I am planning to conduct a research project on the microbial diversity in three different water bodies and I would like to know the optimal number of times I should sample each water body to obtain statistically significant and representative data on microbial diversity. I would also like to know which agar I can use to substitute Endo agar with (if I want to carry out the membrane filtration method), for culturing and sub-culturing, and what is the best method to extract DNA for sequencing?
I think you can follow the following steps to get good results
Number of Samples: Start with 10-20 samples per water body. Adjust based on preliminary results and diversity estimates.
Agar: Use a combination of R2A Agar and Marine Agar to maximize the diversity of cultured microorganisms.
DNA Sequencing Technique: 16S rRNA gene sequencing using Illumina MiSeq is recommended for a balance of cost and information. For more comprehensive data, consider metagenomics using Illumina HiSeq or NovaSeq.
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