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.
TAPHONOMY AND PROVENANCE OF SEDIMENTARY ANCIENT ENVIRONMENTAL DNA
The ability for sediments to preserve DNA across time and scale is still not understood, however ancient environmental DNA (SedaDNA) from sediments has in recent years proven to be an unpreceded resource of information about past ecosystems, ecological communities, and evolutionary inference. The field has undergone a massive development in the bioinformatics pipelines which still needs large investments to handle the complexities of the samples. In contrast, upstream analyses have received little attention and investment and we are currently blind to DNA taphonomy and provenance. If we can address taphonomy and provenance we can obtain a much higher spatial and temporal resolution in the interpretations of the SedaDNA.
I am working on merging interfacial geochemical principles with information from the depositional environments and the stratigraphic units as well as making nano-level experiments to test hypotheses to unravel DNA taphonomy and provenance. My recent studies show that minerals and organic compounds can sequester and preserve very different amounts of DNA and this “lithological bias” prevents us from comparing biodiversity measures across sediment types and depositional systems. To estimate changes in biodiversity across samples composed of different lithologies and or with different sedimentary pathways, we do need to account for the ability of the sedimentary components to retain and preserve DNA.
Dynamics of DNA
In my group we are using atomic force microscopy to study the dynamics of NDA adsorption and desorption as well as processes for enzymatic degradation.
Co-adsorbed organic components
Pre-adsorbed biofilm components are though to enhance the DNA adsorption capacity and influence the preservation potential of the DNA
Interfacial geochemistry
We use interfacial geochemical principles to understand DNA-mineral association at the molecular level as well at the bulk level.
Stratigraphy, sampling and ecological interpretations
I have a thing or 10 to say about procedures of sampling and interpretations of results and how data can be compared across sites.
SHORT STORIES FROM
PAPERS AND PREPRINTS
Our recent study
Application of interfacial geochemical principles to elucidate how depositional processes and the stability of DNA–sediment associations influence our interpretation of pst biodiversity from sedimentary ancient DNA.
We also identify possible interpretational biases arising from neglecting mineral and geochemical controls on eDNA taphonomy.
A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA
A major output of our work so far was exploring why we find 2 Ma old DNA in sediments in Greenland.
We argue that adsorption to mineral surfaces play a role for long term DNA preservation.
Blog post:
36 hours out of the ordinary
