This week we’ve had a lot of calls and emails from people going down to the Gulf to collect oil contaminated water samples, all asking for the same advice: how do I store water filters collected in the field for later extraction of DNA when I get back to the lab? What is the best practice?  Today’s article will share our advice based on the research we have performed in this area. Here is an email from a researcher at the University of Georgia sent to us this week and our answer.

Question:

 I am looking for suggestions for storing filters for subsequent DNA extraction using your PowerWater kit. We are heading out this weekend to the Gulf of Mexico and Florida Keys and will be collecting water samples for microbial analysis. We will be able to filter in the field but not complete the extraction process. Additionally our freezer space is limited. Do you have suggestions for storage of the filters that is not dependent on freezing. Is EtOH a possibility (will it work with the extraction process downstream?)  This is a last minute trip and we are trying to work with materials at hand as best we can.

 Thanks for your insight.

Answer from Heather Callahan, Ph.D.

Thank you for contacting us!  Here are some stabilization recommendations based on work I have been doing for DNA and RNA since last year. 

 These recommendations can be modified to work in Sterivex units or with flat filter membranes.  

Ethanol does not work.  Experiments using either 70% or 100% ethanol resulted in nucleic acids that are completely degraded and lost. 

Clean Water

Clean water samples can be stored dry in the kit bead tubes (or sterivex unit) at either room temperature or cold (refrigerated to -20 C).

Cold is usually best and DNA and most of the time RNA is very stable if the membrane is dry.  These results have been very consistent.  This is the easiest approach because if you are using the flat filter membranes, when you return to the lab, you can just add the lysis buffer and follow the kit protocol without having to transfer the membrane. With Sterivex, you can remove the membrane upon return and place into the PowerWater Bead Tube and begin the prep.

Dirty or Polluted Water

Filters from dirty water samples (muddy or heavily discolored) can be stored dry in the PowerWater bead tube also, but should be stored cold for best results. DNA from dirty samples appears to have the best integrity when the sample is stored at 4C vs. room temperature.  For short periods of time (3 days), room temperature storage may be ok and for long term storage, dry membranes chilled or frozen will result in high quality DNA.

We have also tested the use of LifeGuard Soil Preservation Solution for preserving the DNA and RNA from water filters. For dirty samples, this may be helpful to reduce degradation. Place the water filter into the bead tube and then use 2-4 ml of LifeGuard to saturate the filter. Storage at 4C or colder is still best for long term storage (> 1 week).

To process water filters that have been soaked in LifeGuard, centrifuge the bead tube containing the sample and beads to pellet all bacteria that may have fallen off the filter. Remove as much of the stabilization solution as you can so the lysis reagents are not diluted out significantly.

Alternatively, it would be better to store the filter in stabilizer without the beads so that the solution can be removed efficiently. If you need some empty PowerWater Bead Tubes before your next trip, let us know. If you plan to store the filters dry, then use the bead tube containing beads and then you can begin with the protocol as soon as you return to the lab.

Water Containing Metals

Just a side note regarding water that may be relatively clean from humic substances but contain high amounts of metals, such as water collected in acid mines or underground caves. Feedback from researchers has been to use the PowerWater DNA Isolation Kit.  Scientists have reported back to us that the method incorporating IRT has been successful at providing high quality DNA free of PCR inhibitors.  We are always collecting feedback so please let us know if you are working with metal contaminated water and what works best for you.

Summary

Since each project is different and often times you really have no information in advance about what your water will be like, you can call us to discuss and we can guide you further based on our experience. You may want to try a couple different methods to see which works best for you.

We are always looking for feedback from researchers using products so if you have any results of your own with water filter storage or if you want to try some comparison studies in collaboration with us, please contact us and let us know. 

And for processing DNA from microbes from oil, we have some references and recommendations depending on whether you are working with sediment or water filters. Contact us for advice.

We still have some of our PowerWater T-shirts left. Any blog readers working with the UltraClean Water DNA Kit or the PowerWater or RapidWater DNA Isolation Kits who would like to work with us to compile the results of water DNA purification from various sources of water and the best practices for stabilizing the DNA from those sources will receive one of our t-shirts.  Contact us at technical@mobio.com to discuss your next trip and the water type and filter type and we can provide advice and reagents.

For more information on How to Choose a Water Filter and for a video on how to transfer them from the filter funnel to the bead tube, click this link.

~Suzanne