In sparsely populated countries, many freshwater systems are fairly remote and reachable only by, for example, walking (Fig.1). Therefore, acquiring information about the biological status of these remote systems may pose a challenge if sampling requires carrying a lot of sampling equipment to the site and a lot of sample material back to the lab. This has been the case for traditional monitoring of freshwater invertebrate communities, which is based on extensive sampling of the bottom fauna and storing the collected specimens in ethanol.
The EBAI project will develop and test new ways of monitoring freshwater invertebrates, and we identify species in environmental samples using short, standardized DNA fragments, so called environmental barcoding. By introducing this cost-effective, rapid and repeatable technique in nature management, monitoring may be expanded also to more remote locations.
One way of doing environmental barcoding is to sample DNA that animals shed to their environment, in water in our case. This environmental DNA (eDNA) can be collected to a filter from the sampled water and be extracted from the filter for downstream analyses. Usually, investigators have carried the sampled water to their laboratory for filtration, but carrying liters of water from remote locations is not practical. Thus, we tested if we could carry some filtration equipment to the field (Fig. 2), and do the filtration in the field (Fig. 3), and then carry just the filters to the lab. Filtering in the field allows more sampling in remote locations and therefore, gives more data for the assessments. The critical part in the in-field filtration approach is how to preserve the filters.
In our first experiment, we filtered 64 litres of water in the field and tested how different filtration techniques affect the eDNA-based invertebrate community results (Fig. 4).
We found out that mixed cellulose ester filters preserved either dry or in lysis buffer give the most consistent community composition (Fig. 5). Thus, we advocate filtering in the field, using mixed cellulose ester filters and preserving the filters either dry or in lysis buffer. You can find the results summarized in our recently published article: https://www.nature.com/articles/s41598-018-23052-8.