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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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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.
MOLECULAR GEOBIOLOGY GROUP
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. Link
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. Link
Approach and tools:
Molecular dynamics simulations, AFM imaging and video rate AFM.
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 Link
Approach and tools:
Molecular and microbiology, fluorescent microscopy, atomic force microscopy
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. Link
Approach and tools:
AFM imaging, SEM, EDX, XRD, IR-AFM, ss-ATR-FTIR, Dynamic force spectroscopy.
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.
RECENT GROUP MEMBERS
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 .
Xi Chen
Master student
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.
Magnus August R Harding
Project Student (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
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
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.
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
Project student
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.
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Lasse Nikolajsen
Bachelor 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.
Sept/
KKS to speak about mineral facilitated horizontal gene transfer and its potential impact for the evolution of life. @ the Royal Physiographic Society Jubilee Symposium: Cancer, multicellularity and complex systems.
June/
KKS participating in BLOOM talking about the origin of life.
April/
Congrats to Ann Charlotta on her Bachelor projects on biofilm formation on mineral surfaces.
Congrats to Dr. Vidar Aspelin, Lund University. It was a pleasure to help assess your PhD thesis.
Geomicrobiology Team will join the #DanishBiofilmWorkshop and will be presenting posters and talks.
March/
Diversity Programme Steering Committee at GLOBE Institute will host a workshop on Diversity and belonging in the workplace moderated by Sara Luise Muhr.
January/
Welcome Taru! We now have quite a nice group for advancing our microbiology related studies.
21st: KKS to give seminar in Umeå.
2022/2021
December/
Welcome Ann-Charlotta!
Setting up GMO lab
6th: KKS received a Young Researcher Fellowship Grant from the Carlsberg Foundation (Blog and here)
November/
Welcome Saghar! Look much forward for your next years of Post doc time.
September/
BLOOM: 28th from 17-18
KS discuss biomimicry: Perspectives from an engineer, an architect and a geochemist. Link.
Arranged by BLOOM and IDA
Month of workshops and retreats
August/
19th of August: Final exam for Rocío´s project on "Methods in microbial‐plastic interactions." Hope to see yoiu back using the AFM.
Welcome back Jaime
July/
4th- 9th : Virtual Goldschmidt Conference. We all present the 9th.
At 10 CEST in Room 9, Stan talk about the fate of organic compounds in Precambrian iron formations.
At 10 CEST in Room 10, I will talk about DNA-mineral binding and the role of mineral topography.
At 11.16 CEST in Room 10, Ioannis talk about adsorption characteristics of ssDNA and dsDNA onto mineral surfaces.
June/
4th-9th of June: ISBA9: international symposium on biomolecular archaeology
May/
Welcome Rocío. 2 month PhD course and external experience working on biofilm - plastic interactions in collaboration with POSTH LAB
April/
Good byes and welcomes
Stan is leaving for a grant in Grenoble (Congrats and have fun. You will be missed!). Welcome Toosin, looking much forward to start your MSCA project. Also, welcome back Jaime: It is good to discuss with you again!
Group seminar talks.
The 21st: Willerslev group
The 29th: Kjær group.
March/
Looking forward to assess the PhD thesis of Jennifer Zehner from NTNU, Norway. Topic: Micro-scale studies of microbial-induced carbonate precipitation.
25th: Presenting the work of the group at the NORDBigs seminar series. https://nordbigs.wordpress.com/
26th: Deadline for abstract submissions for our Frontiers Research topic on: Interactions Between Microbes, Minerals, and Molecules Across Scales and Time
29th-31st. Conference on Ancient Biomolecules of Plants, Animals, and Microbes
February/
AFM AFM AFM
January
Welcome back Jaime!
2021/2020
December/
Writing manuscripts
November/
Kamille and I will be setting up
microbial work
October/
Passed with no warning
Magnus handing in.
September/
Welcome Kamille!!
August/
Month of no meetings!
Jaime defending his Thesis.
July/
Welcome Magnus!
Cyphers VRS
June/
Hawaii trip canceled :(
Chloés internship transformed to a literature study.
May/
Zoom meetings
Hellooo Cypher
April/
Zoom meetings
Welcome Ioannis!
March/
"
February/
Proposal writing
Paper writing
Congratulations to Toosin Agbaje on our received Marie Skłodowska-Curie Individual Fellowship for him. Expected Onset October 2020.
January/
Proposal writing
Paper writing
2020/2019
December/
Cypher VRS
Proposal writing
Rejection of 4/5 proposals submitted in 2019
I am giving a heads up on GLOBEs gender initiative, and taking the opportunity to highlight that we need to check our own biases.
November/
Cypher VRS
Jaime joins the group for his masters project on environmental DNA. Welcome!
October/
I am giving seminar at the University of Lund on mineral facilitated horizontal gene transfer and the potential for the evolution of life.
The Cypher arrives!
Proposal time! We are busy writing . We are involved in 7 proposals.
September/
Anne will defend her PhD Thesis the 27th. 14.00 Aud 2 HCØ. CPH.
I am giving an Invited Talk at GSA in Arizona, on the role of geochemistry and mineral facilitated horizontal gene transfer for the evolution of life. Session: "Effects of Mineral-Water Interface Complexity on Geochemical Processes: A Session in Honor of Mineralogical Society of America Awardee for 2018, Laura Nielsen Lammers." Congratulations Laura!
August/
Goldschmidt conference, Barcelona, Spain. Convener: Interactions between Microbes, Minerals, and Molecules Across Space and Time
Willerslev workshop, Camebridge, UK. Stan will talk about propagation of antibiotic resistance genes in the environment. I will talk about mineral facilitated evolution of life.
July/
Stanislav Jelavic will join the groups as a Post Doc for 2 years. He will mainly be looking into the interactions between DNA and minerals.
Anne Rath Nielsen hands in her PhD thesis on the interplay between organic compounds and mineral surfaces. Applications from oil recovery to design of new materials.
May/
Expected onset of VYI project: Distribution of antibiotic resistance genes in the environment: The role of mineral facilitated horizontal gene transfer.
Erasmus student Léa Dieudonné will join the group.
April/
Announcement for a 2 year post doc position in my lab. Expected hire starting 1st of July.
March/
Annual meeting in the Danish Geological Society.
PhD opponent, Norwegian University of Science and Technology
February/
Congratulations to Ioannis Kontopoulos on our received Marie Skłodowska-Curie Individual Fellowship for him. Expected Onset early 2020.
January/
Award Ceremony. Receiving VILLUM YOUNG INVESTIGATOR GRANT.
2019/2018
October/
Onset DFF-Danish ERC-Programme grant: The significance of minerals in horizontal gene transfer: A new
principle for evolution of life?
C A L E N D E R
Ioannis/Toosin
Bia Jaime and Rocio
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.
Svend Harry Canas Weihe
Master student
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
Inorganic componds such as Mg, SO4 and MgSO4 combined show varying degree of inhibition of calcite. Mia did a range of studies to understand the underlying mechanisms behind the inhibition to improve scaling strategies and bio proxies.
Approach and tools:
SEM, EDX, Constant composition method, in-situ UV-VIS, XRD.
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
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. Link
Approach and tools:
Molecular and microbiology, floureescent microscopy, bulk adsorption .
Saghar
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. Link
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 EFECTS 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
On-boarding
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
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