[Coral-List] extraction of bacterial DNA from coral samples.

[buiscuil]

Dear coral-listers,
I am currently working on coral-associated bacteria (not only in mucus) but
am not entirely satisfied by my 16sDNA yields. Having shortly begun, I would
not assert too much, but to my knowledge, no methods comparison has been
published on this particular matter of extracting bacteria from cora
samples. It is most needed though as insufficient yields or unappropriate
protocols can lead to major under-identification of bacterial
associated-communities.

I think my first present objective is to maximize my yield, as coral DNA
largely overwhelms bacterial DNA in a coral sample. I know most people uses
a classical phenol/chloroform technique for coral DNA extraction, but is
there evidence of efficiency of this method in regards to others on coral?
Is there any chance to reach satisfactory results using a DNA extraction
kit?
Also, I understand that the coral species studied can need changements in
the protocol. Personnaly, I temporaly focus on Acropora palmata, A.
cervicornis and Siderastrea siderea.
At least, I wonder if coral squeleton has a negative effect on the DNA
extraction.

If you have any suggestion or reference that would help me I would be very
grateful.
Best wishes,
--
Pascal Mège, PhD candidate
University of Puerto Rico