I am working with a marine non-model organism that has a planktrotrophic larval type and I found out that the larvae are not very selective while feeding. I am planning to do RNAi by feeding them bacteria (E.coli) expressing dsRNA. As a preliminary experiment, I am planning to feed them with bacteria for three hours. I would like to know whether or not they are ingested the bacteria. Is there a method to stain ingested bacteria? The larval type of my organism is transparent and the gut can be visualized using an optical microscope.
Maybe you can engineer your bacteria to express a florescent protein so you can detect them in the cells.
You can just heat kill the bacteria and stain them with DAPI. This has been used in nematodes to check for feeding.
As someone mentioned above, maybe some type of GFP or other color (red/far red) engineered strain of your bacteria. If that is not possible, can you perform sectioning and staining, you could use primary antibodies that specifically target bacterial antigens.
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