Sample Storage - A debate for the ages

Jashan Gokal | 28 February 2016

Going out into the field to sample can be quite an adventure, but it can also be exhausting. On the other hand, when you are also the scientist who has to analyse those samples after a long day of collection, it takes a respectable amount of mental fortitude to not throw in the towel. So…what do you then do when you can’t analyse your samples immediately?

If you plan on storing your sample for physical analysis; it’s best to first fractionate your sample into a liquid and solid phase (by a quick centrifugation), filtering out any microbes in the liquid phase and storing that at -20°C. The solid phase may be oven dried further (if necessary) and can then be frozen at -80°C. The chemical content and solid mass shouldn’t change significantly in the absence of microbial activity although this will have to be verified with your type of sample and storage vessel.

Storing samples for metagenomics analysis or any other purpose becomes slightly trickier. All storage methods will still result in DNA extracts, but whether that DNA is still truly representative of that population is still up for debate. There are 3 main ways for storing a sample:

  1. Drying- This generally refers to drying using dry heat such as that from an oven. The final product may then be stored frozen.
  2. Freezing- can refer to freezing your sample in its native form (which is not recommended due to the high water content), freezing in some kind of cryoprotectant, or freeze-drying. Using cryoprotectants is generally the best way to store metabolically active bacteria for revival at a later stage. Freeze-drying may require special equipment, but it renders the most stable population for downstream metagenomics, and can be stored indefinitely.
  3. Fixing- By mixing the sample with a fixing agent (formaldehyde/ethanol etc.) it “fixes” the cells in the metabolic state they were in at the time of processing. This is best for FISH or RNA analysis, and can be stored for a few months.

Wastewater samples are surprisingly delicate when you consider the environment they come from, and are prone to community shifts. You will have to optimise a storage method based on your sample type and analysis target. Have any storage methods worked well for you or have you seen any significant community shifts?

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