Conclusions: guidelines for optimizing preservation conditions
Standardized protocols are essential for repeatable and reliable
biodiversity monitoring, and our results allow to propose guidelines to
improve and standardize the preservation of soil samples for eDNA
metabarcoding analyses (Fig. 5):
1) If sampling occurs close to lab facilities, or a mobile lab is
available, extracting DNA as soon as possible is the best approach.
Storing samples a few hours at room temperature does not have major
impact on the outcome of analyses, especially if the focus is not on
rare MOTUs;
2) If lab facilities are available after a short-time transportation,
storing samples in the fridge (0-4°C) for a few days is a safe approach
as it does not have a significant impact on community composition, and
only moderately affects MOTUs richness. However, this approach can be
problematic if the aim is to estimate MOTUs richness, and particularly
the occurrence of rare MOTUs. The feasibility of this strategy also
depends on the number and volume of samples, and to the possibility of
maintaining the cold chain;
3) If monitoring in remote areas, sample desiccation (e.g. using silica
gel) and long-term preservation at room temperature is a reasonable
approach, and it is particularly convenient when working with a large
volume of samples. This approach preserves ecological signal, but can
affect the detection of some taxa, particularly among the rarest ones.
Therefore, this approach is suboptimal for monitoring programs aiming at
detecting rare MOTUs.
An effective application of eDNA metabarcoding to biodiversity
monitoring is complex, and protocols of sample preservation are key
methodological choices that has to be taken into account when designing
a metabarcoding-based monitoring. When working in difficult and remote
environments researchers are faced to the trade-offs between a faithful
representation of biodiversity, and multiple logistic constraints in the
field. Accurate a-priori planning is often the basis of successful
monitoring programs and our guidelines can help researchers and
practitioners to identify the best approach to sample preservation,
depending on the studied taxa and research goals.