Open Access Highly Accessed Research article

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

Alexis P Yelton15, Luis R Comolli2, Nicholas B Justice3, Cindy Castelle2, Vincent J Denef46, Brian C Thomas4 and Jillian F Banfield14*

Author Affiliations

1 Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA

2 Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA

4 Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA

5 Current address: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

6 Current address: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA

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BMC Genomics 2013, 14:485  doi:10.1186/1471-2164-14-485

Published: 17 July 2013

Additional files

Additional file 1:

Percent nucleotide identity of 16S rRNA genes in the AMD plasmas relative to one another.

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Additional file 2:

16S rRNA nucleotide identity for AMD Thermoplasmatales organisms and close relatives. Note that all of the organisms in the first column except for Aciduliprofundum boonei are classified as Thermoplasmatales.

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Additional file 3:

Ribosomal protein S15 tree of the AMD plasma archaea and their close relatives.

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Additional file 4:

Average amino acid identity of shared orthologs between the AMD plasma genomes.

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Additional file 5:

Percentage of shared orthologs between the AMD plasma genomes.

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Additional file 6:

Gene order conservation between the AMD plasma genomes. Synt/Orth indicates the number of syntenous orthologs divided by the total number of orthologs.

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Additional file 7:

Average length of syntenous blocks of genes between the AMD plasma genomes. Synt Block indicates the average number of genes of syntenous blocks of genes in each pairwise comparison.

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Additional file 8:

Estimate of genome completeness based on orthologous marker gene homologs. Note that genome estimates of 100% are not exact. These genomes still contain gaps between contigs.

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Additional file 9:

Metabolic and structural features of the AMD plasma organisms. The surface layer proteins are pink. Pili are blue. Flagella are brown. The electron transport chain is yellow. The metal resistance proteins are blue. The archaeal type ATP synthase is yellow. Sulfocyanin is yellow and rusticyanin is blue.

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Additional file 10:

Cluster of unique genes in Gplasma. PUF indicates a protein of unknown function. Bold font indicates gene numbers for proteins detected in proteomic data.

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Additional file 11:

Cryo-EM movie of AMD plasma cell with S-layer proteins.

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Additional file 12:

Genes of metabolic and structural importance in the AMD plasma genomes. * indicates a putative annotation. ** indicates a probable annotation. *** indicates a possible annotation. Gray indicates additional evidence of function via synteny analysis. Bold font indicates gene numbers for proteins detected in proteomic data. “split” indicates a split gene. “fusion” indicates a fused gene.

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Additional file 13:

Structural alignment of blue copper proteins. β-Strands (cupredoxin fold) predicted by YASPIN [118] are highlighted (cyan for β-strand 1, yellow and light green for β-strand 2, pink for β-strand 3, dark blue for β-strand 4, dark green for β-strand 5, purple for β-strand 6 and red for β-strand 7). Amicyanin from Paracoccus denitrificans [GenBank: CAA39199] and Plastocyanin from Synechococcus elongatus GenBank: ABB57 [118] serve as references. Red circles indicate copper-binding ligands. Residues highlighted by light grey correspond to additional β-strands and those in bold orange correspond to α-helices. Sulfocyanin-specific motifs are boxed in red. Black arrows indicate copper-binding ligands. Additional loops are indicated at the bottom of the alignment by a light orange line.

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Additional file 14:

Blue-copper protein motifs found in AMD plasma genes.

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Additional file 15:

AMD plasma blue-copper protein tree. bcp indicates a blue-copper protein of unknown function.

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Additional file 16:

AMD plasma CODH gene tree.

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Additional file 17:

Active site alignment of aerobic CODH catalytic subunit genes. The red box indicates the active site residues. H. pseudoflava is Hydrogenophaga pseudoflava, O. carboxidovorans is Oligotropha carboxidovorans, M. loti is Mesorhizobium loti, B. japonicum is Bradyrhizobium japonicum, and B. fungorum is Burkholderia fungorum.

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Additional file 18:

Ni-CODH catalytic subunit alignment. Genes in this alignment are the Ni-CODH catalytic subunits from R. rubrum (CooS, PDB:1JQK), M. thermoacetica (AcsA, PDB:1MJG) and Fer2 (fer2_31_0047). fer2_31_0047’s secondary structure was predicted by YASPIN [118]. β-strands are shown in green and α-helices are highlighted in cyan. Residues belonging to the D-cluster are boxed in yellow (Cys41 and Cys49). Ligands of the B-cluster are boxed in black (Cys50, Cys53, Cys58 and Cys72). Catalytic residues binding the Ni-Fe-S cluster from C-cluster are boxed in purple (His265, Cys300, Cys338, Cys451, Cys481, and Cys531) and catalyze the oxidation of carbon. His95 and Lys568 (boxed in dark red) are non-coordinating residues conserved in Ni-CODHs and have been suggested to be involved in facilitating the reaction [119]. Residue numbering is from the R. rubrum Ni-CODH.

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Additional file 19:

Cytochrome c oxidase subunit II alignment. * indicates the copper-binding motif found in other cytochrome c oxidase proteins. S. acidocaldarius is Sulfolobus acidocaldarius, A. pernix is Aeropyrum pernix, P. oguniense is Pyrobaculum oguniense, T. thermophilus is Thermus thermophilus, P. denitrificans is Paracoccus denitrificans.

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Additional file 20:

Amino acid identity of AMD plasma cytochrome c oxidase subunit II genes with closely related genes.

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Additional file 21:

AMD plasma gene homologs to genes overexpressed or overtranscribed under anaerobic conditions in T. volcanium and T. acidophilum [75],[76]. Bold font indicates gene numbers for proteins detected in proteomic data.

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Additional file 22:

AMD plasma putative hydrogenase 4 gene tree. Accession numbers are to the left of the species names.

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Additional file 23:

Pili genes in the AMD plasmas. * indicates a putative annotation. ** indicates a probable annotation. *** indicates a possible annotation. Gray indicates additional evidence of function via synteny analysis. “split” indicates a split gene. Bold font indicates gene numbers for proteins detected in proteomic data.

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Additional file 24:

Cryo-EM movie of AMD plasma cells with flagella, pili, and viruses.

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Additional file 25:

Additional information on cryo-EM imaging.

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