whichever - how can you have any form of ownership over a natural bacteria?

1) By keeping the bacteria a secret: not telling which bacteria can be used like this, not telling where you can find it in the nature, not giving anyone a piece of the bacteria culture to use.

2) By patenting the industrial process that makes use of the bacteria, thus gaining an exclusive commercial right to it.

It’s kept by patenting of the process involving the bacteria and the bioreactor, I think. Google Patent query: https://patents.google.com/?assignee=%22Solar+foods%22&oq=%2...

Now CA3153196A1 is the interesting one as it names Xanthobacter sp. VTT-E-193585 as the strain of interest. You even get a 16S rRNA sequence with it for doing some taxonomy! This is not to be confused with FI129574B involving a similar but genetically modified bacterium.