Summary of the experimental workflow.

<p><b>A</b>. Emission spectrum of the UVB lamps used to irradiate the cultured cells of <i>P. angustum </i><b>B</b>. Bacterial cells were collected at the beginning of log phase (OD = 0.1) and cultured either under UVB radiation or in the dark <b>C</b>. After 1.75 h of incubation, quantitative proteomics was performed by using either gel-free (Post-digest ICPL labeling) or gel-based (2D-DIGE) approaches. Quantitative data for ICPL were obtained from the MS spectrum (L: Light label: H: Heavy label).</p

Identification of the two-dimensionally separated protein spots of interest with the average fold change and associated p-values obtained from seven replicates.

<p>The ratio was determined by comparing the peak intensities in LC-MS runs of UVB <i>versus</i> dark conditions (UVB/Dark). The number of peptides assigned a Mascot score above 35, as well as the protein mass, score and empAI value, are also listed for each identified protein. (D: down-regulated; U: up-regulated).</p

UVB protein biomarkers of <i>P. angustum</i> quantified by both ICPL and 2D-DIGE.

*<p>: 2 values are indicated for VAS14_06783 with 2D-DIGE because it was identified under 2 spots (1U, 2U).</p

Venn diagram showing the non-redundant proteins quantified in four biological replicates.

<p>Venn diagram showing the non-redundant proteins quantified in four biological replicates.</p

List of the quantified proteins in four biological replicates using the post-digest ICPL labeling methodology.

<p>Proteins significantly different from the control within a given biological replicate are indicated with bold characters. <b>Ratio</b>: UVB/Dark, <b>SD</b>: standard deviation, <b>#Pept</b>: number of peptides used for protein quantification.</p

A representative standard 2D gel showing protein spots that were down-regulated (A) and up-regulated (B).

<p>Proteins of interest are circled in green, and excised spots are circled in blue or red according their relative spot volumes (D = down-regulated by UVB; U = up-regulated by UVB). Green circles correspond to the up- or down-regulated proteins not excised for MS analysis.</p

Detection of the RecA protein (≈40 kDa) by quantitative fluorescent western blot analysis of both UVB-treated cells and dark control cultures.

<p>Four different biological replicates are shown for each condition.</p

Additional file 1 of Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics

Additional file 1: Table S1. Summary of the metaproteome and metagenome annotations. Including, taxonomic annotations (LCA score ≥80%) and functional annotations (BLASTP, Uniprot) obtained from mPies for the 16S-TaxDB, 18S-TaxDB (note taxonomy is from BLASTP results), MG-DB, and 16S-TaxDB-2nd protein search databases. The metagenome annotations are derived from DRAM and include hits to the KEGG and PFam databases. Table S2. Summary of the taxonomic classifications of the metagenome reads obtained using Kaiju. Table S3. Relative quantification and functional annotations of the expressed Pseudoalteromonas sp. proteins (% relative abundance) using the recovered metagenome-assembled genome as a protein search database

Photosynthetic capacity of <i>Arthrospira</i> sp. PCC 8005 after gamma irradiation.

<p>The data obtained for the irradiated samples were normalized against and are shown as percentage of their representative non-irradiated control (which was put at 100%). Data represent the mean of three independent biological replicates (n = 3) and error bars display the standard error of the mean (SEM). The statistical analysis was calculated on raw data, before normalisation to percentages.</p

Pigment content of <i>Arthrospira</i> sp. PCC 8005 after irradiation.

<p>The data obtained for the irradiated samples were normalized against and are shown as percentage of their representative non-irradiated control (which was put at 100%). Allophycocyanin content, Phycocyanin content, and Chlorophyll A content were measured at T0H, T2H and T5H respectively. Data represent the mean of three independent biological replicates, and error bars present the standard error of the mean (SEM). The statistical analysis was calculated on raw data, before normalisation to percentages. One asterisk indicates a value which is significantly differing (p<0.05) from the non-irradiated control.</p