Hi Saurav,

DNA in water is often less than that in soils or fermentation broth. If you want to do metagenomic, you need to have enough DNA. The first step is to enriched cells. You can filter 5L water to a 0.22nm membrane, and finally collect the membrane. Good luck!

Hi Saurav,

I should stress that this is well outside my area of expertise.  I wonder if it is possible to use the basic principles that are applied in many DNA purification kits : apply an alkaline lysis method to break any cells present (treat with 0.2N NaOH, 1% SDS) and release DNA, then acidify the sample to neutralise (3M Potassium Acetate), (optionally remove any precipitate) and then incubate the neutralised samples with powdered silica and hope that the DNA binds to the silica under these conditions?  The silica slurry could be captured by pouring the sample through a filter and allowing the liquid to drain away, then washed with 70% Ethanol, 100% EtOH and air-dried.  Finally, elute the DNA with 10mM Tris-HCl pH8.5 in a small volume for onward processing.

If the cells are more durable than classic E.coli, perhaps sonicating the samples briefly to begin with may be an approach, although this does risk shearing the DNA that you are hoping to isolate.

Good luck!

Hi Saurav,

DNA in water is often less than that in soils or fermentation broth. If you want to do metagenomic, you need to have enough DNA. The first step is to enriched cells. You can filter 5L water to a 0.22nm membrane, and finally collect the membrane. Good luck!

I recommend you the protocol explained in this article:

Massana R, Murray AE, Preston CM, DeLong E. (1997). Vertical distribution and phylogenetic characterization of marine planktonic archaea in the Santa Barbara Channel. Appl Environ Microbiol 63: 50–56.