In terms of my research, I would say getting DNA out of the microbes that live in extreme environments. For my PhD I worked on soil microbes, which was fairly simple, and I assumed it might be with salty sediments – however, the chemistry of these salts (high salt, sulfur and some heavy metals) interferes with the DNA extraction AND the number of cells is much lower.
I have managed to design some methods to overcome this now but this took a lot longer than I hoped!
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