Master Projects

Analysis and Control of Microbial Systems

Master Projects

 

In focus: Master student Anne Helene Sandmark micropipetting at work under sterile conditions. Photo: K Østgaard. 

 

Ongoing

  • Elin Håberg: The impact of washing routines on nitrifying capacity and bacterial community composition of biofilms in nitrifying biofilters at VEAS
  • Kristin Leonore Lillebo Bentzen: Functional studies of two genes encoding closely related group II silicanins in the diatom Thalassiosira pseudonana
  • Christine Våge Sjevelås: Identification of two group IV silicanins in the diatom Thalassiosira pseudonana
  • Nora Persen Mølmen: Janthinobacterium strains isolated from salmon systems: Violacein production and effect of colonizing Atlantic salmon yolk sac fry
  • Anders Wilhelm Lambine Skovly: Creating a protocol for infection of salmon yolk fry
  • Ann Isabel Carmo Rossvoll: Water microbiota in start feeding of Ballan wrasse
  • Hugues Palandre: Development of molecular tools in the diatom Coscinodiscus wailesii
  • Anne Helene Sandmark: The impact of unsuccessful invasions on an aquatic microbial community in a flow-through system
  • Ingrid Eskerud Harris:
  • Renate Sandberg:
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Graduated / finished:

 

 

Ongoing projects:

 

Elin Håberg: The impact of washing routines on nitrifying capacity and bacterial community composition of biofilms in nitrifying biofilters at VEAS 

Nitrification is the biological process of oxidation of ammonia to nitrate. This process is used in wastewater treatment plants for the conversion of ammonia. At Vestfjorden Avløpsselskap (VEAS) nitrification is done in a fixed film process where lightweight expanded clay aggregate (Leca) is used as carrier material. Backwashing is necessary in these nitrifying bioreactors due to high concentrations of organic material, which can cause fast growing heterotrophic organisms to out-compete slow growing autotrophic nitrifiers. Backwashing routines of the nitrifying filters at VEAS has caused problems at the plant because of loss of Leca from the biofilters during the process of washing. Loss of Leca has led to reduced nitrifying capacity and problems in other parts of the plant. This project aims to investigate different washing routines and their impact on the process of nitrification in Leca biofilm in the nitrifying biofilters at VEAS. This is done by small scale batch experiments to estimate nitrification capacity in Leca, analysis of the microbial community through monitoring of gas kinetics in Leca biofilm and Illumina sequencing of amplicon library from Leca samples.


Kristin Leonore Lillebo Bentzen: Functional studies of two genes encoding closely related group II silicanins in the diatom Thalassiosira pseudonana

Diatoms are unicellular, eukaryotic algae well known for their ability to generate biosilica that constitutes the cell wall, or frustule. Our knowledge of frustule biosynthesis is not yet complete. However, many key components in the biosynthesis process have been identified.    
  
In this project, two genes (Tp24711 and Tp24708) encoding closely related group II silicanins  in the diatom Thalassiosira pseudonana will be studied. Mutated strains will be established by implementing knockout-lines for the two silicanins using the gene editing technique CRISPR/Cas9. The aim is to study how these silicanins affect frustule synthesis and gain a better understanding of the functions and characteristics of the different genes, by looking at frustule morphology and cell growth. In addition, the aim is to verify the localization of two genes in vivo by tagging Tp24711 and Tpbd856-1852 with the fluorescent marker mTurquoise.
 

Christine Våge Sjevelås: Identification of two group IV silicanins in the diatom Thalassiosira pseudonana

Diatoms create most of the organic carbon in the world’s ocean, and they contribute to about one fifth of photosynthesis on earth. Their silicified cell wall have inspired researchers for centuries because of its complex pattern of structures that range from micro- to nanometer scale. Understanding how the complex structures of the cell wall is created can help creating new ways for synthesis of patterned inorganic materials with complex morphologies and advanced properties. The marine diatom Thalassiosira pseudonana is a model species for studies of diatom cell wall synthesis. Several biosilica-associated proteins with unknown functions have been identified. In this thesis, two genes in group IV of the T. pseudonana silicanin protein family, will be knocked out. Characterization of the silicanin knockout mutants will hopefully provide information about the function of these proteins and help with understanding how the structures of the cell wall is created. 

 

Nora Persen Mølmen: Janthinobacterium strains isolated from salmon systems: Violacein production and effect of colonizing Atlantic salmon yolk sac fry.

Janthinobacterium lividum has been found to host the skin of fish, amphibians and humans, producing a purple pigment called violacein. It is believed that violacein production is used as a defense mechanism against infections and diseases, by inhibiting pathogen growth. Previous studies have found violacein to be antifungal, antibacterial, antiviral and antitumoral, supporting that violacein has a diverse range of biological activities and a potential in medical applications. However, the mechanisms driving the violacein production is still not well understood.

In this project, I work with five strains of Janthinobacterium isolated from the skin of Atlantic salmon fry and rearing flasks with salmon yolk sac fry. The main goal for this study is to examine the potential for violacein production and determine how different cultivation conditions influence violacein production by varying cultivation media and incubation temperature.  The relationship between the five different Janthinobacterium strains is investigated based on 16S rRNA gene sequences and sequencing of the entire violacein operon. The correlation between possessing a violacein operon and producing purple colonies have been a main focus in this study. Further work includes examining the effects of colonizing Atlantic salmon yolk sac fry with the different Janthinobacterium strains.
 

Anders Wilhelm Lambine Skovly: Creating a protocol for infection of salmon yolk fry 

My project is a part of Alexander Fiedler's PhD thesis, where the aim is to determine whether or not atlantic salmon yolk fry's natural microbiota has a protective effect against pathogens, and if that is the case, then also determine if bacteriophages are superior to antibiotics in treatment of diseased salmon due to the pathogen-restricted effect of the phages. In order to test if the natural microbiota has a protective effect we first need a consistent infection protocol for the yolk fry, and this is what I am trying to develop. Development is done by keeping the fish in bottles and treating them with different strains of bacteria and then recording the number of deaths among the fishes.

 

Ann Isabel Carmo Rossvoll: Water microbiota in start feeding of Ballan wrasse

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Hugues Palandre: Development of molecular tools in the diatom Coscinodiscus wailesii

The goal of this project is to establish genetic transformation by bacterial conjugation in the giant diatom Coscinodiscus wailesii, thereby opening the way for modification of this species. The species of the genus Coscinodiscus are not only interesting for their great size, but also because of their intricately patterned frustules (cell wall structures made of silicate), which makes them attractive for diverse biotechnological applications.
 

Anne Helene Sandmark: The impact of unsuccessful invasions on an aquatic microbial community in a flow-through system

Microbial invasion is a process where a microorganism is introduced to, established in, grows, spreads, and impacts a new environment or community where it is not present at that particular time (Mallon et al., 2015, Kinnunen et al., 2016). Until recently, few studies investigated the impact that invasion has on the resident community both in regard to community diversity and functionality (Mallon et al., 2018, Buchberger and Stockenreiter, 2018). This project will look at the impact of unsuccessful invasions on microbial composition and functionality in flow-through systems. Mallon et al 2018 observed that an unsuccessful invasion both increased the richness and the average number of carbon sources utilized by the resident community. This increase in niche breadth was hypothesized to be because the invader competed with the resident bacteria which resulted in increased utilization of carbon sources. A new research gap was consequently identified. Does an unsuccessful invasion increase the chance of invasion of success during a secondary invasion? This project will have an overall research goal to test if unsuccessful invasions increase the chance of a successful secondary invasion.

Buchberger F and Stockenreiter M (2018): Unsuccessful invaders structure a natural freshwater phytoplankton community. Ecosphere 9, e02158.

Kinnunen M, Dechesne A, Proctor C, Hammes F, Johnson D, Quintela-Baliuja M, Graham D, Daffoncio D, Fodelianakis S, Hahn N, Boon N and Smets B F (2016): A conceptual framework for invasion in microbial communities. The ISME Journal 10, 2773-2779.

Mallon C A, Elsas J D V and Salles J F (2015): Microbial Invasions: The Process, Patterns, and Mechanisms. Trends in Microbiology 23, 719-729.

Mallon C A, Le Roux X, Van Doorn G S, Dini-Andreote F, Poly F and Salles J F (2018): The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader's niche. Isme J. 12, 728-741.

 

Ingrid Eskerud Harris

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Renate Sandberg:

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Graduated / closed projects:

See earlier Master projects in The archives.