Shared OTUs between all samples.

<p><b>A)</b> Rank abundance curves for all samples at the 97% sequence similarity cut-off. Black depicts the rank abundance curve for all OTUs in all samples. Red indicates the rank abundance curve for the 28 OTUs shared across all samples. In grey the rank abundance curves are plotted for the individual samples <b>B)</b> Venn diagram showing the number of OTUs shared between each of the four groups: Pockmark 0–4 cm (PM04), Pockmark 40 cm (PM40), Reference site 0–4 cm (R04) and Reference site 40 cm (R40).</p

Rarefaction curves of 16S rRNA sequences at the 97% sequence similarity cut-off.

<p>A) Rarefaction curves with singletons included. B) Rarefaction curves with singletons excluded. The sample coloration descriptions are indicated in the figure. Samples are grouped color wise based on location (pockmark vs. reference sediments) and depth (4 cm vs. 40 cm).</p

Overview of a selection of chemical variables measured per sample.

$<p>The value here is the average of the back calculation for both measurements.</p>#<p>Flouride ions were only measured with a 100x dilution. So it is 1 single measurement.</p>*<p>nd: not determined.</p

Relationships between bacterial communities of Oslofjord sediments using constrained correspondence analysis.

<p>Two-dimensional CCA ordination of the samples using one constrained axis (CCA 1) and an unconstrained axis (CA 1). The constraining factor was Total Carbon. Eigenvalue for both axes are indicated beside each axis. Environmental parameters that significantly (p<0.01) correlated with the ordination were fitted using the envfit command (Vegan package). Abbreviations: total nitrogen (TN), total carbon (TC), total organic carbon (TOC).</p

Phylum level abundances of representative OTU sequences.

<p>The Lowest common ancestor algorithm was used to classify OTU sequences with blastN against the SILVA V108 SSURef database. The phylum Proteobacteria was split to accommodate for the different abundances within the various sub clades. OTUs that did not classify to the proteobacterial subclades were assigned to the taxon Proteobacteria. The group “Not assigned” consists of sequences with significant blast hits but could not be classified using the set LCA parameters. The group “Above phylum” contains OTU sequences assigned to either the kingdom Bacteria or to cellular organisms. Note that only the top 25 taxa are indicated for clarity.</p

Diversity estimators for the Oslofjord sediment samples after removal of unique sequences.

<p>Diversity estimators are average values calculated on standardized counts based on the smallest sample with permutations (n = 1000). Standard deviations were omitted for clarity, but can be found in Table S4 in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085990#pone.0085990.s001" target="_blank">File S1</a>.</p>$<p>OTUs⁹⁷: operational taxonomic units at the 97% sequences similarity cut-off.</p>*<p>Distance metrics were calculated after standardization of all samples to the smallest sample (RDC40 = 2071) and bootstrapped (n = 1000).</p>#<p>Non-Parametric Shannon.</p

Principal Coordinates Analysis ordination using weighted Unifrac distances.

<p>The amount of variation explained for each axis is indicated in percentages. Samples are grouped color wise based on location (pockmark vs. reference sediments) and depth (4 cm vs. 40 cm) in the figure.</p

Classical and alternative pathways for antigen presentation.

<p>A) <i>Classical antigen presentation pathways</i>. MHC class I molecules assemble in the ER together with dedicated chaperones (like tapasin) that retain the MHC class I molecules until peptide binding. Ubiquitinated antigens are degraded by the proteasome, and the resulting peptides are transported via the transporters associated with antigen presentation (TAPs) into the ER lumen. Here the peptides are loaded onto MHC class I, tapasin is released and the peptide-MHC class I complex is transported through the Golgi to the cell surface where they are recognized by specific CD8+ T cells. MHC class II molecules also assemble in the ER with the dedicated chaperone Invariant chain (Ii). Ii mediates trafficking of MHC class II from the ER, through the Golgi, and via the cell surface to the endosomal pathway. Ii is exchanged for degraded exogenous antigenic peptides in specialized MHC class II loading compartments (MIIC). Peptide-loaded MHC class II molecules are released from the endosomal compartment to the cell surface where they are recognized by specific CD4+ T cells (reviewed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074004#pone.0074004-Neefjes1" target="_blank">[6]</a>. B) <i>Alternative (Cross-presentation) pathway for exogenous derived peptides by MHC I molecules</i>. MHC class I molecules carrying signal motifs in the cytoplasmic tail are transported to the endosomal pathway where endocytosed antigens are degraded. Peptides can then be loaded directly in the endosomes in a TAP-independent manner, or the antigens can translocate to the cytosol for proteasomal degradation. The processed antigens can then either be loaded on MHC class I in the ER, or transported back via TAP transporters that have been recruited to the endosomal membrane (reviewed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0074004#pone.0074004-Joffre1" target="_blank">[35]</a>). Peptide-loaded MHC class I molecules are subsequently released to the cell surface for antigen presentation to CD8+ T cells.</p

Synonomus (<i>dS</i>) and non-synonomus (<i>dN</i>) mutations in functional sites of MHC I molecules.

<p>Identification of antigen presenting sites (APS and non-APS) follows Kaufmann et. al. (1994), with 37 and 148 sites pr. sequence, respectively. Significant values in bold.</p

Phylogeny of MHC I diversity in Atlantic cod.

<p>A) Unrooted polar cladogram of all unique cDNA sequences of MHC Ia and Ib in Atlantic cod, based on amino acid sequence alignment. Elongated branches illustrate sequences originating from at least two independent PCR reactions. B) Subset of sequences highlighted in a), rooted with additional teleost Ia and Ib sequences from Ensembl. Maximum likelihood (ML) and Bayesian posterior probabilities are shown for the basal branches. Scale bar represents number of amino acid substitutions pr site.</p