Team:Evry/Biology/Chassis/Pseudovibrio

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<h2> <i>Pseudovibrio denitrificans </i> the bacterium to modify</h2>
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== <b><big>From a poorly known genius, a jewel emerged</big></b> ==
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At first glance, working on the microbiome of sponges appears like a hazardous task: 5734 articles for marine sponges, only 51 with microbiome of sponges, only 28 articles mentioning <i>Pseudovibrio genius</i>, only 5 mentioning <i>Pseudovibrio denitrificans</i>, and finally none about a genetic engineering system in it.
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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 <a href="http://www.dsmz.de/catalogues/details/culture/DSM-17465.html"> <b><big>DMSZ</big></b></a>.
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On the other hand <i>Pseudovibrio denitrificans</i>, 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 <i>spongia officinalis</i> resides.
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Now the thorny question is: can it be easily used  in our lab?
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== <b><big>A bacterium we  could work with</big></b> ==
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In the literature <i>Pseudovibrio denitrificans </i> 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 favourable for an iGEM project</i>.
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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 <b><big>RNAseq</big></b> study to discover the transcripts upregulated by the presence of nitrite and clone their promoters as new sensors.
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The following section describes protocols used to optimize (Rich media) & control (Minimal media) growth conditions.
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