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Team:Evry/Biology/CellCharacterization/GenomeAssembly
From 2014.igem.org
De novo Genome assembly
DNA extraction
Assembly Strategy
software used
Velvet for de novo Assembly
best with kmer length 97contigs: 275
Contigs quality
Annotation
Prokka tools for annotation
organism: Pseudovibrio spAssembly Strategy
Antibiotic genes
Restriction enzyme
Cadmium
NItrite
With the help of the 'Molecules of defence and communication in the microbial ecosystems' team of the National museum of natural history of Paris (their web page here), we succeed to cultivate our bacteria Pseudovibrio denitrificans in two medium, the marine broth (MB) and the minimal medium M9 added by 3% of NaCl.
Because of the opaqueness of the marine broth, it's impossible to obtain reliable data of the growth of the bacteria. Thus, the growth curve that we have made, has been made in M9+3%NaCl 1X, with the TECAN infiniteM200.
![Curve TECAN]()
Figure1: Curve of growth in liquid M9+3%NaCl 1X.
The marine broth is more complete than the M9+3%NaCl, even if we have adjusted the salinity. As we can see in the Table2, Pseudovibrio denitrificans grows better on MB media. The number of colony is higher, and they are significantly bigger (Figure2). Moreover, the growth is faster.
![Table+Photos of MB 1X and M9+3%NaCl 1X plates]()
Figure2: Number of CFU and photos of MB 1X and M9+3%NaCl 1X plates.
In the aim to know if we can transfer Pseudovibrio denitrificans from a media, to the other one, we have made some tests and calculate a ratio of survivability. We have made two pre-cultures of Pseudovibrio denitrificans in MB 1X and M9+3%NaCl 1X, and after a culture overnight, we sowed them on plates of MB 1X and M9+3%NaCl 1X (Figure3).
![Table+Photos of ratio of survivability]()
Figure3: Tests of survivability, table of ratio and photos.
Pseudovibrio denitrificans can survive even if we tranfer them from a media to the other one. But we can see that even cells come from a pre-culture of M9+3%NaCl, they grow better and faster on MB plates. Moreover, even if they come from a MB pre-culture, they don't grow very well on M9+3%NaCl plates.
Table1: Composition of used media, marine broth and M9+3% NaCl.
Because of the opaqueness of the marine broth, it's impossible to obtain reliable data of the growth of the bacteria. Thus, the growth curve that we have made, has been made in M9+3%NaCl 1X, with the TECAN infiniteM200.
Figure1: Curve of growth in liquid M9+3%NaCl 1X.
The marine broth is more complete than the M9+3%NaCl, even if we have adjusted the salinity. As we can see in the Table2, Pseudovibrio denitrificans grows better on MB media. The number of colony is higher, and they are significantly bigger (Figure2). Moreover, the growth is faster.
Figure2: Number of CFU and photos of MB 1X and M9+3%NaCl 1X plates.
In the aim to know if we can transfer Pseudovibrio denitrificans from a media, to the other one, we have made some tests and calculate a ratio of survivability. We have made two pre-cultures of Pseudovibrio denitrificans in MB 1X and M9+3%NaCl 1X, and after a culture overnight, we sowed them on plates of MB 1X and M9+3%NaCl 1X (Figure3).
Figure3: Tests of survivability, table of ratio and photos.
Pseudovibrio denitrificans can survive even if we tranfer them from a media to the other one. But we can see that even cells come from a pre-culture of M9+3%NaCl, they grow better and faster on MB plates. Moreover, even if they come from a MB pre-culture, they don't grow very well on M9+3%NaCl plates.
