The Copenhagen Strain

As a side project to the main project we decided to try to find our own strain of magnetic bacteria from within our local environment, isolate and cultivate it.
Cultivating a new strain of magnetic bacteria could have several advantages: its magnetosome might have different properties, copy numbers or way of synthesis, it might grow faster (the strain we used in the other experiments had a generation time of 9 hours (which is long for a bacterium) or the oxygen demands might be different. Also cultivating a new strain will give greater insight into the origin of the magnetosome.

We collected samples from lakes in Copenhagen and from these samples we tried to purify the magnetic bacteria. For the purification we used the protocol from Jove.

We succeeded in enriching the samples for magnetic bacteria. Under light microscope it was clearly seen that the bacteria in the enriched samples moved according to a magnetic field. See video 1, 2 and 3. Based on the morphology we saw at least two different species of magnetic bacteria.



In video 1 it is seen that the bacteria in the sample move toward the South Pole of magnet.
The bacteria are seen as small round “dots” moving toward the top of the picture not being able to move any further than the edge of the water droplet. When the magnet is turned around it is seen that the bacteria start moving away, repelled by the North Pole.

In video 2 a different and significantly larger bacterium (or possibly colony of bacteria) is seen moving towards the South Pole of a magnet.

In video 3 the same bacterium as in video 2 is seen turning very precisely to the movement of a magnet, keeping the same side of itself toward the South Pole of the magnet at all times. Note: the bacteria seemed to die rather fast under the microscope we speculate that this is due to oxygen exposure. This is properly the reason that the bacterium in video 3 stopped moving as video 3 was recorded later than video 2.

The enriched water samples were moved to different sorts of medium previously used to grow magnetic bacteria for cultivation. Until now no growth has been detected.

To get a better idea of what kind of bacteria that were in our enriched samples we sequenced part of the 16S. PCR was preformed with the water samples used as DNA template and the universal 16S primers 907R and GM5F to amplify what ever 16S DNA in the samples. The PCR products were cloned into vectors and sequenced. Click for better view.

Phylogenetic tree of magnetotactic bacteria found in a Copenhagen lake. Click on image for better view.

We sequenced 20 sequences and found 16 of them to originate from different species, indicating that the samples were not as pure as we expected. All the sequences found were compared to known 16S sequences of magnetic bacteria. None of the found sequences seems related to the known sequences. This can mean that none of the bacteria sequenced in this study are in fact magnetic. Another possibility is that some of the bacteria in sample are actually magnetic but they belong to a different clade of magnetic bacteria. This could have happened by horizontal gene transfer. Additional studies are needed to clarify this further.

We are still working with cultivating a strain of magnetic bacteria from Copenhagen, our hope is that we will be able to make it grow under laboratory conditions and then sequence the whole genome. If this is not possible we will try to sequence the genome directly from the enriched water sample. As seen from the 16S sequencing though, we need to enrich the samples further. We hope to have some more results to show at the jamboree.