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.
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MOLECULAR
GEOBIOLOGY
GROUP
Group statement:
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We work across disciplines which makes collaboration and communication essential.
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We make time to play in the lab and test ideas.
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We treat each other as peers and we welcome any interested students, postdocs, scholars or collaborators, regardless the branch of academic training.
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I strive to have a group reflecting the diversity seen in society and I aim to help decrease the extra hurdles STEM women and minorities are facing compared to cis-male colleagues in this otherwise wonderful world of science.
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We all have different ways of learning, we all bring different skills to the table and we all need different input to connect the dots. I am committed to create a learning space where everyone can participate.
GROUP MEMBERS
Oluwatoosin Agbaje
Post doc
Molecules-mineral interactions in historic samples
Toosin´s research will focuses on preservation of DNA and protein in calculus, ceramics, and other fossil samples. ‘Toosin’s expertise across several fields will help to decypher events om the past and in understanding biomolecules preservation across time and space.
Go to project
Approach and tools:
AFM imaging, SEM, EDX, XRD, IR-AFM, ss-ATR-FTIR, Dynamic force spectroscopy.
Saghar
Hendiani
Post doc
Mineral facilitated horizontal
gene transfer
Saghar is studying mineral facilitated horizontal gene transfer and uptake rates in biofilms. This project has relevance for propagation of antibiotic resistance genes in our environments.
Go to project
Approach and tools:
Molecular and microbiology, fluorescent microscopy, atomic force microscopy
Taru
Verma
Post doc
Hgt and dna-mineral fundamentals
Taru is studying mineral facilitated horizontal gene transfer of antibiotic resistance genes. She will work on bridging the microbial observations with the dynamics of DNA-mineral associations
Go to project
Approach and tools:
Molecular and microbiology, fluorescent microscopy, atomic force microscopy
Neethu Rose Sainjan
Post doc
HGT in plastic aggregates
Neethu is investigating bacterial processes and HGT in nanoplastic coronas (NPCs). She will be doing atomic force microscopy work to study selective bacterial growth on NP eco-coronas as a function of environmental parameters and stressors.
Approach and tools:
AFM imaging, sequencing, cloning, meta-omics.
Carlota Carbajo Moral
PhD Student
Quantification of DNA-substrate
bonds and effects on HGT
Carlota is using dynamic force microscopy to quantify DNA-substrate binding parameters. She will link the bond parameters to bulk chemistry kinetics and
nano-level substrate associations. She will work to understand if DNA-substrate binding strength play a role for efficiency bacterial incorporation of substrate adsorbed DNA
Approach and tools:AFM imaging, Dynamic force spectroscopy, ss-ATR-FTIR, UV-vis
Pablo Nicolás Arellano Caicedo
PhD Student
Taphonomy of DNA in sediments
We will be using nano- microlevel analytical approaches to study DNA preservation in sedimentary systems. We will work to broaden our understanding of eDNA taphonomy and address how we can apply taphonomy and sediment provenance to improve biodiversity estimates based on eDNA
Approach and tools:
AFM imaging, SEM, EDX, XRD,
O-PTIR, ss-ATR-FTIR
RECENT GROUP MEMBERS
Ioannis Kontopoulos
Post doc
Dna in sediments
'Ioannis' research focuses on the preservation of DNA in sediments. He bridges across several length scales and combines molecular scale DNA-mineral interactions with DNA extractions and sediment sampling.
Go to project
Approach and tools:
AFM imaging, SEM, EDX, XRD, IR-AFM, ss-ATR-FTIR, Dynamic force spectroscopy .
Bia
Fonseca
PhD Student
Protin-water-mineral interactions
Bia has a background in chemistry and heritage conservation and is using computational and experimental approaches to understand the preservation potential of proteins across time in different environmental settings. Her focus is on collagen and beta lactoglobulin.
Go to project
Approach and tools:
Molecular dynamics simulations, AFM imaging and video rate AFM.
Jaime Quesada Sanz
MSc.
DNA-mineral stability in natural environments
Jaime will be using atomic force microscopy and bulk adsorptio experiments to investigate the nano level interactions between DNA and minerals in a range of environmental solutions. His results can be used to access DNA leaking in sediments and to improve extraction protecols for eDNA
Approach and tools:
AFM imaging, Video rate AFM and force spectroscopy., UV-Vis.
Stanislav
Jelavić
Post doc
DNA-mineral-microbe interactions
Stan is working on DNA-mineral interactions focusing on DNA-mineral binding and stability. He will also help the initiatives of exploring the rate of gene uptake in microbes.
Approach and tools:
AFM imaging, SEM, EDX, XRD, IR-AFM, ss-ATR-FTIR, Dynamic force spectroscopy
Kamille Anna Dam Clasen
PhD Student
Mineral facilitated horizontal gene transfer
Kamille will study the role of mineral structure and surface charge for rates of horizontal gene transfer from mineral adsorbed DNA. This project has relevance for propagation of antibiotic resistance genes in our environments.
Go to project
Approach and tools:
Molecular and microbiology, floureescent microscopy, bulk adsorption.
Rocío Rodriguez Torres
PhD Student
Bacteria-plastic interactions
Rocío is a PhD student at DTU Aqua and she is doing a joint project with the Sand Lab and the Posth Lab about growth of bacteria on microplastics. In this project she will be quantifying binding affinities between relevant bacteria and a range of plastic surfaces.
Approach and tools:
AFM imaging, chemical force microscopy, optical imaging.
Magnus August R Harding
MSc
Degradation kinetics of mineral adsorbed DNA by DNAse
Magnus has a background in geology and palaeontology, and is interested in understanding the processes taking place during fossilization and the fate of organic molecules as they enter the geosphere. Here he will elucidate the preservation potential of environmental DNA.
Approach and tools:
AFM imaging in air, in liquid and using video rate.
Léa
Dieudonné
Erasmus student
DNA conformation
Léa has been looking into DNA conformation on different minerals and explore how we can manipulate the DNA-mineral interaction.
Approach and tools:
AFM imaging and force spectroscopy.
Chloé Martins
Erasmus student
Role of minerals in the origin of life
Chloé was suppose to join the group and do experimental work on propagation of antibiotic resistance genes in the environment. She planned to investigate conformation and behavior of DNA adsorbed to soil minerals. However, because of Covid-19 related lock-downs her project has been transformed to a literature study on the role of minerals in the origin of life.
Approach and tools:
AFM imaging in air, in liquid and using video rate
Urvshi Kaveri Chandra
PhD student
Protein preservation in archaeological artifacts
Urvshi will use her experience with proteins and her molecular biology background to extract proteins from sediments and archaeological artefacts. She will also do fundamental studies of protein-mineral interactions to help optimize extraction methods.
Approach and tools:
AFM (imaging, video rate and force spectroscopy , LC-MS/MS and GC-MS
Anne Rath
Nielsen
PhD student
Artificial nacre
Composite materials are nature’s strategy for creating strong and tough materials. Anne aim to understand the mineralization dynamics of CaCO3 formation on synthetic bio-polymers to develop nacre analog materials.
Anne is currently writing up her PhD thesis.
Approach and tools:
Flow through optical microscopy, AFM imaging, SEM, EDX, Constant composition method, in-situ UV-VIS, XRD.
Kasper Primdal Olesen
Student Project
Heterogeneous nucleation of CaCO3
Kasper studied heterogeneous nucleation and growth of calcite on mineral surfaces and polymers present in the environment. The aim was to elucidate surfaces that inhibit and enhance calcite formation.
Approach and tools:
SEM, EDX, Constant composition, diffusion experiments.
Xi Chen
MSc
Biofilms
Many microbes rely on anchoring themselves to mineral surfaces where they make biofilms enhancing their survival and facilitate gene transfers. Xi will be using her chemistry background to explore the differences in affinities between microbes and minerals and address if there is an interdependence with environmental conditions.
Approach and tools:
Flow through optical microscopy, AFM imaging, SEM, EDX, force spectroscopy.
Lasse Nikolajsen
Ba. Student
Heterogeneous calcite formation
Lasse studied the thermo dynamic barrier to nucleation on a range of substrates. We set up nice system to study nucleation in-situ with optical microscopy under constant flow and steady state conditions.
Approach and tools:
Flow through optical microscopy, SEM, EDX, in-situ UV-VIS, XRD.
Svend Harry
Canas Weihe
MSc
Microbial FeOX reduction
Svend studied the rate of hematite reduction by the reducing bacteria Shewanella. He showed how the presence of organic compounds interfere with the mineral-microbe system paving the way for a better understanding of natural systems.
Approach and tools:
Glove boxes, ferrozine metod, TEM, SEM, EDX.
Mia Nielsen
PhD Student
Inorganic inhibition of carbonates