Growth curves of hbs-LAB in non-supplemented MRS (red) with supplemented-MRS (blue) at measured OD (λ 600 nm).

<p>Growth curves of hbs-LAB in non-supplemented MRS (red) with supplemented-MRS (blue) at measured OD (λ 600 nm).</p

Phylogenetic tree and abundance distribution of hbs-LAB 16S rRNA sequences inferred in this study.

<p>The dendrogram illustrates the phylogenetic relationship of the 22 sequence types. Leaf labels marked with hbs-LAB strain names indicate sequences identical to the reference 16S rRNA sequence. The relative abundance of sequence types for each strain is shown in the heat map (each column represents one strain).</p

Hamming distance between blast queries and hits.

<p>A violin plot of the Hamming distance between the full-length sequence of BLAST queries and hits at a 99% identity cut-off. Inside each violin the boxplot is also depicted.</p

Alpha- and beta-diversity of environmental samples.

<p>(A) Rarefaction curves for OTUs at 97% similarity for environmental samples. (B) NMDA plot of the Bray-Curtis distance between 97%-similarity OTU profiles of the same samples.</p

Ratio between number of unique amplicon sequences and full-length sequences.

<p>The ratio between the number of unique amplicon sequences and unique near full-length sequences (starting at primer 391 and ending at 1786), for different primer pairs and read lengths/types. (A) Paired-end 150 bp reads (B) Paired-end 250 bp reads (C) Single-end 400 bp reads. Paired-end reads are connected by a black dashed line.</p

Taxonomic classification of selected environmental samples Taxonomic classification of selected environmental samples.

<p>(A) Marine water 1 (B) Soil (C) Wastewater sludge 2 (D) Moose rumen 1. An interactive HTML version of these plots and of the other environmental samples at deeper taxonomic resolution can be found as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095567#pone.0095567.s003" target="_blank">File S1</a>.</p

Estimators of alpha-diversity for the environmental samples sequenced.

<p>Estimators of alpha-diversity for the environmental samples sequenced.</p

Taxonomic distribution of sequences matching candidate primers.

<p>The central circle represents the taxonomic distribution of the SILVA eukaryotic database. Each outer ring corresponds to the taxonomic distribution of sequences matching each primer candidate. Primers are marked in the figure and each colour corresponds to a kingdom or phylum as shown in the legend.</p

Specificity of taxonomic annotations at different taxonomic levels.

<p>Specificity of taxonomic annotations at different taxonomic levels, for the different primer pairs and read lengths/types, when requiring 99% identity to the selected match. Only instances where the selected hit sequence was annotated down to family level are shown, which were on average 78% of the cases. Matches to the correct species are depicted in green, and to the right genus in yellow. Matches to the level annotated immediately above genus are marked in orange. All other matches are considered missasignments and depicted in red.</p

Position and coverage of candidate primers.

<p>Eighteen bp oligomers with 12 degrees of degeneracy were designed to match as many of the sequences as possible at each position of an alignment of 31,862 full-length unique eukaryotic 18S rDNA sequences using the DegePrime program. The proportion of the sequences matched by the best oligomer found for each position is depicted in black, with a line connecting adjacent points. The entropy of each position is depicted by a dotted grey line. The position numbering refers to the <i>Saccharomyces cerevisiae</i> strain FM-sc-08 18S ribosomal RNA gene, NCBI accession number Z75578. Dark red horizontal bars represent the oligomers chosen as candidate primers in this study. Primers which were later altered are marked in lighter red. Primers found in the literature are depicted in dark blue. Pink rectangles are used to highlight the hypervariable regions of the gene.</p