Overview of microbial community structure in the EEC, relative to the studied periods and sequencing methods.

<p>Number of OTUs unveiled by pyrosequencing (a) and Illumina (b) methods, and relative number of reads obtained by pyro-sequencing (c) and Illumina (d) methods, based on rDNA sequencing. Number of OTUs (e) and relative number of reads (f) based on rRNA Illumina sequencing. To facilitate reading, the percentage of reads number assigned to a specific group is given when ≥ 1%. Taxonomic affiliation was based on BLASTN searches against the PR2 and Silva databases.</p

Cluster-based microbial community structure in the EEC.

<p>(a) Cluster diagram based on Bray–Curtis dissimilarities calculated based on the non-transformed number of reads for all OTUs found during the study. Red lines in the dendrogram indicate significant differences (p > 0.05) between bifurcations, based on the SIMPROF significance test. ◌ DNA samples, Δ RNA samples. Red dots indicate grouping of samples from the same sampling date (b) Venn diagram of shared diversity between three clusters. The total richness for all groups was 868 OTUs. The number of species shared between the three clusters was 199, corresponding to 23% of the total richness. Similar Bray-Curtis cluster diagrams were constructed from rDNA-based (c) and rRNA-based (d) number of reads.</p

Study area in the eastern English Channel.

<p>The dot (●) indicates the location of the sampling station.</p

Principal Component Analysis (PCA) applied to the environmental variables recorded at SOMLIT station.

<p>Projection of the environmental variables (arrows) and the sampling dates (colored points) on the first factorial plane explaining 58% of the total data inertia. The blue, red and purple ellipses (numbered 1, 2, 3, respectively) correspond to the three groups of sampling dates revealed by the HCA with Ward' method of the PCA dates coordinates on the factorial plane. Most contributing environmental variables to the variability on the first two axes are marked in bold. <b>(a)</b> Sampling dates grouping on each cluster <b>(b)</b> Contributions of each environmental variable on the first two axes of the PCA in percentage. In blue: strong contributions of environmental variables (>10%).</p

Relation between abundance (rDNA reads) and relative cell activity (rRNA reads) for the 100 most abundant OTUs.

<p>(a) Each OTUs was plotted according to their relative number of rDNA (x-axis) and rRNA (y-axis) reads. Each point represents paired percentages (in logarithmic scales) of each taxonomic group from each sample. (b) Boxplot representing rRNA:rDNA ratios for the major taxonomic groups of the 100 most abundant OTUs. The boxplots represent the variation of the rRNA:rDNA ratio around the median for each seasonal clusters (white: all years, green: cluster A representative of <i>P</i>. <i>globosa</i> bloom period, blue: cluster B corresponding to winter conditions, yellow: cluster C corresponding to spring-summer conditions). Whiskers indicate the maximum and minimum values.</p

Taxonomic groups unveiled in the EEC from 77 samples either by pyrosequencing (2011–2013, 47 samples) or by Illumina sequencing (2013–2015, 30 samples).

<p>Taxonomic groups unveiled in the EEC from 77 samples either by pyrosequencing (2011–2013, 47 samples) or by Illumina sequencing (2013–2015, 30 samples).</p

List of environmental variables, means (±SD) of all measurements, minimal and maximal value measured per variable at the SOMLIT station (mean±sd, min-max).

<p>List of environmental variables, means (±SD) of all measurements, minimal and maximal value measured per variable at the SOMLIT station (mean±sd, min-max).</p

Relation between abundance (rDNA reads) and relative cell activity (rRNA reads) for <i>Phaeocystis globosa</i>.

<p>a) Relative rRNA and rDNA reads abundance corresponding to <i>P</i>. <i>globosa</i> between 2013 and 2015. Relative reads abundance for each sample were plotted on logarithmic scale. Considering abundance (rDNA-based data) and relative cell activity (rRNA-based data), four quadrants stand out: rare cells with low activity (DNA<0.01%, RNA<0.01%), rare-active cells (DNA<0.01%, RNA>0.1%), abundant-active cells (DNA>0.1%, RNA>0.1) and abundant cells with low activity (DNA>0.1%, RNA<0.01), respectively. Colors represent rDNA reads abundance (blue: rare, red: abundant), and shades represent rRNA reads abundance as proxy for relative cell activity (dark shade: active, light shade: low activity). b) Schematic representation of <i>P</i>. <i>globosa</i> annual pattern of abundance and activity in the EEC. c) Microscopic counts of <i>P</i>. <i>globosa</i> (dash light grey line: total number of <i>Phaeocystis</i> cells; dash dark grey line: number of <i>Phaeocystis</i> colony) and number of rDNA Illumina reads (black line).</p

Heat-map showing abundance (rDNA-based survey) and relative activity (rRNA/rDNA ratio) of the 100 most abundant OTUs (representing more than 92% of all the reads) detected between 2013 and 2015.

<p>Positive <i>versus</i> negative ratios can be used as an indication of relative cell activity. Negative rRNA:rDNA ratio indicates low cell activity, in contrast to positive ratio which corresponds to higher cells activity (for example, a ratio of -40 corresponds to an OTU having 40-time more rDNA reads than rRNA reads).</p

Diversity indices, based on rDNA and rRNA Illumina sequencing, for samples taken in the EEC (2013–2015).

<p>Curves represent the number of OTUs (solid lines), the richness estimator (S_chao1, dash lines) and indices for diversity heterogeneity (Simpson, Equitability). The rDNA-based dataset is depicted with dark grey lines and the rRNA-based dataset with light grey lines.</p