Universität zu Köln

Förster, Mona ORCID: 0000-0003-0662-6357 (2024). How transformation affects bacterial genome dynamics and opens up alternative evolutionary trajectories. PhD thesis, Universität zu Köln.

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Abstract

For non-sexually reproducing organisms such as bacteria, natural transformation, a common mode of horizontal gene transfer (HGT), plays an important role in increasing genetic diversity, spreading beneficial mutations and curing deleterious ones. However, little is known about the genome-wide barriers, the effects of transformation on fitness and the role of the genetic background of the strains. In the first project, we elucidate the genome-wide barriers of transformation and their dependence on the genetic distance between donor and recipient. We conduct replacement accumulation experiments with Bacillus subtilis as recipient and different Bacillus species as well as a Geobacillus species as donors. For 20 cycles, we allow the recipient to transform for two hours in presence of donor DNA, ensure minimal selection by plating the hybrids directly after transformation, and apply a single cell bottleneck by selecting a monoclonal hybrid for the start of the next cycle. Following cycle 10 and 20, the DNA of the hybrids is sent for whole genome sequencing and the fitness is measured by competition experiments. By pooling all hybrids, we find 96% of core genes affected by replacements when supplying B. subtilis with Bacillus spizizenii DNA, indicating an almost unrestricted exchange between closely related species. In the less-related species Bacillus atrophaeus, we find replacement primarily in regions with high sequence identity, with an overrepresentation of ribosomal genes. A comparison of all donor-recipient pairs reveals an exponential relationship between core genome identity and transfer rate. Core genome identity also affects the length of replaced segments. At a low rate, the replacements entail insertions and deletions of accessory regions. We conclude that transformation between closely related species is strongly dependent on sequence identity and is dominated by replacements. In the second project, we characterize the fitness effects of transformation. To this end, we create a hybrid library with B. subtilis as recipient and B. vallismortis as donor. The distribution of fitness effects (DFE) of the hybrid library is measured via competition experiments under different conditions. These include experiments conducted at varying temperature, with and without lag phase, and in more or less complex media. Two additional libraries, one with random replacement of whole genes and one with B. spizizenii as donor are generated, measured under one condition and compared to the first library. In contrast to the DFE previously reported for mutations, we do not observe a shift towards negative fitness values in most conditions. Instead, we find a predominantly neutral DFE with some beneficial and deleterious outliers in all but one characterized environments. Some of these outliers show antagonistic pleiotropic effects in the different conditions, supporting the idea that a benefit is derived through a shared gene pool between closelyrelated species. Furthermore, we verify the predictive value of the DFEs by Performing an evolution experiment in two of the measured conditions. We conclude that DFEs are a suitable tool for predicting evolution and that transformation has the potential to accelerate adaptation. In the third project, we investigate the role of preceding adaptation on the fitness effects of transformation. For that purpose, we create two hybrid populations with different histories of adaptation, one whose recipient is well adapted to growth in liquid environments and another one whose recipient is well adapted to growth in structured environments. Using these hybrid populations, we address two questions. First, we assess whether Transformation with genomic DNA of B. vallismortis increases the fitness of B. subtilis that were already well adapted to a specific growth condition. By means of laboratory evolution, we find additional benefit of transformation during exponential growth in liquid. Second, we investigate whether transformation speeds up adaption to new growth environments. We find that during adaptation, transformation leads to an increase in fitness in both poorly adapted populations. Interestingly, in the transformed cells different genes are affected by replacements or mutation than in the non-transformed control populations. We conclude that transformation opens up new trajectories of adaptive evolution. To summarize, we find extensive exchange between closely related species, mostly neutrality for fitness of gene replacements and the opportunity for new pathways of adaptive evolution. This indicates that HGT between closely related species is frequent and has a major impact on how bacteria adapt to changing environments.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Förster, Mona mona.foerster@live.de orcid.org/0000-0003-0662-6357 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-732713
Date:	2024
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Physics > Institut für Biologische Physik
Subjects:	Physics Life sciences
Uncontrolled Keywords:	Keywords Language horizontal gene transfer English evolution English bacteria English Bacillus subtilis UNSPECIFIED evolution experiment English fitness English transformation English
Date of oral exam:	16 July 2024
Referee:	Name Academic Title Maier, Berenike Prof. Dr. Gordo, Isabel Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/73271