The role of mathematical modelling in understanding prokaryotic predation

With increasing levels of antimicrobial resistance impacting both human and animal health, novel means of treating resistant infections are urgently needed. Bacteriophages and predatory bacteria such as Bdellovibrio bacteriovorus have been proposed as suitable candidates for this role. Microbes also play a key environmental role as producers or recyclers of nutrients such as carbon and nitrogen, and predators have the capacity to be keystone species within microbial communities. To date, many studies have looked at the mechanisms of action of prokaryotic predators, their safety in in vivo models and their role and effectiveness under specific conditions. Mathematical models however allow researchers to investigate a wider range of scenarios, including aspects of predation that would be difficult, expensive, or time-consuming to investigate experimentally. We review here a history of modelling in prokaryote predation, from simple Lotka-Volterra models, through increasing levels of complexity, including multiple prey and predator species, and environmental and spatial factors. We consider how models have helped address questions around the mechanisms of action of predators and have allowed researchers to make predictions of the dynamics of predator–prey systems. We examine what models can tell us about qualitative and quantitative commonalities or differences between bacterial predators and bacteriophage or protists. We also highlight how models can address real-world situations such as the likely effectiveness of predators in removing prey species and their potential effects in shaping ecosystems. Finally, we look at research questions that are still to be addressed where models could be of benefit

Extended Adolescence: The Ecology and Endocrinology of Facultative Paedomorphosis

Phenotypic plasticity is an adaptation to unpredictable environments whereby an organism of a single genotype may express more than one phenotype under differing environmental conditions. Phenotypic plasticity can manifest as polyphenisms, which is an extreme form of phenotypic plasticity that produces two or more discrete, alternative phenotypes. The expression of alternative phenotypes is controlled by biotic and abiotic environmental factors, which variably affect the strength and direction of phenotypic outcomes. Using a model polyphenic salamander, I sought to understand the ecological and hormonal processes that regulate alternative phenotype expression. The mole salamander (Ambystoma talpoideum) and eastern newt (Notophthalmus viridescens) are facultatively paedomorphic, which is a polyphenism with two alternative adult phenotypes: paedomorphs and metamorphs. Paedomorphs retain juvenile characteristics at sexual maturity (i.e., gills and an aquatic morphology), while metamorphs transition to terrestrial environments. The expressed phenotype depends on the environment context in which the larvae develop, with paedomorphosis often occurring under favorable aquatic conditions. I conducted a series of experiments to investigate the roles of population density, predator presence, hydroperiod, and stress hormones in regulating the expression of paedomorphosis. Results indicated the regulation of paedomorphosis through multiple ecological factors may be reducible to density-mediated effects, with a few notable exceptions. I also show that elevated stress hormones play a central role in regulating metamorphosis suggesting that all ecological factors affecting facultative paedomorphosis may funnel through a simple stress physiology framework. In conclusion, environmental factors affecting this polyphenism may share a comthread of inducing a stress response that initiates metamorphosis, thereby regulating phenotype in the population

The role of mathematical modelling in understanding prokaryotic predation

With increasing levels of antimicrobial resistance impacting both human and animal health, novel means of treating resistant infections are urgently needed. Bacteriophages and predatory bacteria such as Bdellovibrio bacteriovorus have been proposed as suitable candidates for this role. Microbes also play a key environmental role as producers or recyclers of nutrients such as carbon and nitrogen, and predators have the capacity to be keystone species within microbial communities. To date, many studies have looked at the mechanisms of action of prokaryotic predators, their safety in in vivo models and their role and effectiveness under specific conditions. Mathematical models however allow researchers to investigate a wider range of scenarios, including aspects of predation that would be difficult, expensive, or time-consuming to investigate experimentally. We review here a history of modelling in prokaryote predation, from simple Lotka-Volterra models, through increasing levels of complexity, including multiple prey and predator species, and environmental and spatial factors. We consider how models have helped address questions around the mechanisms of action of predators and have allowed researchers to make predictions of the dynamics of predator–prey systems. We examine what models can tell us about qualitative and quantitative commonalities or differences between bacterial predators and bacteriophage or protists. We also highlight how models can address real-world situations such as the likely effectiveness of predators in removing prey species and their potential effects in shaping ecosystems. Finally, we look at research questions that are still to be addressed where models could be of benefit

Nonlinear dynamics of plankton ecosystem with impulsive control and environmental fluctuations

It is well known that the density of plankton populations always increases and decreases or keeps invariant for a long time, and the variation of plankton density is an important factor influencing the real aquatic environments, why do these situations occur? It is an interesting topic which has become the common interest for many researchers. As the basis of the food webs in oceans, lakes, and reservoirs, plankton plays a significant role in the material circulation and energy flow for real aquatic ecosystems that have a great effect on the economic and social values. Planktonic blooms can occur in some environments, however, and the direct or indirect adverse effects of planktonic blooms on real aquatic ecosystems, such as water quality, water landscape, aquaculture development, are sometimes catastrophic, and thus planktonic blooms have become a challenging and intractable problem worldwide in recent years. Therefore, to understand these effects so that some necessary measures can be taken, it is important and meaningful to investigate the dynamic growth mechanism of plankton and reveal the dynamics mechanisms of formation and disappearance of planktonic blooms. To this end, based on the background of the ecological environments in the subtropical lakes and reservoirs, this dissertation research takes mainly the planktonic algae as the research objective to model the mechanisms of plankton growth and evolution. In this dissertation, some theories related to population dynamics, impulsive control dynamics, stochastic dynamics, as well as the methods of dynamic modeling, dynamic analysis and experimental simulation, are applied to reveal the effects of some key biological factors on the dynamics mechanisms of the spatial-temporal distribution of plankton and the termination of planktonic blooms, and to predict the dynamics evolutionary processes of plankton growth. The main results are as follows: Firstly, to discuss the prevention and control strategies on planktonic blooms, an impulsive reaction-diffusion hybrid system was developed. On the one hand, the dynamic analysis showed that impulsive control can significantly influence the dynamics of the system, including the ultimate boundedness, extinction, permanence, and the existence and uniqueness of positive periodic solution of the system. On the other hand, some experimental simulations were preformed to reveal that impulsive control can lead to the extinction and permanence of population directly. More precisely, the prey and intermediate predator populations can coexist at any time and location of their inhabited domain, while the top predator population undergoes extinction when the impulsive control parameter exceeds some a critical value, which can provide some key arguments to control population survival by means of some reaction-diffusion impulsive hybrid systems in the real life. Additionally, a heterogeneous environment can affect the spatial distribution of plankton and change the temporal-spatial oscillation of plankton distribution. All results are expected to be helpful in the study of dynamic complex of ecosystems. Secondly, a stochastic phytoplankton-zooplankton system with toxic phytoplankton was proposed and the effects of environmental stochasticity and toxin-producing phytoplankton (TPP) on the dynamics mechanisms of the termination of planktonic blooms were discussed. The research illustrated that white noise can aggravate the stochastic oscillation of plankton density and a high-level intensity of white noise can accelerate the extinction of plankton and may be advantageous for the disappearance of harmful phytoplankton, which imply that the white noise can help control the biomass of plankton and provide a guide for the termination of planktonic blooms. Additionally, some experimental simulations were carried out to reveal that the increasing toxin liberation rate released by TPP can increase the survival chance of phytoplankton population and reduce the biomass of zooplankton population, but the combined effects of those two toxin liberation rates on the changes in plankton are stronger than that of controlling any one of the two TPP. All results suggest that both white noise and TPP can play an important role in controlling planktonic blooms. Thirdly, we established a stochastic phytoplankton-toxic producing phytoplankton-zooplankton system under regime switching and investigated how the white noise, regime switching and TPP affect the dynamics mechanisms of planktonic blooms. The dynamical analysis indicated that both white noise and toxins released by TPP are disadvantageous to the development of plankton and may increase the risk of plankton extinction. Also, a series of experimental simulations were carried out to verify the correctness of the dynamical analysis and further reveal the effects of the white noise, regime switching and TPP on the dynamics mechanisms of the termination of planktonic blooms. On the one hand, the numerical study revealed that the system can switch from one state to another due to regime shift, and further indicated that the regime switching can balance the different survival states of plankton density and decrease the risk of plankton extinction when the density of white noise are particularly weak. On the other hand, an increase in the toxin liberation rate can increase the survival chance of phytoplankton but reduce the biomass of zooplankton, which implies that the presence of toxic phytoplankton may have a positive effect on the termination of planktonic blooms. These results may provide some insightful understanding on the dynamics of phytoplankton-zooplankton systems in randomly disturbed aquatic environments. Finally, a stochastic non-autonomous phytoplankton-zooplankton system involving TPP and impulsive perturbations was studied, where the white noise, impulsive perturbations and TPP are incorporated into the system to simulate the natural aquatic ecological phenomena. The dynamical analysis revealed some key threshold conditions that ensure the existence and uniqueness of a global positive solution, plankton extinction and persistence in the mean. In particular, we determined if there is a positive periodic solution for the system when the toxin liberation rate reaches a critical value. Some experimental simulations also revealed that both white noise and impulsive control parameter can directly influence the plankton extinction and persistence in the mean. Significantly, enhancing the toxin liberation rate released by TPP increases the possibility of phytoplankton survival but reduces the zooplankton biomass. All these results can improve our understanding of the dynamics of complex of aquatic ecosystems in a fluctuating environment

Colonization History and Alternative Community States in Experimental Microcosms

Using s suite of disparate experimental systems, three tests of the effect of variation in community history on community states were performed. The first test explored the effect of species invasion order on the structure and invasibility in soil microbial communities. Microcosm communities were assembled by augmenting an existing soil community with sequential introductions of three bacterial strains under three alternative sequences. Assembled communities were then probed with a genetically engineered bioremediative bacterium to test the relative vulnerability of these communities to this strain. Results indicated that variation in invasion order resulted in the production of alternative community states with distinct vulnerabilities to invasion. The second test explored the effect of the interaction of variation in invasion sequence with varying productivity level on community composition and media chemistry properties. Detritus- based aquatic communities consisting of bacteria and protists were assembled under two alternative sequences on a gradient of five nutrient concentrations. In total, five unique community states were found to emerge from the interaction of species order and productivity level. Alternative states arising from sequence effects were found at two of the five nutrient levels tested. In addition, sequence effects were found to produce unique biologically-mediated changes to media chemistry. Notably, such effects were not necessarily reflected by observable changes at the species compositional level. The third test evaluated trends in species turnover data for evidence of convergence in community composition among a suite of 15 artificial pond microcosms established at the same location. Ponds were arranged in five clusters of three. Here, an explicit manipulation of invasion sequence was not performed; rather, microcosms are assumed to possess similar histories and similar environments based on spatial proximity. Evidence of convergence was sought using five alternative compositional classification schemes. No evidence for convergence for the overall study site was found. Results of multiple analyses indicated a weak degree of convergence at the cluster level. Disturbance arising from multiple heavy rainfall events, however, had a strong disruptive effect on this convergence. Stronger evidence was found for a divergence in composition between two sets of microcosms that were independent of spatial proximity

Global Positive Periodic Solutions for Periodic Two-Species Competitive Systems with Multiple Delays and Impulses

A set of easily verifiable sufficient conditions are derived to guarantee the existence and the global stability of positive periodic solutions for two-species competitive systems with multiple delays and impulses, by applying some new analysis techniques. This improves and extends a series of the well-known sufficiency theorems in the literature about the problems mentioned previously

Social learning in mixed-species troops of Saguinus fuscicollis and Saguinus labiatus: tests of foraging benefit hypotheses in captivity

The selective costs and benefits affecting the evolution of group living have long interested behavioural ecologists because knowledge of these selective forces can enhance our understanding not only of why organisms live in groups, but also why species exhibit particular patterns of social organisation. Tamarins form stable and permanent mixed-species troops providing an excellent model for examining the costs and benefits hypothesised for group living. However, testing hypotheses in the wild is difficult, not least because participating species are rarely found out of association. In contrast, in captivity it is possible to compare matched single- and mixed-species troops and also to study the same individuals in single and mixed-species troops to see what effect the presence of a congener has on behaviour. In this way, captive work can help us confirm, reject, or refine the hypotheses, and aids in the generation of new ones, for relating back to the wild. The utility of this approach is demonstrated in this thesis which explored some of the foraging benefit hypotheses and, in particular, the underlying notion that individuals in tamarind mixed-species troops can increase their foraging efficiency through social earning. Single and mixed-species troops of Saguinus fuscicollis and S. labiatus were studied at Belfast Zoological Gardens. It was found that social interaction with conspecifics and congeners facilitated learning by individuals of various types of food-related information (food palatability, location, and method of access). However, although social learning operated in mixed-species troops, it did so under the shadow of inter-specific dominance. The results were used, in conjunction with field observations in Bolivia, to make inferences about the adaptive function of social learning in the wild. These findings strengthen the hypotheses which suggest that increased opportunity for social learning, through an increase in troop size and as a result of species divergence in behaviour, is an adaptive advantage of mixed-species troop formation in tamarins

Contributions à l'étude des patrons spatiaux de biodiversité dans les paysages complexes

Les patrons spatiaux issus de processus écologiques naturels et anthropiques constituent une mosaïque complexe dans la nature. Ceci combiné aux conséquences parfois colossales des perturbations anthropiques sur la biodiversité et les services écosystémiques, fait de l'écologie spatiale une science à la fois complexe et urgente dans un contexte de changement global rapide. Dans cette thèse, j’ai essayé de contribuer à notre compréhension de comment la structure spatiale des paysages influence la dynamique des populations, en utilisant des approches innovantes. Dans ce but, j'ai étudié différentes perturbations et différents aspects de la dynamique des populations dans trois chapitres. Les deux premiers chapitres d’analyse portent sur un biome qui fournit de nombreux services écosystémiques. La forêt boréale présente une exploitation en plein développement potentiellement non durable, et est aussi actuellement menacée par des perturbations naturelles sans précédents et exacerbées. J'ai d'abord examiné comment l’habitat naturel et les nombreuses altérations du paysage causées par l'homme influencent une communauté de mammifères de la forêt boréale. Ensuite, je me suis concentré sur une autre perturbation à grande échelle de la forêt boréale en identifiant les éléments du paysage qui limitent la propagation d’un des ravageurs forestiers les plus destructeurs au monde. Enfin, j'ai complété les approches utilisées dans les deux chapitres précédents, en me concentrant sur l'aspect temporel du changement de la dynamique des populations. Je l'ai fait en construisant et en évaluant une méthode capable de détecter des changements de diversité génétique locaux et atypiques, malgré les changements aléatoires omniprésents apportés par la dérive génétique et le flux de gènes. Mes trois chapitres d’analyse ont des implications claires en matière de conservation. Bien que deux d'entre eux soient concentrés sur des systèmes spécifiques, ils peuvent s'appliquer à d'autres paysages, ou du moins fournir une piste pour de futures recherches. Pour conclure ma thèse, j'ai suivi la synthèse de mes chapitres par une discussion sur comment l'interdisciplinarité des disciplines associées à l'écologie spatiale est une force essentielle que nous devrions cultiver. Je termine ma thèse en identifiant certaines des directions de recherche futures les plus excitantes et prometteuses.Natural and anthropogenic spatial patterns create an intricate mosaic. This fact, combined with the sometimes colossal consequences of anthropogenic disturbances on biodiversity and ecosystem services, makes spatial ecology a science of both complexity and urgency in a context of rapid global change. In this thesis, I have tried to contribute to our understanding of how the spatial structure of landscapes influences population dynamics through innovative approaches. Towards this goal, I have investigated different perturbations and different aspects of population dynamics in three chapters. The first two analysis chapters focus on a biome which is a large provider of ecosystem services and resources, featuring rapidly increasing and possibly unsustainable exploitation, but which is also currently under threat from unprecedented and exacerbated natural disturbances. First, I delved into how a community of boreal forest mammals is driven by its natural habitat and the many man-made alterations to the landscape. Then, I focused on another large-scale perturbation of the boreal forest by identifying what elements of the landscape constrain the spread of one of the most destructive forest pests in the world. Finally, I complemented the approaches used the previous two chapters, by focusing on the temporal aspect of population dynamics change. I did this by constructing and evaluating of a method capable of detecting local atypical change in genetic diversity despite the ever-present random changes brought by genetic drift and gene flow. My three analysis chapters have clear conservation implications which, although two of them focused on specific systems, may translate to other landscapes, or at least provide a pipeline for future research. To conclude my thesis, I followed the synthesis of my chapters by a discussion about how the interdisciplinarity of disciplines associated with spatial ecology is an essential strength we should cultivate. I end my thesis by identifying some of the most exciting and promising future research directions