Preservation and storage effects on river sediment microbiomes: Implications for community stability and ecological inference

How river sediment microbial communities are affected by the way they are preserved and stored during laboratory work has significant implications for how scientists interpret data about these communities. We tested how different preservation methods, storage temperatures, and storage times influence the microbial makeup of river sediments using DNA sequencing techniques that target particular genes common to microbes.

Sediment samples were preserved in ethanol, a buffer used to preserve nucleic acids, or without any preservative, and kept at room temperature or frozen at temperatures ranging from -20 to -80 degrees Celsius for up to eight weeks. Our findings reveal that the method used to preserve the samples, the temperature at which they are stored, and the length of time spent in storage all impact the diversity and composition of the microbial communities found in the sediments.

Differences in microbial communities can be seen within a relatively short period of time—around 18 hours—and tend to become more pronounced as the samples are stored for longer. Frozen samples maintained the most similar community makeup to the original samples, while those stored at room temperature, especially without a preservative, showed the most significant changes.

Even with the use of preservatives like ethanol and a buffer, these changes still occurred during storage at room temperature. Additionally, preservation methods also altered the types of microbes identified and the results of statistical analyses used to infer community dynamics. Overall, frozen storage appears to be the most effective way to preserve the microbial communities in river sediment samples, and should be the preferred method when immediate processing of samples is not possible.