Does anyone have experience with DNA extraction from polyps? I would like to look at the microbial community and I am unsure how to handle the mixture hard coral and soft tissue. Thanks for any inspiration!
Maybe, this reference could be useful for you:
*DNA extraction. Flame-sterilized needle-nose pliers were used to snip off
small pieces of all Lophelia samples (live and preserved at depth) and place them in sterile aluminum weigh dishes. Each piece was crushed using a sterile hammer, and the mixture of coral skeleton fragments, polyp tissue, and mucus was transferred to a 2-ml microcentrifuge tube. Microbial community DNA was extracted from the Lophelia samples using the PowerSoil DNA extraction kit (MoBio Laboratories, Inc., Solana Beach, CA), following the manufacturer’s protocol. All samples were processed in triplicate. DNA extracts were frozen (20°C).
*Kellogg, C. A., Lisle, J. T., & Galkiewicz, J. P. (2009). Culture-independent characterization of bacterial communities associated with the cold-water coral Lophelia pertusa in the northeastern Gulf of Mexico. Applied and environmental microbiology, 75(8), 2294-2303.
I've used this kit with another kind of samples but it's very useful to get DNA from complicated samples because this kit has a first essential step: homogenization and lysis produced by action of intense centrifugal process using a kind of beads mixed with lysis buffer. FastDNA® SPIN KIT FOR SOIL (MP Biomedicals) is similar.
To analyze communities I recommend using Next Generation Sequencing techniques instead of DGGE or both of them to compare methods.
I hope you find them useful.
Thank you a lot. That is exactly what I was looking for. I will give it a try and hope it will work out :)
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