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Student projects at CEM

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:


Cable bacteria and Beggiatoa: Competitive exclusion or co-existence

Cable bacteria and Beggiatoa sp. are both filamentous sulfide-oxidizing bacteria able to explore sulfur resources cm deep within the sediment. The two types of bacteria employs different strategies for this exploitation. Beggiatoa can accumulate nitrate in intercellular and migrate to environments with accessible sulfide. Here the organism oxidize the sulfide, using the intracellular nitrate as electron acceptor. Cable bacteria forms centimeter long filaments consisting of thousands of individual cells. The cells with access to sulfide can oxidize the sulfide and pass the electrons over a distance of centimeters to cells with access to oxygen. Both types of organisms can deplete the upper layes of the sediment from sulfide, and in natural environments, they rarely co-exist. At present, there is no knowledge, on conditions that favor one to the other. Proposed hypotheses formulated by the student and supervisors is tested experimentally in laboratory systems, using amongst other micro sensor techniques.

Supervisors: Lars Peter Nielsen and Nils Risgaard-Petersen (contact nils.risgaard-petersen@bios.au.dk)

Methods: microsensors, microscopy

Characterization of the non-canonical nitrate and nitrite reductases in cable bacteria

Many cable bacteria can use nitrate as alternative electron acceptor and reduce it via nitrite to ammonium. Whether they can conserve energy in this step, is currently unclear. The nap operon and an adjacent novel octaheme cytochrome (ohc) are predicted to be responsible for this activity. The goal of this project is to clone and express the predicted catalytic domains (napA, ohc) and the predicted electron donor (napB) in E. coli, to purify the proteins, and to characterize their redox potential, electron flow, and catalytic activity by a combination of electrochemical and biochemical methods. In addition, experiments with uncouplers, quinole inhibitors, and membrane potential stains may shed light on the energetics of the reaction.

Supervisors: Andreas Schramm (contact andreas.schramm@bios.au.dk), Thomas Boesen, Nils Risgaard-Petersen

Methods: cloning, protein expression & purification; microsensors; electrochemistry (in collaboration with the University of East Anglia, Norwich, UK)

Discovering electron transfer mechanisms in isolates associated with cable bacteria

Cable bacteria are long multicellular filaments that grow in sulfidic sediments. It has not yet been possible to create a pure culture of cable bacteria, which suggests that the remaining bacterial community is likely essential for the cable bacteria. Several different types of bacteria live in this community, in which the most interesting ones are the microaerophilic bacteria that we can always see with a microscope because they are forming a so-called microaerophilic veil. We have multiple isolates from this bacterial veil that are supposedly interacting with cable bacteria in an electric way. We suggest that they are associated via interspecies electron transfer. Our hypothesis is that mechanisms of interspecies electron transfer and motility can be found in the genomes of these associated bacteria.
By extracting and sequencing the genomes of these bacteria we can discover what they are capable of and how this might happen via bioinformatics. This project can be extended with creating genomic mutants of the isolates.

Supervisors: Jamie Lustermans (contact jl@bios.au.dk), Andreas Schramm

Methods: DNA/genome sequencing, bioinformatics, (genome manipulation)

Distribution and activity of cable bacteria in natural environments

High biological turnover in the sediment and low frequency of strong waves seem to be important for cable bacteria, but otherwise we do not know much about what determines their distribution. With its uniform water chemistry and great variation between low tide, protected, steep and exposed coasts, Horsens Fjord should be an ideal area for mapping and understanding of the distribution of cable bacteria. The methods will be fieldwork supplemented with laboratory tests. Requires careful prioritization of which environmental parameters should be collected simultaneously.

Supervisors: Lars Peter Nielsen & Nils Risgaard-Petersen (contact nils.risgaard-petersen@bios.au.dk)

Methods: Fieldwork, microsensors, microscopy, microbial community analysis by 16S rRNA gene sequencing.

Extracting high-quality genomic DNA from cable bacteria for long-read sequencing using the Oxford Nanopore MinION

Nanopore long-read sequencing increases our ability to obtain complete genomes from microbial communities. All current cable bacteria genomes are derived from Illumina short-read sequencing, and are thus incomplete. A first step towards using nanopore long-read sequencing for complete cable bacteria genomes will be to extract DNA from cable bacteria in a way that gently preserves long DNA fragments. Current methodology fragments DNA too heavily for nanopore sequencing to be effective. This project will be the development of such a DNA extraction technique as a precursor to long-read sequencing.

Supervisors: Ian Marshall (contact ianpgm@bios.au.dk), Andreas Schramm

Methods: DNA extraction from sediment samples

Finding bacteria living in association with cable bacteria using co-occurrence networks based on microbial community compositions inferred from 16S-rRNA-gene sequencing

It has been hypothesised that cable bacteria live in close metabolic association with other microorganisms in their sediment environment. There may be a role for associate microbes to play either as an intermediate partner to the oxidation at the anoxic end of the cable filament, or as an intermediate partner to the reduction of molecular oxygen at the oxic end of the cable filament. This project involves the mining of existing DNA sequencing databases to find datasets where cable bacteria have been found by sequencing of 16S rRNA genes. The co-occurrence of cable bacteria together with other specific other types of bacteria will then be evaluated to see if there are any candidate taxonomic or physiological groups of microorganisms that may live in close association with cable bacteria.

Supervisors: Ian Marshall (contact ianpgm@bios.au.dk), Andreas Schramm

Methods: Bioinformatics

Metagenomic sequencing of a clonal enrichment of the marine cable bacterium Candidatus Electrothrix aarhusiensis

There is no pure culture of cable bacteria, but there is the next best thing: a clonal enrichment of a single strain of cable bacteria growing in sediment with the rest of the complex microbial community. Much of the high-impact work on cable bacteria to date has been carried out using a clonal enrichment of the freshwater cable bacteria genus Candidatus Electronema from the pond in Vennelystparken on the Aarhus University campus. Using sediment from Løgten Strand north of Aarhus we have now produced a clonal enrichment from Electronema's marine sibling genus, Candidatus Electrothrix, and plan to carry out experiments with this new enrichment. As part of our work with this new strain we would like to sequence its genome by sequencing and analysing a metagenome of the enrichment culture.

Supervisors: Ian Marshall (contact ianpgm@bios.au.dk), Jesper Tataru Bjerg

Methods: DNA extraction, Illumina sequencing library preparation, bioinformatics

Modeling and manipulating pH in sediment and measuring the effect on cable bacteria metabolism

The activity of cable bacteria links two redox half-reactions, transporting electrons from deep, anoxic sediment to shallow, oxic surface sediment. This spatial imbalance in electron consumption and production leads to a concurrent accumulation of hydrogen ions (protons) in deep sediment, making it more acidic, and depletion of protons in shallow sediment, making it more basic. This results in a classic cable bacteria pH profile which has come to be considered diagnostic for the activity of cable bacteria. It has been hypothesised that deliberately manipulating this pH gradient by maintaining a constant pH at all depths or reversing the pH gradient will alter the thermodynamic equilibria that cable bacteria use to conserve energy and survive. This project will involve the testing of this hypothesis, by manipulating pH profiles in sediment and glass slide experimental systems.

Supervisors: Ian Marshall (contact ianpgm@bios.au.dk), Jesper Tataru Bjerg, Lars Peter Nielsen

Methods: microsensors, microscopy

Purification and characterization bacterial protein wires

Cable bacteria are multicellular filamentous bacteria that transport electrons over centimeter distances through an internal wire-like machinery. Bacterial protein wires have been observed in a broad range of organisms from certain Archaea to Geobacter and cable bacteria. The recently published cryo EM structure of Geobacter has revealed that ‘nanowire’ preparations from these bacteria contain polymerized fibers of a multi-heme cytochrome (OmcS). However the bioelectronic conduit forming machinery of cable bacteria still remains a mystery.

Using a combination of omics tools and mass spectrometry, several candidate genes have been identified, ranging from PilA to multi-heme cytochromes. The ultimate goal of this project is to clone, express and purify selected high-priority bacterial protein wire candidates for further investigations by e.g. electron microscopy, cyclic voltammetry and crystallography to obtain a detailed understanding of the conduction mechanisms of these structures at the molecular level.

Supervisors: Thomas Boesen (contact thb@mbg.au.dk), Krutika Bavishi

Methods: molecular cloning, protein biochemistry, crystallography, electrochemistry

Survey of (swarming) motility of microaerophilic bacteria from cable bacteria enrichments

A diverse community of bacteria lives in sulfide rich sediments that contain cable bacteria. Cable bacteria are long filaments consisting of multiple cells and are believed to not need associated bacteria to thrive. These associated bacteria sometimes perform a special type of behaviour, where they purposefully move around the cable bacteria while trying to stay as close to it as possible. This is called swarming. What makes these swarming bacteria even more special is that they are microaerophiles or even aerophiles and that we see them swarming in places where there is no oxygen. The theory for why this is possible is based on the transport of electrons from the swarming bacterium to something else than oxygen, namely an electron shuttle. Electron shuttles are molecules that can transport electrons without being eaten. Our hypothesis is: our bacterial isolates are able to perform swarming based on gradients of these electron shuttles. Some other important questions are: are the isolates motile? How do the bacteria react to opposing gradients of oxygen and sulfide? An experiment like this has never been performed and only partially on communities from marine sediments, but we will work with freshwater sediment cultures. Investigating the motility will require observations through microscopy, where specific glass tools are used to create the gradients. The gradients in the slides could be observed by either microsensors or optodes.

Supervisors: Jamie Lustermans (contact jl@bios.au.dk), Jesper Tataru Bjerg, Andreas Schramm, Nils Risgaard-Petersen

Methods: microscopy, microsensors/optodes