Copper dependent growth rates of <i>Thalassiosira oceanica</i> TO03 and TO05.

<p>Mean values ± standard error are shown; numbers of biological replicates (n) are indicated in brackets. Note that TO05 was not able to grow under 1.96 nM Cu in the medium (indicated by X in the graph). Given the scope of this study, TO03 was not grown under 1.96 nM or 6.08 nM, as it was able to grow under Cu concentrations <1 nM.</p

Comparison between EST-mapped proteomics datasets of TO03 and TO05, emphasizing the similarity in their genomes.

<p><b>A) Results for TO03 (plusEST). B) Results for TO05 (plusEST)</b>. The left side of the panel shows the proportion of identified predicted proteins coming from the TO05 genome <i>vs</i>. the TO03 transcriptome (ESTs). The right side of the panel shows the proportion of the different types of ESTs that have been mapped by the peptides coming from the LC-MS/MS. Even though we used the combined database including all known TO05 and TO03 predicted proteins, neither strain shows bias towards its own subset of proteins.</p

The effects of Cu limitation on growth rate, cell diameter, protein content and a series of photophysiological parameters in two strains of <i>T</i>. <i>oceanica</i>.

<p><b>2A-C</b>, growthrate, cell diameter, and Chl<i>a</i> per cell, respectively; <b>2D-F</b>, gross oxygen production, Fv/Fm, and the absorption cross section of PS II antennae, respectively; <b>2G-I</b>, ¹⁴C PE curve parameters α, P_max, and E_K, respectively; <b>2J-L</b>, ETR_PSII PE curve parameters α, P_max, and E_K, respectively; <b>2M-O</b>, conversion factor, NPQ_NSV, and cellular protein content, respectively. The values are mean ± std. error of three biological replicates. Differing letters above bars represent statistically significant changes (p < 0.05) using a 2-way ANOVA with post-hoc interaction analysis (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181753#sec002" target="_blank">Methods</a> for details). Note that both strains have the same physiological responses under metal replete conditions. Under low Cu conditions, only growth rate and cell size are significantly reduced in the same manner in both strains.</p

Differential expression of proteins involved in the photosynthetic electron transport chain (ETC) in response to chronic Cu limitation in <i>T</i>. <i>oceanica</i>.

<p>Differential expression of proteins involved in the photosynthetic electron transport chain (ETC) in response to chronic Cu limitation in <i>T</i>. <i>oceanica</i>.</p

Overview of expression of all putative LHCs in both strains of <i>T</i>. <i>oceanica</i>.

<p>Overview of expression of all putative LHCs in both strains of <i>T</i>. <i>oceanica</i>.</p

Phylogenetic tree of 48 predicted LHCs from the <i>T</i>. <i>oceanica</i> genome (CCMP 1005) aligned with 41 LHCs from <i>T</i>. <i>pseudonana</i> (CCMP 1335).

<p>Boxed THAOC LHCs have been identified at the protein level in this study. LHCs in grey shaded boxes with bold, black letters are significantly down-regulated and those in black shaded boxes with bold, white letters are significantly up-regulated in response to low Cu in TO03. The only significantly regulated LHC in TO05 is THAOC_08587 (up), which aligns closest to TpFCP7 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181753#pone.0181753.t002" target="_blank">Table 2</a>). Numbers on nodes are based on PhyML alertSH, aBayes, and standard bootstrap (100 replicates) and are expressed as percentages. Bootstrap values below 65% are not shown.</p

Significantly differentially expressed LHCs under chronic low Cu conditions.

<p>Significantly differentially expressed LHCs under chronic low Cu conditions.</p

Bar chart demonstrating the predicted taxonomy of bacterial host genera for assembled Indian Ocean viral metagenomic data.

<p>The area of each bar is proportional to the total number of viral reads contained in the contigs assigned to a particular host genus. Direct assignments are colored green and transitive assignments are colored blue. Direct assignments were made by assigning viral contigs to the host models built on NCBI RefSeq genomes. Transitive assignments were made by assigning viral contigs to models built on large bacterial contigs, and then assigning taxonomy to these bacterial contigs (as described in the text). Twenty top taxa in pairs of green and blue are shown according to the maximum count from either direct or transitive assignment method, respectively. If no bar is shown for one of the methods, the count was zero.</p

Functional characterization of Indian Ocean viral sequences from the viral and larger fractions of metagenomic data in the context of KEGG pathways.

<p>The inset pie charts represent the breakdown of the Metabolism super-pathway (top) and Energy metabolism pathway (bottom). The percentages of viral sequences attributed to the Energy metabolism pathway are indicated on the Metabolism pie charts.</p

A phylogenetic tree built from amino acid sequences using FastTree for the gene encoding the large subunit terminase.

<p>Selected reference sequences are colored red and green. Representative Indian Ocean VF and LF sequences are colored pink and purple respectively. GOS Phase I sequences are colored blue. Confidence values are displayed on the tree.</p