Example of PCR on gill chamber epibionts of <i>R</i>. <i>exoculata</i>.

<p>(A) <i>luxS</i> amplification. <i>luxS</i> genes from <i>Vibrio harveyi</i> and <i>Vibrio parahaemoliticus</i> were used as negative controls. (B) <i>luxR</i> amplification on branchiostegite (br) and scaphognathite (sc) epibionts. (C) <i>luxR</i> amplification on gut (g) and stomach (st) epibionts.</p

Acquisition of symbionts in the gill chamber of <i>Rimicaris exoculata</i>.

<p>(A) Epibiontic colonization through the molt cycle [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174338#pone.0174338.ref022" target="_blank">22</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174338#pone.0174338.ref023" target="_blank">23</a>] compared to (B) biofilm formation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174338#pone.0174338.ref032" target="_blank">32</a>].</p

<i>lux</i> gene PCRs on epibionts of <i>R</i>. <i>exoculata</i> juveniles and eggs.

<p>(A) <i>luxS</i> amplification on scaphognathite and eggs. (B) <i>luxR</i> amplification on scaphognathite and eggs. (C) <i>luxR</i> amplification on (br) branchiostegite and (sc) scaphognathite at the beginning (1) and end (2) of the molt.</p

<i>luxS</i> gene phylogeny (calculated on 550 bp) of symbionts associated with the gill chamber of <i>R</i>. <i>exoculata</i>.

<p>The robustness was tested using 500 bootstraps resampling the tree using the Neighbor-Joining algorithm with the Kimura two-parameter correction matrix. (A) <i>luxS</i> gene affiliated to <i>Proteobacteria</i>. (B) <i>luxS</i> gene affiliated to <i>Epsilonproteobacteria</i>. (C) Localizations of <i>R</i>. <i>exoculata</i> on hydrothermal vents and studied areas; red: Rainbow, green: TAG, blue: Snake Pit, orange: Logatchev (modified from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174338#pone.0174338.ref071" target="_blank">71</a>]). Clone numbers are indicated between brackets.</p

PCR and RT-PCR (end of molt) amplification results per sample of different <i>Rimicaris exoculata</i> parts from different vent sites for the <i>luxR</i> gene analysis.

<p>PCR and RT-PCR (end of molt) amplification results per sample of different <i>Rimicaris exoculata</i> parts from different vent sites for the <i>luxR</i> gene analysis.</p

Example of <i>lux</i> RT-PCR on gill chamber epibionts of <i>R</i>. <i>exoculata</i>.

<p>Free RNAse/DNAse water was used as template for the negative control. (A) <i>luxS</i> amplifications were done on branchiostegite (br), scaphognathite (sc), and gut (g) shrimp epibionts at the end of molt cycle from Rainbow. A1 end of molt and A2 beginning of molt cycle (B) <i>luxR</i> amplification were done on branchiostegite (br), scaphognathite (sc), gut (g), eggs and juvenile (juv) epibionts at the beginning (B2) and at the end (B1) of the molt cycle. The dotted box indicates the correct PCR products size. B2 was more contrasted to try to observe any amplification.</p

<i>Rimicaris exoculata</i> samples used for amplification of <i>lux</i> genes according to the molt stages.

<p><i>Rimicaris exoculata</i> samples used for amplification of <i>lux</i> genes according to the molt stages.</p

NAHSL-breakdown and biocontrol activity of the<i>R.erythropolis qsdA</i> deletion mutant in potato tubers.

<p>(A) The <i>R. erythropolis</i> R138 wild-type (BCA) and the <i>R. erythropolis</i> R138 Δ<i>qsdA</i> (BCA-Δ<i>qsdA</i>) strains were compared for biocontrol activity against <i>P. atrosepticum</i> 6276 (<i>Pa</i>-QS+) 1, 2, 3 and 7 days after inoculation of potato tubers. For the controls, one or both strains were replaced in the inoculum with a 0.9% NaCl solution. Significant differences (Mann and Whitney test; <i>α</i> = 0.05) in maceration symptoms between infected tubers inoculated with the BCA or the BCA-Δ<i>qsdA</i> are indicated with an asterisk. (B) Population dynamics of <i>P. atrosepticum</i> and <i>R. erythropolis</i> bacteria (CFU/g fresh weight of potato tubers; black and red lines respectively), and NAHSL concentrations (ng/g of potato tubers; black and white bars) were determined for each condition in potato tubers. For lines and bars, each value is the mean of three replicates with the standard deviation indicated. NS, non-significant; NAHSL, <i>N</i>-acyl homoserine lactone.</p

Bacterial strains and plasmids.

<p>Km^R, Ap^R, Gm^R and Tc^R indicate resistance to kanamycin, ampicillin, gentamicin and tetracycline, respectively. NAHSL, <i>N</i>-acyl homoserine lactone; CFBP, Collection Française de Bactéries associées aux Plantes, Institut National de la Recherche Agronomique (INRA), Angers, France.</p

NAHSL-breakdown and biocontrol activity of the QsdA-expressing<i>E. coli</i> strain in potato tubers.

<p>(A) <i>E. coli</i> DH5α(pUC19) (<i>Ec</i>) and <i>E. coli</i> DH5α(pUC19-<i>qsdA</i>) (<i>Ec-qsdA</i>) were compared for biocontrol activity against <i>P. atrosepticum</i> 6276 (<i>Pa</i>-QS+) 1, 2, 3 and 7 days after inoculation of potato tubers. For the controls, one or both strains were replaced in the inoculum with a 0.9% NaCl solution. Significant differences (Mann and Whitney test; <i>α</i> = 0.05) in maceration symptoms between infected tubers inoculated with the <i>Ec</i> or the <i>Ec-qsdA</i> strains are indicated with an asterisk. (B) Population dynamics of <i>P. atrosepticum</i> and <i>E. coli</i> bacteria (CFU/g fresh weight of potato tubers; black and blue lines respectively), and NAHSL concentration (ng/g of potato tubers; black and white bars), were determined for each condition in potato tubers. For lines and bars, each value is the mean of three replicates with the standard deviation indicated. NS, non-significant; NAHSL, <i>N</i>-acyl homoserine lactone.</p