Monitoring Biodiversity using Environmental DNA

As any species interacts with its environment, most of them will at some point expel DNA to their surroundings. Such DNA can be picked up in environmental samples, isolated and analysed. Within the last decade, this has become a multidisciplinary research field known as Environmental DNA (eDNA). Especially the advance in DNA sequencing technology has revolutionized this field and
opened new frontiers in ecology, evolution and environmental sciences. Also, it is becoming a powerful tool for field biologist, with new and efficient methods for monitoring biodiversity.
This thesis focuses on the use of eDNA in monitoring of biodiversity in different settings. First, it is shown that a diversity of rare freshwater animals – representing amphibians, fish, mammals, insects and crustaceans – can be detected based on eDNA obtained directly from 15 ml water samples of lakes, ponds and streams. For the amphibians there is a quantitative relationship
between species-specific eDNA molecules and population sizes. Furthermore, it is demonstrated that entire faunas of amphibians and fish can be detected by next-generation sequencing (NGS) of eDNA from pond water.
Secondly, the method is applied in a marine setting, showing that eDNA obtained directly from ½ l seawater samples can account for marine fish biodiversity using NGS. Promisingly, eDNA covered the fish diversity better than any of 9 methods, conventionally used in marine fish surveys.
Additionally, it is shown that even short 100-bp. fish eDNA sequences in seawater degrades beyond detectable levels within days. In seawater, the method is also used for detection of marine mammals focusing on the cetacean species harbor porpoise. The eDNA approach consistently detected the
porpoise under controlled conditions, but in natural environments the method was less successful than acoustic detections. However, at one site, long-finned pilot whale – a species rarely sighted in the target area – was detected.
Another study examines DNA extracted from leeches to account for biodiversity of terrestrial mammals, on which they have been feeding. The persistence of mammalian DNA in leech guts is shown to persist for at least 4 months post feeding. Subsequently, it is shown that DNA from wild leeches, collected in tropical rainforest in Vietnam, contains DNA from wild mammals living in the
area, representing poorly known, cryptic and threatened species.
Finally, a study tests the applicability of non-destructive DNA extraction from old and ancient insect remains. DNA is successfully retrieved, amplified and equenced from dried museum beetle specimens up to 188 years old, ermafrost-preserved macrofossils up to 26.000 years old and directly from 1800-3000 years old temperate soil sediments from New Zealand.