1,721,023 research outputs found
Temperature dependence of trophic interactions are driven by asymmetry of species responses and foraging strategy
No full textEnvironmental temperature has systematic effects on rates of species interactions, primarily through its influence on organismal physiology. We present a mechanistic model for the thermal response of consumer-resource interactions. We focus on how temperature affects species interactions via key traits - body velocity, detection distance, search rate and handling time - that underlie per capita consumption rate. The model is general because it applies to all foraging strategies: active-capture (both consumer and resource body velocity are important), sit-and-wait (resource velocity dominates) and grazing (consumer velocity dominates). The model predicts that temperature influences consumer-resource interactions primarily through its effects on body velocity (either of the consumer, resource or both), which determines how often consumers and resources encounter each other, and that asymmetries in the thermal responses of interacting species can introduce qualitative, not just quantitative, changes in consumer-resource dynamics. We illustrate this by showing how asymmetries in thermal responses determine equilibrium population densities in interacting consumer-resource pairs. We test for the existence of asymmetries in consumer-resource thermal responses by analysing an extensive database on thermal response curves of ecological traits for 309 species spanning 15 orders of magnitude in body size from terrestrial, marine and freshwater habitats. We find that asymmetries in consumer-resource thermal responses are likely to be a common occurrence. Overall, our study reveals the importance of asymmetric thermal responses in consumer-resource dynamics. In particular, we identify three general types of asymmetries: (i) different levels of performance of the response, (ii) different rates of response (e.g. activation energies) and (iii) different peak or optimal temperatures. Such asymmetries should occur more frequently as the climate changes and species' geographical distributions and phenologies are altered, such that previously noninteracting species come into contact. By using characteristics of trophic interactions that are often well known, such as body size, foraging strategy, thermy and environmental temperature, our framework should allow more accurate predictions about the thermal dependence of consumer-resource interactions. Ultimately, integration of our theory into models of food web and ecosystem dynamics should be useful in understanding how natural systems will respond to current and future temperature change
Ecological landscapes guide the assembly of optimal microbial communities
Full text linkAssembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia
The effects of foraging behaviour on food-web structure and dynamics
Full text linkA food web summarises the foraging relationships among creatures within a community. Therefore, to understand how food-web structural and dynamical properties emerge, it is essential to clarify how foraging behaviour (as the underpinning driver) shapes the properties at the level of the whole food web. In this thesis, we examine the influence of several behavioural aspects of foraging on food webs, as well as the mechanisms that cause these influences. In Chapter 2, by conducting food-web dynamical modelling that is constrained by species’ metabolism (following Metabolic Theory of Ecology, MTE), we bring to light how the foraging strategy and dimensionality interact with food-web structures to determine species coexistence in food webs. In Chapter 3, by further introducing Optimal Foraging Theory (OFT) as a diet choice mechanism, we explore the food-web structural and dynamical consequences when species are able to adjust their diet depending on resource abundances. We show that incorporating OFT indeed significantly affect both the structure and the dynamics of food webs, while the impacts can be varied and dependent on parameters that control the properties of both the community and its species’ behaviour. We then proceed in Chapter 4, by modelling using the same MTEOFT framework, to investigate the emergent food-web structure under conditions where species cannot fully comply with OFT but rather are constrained by the predation risk they undertake. We develop a new model that describes consumers’ diet choice under this predation-risk effect, and find that we can capture better the empirical food-web structure than can the classical OFT model without predation-risk considerations. By showing how foraging strategy and dimensionality, adaptive diet choice, and predation risk-driven response scale up their effect to determine food-web properties, overall, the findings of this thesis shed light on how food-web properties emerge from organismal foraging behaviour. Also, the present thesis lays a firm quantitative foundation for future work in food-web ecology.Open Acces
Predicting the effects of environmental variation on Atlantic salmon (Salmo salar) population dynamics
No full textRapid environmental change is causing dramatic declines in marine and freshwater fish populations across the globe. Atlantic salmon populations, which have a life cycle that spans both marine and freshwater ecosystems, have declined by around 70% in the last 25 years. Understanding the factors that drive Atlantic salmon population dynamics are crucial to ultimately mitigate these declines. Within this thesis, we develop a novel mechanistic model by combining the Metabolic Theory of Ecology with Integral Projection Models, giving a Metabolic IPM (termed MIPM). In Chapter 2, we develop the MIPM and derive the thermal performance curve of Atlantic salmon population fitness, independently predicting the thermal niche across their geographical range. We find that under future global warming scenarios, the fitness of many populations will be negatively impacted, compounded by resource supply and thermal fluctuations. In Chapter 3, we evaluate the value of existing population data and compare different possible expansions to better inform the MIPM. We find that sampling in an additional month during the field season has greater power in uncovering model parameters, compared to deploying the same field effort to generate a longer time series, or more intensive sampling according to current practices. Finally, in Chapter, 4 we investigate the drivers of existing populations by comparing empirical juvenile Atlantic salmon data from populations that span their latitudinal distribution. We find that temperature is a governing factor, however, temperature-independent resource availability plays a significant role, having implications on the fitness of populations and the ability to adapt to climate change. Overall, our results provide novel insights from a model that can capture environmental constraints on Atlantic salmon populations, and we hope that our results can be used to better inform management programmes. Furthermore, our modelling framework is adaptable for predicting the impacts of environmental change on other focal species.Open Acces
Population and community body size structure across a complex environmental gradient
No full textWe monitored the invertebrate community of leaf litter in and around a drying intermittent pool bed to explore patterns of ecological organisation across a complex environmental gradient, with particular focus on population and community size structure. We measured the body size of 24,609 individuals from 313 taxa ranging over 6 orders of magnitude in size to explore how the functional properties of individuals, populations and communities are affected by moisture (aquatic vs. terrestrial) and light (diurnal vs. nocturnal), and how these properties change across the aquatic–terrestrial habitat transition that occurs as the pool bed dried. We found strong effects of moisture on some population (size structure) and many community (species richness, abundance, evenness, biomass and size structure) properties, with additional temporal effects across the aquatic–terrestrial ecotone. There was no difference between diurnal and nocturnal populations or communities. Our results facilitate understanding of how the physical environment influences functional attributes, and particularly the size structure, of natural populations and communities
The effect of temperature on the dynamics and functioning of microbial communities
No full textTemperature is arguably the most important environmental driver in ecological systems. It acts across multiple scales to affect everything from individual physiological rates to populations dynamics and the functioning of ecosystems. Despite this, there is still uncertainty surrounding the mechanisms through which temperature acts, especially on microbial communities whose contributions to the cycling of energy and nutrients make them a crucial part of global biogeochemical cycles. In this work I use mathematical modeling and empirical data to investigate the effects of temperature on microbial communities and their emergent structure, dynamics and functioning. I focus particularly on two features of microbial communities and how they modify this response, interactions between populations and the variation in thermal responses between different taxa. I first examine the effects of temperature on the feasibility of microbial communities. Using a general model of community dynamics I show how the effects of temperature on populations and their interactions can predict species richness across temperature gradients. Crucially I reveal the importance of variation in thermal sensitivity between populations in determining the shape of this relationship. I then look at the effects of temperature on respiration in microbial communities, using a model of interaction-driven community dynamics combined with microbial microcosm experiments. I show theoretically how interactions can dampen or amplify the sensitivity of community respiration depending whether they are competitive or facilitatory in nature and that these predictions are matched in an experimental microbial heterotroph system. Finally I look at the effects of temperature on functioning and richness in more complex models of microbial communities that explicitly include competition and facilitation via the exchange of metabolic byproducts. I show how increases in temperature consistently lead to the break down of facilitation in microbial communities leading to simplified structure and reduced richness. Overall my work demonstrates how both interactions and variation in thermal responses between taxa can have large impacts on the thermal responses of microbial community properties.Open Acces
Swimming with microbes: an individual-based modelling approach to ocean microbial ecology across scales
Full text linkMicrobial ecosystems, both on land and in the oceans, are the staging ground for the biogeochemical activity that sustains habitable conditions on Earth. Ocean microbes are of particular importance; the primary producers that drive biogeochemical ocean processes are almost entirely microbial, and are collectively responsible for about half of global net primary production. These ecosystems are extraordinarily complex, by virtue of being driven by very large numbers of living individuals, constantly interacting with each other and their highly dynamic physical environment. Much uncertainty remains about how these dynamics, from micro- to macro-scales, ultimately impact key ecosystem properties such as spatial dynamics and growth rates of populations and communities. In this project I use individual-based modelling (IBM) across a range of spatial and temporal scales, leveraging large, high-resolution physical and biological datasets along with advancements in modelling tools to shed light on spatial and temporal dynamics of microbial populations in inherently fluctuating environments. In doing so I clarify and quantify hitherto unresolved ecological questions relating to interactions between microbes and turbulence, inaccuracies in conventional modelling approaches, and the balance of competition and coexistence between microbes in the marine environment.
In the Introductory Chapter, I review our current understanding of microbial ecology in the oceans, and illustrate how complex ecological behaviour emerges from the constant interaction of microbial individuals with each other and with their environment.
In the Second Chapter, I begin at the smallest scales directly relevant to ocean microbes, investigating the impact of turbulence on microbial spatial dynamics and patchiness. I adopt an existing mathematical framework for modelling microbes capable of gyrotactic locomotion, with an IBM to reproduce their motion within a fully-resolved 3D simulation of convective turbulence. This work clarifies and extends to more realistic flow regimes the existing theory connecting micro-scale microbe patchiness to a coupling of turbulence and individual motility. Interpreting my results in the context of varying turbulent conditions from the surface to the bottom of the mixed layer, I propose that this turbulence-driven patchiness is ephemeral, non-ubiquitous, and depth-dependent.
In the Third Chapter, I transition to larger spatial and temporal scales, and develop an IBM on top of the NEMO-MEDUSA oceanographic model and the global Biotraits database. I use this model to quantify, for the first time, to what degree fluctuating environmental conditions can influence estimates of a microbe's growth rate, due to nonlinear averaging effects similar to the phenomenon known as Jensen's Inequality. In a microbial growth context, such effects predict that growth rate estimates based on mean environmental conditions will differ from realised growth rates in a dynamic environment. I substantiate this prediction by simulating populations of marine phytoplankton following ocean currents, and demonstrating that realised growth differs substantially from mean-environment growth estimates for a clear majority of these simulated populations. I quantify the relative contributions of temperature and nutrient fluctuations to this microbial ``growth gap'' -- the magnitude of the difference between realised and mean-environment growth rates, and discuss the implications of my findings under a warming climate.
In the Fourth Chapter, I apply my NEMO-MEDUSA-Biotraits IBM to investigate the ‘Paradox of the Plankton’ -- the puzzling absence of competitive exclusion among ocean microbes. I simulate populations of distinct species with thermal histories which significantly overlap in both space and time within the IBM, which I treat as competitors. I then examine whether the distinct thermal adaptations of these competitors can cause competitive advantage to shift back and forth over time as environmental conditions fluctuate, thus preventing any individual species from permanently outcompeting others.
In the Final Chapter, I link my findings to each other and to the bigger picture of microbial ocean ecology, emphasizing how a maturing body of mathematical ecological theory, increasingly large and detailed datasets, and modern computational tools, allow us to shed light on long-standing questions by closely examining interactions between individuals and a dynamic environment.Open Acces
Effects of temperature on microbial metabolic rates
Full text linkProkaryotes (bacteria and archaea) are globally ubiquitous micro-organisms which play fundamental roles in biogeochemical cycles and ecosystem functioning. Understanding how these microbes are affected by temperature is key to our understanding of how ecosystem processes will be affected by and respond to climate change. This includes understanding both how temperature directly affects the biological rates of prokaryotes through to how community composition may change with temperature and the impacts that these responses have on overall community functioning. Combining meta-analyses with experimental work and mathematical modelling, I assessed the direct impacts of temperature on microbial biological rates, with the aim of understanding how these effects translate to community and ecosystem level changes. I performed a meta-analysis of prokaryotic growth and metabolic rates, spanning the entire temperature spectrum of life on earth, revealing that the metabolic rates of mesophilic prokaryotes are likely to rise with climate warming. I used experimental methods to reveal the phenotypic
diversity of temperature fitness in microbial communities, suggesting that species sorting rather than direct thermal adaptation may play a major role in how ecosystems respond to climate change. This work also revealed a disparity in phylogenetic groups associated with cooler and warmer temperatures as well as a divergence in their growth strategies, with warmer adapted taxa tending towards growth specialism rather than yield specialism. I also tested how microbial carbon use efficiency — the proportion of carbon uptake allocated to growth — varies with temperature. I found a unimodal temperature dependence of this trait, a departure from previous understanding. This work shows that changes in the composition and function of microbial communities with global change are likely to have a profound impact on ecosystem responses to warming. I propose that through species sorting processes, microbial communities are likely to shift to warmer adapted taxa with higher metabolic rates on average, which tend
to be less carbon efficient in their growth. Ultimately, this may lead to increased carbon efflux versus sequestration by the microbial components of ecosystems with climate warming.Open Acces
Towards a non-equilibrium thermodynamic theory of ecosystem assembly and development
Full text linkNon-equilibrium thermodynamics has had a significant historic influence on the development
of theoretical ecology, even informing the very concept of an ecosystem. Much of this influence
has manifested as proposed extremal principles. These principles hold that systems will tend
to maximise certain thermodynamic quantities, subject to the other constraints they operate
under. A particularly notable extremal principle is the maximum entropy production principle
(MaxEPP); that systems maximise their rate of entropy production. However, these principles
are not robustly based in physical theory, and suffer from treating complex ecosystems in
an extremely coarse manner. To address this gap, this thesis derives a limited but physically
justified extremal principle, as well as carrying out a detailed investigation of the impact of
non-equilibrium thermodynamic constraints on the assembly of microbial communities. The extremal
principle we obtain pertains to the switching between states in simple bistable systems,
with switching paths that generate more entropy being favoured. Our detailed investigation
into microbial communities involved developing a novel thermodynamic microbial community
model, using which we found the rate of ecosystem development to be set by the availability
of free-energy. Further investigation was carried out using this model, demonstrating the way
that trade-offs emerging from fundamental thermodynamic constraints impact the dynamics of
assembling microbial communities. Taken together our results demonstrate that theory can be
developed from non-equilibrium thermodynamics, that is both ecologically relevant and physically
well grounded. We find that broad extremal principles are unlikely to be obtained, absent
significant advances in the field of stochastic thermodynamics, limiting their applicability to
ecology. However, we find that detailed consideration of the non-equilibrium thermodynamic
mechanisms that impact microbial communities can broaden our understanding of their assembly
and functioning.Open Acces
Limits to thermal adaptation in ectotherms
Full text linkClimate change is expected to affect biological systems across multiple scales through its direct effects on the physiology of individual organisms. Therefore, to predict how communities and ecosystems will be impacted by changes in climate, it is key to understand the extent to which ectotherm physiology can change through thermal adaptation. In this thesis, we examine the influence of possible constraints on thermal adaptation, as predicted by the Metabolic Theory of Ecology. In Chapter 2 we describe the consequences of violating a key assumption of a model used for quantifying the thermal performance curve, i.e., the relationship of biological rates with temperature. We then proceed in Chapter 3 to evaluate the impact of thermodynamic constraints on the evolution of the thermal performance curves of phytoplankton. We show that thermodynamic constraints have a very weak effect on thermal adaptation, with phylogenetically structured variation being present across the entire thermal performance curve. Further support for such a conclusion is obtained in Chapter 4 through a phylogenetic comparative analysis of the evolution of thermal sensitivity across prokaryotes, phytoplankton, and plants. This reveals that thermal sensitivity is much more variable than expected, as it can change drastically within short amounts of evolutionary time. In Chapter 5, we finally investigate thermal adaptation at the molecular level, examining if changes in temperature can alter the effects of nonsynonymous mutations. We show that across prokaryotes, mutations become increasingly detrimental to the stability of proteins with temperature. In response, thermophile species evolve enzymes that are more robust to mutations and exhibit low substitution rates. Overall, these results further our understanding of how thermal physiology evolves and indicate areas where the theory – as it currently stands – may need to be modified.Open Acces
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