Home 

Consortium

Descriptions of  PhD projects

Application

Contact

The program offers PhD positions  the following. Feel free to contact respective supervisors for more details.

1) Accumulation of mutations and the robustness of genetic systems
2) Monitoring of metal availability thresholds causing changes in insect larval community structure in metal-contaminated stream systems
3) Impact of industrial pollution (heavy metals) on stoichiometry of soil-litter food webs in forests
4) Metabolic performance and susceptibility to pollution in voles: an experimental evolution approach
5) Role of anti-competitor toxins in the origin and maintenance of diversity in structured microbial populations
6) Relationship between the diversity of soil microbial communities and their resistance to different stressors
7) Interaction between natural and sexual selection in adaptation to novel, stressful environment



1) Accumulation of mutations and the robustness of genetic systems (supervisors: Ryszard Korona; Arjan de Visser, Wageningen)
It is commonly observed that an organism can accommodate a mutation, or even several mutations, without a visible phenotypic effect. Robustness of genetic systems is likely rooted in basic features of metabolic networks and therefore is intensely studied by theoreticians. Understanding the causes and limits of robustness is especially important in case of species in which mutations are accumulating and whose environment fluctuates, because genetically compromised organisms are less resilient to environmental stress. Empirical studies of genetic robustness are still in an initial phase. The traditional approach was to introduce multiple random mutations whose location and function were largely unknown. New technologies allow planned mutagenesis, but its application has been restricted to one or very few genes per organism. The planned research will be the first attempt to blend both approaches by generating a large number of organisms with different combinations of multiple but individually recognizable mutations. Budding yeast is currently the best model for such a study. A complete collection of strains in which every native gene is replaced by the same marker gene is available. A selected marked gene will be replaced by a cassette which can be then easily removed from the genome. (The cassette has already been constructed in the laboratory of RK.) Iteration of this procedure will generate strains in which random or selected combinations of genes are deleted. Two hypotheses, crucial for the current debate about robustness, will be tested. Firstly, most existing models suggest that trajectories of fitness decay are in general not gradual but treshold-like, that is, phenotypic collapse is greatly accelerated after a critical number of mutations is accumulated. Secondly, the decline in fitness is accelerated by mutations with highly pleiotropic effects, such as those located in genes related to chromatin restructuring, transcription and translation, protein maturation and degradation.

 2) Monitoring of metal availability thresholds causing changes in insect larval community structure in metal-contaminated stream systems (supervisors: Wojciech Fiałkowski; Philip Rainbow, London)
Trace metal contamination of aquatic biota strongly impacts the taxonomic diversity of macrobenthic assemblages. However, very rarely do the metals constitute the only source of pollution in a given ecosystem. The aim of this project is to find a way of telling apart the influence of metals from that of other contaminants. We plan to use a Hydropsyche – mayfly model in a metal-rich streams draining the industrial region of Upper Silesia in Poland. Hydropsychid caddisflies are widespread in metal contaminated streams and are excellent biomonitors of toxic metals like Cu (Cain et al., 1992; Gower et al., 1994). Their larvae are hardy and tolerate local trace metal availabilities to a much greater extent than do more metal-sensitive members of stream insect larval communities such as ephemerellid and heptageniid mayflies. Thus the latter will be eliminated from stream benthic communities at metal levels (reflected in bioavailabilities) still tolerated by Hydropsyche larvae. We intend to test the hypothesis that the threshold bioavailabilities for mayflies mentioned above will be consistently correlated with particular accumulated metal concentrations in the Hydropsyche larvae, given that these accumulated metal concentrations are integrated measures of the metal bioavailabilities to which the larvae have been exposed (Rainbow, 2006). Thus it is further hypothesised that there will be a correlation between the bioaccumulated concentration in hydropsychids and the abundance of ephemerellid and heptageniid mayflies in a metal-contaminated stream, system (Maret et al., 2003).
It is intended to use the metal-rich streams draining the Upper Silesia industrial region to investigate this hypotheses. Measures of community structure will be made (with particular reference to the presence and abundance of ephemerellid and heptageneiid mayflies) along metal gradients of several streams, and sympatric larvae of Hydropsyche will be collected for metal analysis by means of ICP-OE spectroscopy. From previous studies (Fialkowski et al., 2003a,b), it is expected that the trace metals As, Cu, Pb and Zn will be of particular relevance in addressing this hypothesis.

3) Impact of industrial pollution (heavy metals) on stoichiometry of soil-litter food webs in forests (supervisors: Anna Rożen; Stefan Sheu, Goettingen)
Ecological stoichiometry investigates energy and selected elements balance in ecological interactions. It assumes that consumers maintain elemental homeostasis in body composition within limited bounds. Chemical composition of organisms (stoichiometric ratio of elements mass in organism) is diversified and may be different on particular trophic levels. Therefore some elements may constitute a factor limiting growth of organisms, whereas others are in excess. The stoichiometry of elements in food may influence species composition of consumers and affect the biodiversity. We know from previous studies that in the polluted sites the density of soil invertebrates is lower while their diversity is higher. Some elements (egzobiotics) may interact with nutrients influencing species composition of soil-litter community and, in consequence, biodiversity. It is hypothesised that in stressed environments the stoichiometry of some elements in food webs may be affected as a result of interaction between nutrients and heavy metals (i.e. antagonism Cd/Ca – increased excretion of calcium).
The project is aimed at explaining how pollution affects the stoichiometry of terestrial (soil/litter) trophic webs which have not yet been studied in that respect (therefore no precise hypotheses as to particular elements affecting stoichiometric balances of particular taxonomic groups cannot be made before pilot experiments are done). The research will be conducted both in the field and in laboratory. The field studies will be done in forests polluted by zinc smelter (high concentrations of Zn, Cd, Pb ) and those polluted by copper smelter (high concentration of Cu), where the structure of soil-litter food webs will be assessed and samples of invertebrates will be taken. In the animals, litter and soil stoichiometric ratios of elements (C,N,S, P as well as selected microelements and xenobiotcs) will be measured using appropriate analytical methods. The stoichiometric relations in two polluted forests will be compared with those form unpolluted ones. The hypothesis will be tested that in result of heavy metal loads the balances of some nutrients will be changed, resulting in connection with different taxonomic composition of the biota. In the laboratory simple experimental food chains will be composed from forest soil invertebrates to learn about the impact of heavy metals on stoichiometric relations under controlled conditions. This would provide quantitative data on stoichiometric balances in taxonomically different trophic chains which are necessary to verify the hypotheses on stoichiometric effects in community composition.

4) Metabolic performance and susceptibility to pollution in voles: an experimental evolution approach (supervisors: Paweł Koteja; Theodore Garland, University of California, Riverside, USA)
It is a trivial notion that the effects of environmental stressors on organisms depend on life strategy of the organisms and their characters associated with activity pattern, food habits, rate of metabolic processes, adaptations to local habitat, etc., but the knowledge of specific patters of the relations is still limited. One approach to investigate such relations is to compare the effects of particular stressors across different species, representing alternative adaptive strategies. However, species usually differ simultaneously in many aspects of adaptive characters and have a different and usually only poorly known history. Thus, correlations observed in comparative studies do not allow strong inferences concerning casual relations. On the other hand, typical experiments are based on studying the effects of alternative conditions at the level of phenotypic plasticity, which does not allow predictions concerning correlated evolution, because the phenotypic correlations do not necessarily reflect genetic ones. A promising tool to resolve the difficulties is to apply "experimental evolution", i.e., to compare lines of organisms representing different adaptations acquired under controlled laboratory conditions. An ongoing multidirectional artificial selection experiment, in which bank voles (Myodes glareolus) are selected towards high aerobic metabolism achieved during locomotor activity (A), predatory behavior (P), and ability to cope with herbivorous diet (H), provides a unique opportunity to perform such a research, without the need to bear the high costs of establishing experimental colonies. Four lines for each of the selection directions and four unselected, control lines (C), have been maintained for 10 generations. Direct effects of selection have been significant already after three generations, and several correlated responses have been observed in subsequent generations. As of now (generation 10), results of the controlled evolution are most evident in the "high aerobic metabolism" lines (A), in which basal metabolic rate, food consumption rate, spontaneous locomotor activity, and maximum forced-exercise metabolism are higher than in the unselected control lines.
The "high aerobic" lines of the voles provide an elegant model to find out whether and how the susceptibility to environmental stressors such as pollutants changes as a consequence of evolution towards high overall rate of metabolism. The question is intriguing because contradictory hypotheses concerning the effects can be proposed. High metabolism and increased food consumption in the A lines should result in a higher intake of pollutants, regardless of whether the source is in food, water or air. Moreover, specific physiological adaptations related to locomotor performance could be traded-off for a decreased capabilities of decontamination mechanisms, and biochemical machinery tuned to achieve maximum rates of aerobic metabolism could be more sensitive to a wide range of toxicants (especially those interfering with aerobic metabolic paths). Both of the above mechanisms would lead to a prediction that voles from A lines, and generally animals with high metabolic rates, should be more prone to adverse effects of pollution. On the other hand, however, the high rate of metabolic turn-over can be also associated with a higher capacity of removing or neutralizing the toxicants, which would lead to an opposite prediction. The aim of the project will be to compare the effect of toxicants (inorganic: heavy metals; organic: pesticides) in voles from the A and C lines. The specific tasks will be to compare 1) the rates of accumulation and elimination of the pollutants, 2) effects of the pollutants on organismal performance (aerobic capacity, locomotor performance, thermoregulatory capacity), and 3) underlining biochemical and molecular mechanisms (expression of genes evolved in detoxication, oxidative damage, etc.).

5) Role of anti-competitor toxins in the origin and maintenance of diversity in structured microbial populations (supervisors: Ryszard Korona; Arjan Visser, Wageningen)
Interference competition via anti-competitor toxins is wide spread among bacteria and eukaryote microbes, but its ecological role is not well understood. Toxins are costly to produce, leading to lower resource competitive ability, but may provide benefits as well by eliminating resource competitors. This leads to the prediction that anti-competitor toxins have an important role in the evolutionary maintenance of microbial diversity because neither toxin producers nor non-producer can eliminate one another. These theoretical predictions have hardly been tested. Previous collaborative work between our institutes using toxin-producing (“killer”) yeast has shown that one condition that is crucial for such benefit is fragmentation of the spatial structure of the population.
The present project will use laboratory evolution experiments with the killer yeast system to study three main hypotheses. (i) The costs of toxin production differ significantly under various environmental conditions. (ii) Coexistence of toxin producer and sensitive strain is restricted to a set of environmental conditions and population densities predicted by existing mathematical models. (iii) Toxin producers and non-producers are able to co-evolve effectively towards new equilibria predicted for altered environmental conditions.
Monocultures and mixed populations of differently marked toxin producers and non-producers will be allowed to evolve under various scenario’s of population structure and density by serial transfer for hundreds of generations. Samples from these populations will be analyzed for changes in resource competitive fitness and changes in interference competitive ability (i.e. killing ability and toxin resistance/sensitivity). Evolution will be tracked at the level of phenotype level (e.g. growth rate, morphology, metabolism), mRNA expression profiles, and DNA sequence. (It is estimated that funds accessible in the requested grant are already sufficient for sequencing and quantification of cDNA libraries from dozens of strains. The fast development of rapid DNA sequence analysis will likely make this figure considerably higher.)

6) Relationship between the diversity of soil microbial communities and their resistance to different stressors (supervisors: Ryszard Laskowski; Nico Van Straalen; Kees van Geestel, Amsterdam)
The most of soil microbes are functionally redundant and replaceable with other species without any change in general soil function. According to recent estimation, the reduction of taxonomic diversity in metal polluted soils can reach 99.9%, with most species belonging to rare taxa, but the functional importance of these rare taxa for soil nutrient cycling and ecosystem resilience is unknown. Changes in the relative diversity and functional characteristics of microbial communities might have unpredictable consequences for nutrient cycling and thus productivity.
Based on previous work done in our research group we found the soil bacterial functional diversity to be a good indicator of effects of different metal pollution, ecosystem type or ecosystem management. We expect that changes in the abiotic factors (temperature, moisture) may stronger affect less diverse soil microbial communities. The project will be focused on:
1. Resistance of the microbial communities in soils differing in chemical, physical and biological properties to natural stressors and/or disturbances (temperature, soil moisture, toxic compounds)
2. Resistance of the microbial communities in long term polluted soils (e.g. heavy metals) to an additional stressors and or disturbances (temperature, soil moisture, toxic compounds)
3. Linking the genetic and functional diversity of soil microbial communities to their resistance to different stress or disturbance and to ecosystem functions.
The project will enable us to assess relative risk for stability and functioning of soil in forest and agricultural ecosystems caused by potential additional stressors (human activities or climate change).

 7) Interaction between natural and sexual selection in adaptation to novel, stressful environment (Supervisors: Jacek Radwan; David Hosken, Nina Wedell, Exeter).
This project has two aims. Firstly, it will investigate life-history costs of adaptation of Drosophila simulans to an insecticide (methoprene); secondly, it will examine the role of sexual selection in promoting such adaptation. This project is interconnected with project (10) which will investigate molecular basis for the adaptation.
Adaptation to novel environment, such as that created by the use of pesticides by humans, has implication both for agriculture and biological conservation. While species may adapt to polluted environment, the adaptation is likely to be associated with life-history costs. Such costs have important implications. Firstly, such costs will affect population dynamics and possibility of pesticide adapted organisms (or just the underlying genes) to spread to other environments (species). Secondly, the use of pesticides often affects endangered species inhabiting neighboring habitats. While such species may adapt to pesticides, the life-history costs of adaptation may affect their chances of extinction. Furthermore, adaptation may be promoted or slow down by sexual selection. Sexual selection has a major long-term effect on biodiversity, influencing both speciation and extinction. The so called “good genes hypothesis” of sexual selection predicts that males possessing well adapted genes will achieve highest reproductive success, in which case adaptation to novel environment should be promoted. However, this prediction has been tested in only a handful of studies, which gave inconsistent results.
The project on Drosophila simulans will trace adaptation to an insecticide (methoprene) for a minimum of 15 generations. Flies will be reared in replicate populations under either standard laboratory environmental conditions, or under methoprene exposure, with and without sexual selection. Methoprene is a synthetic analogue of juvenile hormone frequently used as an insecticide and will be added to the fly food. Sexual selection will be either excluded by enforcing monogamy, or allowed by allowing 4 males to compete for reproductive success over one female. Adaptation to novel environment will be assessed by measuring several fitness components (lifetime reproductive success, development time, developmental stability). The costs of adaptation will be assessed by measuring the same life-history traits in methoprene-free environment. Two major hypotheses will be tested: (i) Adaptation to an insecticide entails substantial life history costs and (ii) sexual selection promotes adaptation to novel environment.

 

International PhD Program:

Environmental stress, population viability and adaptation