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Tanentzap Group: Evolutionary ‘omics of adaptation in environmental microbiomes


Supervisor: Andrew Tanentzap (Plant Sciences)

Project outline:

Recent advances in ultrahigh-resolution mass spectrometry (UHR-MS) have shown that just a few mL of freshwater contains thousands of dissolved organic molecules of varying origin and composition. But the biological significance of this chemical diversity is largely a mystery. Chemical diversity in dissolved organic matter (DOM) should have far-reaching consequences for the functioning of freshwater ecosystems that support life on Earth by interacting with microbial diversity. Microbes both alter the structure of DOM molecules through decomposition and release new molecules into the environment, such as for communication or defence. A greater diversity of DOM molecules can also offer more niches for microbes to live upon.

The aim of this PhD is to understand how microbes and DOM interact from the lab into the field. Outcomes of this research will be relevant for human health and wellbeing and industrial biotechnology.

The first part of this PhD will test whether bacteria evolve adaptations faster when grown on more complex mixtures of DOM. Using an experimental evolution approach, the student will rear replicated cultures of Pseudomonas fluorescens for 5,000 generations on 5 natural DOM sources and map their transcriptomic and phenotypic responses.

RNA-Seq approaches are yet to be widely used in experimental evolution.

By simultaneously manipulating biological diversity of the cultures with other model Proteobacteria that span a large range of functions and life history strategies, we will also determine how evolutionary responses to DOM vary with biological interactions and functions that characterise natural communities. More broadly, this project will address a long-standing question in biology about when deterministic processes are more important than chance in underlying genomic adaptation.
The remainder of the PhD can be tailored to the student's interests and build on the earlier work in two ways. First, our group is performing a field manipulation of DOM in a real lake to test the extent to which microbes are responding to versus creating chemical diversity. The student could use this platform to test predictions from their earlier experiment about how complex communities of microbes and chemicals co-vary. By discovering which microbial taxa change freshwater DOM more favourably for human consumption, we could try and culture these taxa in the lab and test their potential for water purification technologies.

Second, microplastics are a major emerging environmental issue but their influence on biological life remains largely unknown. We have recently found that microplastics leach considerable DOM and influence microbial activity. The student could use a similar experimental evolution approach to understand how microplastics influence microbial adaptation as a specific environmental perturbation


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