Isotopic composition of E. coli cells measured with EA-IRMS.

<p>Isotopic composition of untreated, fixed, and fixed/hybridized <i>E. coli</i> cells measured with EA-IRMS on dried cells pellets. Standard deviation is given in parentheses.</p

NanoSIMS images obtained for mixed untreated and fixed/hybridized cells grown in enriched culture media.

<p>NanoSIMS images obtained for mixed untreated and fixed/hybridized cells grown in enriched culture media with nominal ¹³C abundance of 10.9, 20.7, 40.3 and 79.4%. Panel (a) shows the secondary ion of ³²S⁻ image as an image of total biomass (scale bar : 5 µm). Panel (b) shows the secondary ion of ¹²⁷I⁻ image as an indication of hybridized cells. (c) ¹³C Isotopic abundance map of corresponding area.</p

Mean isotopic composition of individual cells measured with nanoSIMS.

<p>Mean isotopic composition of untreated and fixed/hybridized <i>E. coli</i> cells measured with nanoSIMS on individual cells. Standard deviation is given in parentheses.</p

NanoSIMS images obtained from a double-labelled complex sample (¹³C-labeled methanol degrading anaerobic digester).

<p>NanoSIMS images obtained from acomplex sample(¹³C-labeled methanol degrading anaerobic digester) labelled with a generalist bacterial iodinated probe (EUBI) and a Methanosarcina genera specific brominated probe (MS1414). Panel (a) shows the secondary ion of ³²S⁻ image as an image of total biomass. Panel (b) shows the secondary ion of ⁸¹Br⁻ image as an indication of archaeal cell identity. Panel (c) shows the secondary ion of ¹²⁷I⁻ image as an indication of total bacteria. Panels (d) shows the ¹³C Isotopic abundance map.</p

Other cellulosomal proteins with significantly different levels when comparing Tissue and Whatman Paper incubations.

<p>Other cellulosomal proteins with significantly different levels when comparing Tissue and Whatman Paper incubations.</p

Growth and fermentation dynamics of <i>R</i>. <i>cellulolyticum</i> on Tissue (black symbols), Whatman Paper (grey symbols) and Cotton (light grey symbols).

<p>Acetate (A), ethanol (B) and lactate (C) are the three most abundant fermentation products and their concentration ratios are shown in (D-E). Genome copy numbers estimated from the amount of total extracted DNA are shown in (F). Error bars indicate standard deviations calculated from triplicate samples, except in F (duplicate samples). Light grey areas indicate the time points selected for subsequent proteomic analyses.</p

ABC transporter proteins with significantly different levels when comparing Tissue and Whatman Paper incubations.

<p>ABC transporter proteins with significantly different levels when comparing Tissue and Whatman Paper incubations.</p

Cellulosomal endoglucanases with significantly different levels when comparing Tissue and Whatman Paper incubations.

<p>Cellulosomal endoglucanases with significantly different levels when comparing Tissue and Whatman Paper incubations.</p

Non-cellulosomal CAZymes with at least one statistically significant effect when comparing incubations on Tissue and Whatman Paper.

<p>Non-cellulosomal CAZymes with at least one statistically significant effect when comparing incubations on Tissue and Whatman Paper.</p

Proteins with significant effects when comparing growth on Tissue and Whatman Paper mapped over <i>R</i>. <i>cellulolyticum</i> glucose and xylose catabolic pathways.

<p>Statistically significant substrate and substrate-by-time interaction effects were considered. The green color indicates positive effects while the red color indicates negative effects. Positive effects correspond to quantified protein levels higher in Tissue incubations than in Whatman Paper incubations (substrate effect) and to quantified protein levels increasing more or decreasing less in Tissue incubations than in Whatman Paper incubations (substrate-by-time interaction effect). The statistical models (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170524#sec002" target="_blank">Materials and Methods</a>) take into account the replicates and their variability. Protein names and EC numbers are indicated in grey. * indicate effects not significant when adjusting for multiple comparisons (Q-values > 0.01) but still supporting the overall trend (p-values < = 0.05). ** indicate a significant negative substrate effect (q-value ≤ 0.01) and a positive interaction effect (q-value > 0.01 but p-value ≤ 0.05). Pathways were adapted from the Biocyc website (<a href="http://biocyc.org/" target="_blank">http://biocyc.org/</a>).</p