DISTRIBUTION OF ANTIBIOTIC RESISTANCE GENES IN THE ENVIRONMENT:
THE ROLE OF MINERAL FACILITATED HORIZONTAL GENE TRANSFER
Combining recent research across disciplines, I see evidence that minerals hold a high and unrecognized potential for enhancing the distribution of the ARg in the environment. Adsorption of ARg to minerals significantly increases the ARg’s lifetime and facilitates their distribution by sedimentary transport processes. In addition, minerals also serve as a) sites for horizontal gene transfer (HGT), b) platforms for microbial growth and, hence 3) act as hot spots for propagation of adsorbed ARg to other microbes. However, some minerals and ARg are bound more strongly than others and various bacteria have different affinities toward various minerals. Those variations in affinity are poorly quantified but vital for predicting the distribution of ARg in the environment.
Bacterial colony formation.
Image by Lisselotte Jauffred (collaborator from NBI)
The spread of antibiotic resistance genes (ARg) is a worldwide health risk1 and is no longer only a clinical issue. Vast reservoirs of ARg are found in natural environments2–4 such as soils, sediments and oceans. The emergence and release of ARg to the environment is in particular caused by extended use of antibiotics in farming, e.g. where the genes dissipate from the manure.5 Once in the environment, the ARg are surprisingly rapidly propagated. It is well known that the ARg are distributed to neighbour bacteria through processes of both cell sharing or through horizontal gene transfer (HGT) where one species acquirer resistance from another.6,7 Most HGT responsible for the spread of ARg are assumed to be through direct microbe-microbe contact. However, I find that the outcome of non-contact transfer is grossly underestimated. In the HGT mechanism called “Transformation”, free ARg in suspension or adsorbed to a mineral can be picked up and incorporated into non-related organisms. Considering that free DNA only can survive for a few weeks in sea- and freshwater environments,8–10 any HGT from free DNA can rightly be assumed to be local, but if the DNA gets adsorbed to a mineral, it can survive for several hundred thousands of years.11–14 If this also holds for ARg, then minerals offer a potent mechanism for distributing ARg through our environments my means of sedimentary processes.
KARINA K. SAND
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.
APPROACH
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.
FUNDING
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:
PROJECT IMPACT
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
NEWS
STUDENT PROJECTS
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: kks@sund.ku.dk