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Tanentzap Group: Evolutionary ‘omics of adaptation in environmental microbiomes

NERC / GFC / OTHER

Supervisor: Andrew Tanentzap (Plant Sciences)

Importance of the area of research concerned:

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 (Kellerman et al. 2014). 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.

Project summary:

This PhD specifically aims to understand how microbes and DOM interact, but also addresses broader questions about when deterministic processes underlie genomic adaptation. The first part of this PhD will test if bacteria evolve faster when grown on more complex DOM mixtures. Using an experimental evolution approach (Elena & Lenski 2003), the student will rear replicated Pseudomonas fluorescens cultures on different natural DOM sources and map their transcriptomic and phenotypic responses. By varying species diversity of the cultures, they will also test how evolutionary responses to DOM vary with biological interactions that characterise natural communities. The rest of the PhD will build on work in our group to test experimental predictions in field settings (e.g. Fitch et al. 2018) or explore how anthropogenic DOM sources (e.g. microplastics) influence microbial adaptation.

What will the student do?:

For the first part of the project, the student will help maintain the evolution experiment. This involves daily transferring of bacterial cultures to new microplates and regularly preserving cultures for phenotyping and genotyping. The student will run fitness assays of preserved colonies on different DOM sources to test if populations are adapting or showing plasticity. In the lab, the student will extract RNA and sequence transcriptomes to identify the genetic basis for adaptation. They will be responsible for performing the required bioinformatics. For the second part of the project, the student will design a suitable sampling strategy and carryout data collection and analysis tied to their specific interests.

References:

  • Kellerman, A.M., Dittmar, T., Kothawala, D.N. & Tranvik, L.J. 2014. Chemodiversity of dissolved organic matter in lakes driven by climate and hydrology. Nature Communications, vol. 5, pp.3804, DOI 10.1038/ncomms4804
  • Elena, S.F. & Lenski, R.E. 2003. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Reviews Genetics, vol. 4, pp.457–469, DOI 10.1038/nrg1088
  • Fitch, A., Orland, C., Willer, D., Emilson, E.J.S. & Tanentzap, A.J. 2018. Feasting on terrestrial organic matter: Dining in a dark lake changes microbial decomposition. Global Change Biology, vol. 24, pp.5110-5122. DOI 10.1111/gcb.14391