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Team:Evry/Biology/Chassis/Pseudovibrio
From 2014.igem.org
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| + | At first glance working on the microbiome of sponges seems like an hasardous task : 5734 articles for marine sponges, only 51 with microbiome of sponges, 28 articles mentionning <i>Pseudovibrio genius</i>, 5 mentionning <i>Pseudovibrio denitrificans</i> | ||
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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 (cf <b><big> toxic compound</big></b>) and easy to sourced at <b><big>DMSZ</big></b>. | 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 (cf <b><big> toxic compound</big></b>) and easy to sourced at <b><big>DMSZ</big></b>. | ||
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Revision as of 16:40, 12 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 seems like an hasardous task : 5734 articles for marine sponges, only 51 with microbiome of sponges, 28 articles mentionning Pseudovibrio genius, 5 mentionning Pseudovibrio denitrificans
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 (cf toxic compound) and easy to sourced at DMSZ.
On the other hand to that Pseudovibrio denitrificans or strains related to the species has been shown as majoritary in at least six microbiomes of sponges in the mediterrean sea, where spongia officinalis reside.
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 (cf toxic compound) and easy to sourced at DMSZ.
On the other hand to that Pseudovibrio denitrificans or strains related to the species has been shown as majoritary in at least six microbiomes of sponges in the mediterrean sea, where spongia officinalis reside.
== A bacterium we could work with ==
Stained as a Gram-negative, the cells in late exponential to early stationary phase of growth were predominantly straight or curved rods. They were motile by means of one to several lateral or subpolar flagella. Both strains required NaCl for growth and exhibited optimal growth at about 30 degrees C, pH 8 and 3 % NaCl.
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.
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.
- be massively present on the sponge surface / avoiding being in an unfavorable position for food competition.
- be found mainly in sponges / avoid spreading to species in contact with sponges.
- be the phenotypically closest possible to a known bacterium. / avoid cell cultures difficulties.
