Fig 1.
Acquisition of symbionts in the gill chamber of Rimicaris exoculata.
(A) Epibiontic colonization through the molt cycle [22–23] compared to (B) biofilm formation [32].
Table 1.
Primers used (all sequences were designed during the study).
Table 2.
Rimicaris exoculata samples used for amplification of lux genes indicating parts sampled from different vent sites.
Table 3.
Rimicaris exoculata samples used for amplification of lux genes according to the molt stages.
Table 4.
Clone library for the lux genes of Rimicaris exoculata epibionts.
Fig 2.
Example of PCR on gill chamber epibionts of R. exoculata.
(A) luxS amplification. luxS genes from Vibrio harveyi and Vibrio parahaemoliticus were used as negative controls. (B) luxR amplification on branchiostegite (br) and scaphognathite (sc) epibionts. (C) luxR amplification on gut (g) and stomach (st) epibionts.
Fig 3.
lux gene PCRs on epibionts of R. exoculata juveniles and eggs.
(A) luxS amplification on scaphognathite and eggs. (B) luxR amplification on scaphognathite and eggs. (C) luxR amplification on (br) branchiostegite and (sc) scaphognathite at the beginning (1) and end (2) of the molt.
Table 5.
PCR and RT-PCR (end of molt) amplification results per sample of different Rimicaris exoculata parts from different vent sites for the luxS gene analysis.
Table 6.
PCR and RT-PCR (end of molt) amplification results per sample of different Rimicaris exoculata parts from different vent sites for the luxR gene analysis.
Fig 4.
Example of lux RT-PCR on gill chamber epibionts of R. exoculata.
Free RNAse/DNAse water was used as template for the negative control. (A) luxS 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) luxR 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.
Fig 5.
luxS gene phylogeny (calculated on 550 bp) of symbionts associated with the gill chamber of R. exoculata.
The robustness was tested using 500 bootstraps resampling the tree using the Neighbor-Joining algorithm with the Kimura two-parameter correction matrix. (A) luxS gene affiliated to Proteobacteria. (B) luxS gene affiliated to Epsilonproteobacteria. (C) Localizations of R. exoculata on hydrothermal vents and studied areas; red: Rainbow, green: TAG, blue: Snake Pit, orange: Logatchev (modified from [71]). Clone numbers are indicated between brackets.
Fig 6.
luxR gene phylogeny (calculated on 560 bp) of symbionts associated with the shrimp R. exoculata.
The robustness was tested using 500 bootstraps resampling the tree using the Neighbor-Joining algorithm with the Kimura two-parameter correction matrix. (A) luxR affiliated to Proteobacteria. (B) luxR affiliated to Gammaproteobacteria. (C) Localizations of R. exoculata on hydrothermal vents and studied areas; red: Rainbow, green: TAG, blue: Snake Pit, orange: Logatchev (modified from [71]). Clone numbers are indicated between brackets.