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Experimental Evolution of Thaumarchaeota


Project Description

The fundamental aim of this project is to determine the process of adaptive diversification and associated trade-offs in fitness, by studying microbial evolution experimentally.

Using microbes to test theory in evolutionary biology has led to major scientific advances. In particular, microbial experimental evolution has allowed analysis of both microbial adaptation (genomic and phenotypic changes) and diversification (phenotypic evolution and lineage-splitting) using controlled environments, through increased understanding of the nature and frequency of genomic substitutions, their effects on microbial fitness and the mechanisms by which diversity is created and maintained in microbial populations. These concepts were established from studies of bacteria, fungi, viruses and phage, focussing mainly on a few bacterial model organisms (1, 2). However, an entire domain of life, the Archaea (3), has largely been ignored by evolutionary biologists, despite their widespread distribution in natural environments, high abundance and essential contribution to global ecosystem functioning that sustains the planet. A priori, no clear reasons for different evolutionary processes between archaea and bacteria can be advanced, but their ancient evolutionary divergence (despite the existence of lateral gene transfer between domains) suggests that the relevance of established microbial models of adaptation and diversification should be tested on these organisms if they are to be considered universal. Indeed, despite the global importance and diversity of archaea, our understanding of the ecological and evolutionary processes generating their high diversity is scarce compared to that of eukaryotes and, to a lesser extent, bacteria.

This project will focus on members of a key microbial phylum, the Thaumarchaeota (4, 5), which are abundant and ubiquitous and perform a critical ecosystem function, ammonia oxidation. The distribution of natural microbial communities is influenced by environmental characteristics, and pH is the major abiotic factor influencing extant thaumarchaeotal niche specialisation (4), and has also influenced their diversification and patterns of lineage formation through deep evolutionary time (5).

This project aims to study the evolution of these microbes experimentally (6). Experimental evolution will be performed by imposing environmental changes under controlled conditions and the evolutionary mechanisms of adaptation and diversification as well as the existence of trade-offs will be determined using genomic and fitness changes over time.

The PhD student will join a dynamic team of researchers led by Dr Cécile Gubry-Rangin (https://www.abdn.ac.uk/ibes/people/profiles/c.rangin) and will benefit from the presence of strong groups in the department working on related topics as well as being embedded in a strong network of international collaborations. The University of Aberdeen provides an excellent scientific environment, state-of-the-art technological support facilities and diverse training opportunities for all aspects of research and for transferable academic and generic skills.

Candidate should have (or expected to achieve) a minimum of 2:1 Honours degree, ideally (but not required) an MSc in evolution, ecology or related, strong theoretical skills and enthusiasm for learning and developing microbial experimental evolution.

Funding Notes

The PhD is funded 100% by The Royal Society and the funding has already been secured. The studentship covers the registration fees, the students salary for 4 years, experimental costs and travel for training and conference attendance for the student.

References

1. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461(7268):1243-7
2. Rainey PB, Travisano M. (1998) Adaptive radiation in a heterogeneous environment. Nature 394:69. 394(6688):69-72.
3. Spang A, Caceres EF, Ettema TJG. (2017) Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357(6351). pii: eaaf3883.
4. Gubry-Rangin C, Hai B, Quince C, Engel M, Thompson BC, James P, Schloter M, Griffiths RI, Prosser JI, Nicol GW. (2011) Niche specialization of terrestrial archaeal ammonia oxidizers. Proc Natl Acad Sci USA 108(52):21206-21211.
5. Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ. (2015) Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proc Natl Acad Sci USA 112(30):9370-9375.
6. Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW. (2011) Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci U S A 108(38):15892-7.

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