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.
QUANTIFICATION OF MOLECULAR BONDING
Higher organisms rely on mineral-polymer interactions for their skeletal structures and anchoring to their habitat. Medical and technological applications such as nanoparticles for ingestion and bioinspired and responsive materials are built on mineral-polymer interactions. However, the mechanistic understanding of these interactions is poorly constrained. Dynamic force spectroscopy (DFS) can probe the free energy landscape of interacting bonds and provide the underlying mechanistic information. However, obtaining qualitative thermodynamic and kinetic parameters from Polymer-linked DFS, has proven troublesome and erroneous data are currently being presented in the literature.
We have developed a protocol for obtaining quantitative insight into polymer-mineral binding. We used theoretical calculations to prove the appropriate protocol of data analysis and demonstrate the approach by analyzing DFS data for literature and newly obtained data on mineral binding by biopolymers in microbial systems. Beside restating an appropriate method to tackle analyses of DFS data we have addressed 3 common difficulties’ in the DFS analyses:
- determining the amount of bonds interacting
- addressing the non-linear dependence of extension on applied force for biopolymers
- how to approach the overlooked equilibrium regime for polymer-based force spectroscopy
Our findings provide new insights into (bio)polymer-mineral interactions and both the conclusions and the approach are directly applicable to a broad range of disciplines, ranging from intracellular biomineralization to design of bioinspired functional materials for technologies, such as development of nanoparticles for biomedical applications.
https://www.nature.com/articles/s41598-017-09041-3
a) Schematic of DNA fixed to an AFM probe (in reality more molecules will be clustered at the probe. b) Energy landscape of a bond. The energy well defines the bound state at a distance xt away from the transition state. The energy difference between the bound and the transition state is ΔGbu. The intrinsic rate of unbinding, koff, describes the speed at which the unbinding occurs without an applied external force. c) The force spectrum can be divided in two regions: the near equilibrium regime and the kinetic regime where a bond breaks faster than it reforms. The intercept between the plateau of rupture forces in the near equilibrium regime and the y-axis defines the feq, the slope of the kinetic regime defines the xt and the intercept between a tangent of the kinetic regime and the x-axis defines the koff.
Mechanistic insight into biopolymer induced iron oxide mineralization
through quantification of molecular bonding
We recently published our work on quantification of mineral-biomolecular bonding and its role for nucleation.
We used dynamic force spectroscopy to directly probe binding between complex, model and natural microbial polysaccharides and common iron (oxyhydr)oxides. Applying nucleation theory to our results demonstrates that if there is a strong attractive interaction between biopolymers and iron (oxyhydr)oxides, the biopolymers decrease the nucleation barriers, thus promoting mineral nucleation. These results are also supported by nucleation studies and density functional theory. Spectroscopic and thermogravimetric data provide insight into the subsequent growth dynamics and show that the degree and strength of water association with the polymers can explain the influence on iron (oxyhydr)oxides transformation rates.
Figure 1. Polysaccharide stalks from Gallionella and EPS produced by Shewanella are both associated with iron (oxyhydr)oxide formation. We covalently attached alginate and EPS to an AFM tip and brought the polymers in contact with ferrihydrite and hematite and obtained dynamic force spectra. d) Force curves typical for interaction between polymer brushes and minerals. Distance along the y-axis is the length between the surface and the tip pulling away from the surface. To derive single polymer binding events, we applied worm-like chain fits (black curve) for the last rupture event for each force curve.
Combined, our results provide a mechanistic basis for understanding how polymer-mineral-water interactions alter iron (oxyhydr)oxides nucleation and growth dynamics. Our work pave the way for an improved understanding of the consequences of polymer induced mineralization in natural systems and have implications for the global iron cycle and as well as understanding formation of banded iron formations (https://eartharxiv.org/pd73x/).
https://pubs.rsc.org/en/content/articlepdf/2020/NA/D0NA00138D
Blog post link: https://www.kksand.com/post/quantification-of-molecular-bonding
