Dr Jon Pittman, Dr C Knight
No more applications being accepted
Competition Funded PhD Project (European/UK Students Only)
About the Project
Pollution from waste-streams such as abandoned mine sites is a major environmental problem that has deleterious consequences for aquatic and terrestrial ecosystems throughout the world. Freshwater resources are negatively impacted by such pollution reducing the value of the water for agricultural, recreational or industrial uses, rendering it unsafe for humans [1]. Biodiversity is significantly impaired in polluted environments, yet some organisms can adapt to tolerate the stress conditions. Organisms can display shorter-term protective responses that occur through non-genetic phenotypic plasticity (also called acclimation), as well as adaptation and evolution over many generations through heritable genetic alterations [2-4]. While extremophile prokaryotic microorganisms have been extensively studied, much less is known regarding mechanisms of adaptation by eukaryotic photosynthetic microorganisms to extreme stress conditions. Evaluating such processes helps us to understand how ecosystems respond to environmental change. Furthermore, there are applications to the use of extremely stress tolerant microorganisms such as for pollutant bioremediation.
Project Summary:
Many abandoned mine sites have pit lakes and ponds containing volumes of metal-rich acid mine drainage (AMD) with extremely poor biodiversity. At one such site with high concentrations of dissolved metals and high acidity (~pH 2), we have recently identified a strain of microalgae (Chlamydomonas acidophila) that displays high tolerance to this environment, and shows evidence of adaptation to the copper stress in comparison to other strains of the same species [2]. Our hypothesis is that this strain of microorganism has adapted to survive in the AMD environment through genetic alterations and that the plasticity of this taxa can be exploited to understand the mechanisms and the limits of tolerance traits through ‘artificial’ experimental evolution.
The aims of this PhD project are to determine the adaptation mechanism of the strain and to explore the plasticity of Chlamydomonas taxa to ionic stresses by experimental evolution under lab conditions. Recently we demonstrated that AMD pollution can substantially alter bacterial community composition and predicted enzymatic function of the community through the use of metabolic reconstruction analysis [5]. Likewise, an additional objective of the project will be to perform a metagenomics analysis of AMD environment samples to gain a better understanding of eukaryotic extremophile community structure within these environments and predict functional traits. Artificial evolution experiments will be performed on the already naturally adapted strain and on non-adapted, AMD stress sensitive strains, to quantify tolerance and physiological response to increasing metal exposure over generations. Genomic and bioinformatics approaches will be used to analyse strains from the field-collected samples and laboratory-based evolution experiments to determine adaptive mechanisms. These will be performed alongside functional analyses of the strains using metabolic and metal biochemistry approaches. Together these experiments will provide an in-depth understanding of stress adaptation processes in aquatic systems subject to long-term metal pollution. The assessment of the degree to which microalgae strains can tolerate and enhance metal removal from the water column due to the selection for tolerant microorganisms will also facilitate the development of microbial bioreactors as a bioremediation strategy [2]. We will also work with organisations including the Environment Agency and Natural Resources Wales with regard to the development of future remediation approaches at abandoned UK mine sites.
The student will receive training in a range of physiological, analytical, and molecular biology techniques, including bioinformatics. The research team has an excellent track record in environmental pollution analysis, microbial ecology and evolution. Jon Pittman (primary supervisor) has experience examining responses of metal pollution and bioremediation by microorganisms. He will provide training in microalgal physiology, molecular biology and some analytical techniques. Co-supervisors Chris Knight and Andrew Dean will provide aquatic biology, water chemistry, microbiology and evolutionary biology techniques. Access to genome sequencing and spectroscopy analysis core facilities will also be available from collaboration with both universities. The supervisor’s labs have MSc, PhD students and postdoctoral scientists working on related projects and using relevant techniques, and together the labs will provide an excellent training environment for the student to gain a unique set of cutting edge, multidisciplinary skills.
Funding Notes
Studentships will provide a stipend (currently £14,553 pa), training support fee and UK/EU tuition fees for 3.5 years. Candidates from the UK and European Union are eligible for full studentship awards.
There will be a fixed date of 26th February 2019 for interviews; successful candidates will be invited by 19th February.
References
[1] Dean AP, Lynch S, Rowland P, Toft BD, Pittman JK, White KN (2013) Natural wetlands are efficient at providing long-term metal remediation of freshwater systems polluted by acid mine drainage. Environmental Science & Technology 47: 12029-12036
[2] Dean AP, Hartley A, McIntosh OA, Smith A, Feord HK, Holmberg NH, King T, Yardley E, White KN, Pittman JK. (2019) Metabolic adaptation of a Chlamydomonas acidophila strain isolated from acid mine drainage ponds with low eukaryotic diversity. Science of The Total Environment 647: 75-87
[3] Osundeko O, Dean AP, Davies H, Pittman JK (2014) Acclimation of microalgae to wastewater environments involves increased oxidative stress tolerance activity. Plant and Cell Physiology 55: 1848-1857
[4] Krašovec R, Richards H, Gifford DR, Hatcher C, Faulkner KJ, Belavkin RV, Channon A, Aston E, McBain AJ, Knight CG (2017) Spontaneous mutation rate is a plastic trait associated with population density across domains of life. PLoS Biology 15: e2002731
[5] Aguinaga OE, McMahon A, White KN, Dean AP, Pittman JK (2018) Microbial community shifts in response to acid mine drainage pollution within a natural wetland ecosystem. Frontiers in Microbiology 9: 1445