The Caulobacteraceae is an environmentally prevalent bacterial family that includes Caulobacter crescentus, a model organism well known for its complex lifecycle comprising motile non-reproductive cells and reproductive cells with stalks. However, despite their importance, surprisingly little is known about their phenotypic range, ecology, and evolution. To bridge this gap, this thesis characterizes the genotypic and phenotypic diversity of the Caulobacteraceae and investigates how they adapt to environmental changes across physiological and evolutionary timescales, significantly advancing our understanding of this widespread lineage.

In study I, we show that C. crescentus adapts to different forms of starvation by arresting its lifecycle at distinct points through differential regulation of cell differentiation and the replication initiator DnaA, which triggers either an accumulation of non-reproducing motile or sessile stalked cells.

In study II, we map out the evolutionary history, environmental distribution, and genetic potential of the order Caulobacterales. This uncovers convergent loss of the dimorphic lifecycle, crescentin-mediated cell curvature among other alphaproteobacteria, and widespread phototrophy, which includes the new genus Acaudatibacter—the first Caulobacterales lineage with photoautotrophic potential.

In study III, we expand the phenotypic and genomic repertoire of the Caulobacteraceae by isolating 58 new strains and describing 15 novel species. This uncovers previously unrecognized traits, including widespread quorum sensing modules and biofilm formation through later cell–cell interactions, likely involving giant secreted adhesins.

In study IV, we provide the first detailed portrait of the natural plasmids of the Caulobacteraceae. We identify their core propagation modules, uncover genes for novel antimicrobial compounds and distinct stress adaptation modules, and find evidence for these plasmids being regulated by the dimorphic lifecycles of their hosts. Our work reveal that plasmids have played key roles in the evolution of the Caulobacteraceae.

In study V, I synthesize knowledge on the evolution and diversity of alphaproteobacterial dimorphism. In particular, I delineate the defining characteristics of dimorphism, highlight analogous lifecycles across bacteria, and emphasize that prosthecae (stalks) are not inherently linked to dimorphism. Lastly, I underscore the value in establishing complementary model organisms to unravel the evolution of lifecycle complexity.

Caulobacteraceae är en vitt förekommande bakteriefamilj som innefattar modellorganismen Caulobacter crescentus, känd för sin komplexa livscykel med en motil icke-reproduktiv fas och en reproduktiv fas med stjälkceller. Trots dess betydelse för forskningen är kunskapen om familjens fenotypiska bredd, ekologi och evolution begränsad. Denna avhandling överbryggar denna kunskapsklyfta genom att karaktärisera den genotypiska och fenotypiska diversiteten hos Caulobacteraceae samt undersöka hur de anpassar sig till miljöförändringar över fysiologiska och evolutionära tidsskalor. Arbetet bidrar därmed till en väsentligt fördjupad förståelse för denna vitt utbredda bakteriefamilj.

I studie I visar vi att C. crescentus anpassar sig till olika svältförhållanden genom att stoppa sin livscykel vid specifika stadier genom reglering av celldifferentiering och replikationsinitiatorn DnaA, vilket antingen triggar en ackumulering av icke-reproduktiva motila celler eller fastsittande stjälkceller.

I studie II kartlägger vi den evolutionära historian, miljöförekomsten, och genetiska potentialen hos ordningen Caulobacterales. Resultaten visar att den dimorfa livscykeln har gått förlorad genom konvergent evolution, att crescentinförmedlad cellkrökning förekommer hos andra alfaproteobakterier samt att fototrofi är utbrett. Detta inkluderar det nya släktet Acaudatibacter, ordningens första rapporterade evolutionära linje med gener för fotoautotrofi.

I studie III expanderar vi Caulobacteraceae-familjens fenotypiska och genomiska repertoar genom att isolera 58 nya stammar och därav beskriva 15 nya arter. Dessa uppvisar tidigare okända egenskaper, såsom kvorumavkänning (quorum sensing) och biofilmproduktion via laterala mellancellsinteraktioner, vilket sannolikt involverar enorma utsöndrade adhesiner.

I studie IV framför vi det första detaljerade porträttet av naturliga plasmider hos familjen Caulobacteraceae. Vi identifierar deras fortplantningsmoduler, upptäcker gener för nya antimikrobiella ämnen och diverse stressanpassningsmoduler, samt finner bevis för att plasmiderna regleras av sina värdcellers dimorfa livscykler. Våra resultat visar att plasmider har spelat nyckelroller under Caulobacteraceae-familjens evolution.

I studie V presenterar jag en syntes av evolutionen av alfaproteobakteriell dimorfism och dess diversitet. Detta gör jag genom att beskriva de definierande egenskaperna hos celldimorfism, belysa analoga livscykler hos andra bakterier, samt understryka att prosteker (stjälkar) inte har en inneboende koppling till dimorfism. Slutligen poängterar jag vikten av att utveckla nya, komplementära modellorganismer för att klarlägga hur komplexa livscykler har utvecklats.

In a recent article published in Nature Communications, we proposed several revisions to the taxonomy of the bacterial order Caulobacterales1. To meet the criteria for an ‘effective publication’ according to the International Code of Nomenclature of Prokaryotes (ICNP), we here provide protologues for the proposed taxonomic revisions, which were originally included in the electronic supplementary material rather than the main article (see Note 1 to Rule 25a of the ICNP)2. Motivations for these proposals are based on our phylogenomic analyses and are found in the ‘Supplementary Note 2’ of Hallgren et al.1.

Many bacteria have complex pleomorphic lifecycles — a feature particularly widespread across the class Alphaproteobacteria of the phylum Pseudomonadota. While research on bacteria with pleomorphic lifecycles has for many years focused on the dimorphic bacterium Caulobacter crescentus, more recent studies on less established alphaproteobacterial model bacteria have uncovered diverse variations of bacterial pleomorphism. Here, we provide an overview of the diversity and evolution of the complex lifecycles among dimorphic Alphaproteobacteria and highlight the presence of analogous lifecycles in unrelated bacteria across the bacterial domain. We discuss the commonalities and differences between dimorphic species, as well as the selective pressures that might have sculpted their lifecycles. Furthermore, we exemplify how the cellular appendages common among dimorphic Alphaproteobacteria, referred to as prosthecae, are not inherently linked to dimorphism. Finally, we highlight how the large diversity of dimorphic Alphaproteobacteria can be used to shed light onto the evolution of bacterial cell biology.

Model bacteria are fundamental for research, but knowledge about their ecology and evolution is often limited. Here, we establish an evolutionary and ecological context for the model organism Caulobacter crescentus—an alphaproteobacterium intensively studied for its dimorphic lifecycle. By analyzing the phylogenetic relatedness and genetic potential of hundreds of Caulobacterales species, we reveal substantial diversity regarding their environmental distribution, morphology, cell development, and metabolism. Our work provides insights into the evolutionary history of morphological features such as the cell curvature determinant crescentin and uncovers a striking case of convergent loss of traits for cellular dimorphism among close relatives of C. crescentus. Moreover, we find that genes for phototrophy are widespread across Caulobacterales and that the new genus Acaudatibacter, described here, includes the first reported Caulobacterales lineage with photoautotrophic potential. Our study advances our understanding of an environmentally widespread bacterial order and sheds light on the evolution of fundamental prokaryotic features.

Here, we report the complete genome sequences of the dimorphic prosthecate bacterial species type strains Brevundimonas intermedia CB63T and Brevundimonas staleyi FWC43T, isolated from pond water and wastewater, respectively. B. intermedia CB63T contains a chromosome of 3.60 Mb, and B. staleyi FWC43T contains a chromosome of 3.97 Mb and a 157-kb plasmid.

All cells must ensure precise regulation of DNA replication initiation in coordination with growth rate and in response to nutrient availability. According to a long-standing model, DNA replication initiation is tightly coupled to cell mass increase in bacteria. Despite controversies regarding this model, recent studies have provided additional support of this idea. The exact molecular mechanisms linking cell growth with DNA replication under different nutrient conditions remain elusive. However, recent studies in Caulobacter crescentus and Escherichia coli have provided insights into the regulation of DNA replication initiation in response to starvation. These mechanisms include the starvation-dependent regulation of DnaA abundance as well as mechanisms involving the small signaling molecule (p)ppGpp. In this review, we discuss these mechanisms in the context of previous findings. We highlight species-dependent similarities and differences and consider the precise growth conditions, in which the different mechanisms are active.

Upon nutrient depletion, bacteria stop proliferating and undergo physiological and morphological changes to ensure their survival. Yet, how these processes are coordinated in response to distinct starvation conditions is poorly understood. Here we compare the cellular responses of Caulobacter crescentus to carbon (C), nitrogen (N) and phosphorus (P) starvation conditions. We find that DNA replication initiation and abundance of the replication initiator DnaA are, under all three starvation conditions, regulated by a common mechanism involving the inhibition of DnaA translation. By contrast, cell differentiation from a motile swarmer cell to a sessile stalked cell is regulated differently under the three starvation conditions. During C and N starvation, production of the signaling molecules (p)ppGpp is required to arrest cell development in the motile swarmer stage. By contrast, our data suggest that low (p)ppGpp levels under P starvation allow P-starved swarmer cells to differentiate into sessile stalked cells. Further, we show that limited DnaA availability, and consequently absence of DNA replication initiation, is the main reason that prevents P-starved stalked cells from completing the cell cycle. Together, our findings demonstrate that C. crescentus decouples cell differentiation from DNA replication initiation under certain starvation conditions, two otherwise intimately coupled processes. We hypothesize that arresting the developmental program either as motile swarmer cells or as sessile stalked cells improves the chances of survival of C. crescentus during the different starvation conditions.