The passage of genes from parents to offspring is a fundamental rule of heredity. However, bacteria violate this rule of strict vertical inheritance by shuttling DNA between cells through horizontal gene transfer (HGT). Common vehicles for HGT are conjugative plasmids, extrachromosomal pieces of DNA encoding the machinery for their own transfer. In addition to standard vertical transmission,...
In their natural habitats, bacteria live in close contact with other species. Genomic studies reveal plentiful evidence of horizontal gene transfer across different species. However, little is known about its rates and fitness effects. What are limiting factors of cross-species gene transfer? How does gene transfer affect bacterial fitness? While gene transfer can benefit bacteria during...
While independently replicating sequences, such as transposons, are common in bacterial genomes, they usually do not persist for long periods of time. To be maintained in the gene pool bacterial mobile genetic elements require to jump hosts. In contrast, short sequence repeats known as REPINs – whose replication is dependent on a non-jumping RAYT transposase – persist for millions of years in...
Microbes living in natural communities develop antimicrobial resistance (AMR) through complex evolutionary trajectories. Fundamental features of this process emerge only in natural settings and therefore remain poorly understood. How are real-world AMR-associated genetic traits distributed between genes, intergenic regulatory regions, and mobile elements? Following an antibiotic exposure, are...
While we often track evolution for single traits in microbes, understanding and projecting their ecological functions often requires considering their integrated multitrait phenotypes. For example, understanding how the responses of phytoplankton to environmental change translate into changes in ocean primary production changes depends not only on the direct responses to selection (e.g....
No two cells are identical, even when sharing the same genetic code. This variability among phenotypes can be found in cell populations regardless of the complexity of the organism — from mammalian neural tissues to bacterial colonies. In the latter, genetically and morphologically identical bacteria often exhibit a myriad of growth states, resulting in drastic fitness variability. Most of...
The fitness effects of all possible mutations available to an organism largely shapes the dynamics of evolutionary adaptation. Tremendous progress has been made in quantifying the strength and abundance of selected mutations available to single microbial species in simple environments, lacking strong ecological interactions. However, the adaptive potential of strains that are part of...
Biological functions of many cellular assemblages, ranging from multicellular organisms to microbial communities, rely on diversity among the composing units. Such division of labour is often seen through the lens of game theory, where the accent is posed on the success of different strategies in short-term competition (e.g. one cell type grows faster than another - like in cancer). Such...
Bacterial genes can either reside on the chromosome or on plasmids, extrachromosomal genetic structures that can be transferred from cell to cell. The distribution of genes between plasmid and chromosome is not random: certain types of genes are particularly likely to be plasmid-associated. This includes a number of clinically important traits, such as antibiotic resistance and virulence...
The evolution of multicellularity has opened new evolutionary paths to increased diversity and complexity. This transition from single cells to multicellularity involved three processes: cells remained attached to one another and formed groups, cells within these new groups differentiated to perform different tasks, and the emergent groups adapted their life cycles by evolving new reproductive...
The origin of multicellularity was one of the most significant innovations in the history of life. Our understanding of the evolutionary processes underlying this transition remains limited, however, mainly because extant multicellular lineages are ancient and most transitional forms have been lost to extinction. We bridge this knowledge gap by evolving novel multicellularity in vivo, using...
The evolutionary battle between viruses and the immune system is likened to a high-stakes arms race. The immune system makes antiviral proteins, called restriction factors, which can stop the virus from replicating. In response, viruses evolve to evade the effects of restriction factors. To counter this, restriction factors evolve too, and the cycle continues, in which both sides rapidly...
Large-scale duplications are a highly dynamic class of mutation. They arise and are subsequently lost – often without a trace – at rates far exceeding those typically observed for SNPs. The transient nature of large duplications means that their contribution to evolutionary processes is often overlooked. We are following the dynamics of adaptive, large-scale duplications in evolving...
In response to infection or vaccination, our immune system creates antibodies that bind strongly to relevant antigens through an evolutionary process called affinity maturation, which involves rounds of somatic hypermutation and selection. A key aspect of this process is the binding affinity landscape, which describes the mapping between antibody sequence and binding affinity to various...
From phytoplankton producing the planet’s oxygen to wildebeest grazing the Serengeti, each species modifies their ecosystem. These ecological changes can precipitate adaptive evolution, which in turn can lead to further changes in the ecosystem. Previous studies have shown that this coupling between ecological and evolutionary processes is often driven by interactions between species. While...
Author: Sotaro Takano, Jean C.C. Vila, Alvaro Sanchez, Djordje Bajić
Microorganisms typically display a wide, and often overlapping, range of metabolic capabilities. In theory, this should favor competitive exclusion, and thus seems at odds with the pervasive coexistence and the diversity observed in natural microbiomes. One form of resource specialization that could partly explain the...
There is great deal of interest in exploiting evolutionary tradeoffs to combat drug resistance. Instances of drug resistance have been steadily increasing creating considerable human health and economic impacts. In the United States, the CDC reports that ~35,000 deaths and $55 billion can be attributed to drug resistant infections per year. Collateral sensitivity (CS), where developing...
Gene regulatory networks are essential to organism survival as they allow rapid adaptation through altering gene expression profiles. These regulatory networks can be key sites of evolutionary change and they provide important insights into the adaptability of various organisms to environmental shifts such as climate change. Mutations drive their evolution, but mutation biases can drive...
Tremendous progress has been made in quantifying fitness landscapes and elucidating how the effects of available mutations affect the dynamics of single microbial species in simple environments lacking strong ecological interactions. However, it remains largely unclear how natural selection depends and feeds back onto the spatial and community structure characteristic of most natural...
Populations are fundamental units of ecology and evolution, and delineating ecologically meaningful populations among microbes is important for identifying how they adapt to and interact with their local environment. Here, we develop a method to assign closely related isolates to populations by inferring their gene flow information through a tri-partitioning of SNPs distributed across the...
Whether evolution is predictable has become an outstanding question in the field of evolutionary biology and requires knowledge of the complex genotype-fitness map. Experimental evolution studies have begun to shed light on this, but it has not yet been determined if predictions can be extended between different species. Here, we use the Pseudomonas fluorescens SBW25 wrinkly spreader (WS)...
Random mutations and demographic events make evolution inherently stochastic, despite the deterministic force of natural selection. In order to better understand the genetic and ecological factors that drive evolutionary predictability, we use the evolution of resistance to beta-lactam antibiotics in Escherichia coli as experimental model. I will present recent work on the joint effect of...
Fitness landscapes map genotypes to fitness, visualizing possible evolutionary paths. These landscapes are studied both at the conceptual level and made explicit by measuring the fitness of nearby genotypes to create empirical fitness landscapes. Since the mapping of the genotype to fitness depends on the environment, several approaches have been taken to include the environment. One of them...
The evolution of multicellularity created new ecosystems, fundamentally changing Earth’s ecology (Szathmáry & Smith, 1995). While multicellularity has evolved numerous times in diverse lineages (Knoll et al. 2011), no prior work has directly examined the impact of this major evolutionary transition on multicellular diversity. Using long-term experimental evolution, we show that the evolution...
Drug resistant pathogens are a wide-spread and deadly phenomenon that infect nearly 3 million individuals in the United States each year. If microbial resistance continues to develop at the current rate, bacterial infections are expected to surpass cancer as the leading cause of death worldwide by 2050. Novel approaches to designing therapy that explicitly take into account the adaptive nature...
Evolution can be viewed as a game where the object is to keep playing. From this perspective, focus is brought to the properties of lineages that enable their success over long spans of evolutionary time, rather than the phenotypes and performance of individuals in the contemporary environment. One property required for long-term evolutionary success is the ability of a lineage to translate...
Many cellular populations are tightly packed, including microbial colonies and biofilms, or tissues and tumours in multicellular organisms. However, little is known about how ensuing mechanical cell-cell interactions reshape evolutionary dynamics and critical outcomes, such as drug resistance. Here, I will show how growth-induced collective motion inherently suppresses the differential...
Microbes inhabit natural environments that are remarkably dynamic, with sudden environmental shifts that require immediate action by the cell. The genetic control of cellular responses therefore evolve according to the specific demands of their environment, resulting in different strategies such as transcriptional regulation or stochastic switching. However, when microbes are exposed to...
History, chance, and selection are the fundamental factors that drive and constrain evolution. We designed evolution experiments to disentangle and quantify effects of these forces on the evolution of antibiotic resistance. Previously, we showed that selection of the pathogen Acinetobacter baumannii in both structured and unstructured environments containing the antibiotic ciprofloxacin...
Eukaryotes and prokaryotes have distinct genome architectures, with marked differences in genome size, the ratio coding/non-coding DNA, and the abundance of transposable elements (TEs). As TEs replicate independently of their hosts, the proliferation of TEs is thought to have driven genome expansion in eukaryotes. However, prokaryotes also have TEs in intergenic spaces, so why do prokaryotes...
Plasmids are mobile genetic elements that horizontally transfer antibiotic resistance and virulence factor genes among bacteria. It's unclear if plasmids persist only through selection for the genes they carry or if they are infectious enough to persist as genomic parasites. Here we show that plasmids' infectious potential is severely underestimated by theoretical models and experimental...
