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Team:Evry/Biology/Chassis/Pseudovibrio
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| - | Moreover with only 12 species in the genius, and 2 strains sequenced (Pseudovibrio sp. FO-BEG1, Pseudovibrio sp. JE062) we knew we would have to sequence our strain of <i>Pseudovibrio denitrificans </i> with a mapping to one of the 2 strains references. A formidable drawback even considering that in the first place the species was chosen because of its natural denitrification ability (see <a href="https://2014.igem.org/Team:Evry/Biology/ToxicCompounds"> <b><big> toxic compound</big></b></a>) and easy to source at <b><big>DMSZ</big></b>. | + | Moreover with only 12 species in the genius, and 2 strains sequenced (Pseudovibrio sp. FO-BEG1, Pseudovibrio sp. JE062) we knew we would have to sequence our strain of <i>Pseudovibrio denitrificans </i> with a mapping to one of the 2 strains references. A formidable drawback even considering that in the first place the species was chosen because of its natural denitrification ability (see <a href="https://2014.igem.org/Team:Evry/Biology/ToxicCompounds"> <b><big> toxic compound</big></b></a>) and easy to source at <a href="http://www.dsmz.de/catalogues/details/culture/DSM-17465.html"> <b><big>DMSZ</big></b></a>. |
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Revision as of 02:22, 18 October 2014
Pseudovibrio denitrificans the bacterium to modify
== From a poorly known genius, a jewel emerged ==
At first glance, working on the microbiome of sponges appears like an hazardous task: 5734 articles for marine sponges, only 51 with microbiome of sponges, only 28 articles mentioning Pseudovibrio genius, only 5 mentioning Pseudovibrio denitrificans, and finally none about a genetic engineering system in it.
Moreover with only 12 species in the genius, and 2 strains sequenced (Pseudovibrio sp. FO-BEG1, Pseudovibrio sp. JE062) we knew we would have to sequence our strain of Pseudovibrio denitrificans with a mapping to one of the 2 strains references. A formidable drawback even considering that in the first place the species was chosen because of its natural denitrification ability (see toxic compound) and easy to source at DMSZ.
On the other hand Pseudovibrio denitrificans, or strains related to the species, has been shown to be in the majority in at least six microbiomes of sponges in the Mediterranean Sea, where spongia officinalis resides.
Now the thorny question is: can it be easily used in our lab?
== A bacterium we could work with ==
In the literature Pseudovibrio denitrificans is described as a Gram-negative, motile by means of one to several lateral or subpolar flagella requiring NaCl for growth. It exhibits optimal growth at about 30 C°, pH 8 and 3 % NaCl, and a doubling time of 45 min in rich media. In a nutshell the conditions seem favorable for an iGEM project.
They are known to be capable of anaerobic growth by carrying out denitrifying metabolism using nitrate, nitrite or nitrous oxide as terminal electron acceptors. Being consequently a main reason for our RNAseq study to discover the transcripts upregulated by the presence of nitrite and clone their promoters as new sensors.
The following section describes protocols used to optimize (Rich media) & control (Minimal media) growth conditions.
