Master's Thesis: Ecological and Genomic Characterization of Streamlined, Rhodopsin-bearing Freshwater Microbes
’Candidatus Methylopumilus sp.’ is a proposed bacterial taxon isolated from the plankton of lakes. This genus includes two suggested species, which are tentatively named ’Candidatus Methylopumilus planktonicus’ and ’Candidatus Methylopumilus turicensis’. They are characterized by a small, streamlined genome (1.3 Mb and 1.75 Mb, respectively) and methylotrophic lifestyle, which allows them to utilize substrates without carbon-carbon bounds for assimilation, i.e. methanol or methylamine.
In the scope of the presented thesis, more strains of ’Ca. Methylopumilus planktonicus’ were sequenced and put in phylogenomic relation to each other, and to the closely related, marine OM43 clade.
Another feature of ’Ca. Methylopumilus sp.’ is the presence of rhodopsins (light-driven proton pumps), meaning that the candidate genus can further utilize light to produce energy in the form of ATP. To examine the influence of rhodopsins on growth of ’Ca. Methylopumilus planktonicus’, a growth assay was conducted with conditions varying in light-exposure and carbon concentration. The response of the bacteria to the various conditions was quantified by measuring their cell densities by flow cytometry, and additionally by assessing the cell volumes and morphotypefrequencies by epifluorescence microscopy of DAPI-stained cells.
There were tendencies of a fitness-advantage in light-grown cultures, as the cell densities were higher, more biomass could be assimilated, and the carbon uptake was higher when exposed to light. Furthermore, there was a shift from Vibrio-shaped forms to rounder morphotypes over time in both light- and dark-grown cultures.
All in all, this thesis presents an extensive characterization of ’Ca. Methylopumilus planktonicus’ in terms of genomic properties and growth behavior in varying conditions and can thus contribute to the official approval of the novel species description.
This repos includes the written thesis, and also a selection of scripts used for the graphical and statistical analysis. These files aim to present a fraction of the work I have done during the Master's project.