Abundance and α-diversity comparison of bacteriome and mycobiome between PMA-pretreated and untreated samples.

<p>Abundance and α-diversity comparison of bacteriome and mycobiome between PMA-pretreated and untreated samples.</p

Venn diagram representing number of shared and specific bacterial (A) and fungal (B) genera between PMA-treated and untreated samples.

<p>In each case, the first 5 most prevalent genera are listed.</p

Effect of PMA on the composition of mycobiome of each sample.

<p><b>(A)</b>: Relative abundance of fungal genera of each sample (“yes” or “no” indicates the samples with or without PMA-pretreatment). <b>(B)</b>: PCA plot of the first two components of mycobiome of samples with and without PMA-pretreatment. Each marker represents treatment conditions (filled triangle symbols PMA-treated samples, filled square symbols untreated samples). Each color represents a given sputum sample (G040.III: dark blue; G088.II: chartreuse; G088.III: dark green; G172.I: yellow; G172.II: orange; G172.III: dark orange; G014.II: dark grey; G014.III: black; G176.II: firebrick; G176.III: dark red).</p

Comparison of the enumeration of <i>P</i>. <i>aeruginosa</i> cells between cultures and qPCRs of PMA-treated and untreated sputum samples.

<p>Comparison of the enumeration of <i>P</i>. <i>aeruginosa</i> cells between cultures and qPCRs of PMA-treated and untreated sputum samples.</p

<i>p-values</i> and <i>r-values</i> of similarity analysis (one-way ANOSIM) of the bacterial and fungal OTU data.

<p><i>p-values</i> and <i>r-values</i> of similarity analysis (one-way ANOSIM) of the bacterial and fungal OTU data.</p

Abundance and α-diversity comparison of bacteriome and mycobiome between PMA-pretreated and untreated samples.

<p>Abundance and α-diversity comparison of bacteriome and mycobiome between PMA-pretreated and untreated samples.</p

<i>In situ</i> survey from morphological observations.

<p>Temporal variation of biomasses (µg C L⁻¹) of (a) Phytoplankton and (b) micro- (ciliates and dinoflagellates) and nanoheterotrophic protists (represented mainly by heterotrophic nanoflagellates HF) at the coastal station R1 (50°48′ N, 1°34′ E) in the eastern English Channel (Strait of Dover) from March to April 2009. Results are shown here in terms of biomass – calculated based on abundance and cell size – (see Method section) and to better represent the stocks of the different compartments.</p

Rarefaction curves and richness estimator.

<p>Rarefaction curves representing the numbers of Operational Taxonomic Units (OTU) <i>versus</i> the number of reads plotted from tag pyrosequencing data. The OTUs were determined using the program Uclust <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039924#pone.0039924-Edgar1" target="_blank">[38]</a>, with a cutoff value set to 0.03 (OTUs were grouped when their level of sequence similarity ≥97%) for the analysis. The table indicates the number of reads, the number of OTU, the richness estimator (Schao1 and Margalef indices), and the heterogeneity of the diversity (Shannon and Simpson indices) for each sampling date.</p

Differential infra-specific diversity of Haptophyceae before and during their spring bloom.

<p>Tag pyrosequencing reads assigned to the group of Haptophyceae were independently extracted for both sampling dates. Reads sharing more than 97% sequence identity were grouped under the same OTUs using Uclust <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039924#pone.0039924-Edgar1" target="_blank">[38]</a>. All the reads having a size above 400bp and representative of an OTU were aligned together with reference sequences using Clustalw <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039924#pone.0039924-Thompson1" target="_blank">[84]</a>. The representative sequences and reference sequences were aligned using Muscle <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039924#pone.0039924-Edgar1" target="_blank">[38]</a>. The resulting alignments, manually curated using the Bioedit software (<a href="http://www.mbio.ncsu.edu/bioedit/bioedit.html" target="_blank">http://www.mbio.ncsu.edu/bioedit/bioedit.html</a>), were used to build phylogenetic trees. For tree construction, the Seaview 4.0 software (<a href="http://pbil.univ-lyon1.fr/software/seaview.html" target="_blank">http://pbil.univ-lyon1.fr/software/seaview.html</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039924#pone.0039924-Gouy1" target="_blank">[39]</a> was used with Neighbor-joining (NJ) and K2P substitution method. Bootstrap values were estimated from 1000 replications. The unrooted phylogenetic tree displayed 21 OTUs inferred from 299 reads corresponding to March 31^st sample, and 56 OTUs inferred from 2,759 reads for April 21^st sample. On each branch are indicated the sampling dates with “1-” corresponding to March 31^st and “2-” to April 21^st, the reads I.D. as it was submitted into the SRA database (SRX031036) and between brackets the number of reads composing the OTU. The taxonomical subdivisions are indicated on the left side of the figure. For relevant clades, the sum of reads “n” composing a cluster was given for each sampling dates.</p

Proportion of taxonomic groups identified in the English Channel using pyrosequencing of 18S rRNA gene hypervariable regions.

<p>The reads obtained from pyrosequencing of 18S rRNA hypervariable region were subject to BlastN <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039924#pone.0039924-Altschul1" target="_blank">[34]</a> search against the Silva SSU rRNA database (<a href="http://www.arb-silva.de/" target="_blank">http://www.arb-silva.de/</a>) to assign a taxonomic group. The pie diagram displayed the proportion of reads, obtained at both sampling dates, belonging to a particular taxonomic group (threshold E = 10⁻⁵). The composition of the Alveolates, being the most dominant group, was displayed on an additional smaller pie diagram. “Not assigned” correspond to reads having a match in the Silva database, but without a precise taxonomic assignment. The percentage of reads assigned to a specific group was given when above 1%.</p