How do researchers avoid over-amplification of eukaryotic chloroplast 16S rDNA when classifying prokaryotic microbial communities in algal bloom experiments?

For example, if I need to amplify bacterial DNA living on a certain green algae, it's inevitable that chloroplast DNA will also be amplified. This results in sequencing data being predominantly chloroplast DNA, with only a small portion being bacterial. What are some solutions to this?

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