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

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

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

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

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

Table_3_A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations.XLSX

<p>Atlantic cod (Gadus morhua) provides an interesting species for the study of host-microbe interactions because it lacks the MHC II complex that is involved in the presentation of extracellular pathogens. Nonetheless, little is known about the diversity of its microbiome in natural populations. Here, we use high-throughput sequencing of the 16S rRNA V4 region, amplified with the primer design of the Earth Microbiome Project (EMP), to investigate the microbial composition in gut content and mucosa of 22 adult individuals from two coastal populations in Norway, located 470 km apart. We identify a core microbiome of 23 OTUs (97% sequence similarity) in all individuals that comprises 93% of the total number of reads. The most abundant orders are classified as Vibrionales, Fusobacteriales, Clostridiales, and Bacteroidales. While mucosal samples show significantly lower diversity than gut content samples, no differences in OTU community composition are observed between the two geographically separated populations. All specimens share a limited number of abundant OTUs. Moreover, the most abundant OTU consists of a single oligotype (order Vibrionales, genus Photobacterium) that represents nearly 50% of the reads in both locations. Our results suggest that these microbiomes comprise a limited number of species or that the EMP V4 primers do not yield sufficient resolution to confidently separate these communities. Our study contributes to a growing body of literature that shows limited spatial differentiation of the intestinal microbiomes in marine fish based on 16S rRNA sequencing, highlighting the need for multi-gene approaches to provide more insight into the diversity of these communities.</p

Table_9_A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations.XLSX

<p>Atlantic cod (Gadus morhua) provides an interesting species for the study of host-microbe interactions because it lacks the MHC II complex that is involved in the presentation of extracellular pathogens. Nonetheless, little is known about the diversity of its microbiome in natural populations. Here, we use high-throughput sequencing of the 16S rRNA V4 region, amplified with the primer design of the Earth Microbiome Project (EMP), to investigate the microbial composition in gut content and mucosa of 22 adult individuals from two coastal populations in Norway, located 470 km apart. We identify a core microbiome of 23 OTUs (97% sequence similarity) in all individuals that comprises 93% of the total number of reads. The most abundant orders are classified as Vibrionales, Fusobacteriales, Clostridiales, and Bacteroidales. While mucosal samples show significantly lower diversity than gut content samples, no differences in OTU community composition are observed between the two geographically separated populations. All specimens share a limited number of abundant OTUs. Moreover, the most abundant OTU consists of a single oligotype (order Vibrionales, genus Photobacterium) that represents nearly 50% of the reads in both locations. Our results suggest that these microbiomes comprise a limited number of species or that the EMP V4 primers do not yield sufficient resolution to confidently separate these communities. Our study contributes to a growing body of literature that shows limited spatial differentiation of the intestinal microbiomes in marine fish based on 16S rRNA sequencing, highlighting the need for multi-gene approaches to provide more insight into the diversity of these communities.</p

Table_11_A Single Vibrionales 16S rRNA Oligotype Dominates the Intestinal Microbiome in Two Geographically Separated Atlantic cod Populations.XLSX

<p>Atlantic cod (Gadus morhua) provides an interesting species for the study of host-microbe interactions because it lacks the MHC II complex that is involved in the presentation of extracellular pathogens. Nonetheless, little is known about the diversity of its microbiome in natural populations. Here, we use high-throughput sequencing of the 16S rRNA V4 region, amplified with the primer design of the Earth Microbiome Project (EMP), to investigate the microbial composition in gut content and mucosa of 22 adult individuals from two coastal populations in Norway, located 470 km apart. We identify a core microbiome of 23 OTUs (97% sequence similarity) in all individuals that comprises 93% of the total number of reads. The most abundant orders are classified as Vibrionales, Fusobacteriales, Clostridiales, and Bacteroidales. While mucosal samples show significantly lower diversity than gut content samples, no differences in OTU community composition are observed between the two geographically separated populations. All specimens share a limited number of abundant OTUs. Moreover, the most abundant OTU consists of a single oligotype (order Vibrionales, genus Photobacterium) that represents nearly 50% of the reads in both locations. Our results suggest that these microbiomes comprise a limited number of species or that the EMP V4 primers do not yield sufficient resolution to confidently separate these communities. Our study contributes to a growing body of literature that shows limited spatial differentiation of the intestinal microbiomes in marine fish based on 16S rRNA sequencing, highlighting the need for multi-gene approaches to provide more insight into the diversity of these communities.</p