Applying DNA methods in the assessment of aquatic ecosystem status and biodiversity (eDNA-monitor)
Traditionally, analyses of monitoring data with light microscopy require long experience and strong taxonomic skills. Identifying species with few distinguishing features or very small size can be difficult or even impossible, even under a microscope. Differences in techniques and taxonomic resolution often limit comparability, while sample analysis is time-consuming and expensive. For this reason, new methods are needed to complement traditional approaches.  DNA- and RNA-based molecular techniques offer a cost-efficient way to complement, update, and enhance monitoring, while also improving the comparability of results. In these methods, DNA from specific gene regions is extracted and amplified, and the resulting sequences are compared with reference data stored in sequence databases.  The project builds on data from SYKE's open Hertta database, which contains information produced with traditional taxonomic methods. By applying DNA analyses to the same samples, it becomes possible to directly compare the two approaches.  The main objective is to test, develop, and validate the use of DNA methods for assessing both the ecological status of waters and biodiversity. The project also aims to create guidelines for DNA-based monitoring of different biological quality elements—phytoplankton, benthic diatoms, benthic invertebrates, and zooplankton—in lakes, rivers, and in both coastal and offshore areas of the Baltic Sea. Another goal is to investigate whether analyses generated with traditional methods, which are limited in taxonomic resolution and demand considerable work time, can be complemented or ultimately replaced by automated, standardized, and precise numerical DNA methods. The project will also explore alternative ways of interpreting DNA results (such as Operational Taxonomic Units, OTUs, or Amplicon Sequence Variants, ASVs), contribute to the expansion of reference sequence databases, and pilot the use of DNA techniques in zooplankton monitoring in inland waters.