A computational biology approach to studying algae-bacterial interactions
type: CreativeWork
description: Microalgae have a profound effect on the world due to their large contribution to net carbon fixation. Although they are phototrophic, more than 50% of microalgae are thought to depend on external supply of metabolites such as B-vitamins. In oceans, algae are therefore often found together with a community of bacteria and form intricate networks where metabolites are exchanged. Currently, only a fraction of the related mechanisms and metabolite exchanges between algae and bacteria have been uncovered and many more are likely to exist. The work presented in this thesis is based on a model system for algae-bacterial interactions made up of the green alga, Lobomonas rostrata and the alpha-proteobacterium Mesorhizobium loti. In the model system, it is known that the bacterium provides vitamin B12 to the alga and itself, whilst the alga provides fixed carbon. I have applied methods from the field of computational biology to study the interactions between these organisms and other similar partnerships, with the aim of uncovering new insights. The thesis is made up of three research chapters, each focused on using a specific method to study algae-bacterial interactions. I developed a genome scale metabolic model of metabolism of M. loti that enabled simulation of growth. The model simulates 1908 enzymatic reactions and takes 1804 metabolites into account. Using the model, I simulated growth of the bacterium on 1018 different substrates with the aim of identifying substrates supplied by L. rostrata when the two organisms are co-cultured. In addition, I carried out a set of simulations studying the bacterium’s ability to produce B12 from 1368 different substrates. The modelling efforts in this project was successful in enabling simulations, but it was not possible to validate the simulations with experimental data. A transcriptomics experiment was undertaken with the aim of identifying genes related to the interaction between L. rostrata and M. loti. In the experiment, the p…
abstract: Microalgae have a profound effect on the world due to their large contribution to net carbon fixation. Although they are phototrophic, more than 50% of microalgae are thought to depend on external supply of metabolites such as B-vitamins. In oceans, algae are therefore often found together with a community of bacteria and form intricate networks where metabolites are exchanged. Currently, only a fraction of the related mechanisms and metabolite exchanges between algae and bacteria have been uncovered and many more are likely to exist. The work presented in this thesis is based on a model system for algae-bacterial interactions made up of the green alga, Lobomonas rostrata and the alpha-proteobacterium Mesorhizobium loti. In the model system, it is known that the bacterium provides vitamin B12 to the alga and itself, whilst the alga provides fixed carbon. I have applied methods from the field of computational biology to study the interactions between these organisms and other similar partnerships, with the aim of uncovering new insights. The thesis is made up of three research chapters, each focused on using a specific method to study algae-bacterial interactions. I developed a genome scale metabolic model of metabolism of M. loti that enabled simulation of growth. The model simulates 1908 enzymatic reactions and takes 1804 metabolites into account. Using the model, I simulated growth of the bacterium on 1018 different substrates with the aim of identifying substrates supplied by L. rostrata when the two organisms are co-cultured. In addition, I carried out a set of simulations studying the bacterium’s ability to produce B12 from 1368 different substrates. The modelling efforts in this project was successful in enabling simulations, but it was not possible to validate the simulations with experimental data. A transcriptomics experiment was undertaken with the aim of identifying genes related to the interaction between L. rostrata and M. loti. In the experiment, the p…
author: Kudahl, Ulrich Johan
language: en
keywords: Computational Biology, Algae, Bacteria, Vitamin B12
license: https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/27f030b0-a85b-455e-ae0c-757aa0a47914/download
license: https://www.rioxx.net/licenses/all-rights-reserved/
date published: 2018-07-20
date modified: 2026-07-22T22:24:06Z
provider: Cambridge University
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Cambridge

PropertyValue
property ID: DOI
value: 10.17863/CAM.24234