2-DE electrophoresis gels of the soluble fractions of proteins extracted from CON after 4 and 15 days of incubation.

<p>The marked spots were analyzed by MALDI TOF/TOF MS/MS. The identified spots are shown in red, and the ones with a low score shown in green were unidentified. The numbers match with the numbers in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0184505#pone.0184505.t002" target="_blank">Table 2</a>.</p

Dioxygenase enzymes codified in the genome of <i>Sphingobium</i> sp. AM strain and its putative substrates.

<p>Dioxygenase enzymes codified in the genome of <i>Sphingobium</i> sp. AM strain and its putative substrates.</p

Bacterial counts in CON and SC cultures in phenanthrene-supplemented cultures.

<p>Heterotrophic viable bacteria (A) and PAH-degrading bacteria (B) counts in CON and SC cultures growing in LMM with phenanthrene as a sole carbon and energy source during 15 days of incubation. Yellow colony (YC) counts in CON and SC during phenanthrene degradation (C). The results are the means of triplicate independent experiments. The bars represent standard deviations.</p

Mascot results of identified and non-identified proteins found in 2-DE electrophoresis gels of CON cultures.

<p>Summary of the Mascot search results of identified (shaded grey) (high score and/or high sequence coverage) and non-identified proteins (low score) found in 2-DE electrophoresis gels of CON cultures after 4 and 15 days of incubation and analyzed by MALDI TOF/TOF MS/MS. The “x” indicates proteins present in each condition. The lower the expectation value (e-value), the more significant is the score.</p

Metabolic reactions that could involve proteins codified in the ORFs found in S1P3.

<p>(1) The upper degradation pathway of aromatic compounds: A1 to A6, which were initial dioxygenase, dehydrogenase, extradiol dioxygenase, isomerase, hydratase/aldolase and aldehyde dehydrogenase, respectively. (2) The lower degradation pathway (meta-cleavage of catechol): B1 to B8, which were catechol 2, 3-dioxygenase, hydroxymuconic- semialdehyde dehydrogenase, hydroxymuconic-semialdehyde hydrolase, 4-oxalocrotonate isomerase, 4-oxalocrotonate decarboxylase, 2-keto-4-pentenoate hydratase, 2-oxo-4-hydroxypentenoate aldolase and acetaldehyde dehydrogenase, respectively.</p

Gene organization of S1P3 fragment.

<p>The predicted coding sequences are shown with arrows and are colored by groups: genes codifying for hypothetical proteins (gray), genes codifying for aromatic compound degradation (red), genes codifying for the hydrocarbon bacterial response (light blue), genes not directly involved in aromatic compound degradation proteins (violet) and genes for mobile elements and associated proteins (green). Coding sequences are numerated every three. The black box highlights a complete gene cluster with ORFs related to a lower pathway involved in PAH degradation.</p

Concentration of phenanthrene and 1-hydroxy-2-naphthoic acid (HNA) in AM, CON and SC in phenanthrene-supplemented cultures.

<p>The (A) phenanthrene and (B) 1-hydroxy-2-naphthoic acid (HNA) concentrations in AM, CON and SC cultures growing in LMM with phenanthrene as a sole carbon and energy source during 15 days of incubation. The results are the means of triplicate independent experiments. The bars represent standard deviations.</p

Functional assignment of the identified coding sequences found in S1P3.

<p>Functional assignment of the identified coding sequences found in S1P3.</p