(e)DNA barcoding: screening for species presence and diversity
Besides screening for variation between individuals of the same species, markers can also be developed specifically to differentiate at species level.
Such so-called DNA barcodes can then be applied to identify specimens in a cheap and rapid fashion, and allows identification in case morphological identification is not possible (e.g. tissue or leaf fragments, or products made from biomaterial). DNA barcoding can not only be useful for answering all kind of taxonomic questions and for assessing levels of diversity in ecosystems, but also for very applied purposes, such as the detection of invasive species or pests and diseases in trade or in the environment. Due to availability of new techniques for high-throughput sequencing of DNA-fragments, standardized barcodes are currently produced world-wide in great numbers for numerous species. Libraries containing such barcodes can then be used as a reference to identify new specimens. Reference libraries and easy-to-use diagnostic tools are now rapidly being developed, and will soon be available for many taxonomic groups. Alterra is actively involved in such efforts, as we harbour an essential but unique combination of strong taxonomic expertise, up-to-date molecular facilities and broad experience with applied research questions.
Example: Detecting elusive aquatic species based on environmental DNA (eDNA)
A novel but promising approach for the detection of elusive species is the use of environmental DNA (eDNA). Using taxon-specific PCR assays (qPCR or ddPCR), we can assess the presence of a particular type of organism in a pond, lake or river, based on a small water sample. At the moment we have eDNA-detection methods available for six species: Red swamp crayfish (Procambarus clarkii), Common spadefoot toad (Pelobates fuscus), Great crested newt (Triturus cristatus) and European weather loach (Misgurnus fossilis), Atlantic Salmon (Salmo salar) and Round goby (Neogobius melanostonomus).
Example: High-throughput screening of soil faunal communities based on DNA metabarcoding
Within the EU FP7-project EcoFINDERS, various European partners collaborated to gain more insights in links between soil diversity and ecosystem services, across different soils, climate types and land uses. To allow rapid diversity screening of many soils throughout Europe, new tools were developed for high-throughput species identification based on the DNA contained in soil extracts. Alterra participated in this DNA metabarcoding project by coordinating validation tests based on high-throughput sequencing of mock communities, and developed a new approach for DNA metabarcoding of soil mites (Oribatida, Astigmata, Mesostigmata and Prostigmata).