Hai
Anyone can explain the genomic DNA isolation methodology of net
collected zooplankton samples for Metagenomics (diversity) studies.
I am facing an issue in DNA isolation from net collected samples due to high biomass.
Anyone have experience in the Metagenomics studies in zooplankton; please suggest some tips to handle the large volume and effective DNA isolation for Metagenomics studies.
Thanks
Qiagen DNeasy Blood and Tissue kit is good for DNA isolation from Zooplankton sample.
other wise u can try with CTAB DNA extraction method that was modified from the method established by Winnepenninckx et al. (1993), modified phenol chloroform DNA extraction method from Pearson and Stirling (2003).
There are lot of kits out there that can help you get genomic DNA. It depend on what quality of DNA are you looking for, surely you need un-smeared DNA if you are working with metagenomics. You can refer the papers based on the work done on zooplanktons, even if its not metagenomic. Because you need some DNA to start with.
Check Di Capua et al 2017 (Plos One 10.1371/journal.pone.0175662) where they extracted DNA from zooplanktons for phylogenetic studies.
another suggestion is DNA extraction efficiency is directly related to sea water and salt content. SO if you want to extract DNA from net sample, first thing you can try is to centrifuge or filter your net sample to remove any sea water from the sample and then proceed to lysis step. This step will help that the salts from sea water do not interfere your DNA extractions.
Gud luck
I understand that you are reading specialised literature, that's why I share some tips for help you.
Be carefull in the fixation of the samples, I work with some species, not metagenomics. But in the successful cases always have been the the sample with no fixing substance , in some cases I have used alcohol 96% but after that I washed my samples and put them during 15 minutes in 50°C.
Well, L. Jagadeesan in my point of view this DNA that you are trying to extract is environmental DNA (eDNA), that is probably captured by the net, to extract this, I suggest you cut a little part of the net, grind it in some way you can, and I also recommend the Qiagen Blood and Tissue DNA extraction kit. If you are not going to extract the DNA right away, you should preserve it on -20°. I hope it could help you.
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