Changing filter method on 40ga. Nano

I have a built-in wet/dry filter on the back of my nano tank. I want to remove the hood lighting and filter so I can get a skimmer, new lighting and new filter. What is the best way of acheiving this without losing any of my bacteria? Also what kind of filter would be recommended? I'm a newbie at this still

 

For a 40 gallon I think a aqua c remora skimmer would be a great choice for a skimmer on a 40. I use to use a HOB filter, just a cheap one and it worked fine cleared up my water a bit. But now that I have a good amount of flow the protein skimmer is the only filtration on the tank. I took the filter off a while back, really made no difference now I just have one thing less to clean.