What is the most effective treatment for maintaining soil microbial community structure during field sampling expeditions?

Microbial ecology is dependent upon environmental samples collected in the field. However, field trips in remote locations present a number of logistical problems which can compromise sample integrity and lead to unreliable conclusions. Microbial communities continue to live after sample collection and, now under different conditions, may shift their composition. In the laboratory environment, the microbial community can be held constant through techniques such as freezing which may not be available for several days during sampling trips. There are several treatments which claim to preserve samples without refrigeration but most are (1) not designed for soil communities and (2) have not been independently tested.

We compare five treatments—DNA/RNA Shield (Zymo Research), PowerProtect DNA/RNA (Qiagen), Phoenix Protect (Procomcure Biotech), DESS and silica gel packets—on the basis of ease-of-use, cost-effectiveness and preservation effectiveness to make a final recommendation of the best choice for preserving microbial soil communities during field trips. Soil samples were collected, treated with one of the five treatments and incubated at either 5 °C or 22 °C. DNA was isolated from controls at the beginning of the experiment and from the treated samples at 7, 14, 28 and 56 days after sampling. Amplicons of the bacterial 16S ribosomal gene and fungal ITS region were sequenced and analysed to compare how the microbial communities in different treatments changed over time in terms of their richness and overall beta diversity. In addition, we checked for differential abundance of individual taxa.

With this work, we hope to inform researchers about which microbial preservation treatments are most appropriate for soil samples and which taxa might still change despite their use. We hope that this will aid researchers better plan field trips into remote locations and will improve the quality of data produced from such trips.