE 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. The taxonomy is based on GTDB taxonomy r214. ZetaOTU categorization of Zetaproteobacteria is based on 16S rRNA genes extracted from MAGs. Zetaproteobacteria in culture are marked with yellow stars, along with the stated known iron oxide morphology.

References:

Hribovšek, P. et al. Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field. mSystems 8, 2023.06.20.545787 (2023).