Supplementary materials for: Genomic reconstruction of a novel, deeply-branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction

Kiley W. Seitz1, Cassandre S. Lazar2,3,4, Kai-Uwe Hinrichs3, Andreas P. Teske2, and Brett J. Baker1*

1Department of Marine Science, University of Texas Austin, Marine Science Institute, Port Aransas, TX 78373, USA2Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, USA3MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany4Institute of Ecology, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany*phone 510-333-5254, email acidophile@gmail.com. To whom correspondence should be addressed.

Additional information regarding the distribution of ribosomal proteins in the genomes. The

majority of the genomic bins (52.60%) did not have all 16 ribosomal genes. 4% of sequences

were only missing one gene and 21.9% were missing less then 3 conserved proteins. 10.9% of

sequences only had 8 of the 16 ribosomal genes. The number of ribosomal genes identified in

Thorarchaea were 9, 9 and 8 for SMTZ1-83, SMTZ1-45 and SMTZ-45 respectively. The number of

absent ribosomal proteins varied but the majority of ribosomal genes present in the genomes

was consistent in the phyla. Sequences for rpL2, 14, 22 and 24 and rpS3 and 17 were in all three

genomes. Sequences rpL5 and rpS8 were seen in at least two of the Thorarchaeal genomes.

Supplementary Figure S1. Tetranucleotide based ESOM (emergent self-organizing map) of 5kb fragments from the SMTZ sediments. Contigs belonging to Thorarchaeota bins, SMTZ-83 and a bin containing both SMTZ1-45 and SMTZ-45 fragments are labeled. Other bins that were well defined in this area of the map are colored.

Supplementary Figure S2. Rank abundance plot of all genomic bin in the WOR SMTZ (24-32 cm) based on recruitment of reads to ribosomal protein S3 genes. The three Thorarchaeota bins are labeled.

Supplementary Figure S3. Phylogenetic analysis of identified hydrogenase protein sequences from the Thorarchaeaota genomes. The tree was generated using Phylip PROML in the ARB software package. Closed circles represent bootstrap values of >70 and open circles represent values >50.

Supplementary Table S1. CAZy server was used to identify the presence and quantity of various carbohydrate-degrading enzymes in all three archaeal bins

Supplementary Table S2. List of genes identified in the bin SMTZ1-83 and used to reconstruct the physiological pathways shown in Figure 4.

Supplementary Table S3. Distribution of key metabolic genes within the three Thorarchaeota bins. Those highlighted in yellow are present in all three of the bins.