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Open PostDoc position

Are you interested in cable bacteria and their transport of electrons? We have an open PostDoc position (2 years) where you will be investigating how internal electric wires of cable bacteria conduct electrons and connect with metabolic processes. Read more and apply here.

Open positions

CEM are always looking for skilled candidates, and are eager to start new collaborations. If you have an idea for a project or a funding application, we are very interested in hearing from you. Please contact us for further information.

Student projects at Center for Electromicrobiology

If you are interested in pursuing one of these projects please contact the supervisor whose email address is listed below the relevant project description.

All projects can be scaled to become biological projects, bachelor's projects, or masters' projects depending on what stage the student is at. 

We also welcome external students from universities other than Aarhus University who are interested in carrying out these projects as internships or thesis projects, although we regret that we cannot fund travel or living expenses for such short-term stays.  

Read our ideas for projects below:

Identification of electro-active microbial players in contaminated soil (BIOMAP project)

Electro-active microorganisms are defined as bacteria able to drive electric currents over mineral or biological conductors. Contaminated soils are generally characterized by highly reduced conditions (large availability of electrons) and therefore represent favourable sites for electro-active bacteria, where they can contribute to the “export” of excess electrons thereby stimulating the oxidation of the contaminants. Electric currents mediated by electro-active bacteria can be detected as alteration of the electric field on the soil surface. This principle is at the basis of a novel mapping technology current under development at the Center for Electromicrobiology.

Here we seek for a motivated student who will engage in our current effort to detect and describe the diversity of electro-active microbes in polluted soils. Within this project, the student will acquire hands-on experience on molecular (DNA and RNA-based) and microscopy tools for the characterization of bacterial diversity. Depending on the starting time of the project, there may be opportunities to participate in sampling campaigns and in situ measurements of the electric fields.

Supervisors: Lars Riis Damgaard, Ugo Marzocchi, Andreas Schramm, Ian Marshall

Methods: DNA/RNA extraction, Illumina sequencing, Fluorescence microscopy, bioinformatics

Contact: Ugo Marzocchi (ugomar@au.dk)

Electroactive bacteria for the remediation of harmful contaminants

The degradation of a large array of contaminants occurs via oxidative processes where electrons are “extracted” from the contaminant via chemical or biological processes. The ability of certain bacteria to drive electric current through biological or mineral conductive structures allows them to accelerate such oxidative processes. This project(s) aims to investigate the relevance of such bio-electrochemical currents for the natural self-remediation capacity of sediments and soil and its potential application to further stimulate the degradation of harmful contaminants in engineered system.

Supervisors: Ugo Marzocchi and Lars Riis Damgaard

Methods: Microsensors, electrochemistry, analytical chemistry

Contact: Ugo Marzocchi (ugomar@au.dk)

Effect of changing pH on cable bacteria activity in surface sediment

Cable bacteria are filamentous bacteria that couple sulfide oxidation in deep sediment with oxygen reduction at the sediment surface. These two independent redox half-reactions result in the consumption of protons at the surface and production of protons at depth, leading to a pH peak signature of cable bacteria activity. Thermodynamic theory says that manipulating the pH profile of the sediment will inhibit or promote the growth of cable bacteria, but this has never been tested before. In this project, the student will manipulate the pH profile of a sediment microcosm with acids, bases, and buffers and monitor the response of the cable bacteria using qPCR, microsensors, and planar optodes to monitor cable bacteria abundance, pH, O2, H2S, and electric potential. This will enhance our understanding of cable bacteria growth in environments with steep pH gradients, such as the rhizosphere of aquatic plants.

Supervisors: Ian Marshall, Klaus Koren

Methods: qPCR, microsensors, planar optodes

Contact: Ian Marshall (ianpgm@bios.au.dk)

Predation of cable bacteria

It is currently unknown what factors control cable bacteria population size. One hypothesis is that other microorganisms (either eukaryotes or prokaryotes) act as cable bacteria predators, and thus have an important role in cable bacteria population control. In this project, you will release cultures of potential cable bacteria predators into microcosms of cable bacteria, track their progress and determine the role they play in cable bacteria mortality.

Supervisors: Ian Marshall, Andreas Schramm

Methods: FISH, qPCR, SEM, microsensors

Contact: Andreas Schramm (andreas.schramm@bios.au.dk)

Cable Bacteria and the climate consequences of melting permafrost

Cable bacteria have recently been shown to limit methane emissions from rice paddies (www.nature.com/articles/s41467-020-15812-w). One of the biggest threats to the climate currently is methane emissions from melting permafrost. What role might cable bacteria play in limiting methane emissions from these environments? This project will combine surveys of existing sequencing datasets from permafrost areas with laboratory-based tests of cable bacteria's ability to recover from freezing to see what role they might play in limiting methane emissions from melting permafrost.

Supervisor: Ian Marshall (ianpgm@bios.au.dk)

Methods: microsensors, bioinformatics, amplicon sequencing, qPCR

Hunting for the proteins associated with the conductive fibers of cable bacteria

Cable bacteria transport electrons over centimeters along periplasmic “fibers” but the biomolecules and mechanism behind this unique property are still enigmatic. This project aims at developing a method to selectively extract proteins building (or associated with) these fibers for identification by proteomics/MS 

Supervisors: Thomas Boesen, Andreas Schramm

Methods: protein extraction & purification, selective protein enrichments, mass spectrometry

Contact: Andreas Schramm (andreas.schramm@bios.au.dk)

Developing genetic methods for cable bacteria

Cable bacteria apparently have a fascinating physiology but many of their traits remain hypothetical predictions based on genome/transcriptome analyses. The goal of this project is to develop methods to generate cable bacteria mutants or reporter strains to verify predicted functions or localizations of certain proteins. This is a great challenge given that we cannot currently grow cable bacteria in pure culture (only as enrichment), that they have to be grown in a gradient system (they do not form colonies on plates), they are filamentous (multicellular!), and no genetic system is so far available. So the ideal student for this project is the adventurous type, ready for a "high risk - high gain" project!

Supervisors: Thomas Boesen, Ian Marshall, Andreas Schramm

Methods: molecular biology & microbiology, fluorescence microscopy (CRISPR-Cas9, GFP, knock-out mutants...)

Contact: Andreas Schramm (andreas.schramm@bios.au.dk)

Functional characterization of the putative nitrate-reduction system of cable bacteria

Cable bacteria can electrically couple the oxidation of sulfide to the reduction of nitrate to ammonium. The key enzymes for nitrate reduction, NapA, NapB, and a unusual periplasmic octaheme cytochrome (pMHC), are currently expressed E. coli for downstream structural, functional, and interaction studies. The goal of this project is to functionally characterize these proteins, i.e. to prove (in enzyme assays) that they indeed can reduce nitrate to nitrite and nitrite to ammonium, respectively, and to test if and how the proposed electron donor NapB can interact with the catalytic domains NapA and pMHC.

Supervisors: Thomas Boesen, Krutika Bavishi, Andreas Schramm

Methods: protein purification, enzyme assays, protein interaction assays

Contact: Andreas Schramm (andreas.schramm@bios.au.dk)