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.
Gene transfer in the Plastisphere
THE KALØVIG PROJECT:
MERGING OF KNOWLEDGE
Project partners & expertise:
Field site
Assoc. Prof. Katrine J. Andresen
Marine geophysics and sedimentary processes
The seafloor in this shallow water is dominated by fine-grained muddy Holocene sediments (Fig. 1). At the end of WWII, several
thousand tons of ammunition was dumped in ‘Koraldybet’, which today is a restricted access area due to the potential risk of explosions and pollution from the ammunition. The bay further hosts the Studstrup Combined Heat and Power Plant that since 1968 has produced electricity and district heating by burning wood pellets, straws and coal.
Exploring the micro niche
Assoc. Prof. Nicole Posth& Posth Lab
Geomicrobiology and the Plastisphere
In the environment, the surfaces of plastic debris quickly become coated with biofilm and mineral coatings, an ecological niche referred to as the Plastisphere (Fig from Dodhia et al, (7)). The plastisphere effectively turns plastics into biogeochemically-active “micro niches” composed of microbes, organic matter, metals, minerals, metals and salts reflective of the host environment, and increases the effective surface area of the original plastic particles, i.e. calcite, iron oxides and carboniferous compounds have up to 2000 times the adsorption capacity as plastic particles (unpublished data).
DNA transfer to bacteria
Post doc Saghar Hendiani& SandLab
Mineral facilitated horizontal gene transfer and DNA dynamics
Saghar will use a range of surface characterization tool on pristine plastic samples and samples who have been inserted into Kalø Vig for 2 months.
She will further investigate if and how efficient the samples can transfer mineral adsorbed ARg to 2 types of bacteria.
We will explore which surface characteristics decrease the transfer efficiency and explore those features and potential mitigation strategies in follow up proposals
Fieldwork in Kalø vig
Plan: Position plastic samples on bottom sediments using Paul-the-diver and insert plastic in the water column on 4 ropes.
After weeks of preparations we set off. Very sunny, slightly windy.
At site one all went according to plan.
Slightly windy turned into quite windy and diving at site two was aborted.
Check photos of a beautiful day o What a great team effort. Sincerely thanks to Paul and Per for boat, diving and logistic support.
Preparations
Stitching
Frame ready
Different types of plastics, quartz and cotton
Getting ready
Slightly windy
Action
Getting ready to deploy
Paul gearing up
Time to get in..
See you in 2 month
We hope..
Purpose and background
The spread of antibiotic resistance genes (ARg) is a worldwide health risk (1) and no longer only a clinical issue. Vast reservoirs of ARg are found across natural environments (2), such as soils, sediments and oceans. As such, the geologic perspective and methodological approach can be used to study these environments and inform management strategies for the protection of water resources and ecosystems.
Once in the environment, ARg are surprisingly rapidly propagated- at a rate that is enhanced by the concurrent presence of heavy metals (3). ARg are efficiently distributed between bacteria through horizontal gene transfer (HGT), where one species acquires resistance through gene transfer from other resistant bacteria. Most HGT responsible for the spread of ARg is assumed to be through direct microbe-microbe contact. ARg acquisition by uptake of extracellular DNA shed to the environment is traditionally not considered an effective mode of transfer, simply because extracellular DNA degrades in a matter of days when it is suspended in e.g. seawater (4). However, colleagues and I just showed that sedimentary DNA can be preserved in the environment for geological relevant timescales (at least 2 Ma years) and we have assigned adsorption to minerals as a key for DNA preservation (5)
My group and I found that two environmentally-relevant bacteria can successfully incorporate mineral adsorbed ARg as well as 60bp (fragmented) DNA (6). Our results show that bacteria acquire and incorporate extracellular DNA adsorbed to mineral surfaces to gain an evolutionary advantage. This pathway of evolution is currently not recognized, although reuse of genetic invention could be an effective means of obtaining evolutionary fitness for microorganisms. In the environment, DNA associated to minerals could be transported and deposited according to sedimentary processes. Bacteria could access and pick up ARg along these transport pathways and at deposition sites, explaining the vast propagation of ARg in the environment.
Expected scientific outcome
Following our results we expect to establish if a) plastic-micro-niches facilitate HGT and if build-up enhance or inhibit gene acquisition, b) which substrate types have the highest and lowest uptake efficiency, and c) if polluted point sources are hotspots for ARg propagation in Kalø Vig.
Knowledge of which type of particles inhibit or decrease gene transfer efficiency can be important for mitigation strategies. Importantly, our study can help elucidate the mechanisms behind the rapid ARg propagation in our environment.
Funding
Building on expertise funded by:
References
1. Hatosy, S. M. & Martiny, A. C. The Ocean as a Global Reservoir of Antibiotic Resistance Genes. Appl. Environ. Microbiol. 81, 7593–7599 (2015)
2. Martínez, J. L. Antibiotics and Antibiotic Resistance Genes in Natural Environments. Science 321, 365–367 (2008)
3. Hemme, C. L. et al. Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community. mBio 7, e02234-15 (2016).
4. Dejean, T. et al. Persistence of Environmental DNA in Freshwater Ecosystems. PLOS ONE 6, e23398 (2011)
5. Kjær, K. H. et al. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 612, 283–291 (2022)
6.Verma, T., Hendiani, S., Andersen, S. B., Burmoelle, M. & Sand, K. K. Sedimentary DNA can influence evolution: Establishing mineral facilitated horizontal gene transfer as a route to bacterial fitness. 2023.01.24.525235 Preprint (2023)
7. Dodhia MS, Rogers KL, Fernández-Juárez V, Carreres-Calabuig, JA, Tisserand AA, Keulen N, Riemann L, Shashoua Y, Posth NR. Microbe-Mineral interactions in the Plastisphere: coastal biogeochemistry and consequences for plastic fate. Frontiers in Marine Science, 10 (2023)
