Cooperative and harmful behaviour in the bacterial world

Tese de doutoramento, Biologia (Biologia Evolutiva), Universidade de Lisboa, Faculdade de Ciências, 2017Bacteria are social organisms capable of displaying a multiplicity of complex behaviours, some of them with a significant impact on human lives. Antibiotic resistance, for one, is currently a major health menace and is typically envisioned as an asocial behaviour. Yet, sensitive bacteria can survive the action of antibiotics, given that their social entourage gathers the right characteristics. In this thesis social behaviour of bacteria, ranging from altruistic to spiteful, are shown to affect not only their survival, but also their ability to counterattack the invasion of competing bacteria, and ensure the preservation of social traits, such as antibiotic resistance. To ascertain the complexity and relevance of social behaviours on the bacterial world we studied two types of Escherichia coli mobile genetic elements: bacteriophages and plasmids. Such elements, are not only able to transmit horizontally between different bacterial lineages, but are also able to promote social behaviour in bacteria. In this thesis, both a temperate bacteriophage and three different conjugative plasmids were shown to act as promotors of bacterial social behaviours – both cooperative and harmful. Lysogenic bacteria were shown to use the λ bacteriophage as an allelopathic agent able to harm susceptible cells in their vicinity. This behaviour is of a spiteful nature towards the killed susceptible cells, but also proves to be altruistic towards surviving lysogenic bacteria in the population. Similarly, ampicillin-resistant bacteria, carrying conjugative plasmids, were able to cooperate in the detoxification of ampicillin enriched environments, which led to the survival of genetically sensitive bacteria. However, such sensitive hitchhikers did not remain unharmed for long. In fact, the resistant bacteria were able to use plasmids as a mechanism to harm plasmid-free bacteria and also to restore the cooperative antibiotic-resistance in the population. There is a great need to increase the general knowledge about bacterial social behaviours, since they are involved in well-known threats to public’s health. As far as bacteria are concerned, especially pathogenic bacteria, it is urgent to understand how social behaviours influence the ability of strains to survive the action of antibiotics, but also how they are able to cope when competing against non-pathogenic strains.As bactérias são organismos sociais capazes de desempenhar uma multiplicidade de comportamentos complexos, alguns dos quais com um impacto significativo na vida dos seres humanos. A resistência a antibióticos, por exemplo, é uma das maiores ameaças à saúde pública da atualidade e é tipicamente vista como um comportamento associal. Porém, bactérias sensíveis podem sobreviver à ação de antibióticos, se o seu enquadramento social reunir as características necessárias. Nesta tese, mostra-se que comportamentos sociais bacterianos, desde altruísmo a malícia, são capazes de afetar não só a sua sobrevivência como também a sua habilidade de contra-atacar a invasão de bactérias competidoras, assegurando a preservação de traços sociais, tais como a resistência a antibiótico. Por forma a desenvolver os conhecimentos relativos à complexidade e relevância dos comportamentos sociais no “mundo bacteriano”, estudamos dois tipos de elementos genéticos móveis de Escherchia coli: bacteriófagos e plasmídeos. Esses elementos são, não só capazes de ser transferidos horizontalmente entre diferentes linhagens bacterianas, como também são capazes de promover comportamentos sociais em populações bacterianas. Nesta tese, demonstra-se que, tanto um bacteriófago temperado como três plasmídeos conjugativos, atuam como promotores de comportamentos sociais – sejam cooperativos ou prejudiciais. É demonstrado que bactérias lisogénicas podem usar o fago λ como um agente alelopático capaz de prejudicar células suscetíveis na sua vizinhança. Este comportamento é de uma natureza maliciosa do ponto de vista das bactérias suscetíveis, mas também se mostra altruístico para com as outras bactérias lisogénicas que existem na população. Da mesma forma que bactérias resistentes a ampicilina, que possuem plasmídeos conjugativos, foram capazes de cooperar na destoxificação de um ambiente suplementado com ampicilina, o que por sua vez levou à sobrevivência de bactérias geneticamente sensíveis à ampicilina. No entanto, essas bactérias sensíveis oportunistas não permaneceram impunes por muito tempo. De facto, as bactérias resistentes foram capazes de usar os plasmídeos como uma forma de prejudicar as bactérias inicialmente sem plasmídeo e também como forma de restaurar o comportamento cooperativo de resistência a antibióticos na população. Existe uma grande necessidade em aumentar o conhecimento geral acerca de comportamentos sociais bacterianos, uma vez que estes organismos estão envolvidos em ameaças à saúde pública bem conhecidos. Em relação a bactérias, especialmente bactérias patogénicas, é urgente perceber como é que comportamentos sociais influenciam a capacidade de sobrevivência de estirpes à ação de antibióticos, mas também como é que elas essas estirpes são capazes de lidar quando em competição com bactérias não patogénicas

Cyanobacterial Toxins as Allelochemicals with Potential Applications as Algaecides, Herbicides and Insecticides

Cyanobacteria (“blue-green algae”) from marine and freshwater habitats are known to produce a diverse array of toxic or otherwise bioactive metabolites. However, the functional role of the vast majority of these compounds, particularly in terms of the physiology and ecology of the cyanobacteria that produce them, remains largely unknown. A limited number of studies have suggested that some of the compounds may have ecological roles as allelochemicals, specifically including compounds that may inhibit competing sympatric macrophytes, algae and microbes. These allelochemicals may also play a role in defense against potential predators and grazers, particularly aquatic invertebrates and their larvae. This review will discuss the existing evidence for the allelochemical roles of cyanobacterial toxins, as well as the potential for development and application of these compounds as algaecides, herbicides and insecticides, and specifically present relevant results from investigations into toxins of cyanobacteria from the Florida Everglades and associated waterways

Mathematical Modelling of Predatory Prokaryotes

Predator–prey models have a long history in mathematical modelling of ecosystem dynamics and evolution. In this chapter an introduction to the methodology of mathematical modelling is given, with emphasis on microbial predator–prey systems, followed by a description of variants of the basic two-species system. Then the two-species system is extended to incorporate effects such as predator satiation and prey escape strategies, after which multi-species effects, including alternative prey, protector species and decoy effects, are discussed. Simulations are used to discuss the effect of several model parameters

Systems biology of lactic acid bacteria: a critical review

Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute

The ecology and evolution of diversity and cooperation in bacterial public-goods

Explaining why cooperation exists despite the persistent advantage of cheats has been the focus of much theoretical and empirical attention in biology. Using the bacterium Pseudomonas aeruginosa as a model system for the evolution of cooperation, I investigate two distinct phenomena which may develop our understanding of how cooperation is maintained; 1) tag-based cooperation and diversity; and 2) environmental heterogeneity. The first investigates how diversity in cooperative systems may be a response to the selective pressure exerted by cheating, and how cheats may then regulate communities to maintain diversity: I demonstrate that in competition, tag-based cooperation is able to evade parasitism, provided the public-good is only accessible to producer strains, i.e., the cheat possesses the “wrong” tag. I also demonstrate that cheats can have a marked influence on diversity: In a community of two producer strains with different tags, if a third cheater strain is introduced, it will drive both its own producer and itself extinct. I do not find that the presence of cheats maintains diversity in either structured or unstructured environments, and discuss the possible causes of this. In the second topic of this thesis, I investigate the effect of environmental heterogeneity in resource availability, through space and time, on the evolution of cooperation. Environmental heterogeneity is a ubiquitous feature of natural landscapes, yet its effect on the evolution of cooperation has not been extensively studied. I demonstrate that resource availability heterogeneity, in both time and space, acts to maintain cooperation at higher levels than homogeneous environments of the same total resource value. This effect is due to the covariance between productivity and the cost of cooperation: high resource availability periods and spaces are highly productive, and also incur a relatively lower cost of cooperation.BBSR

Model of bacterial toxin-dependent pathogenesis explains infective dose

The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics