MINERAL PRESERVED eDNA
Extracting ancient environmental DNA (eDNA) from soil and lakebed sediments has provided a whole new insight into mega-faunal demography, plant, animal and microbial diversity.
The starting point of the eDNA research is the extraction of DNA from associated sediments. The extraction procedures are optimized as far as the current knowledge allows, but the extractions still introduce a bias in the extracted data, simply because some mineral-DNA bonds are stronger than others and respond differently to extraction solutions. The few approaches taken to study the strength and stability of the DNA-mineral bonds treat the adsorption of DNA to minerals at the bulk level and the information obtained is mostly qualitative and, therefore, hard to extrapolate to systems outside the range of the experimental system and conditions. Additionally, this lack of understanding prevent us from quantifying if the extracted DNA is of primary origin or if has been remobilized and also limit our focus to well preserved deposits and therefore limit the scope.
My group and I are using nanoscale techniques in combination with environmental samples to unravel the DNA-mineral affinities at different environmental settings. Techniques include atomic force microscopy, FTIR and XRD.
Ioannis Kontopolos has started his postdoctoral experience
in April 2020 to work on reaction kinetics of DNA-mineral
associations in the environment. He was awarded a Marie
Skłodowska-Curie Individual Fellowship (H2020-
MSCA-IF-EF-ST) for our DENMARK project (below).
THE DENMARK PROJECT
Environmental DNA (eDNA) is trace amounts of DNA released by organisms into water and sediments. It has recently attracted a lot of attention as it can be a valuable tool for detecting present and past organisms without the need to directly sample them. However, biotic and abiotic decay has severe effects on DNA survival. The adsorption of DNA to mineral surfaces in sediments have been shown to protect DNA molecules and decrease the DNA decay rate. Understanding which minerals and environmental conditions provide the best preservation of adsorbed DNA can thus allow us to:
a) target such environments for paleoecological and palaeogenetic studies;
b) serve as a quantitative tool for assessing DNA migration, i.e. is the recovered eDNA autochthonous?;
c) significantly advance eDNA extraction and analysis protocols by targeting and extracting eDNA from specific minerals.
Ioannis approaches will include extraction techniques, atomic force microscopy, and in-situ liquid cell FTIR
I am looking for students with knowledge of
geology, chemistry, bioinformatics or microbiology
to look into different aspects of how to optimize retrieval of DNA from sediments.
We will be using surface science and a range of spectroscopy and microscopic approaches. No knowledge of those is required beforehand.
Send an informal email for for more info: