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Reconstructing past thaumarchaeotal ecology and evolution in peatland soils

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  • Full or part time
    Dr C Gubry-Rangin
    Dr D Mauquoy
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Analyses of past ecological and evolutionary adaptation processes are essential to understand present and future biodiversity processes. Microbial analyses often lack dating on medium to long-term timescales, but such knowledge would strongly benefit to the understanding of ecosystem development.

This project therefore aims to embed cutting-edge genomics tools with modern radiocarbon dating to understand the past ecology and evolution of microbial communities, especially those with unknown (but potentially important) ecosystem functions. This project will focus on UK peatland ecosystems which have accumulated peat over the course of the Holocene epoch. Peatland ecosystems form the most efficient carbon sink on the planet and cover a total of around 2% of the global land area. Most peat bogs formed ~12,000 years ago in high latitudes and peat forms due to the slow decay rates under acidic and anaerobic conditions. Microbial analyses have been undertaken to understand the role these organisms play in peatland carbon cycling, but more research is required to identify this in more detail.

Thaumarchaeota is likely an ancient phylum, with a history stretching back to 1.2 – 2 Gyr (Gubry-Rangin et al., 2015). Thaumarchaeota form a highly diverse phylum and their evolutionary breadth suggests that there is significant potential for important metabolic diversity within this phylum. While Thaumarchaeota are usually described as ammonia oxidisers which derive energy from the oxidation of ammonia under aerobic conditions, a deeply-rooted and diverse group of Thaumarchaeota (the Group I.1c) do not require ammonia oxidation to grow (Weber et al., 2015). These Group I.1c microorganisms are ubiquitous in acidic environments and their presence has been detected in a diverse range of ecosystems, including peat, boreal forest, agricultural and grassland soils. In addition, Group I.1c is phylogenetically diverse (Vico Oton et al., 2016), despite being present only in acidic environments. This high phylogenetic diversity is consistent with the hypothesis of unexplored, but potentially considerable, metabolic diversity within Group I.1c. Several Group I.1c ecosystem functions have been hypothesised, with suggested roles in methane oxidation and anaerobic fermentation. However, only one genome has been reconstructed to date (Lin et al., 2015) and no culture or microbial enrichment is available. This lack of cultivation probably results from major gaps in knowledge of their physiology preventing successful enrichment. This project will therefore target a ubiquitous and abundant group of archaeal microbes in peatland ecosystems, whose ecosystem function is not yet understood.

Although dating the origin of prokaryotic groups is extremely difficult, majority of microbial studies haven’t really taken advantage of the potential age/depth models provided by the radiocarbon dating of plant macrofossils. Indeed, while direct microbial dating is challenging due to lack of microbial fossils, radiocarbon dating of the former peat forming vegetation can provide accurate and precise chronologies spanning centennial and millennial timescales (McClymont et al., 2008) and can be successfully applied as an indirect measure to determine the age of microbes. Therefore, chronosequences spanning deep peat profiles can shed light on the evolution of this microbial group but can also be used as a proof of concept for microbial dating.

The fundamental aim of this project is to understand the ecology and recent evolution of deeply-rooted unexplored Thaumarchaeota in peatland soils, especially their metabolism and ecosystem function across geographical landscapes.

The PhD student will join a dynamic team of researchers headed by Dr Gubry-Rangin. This well-established group with world-wide recognised reputation in microbial ecology and a high-impact track record focuses on ecology and evolution of ammonia oxidisers in various terrestrial ecosystems. The student will also strongly interact with the research group of Dmitri Mauquoy, widely renowned for peat ecosystems and radiocarbon dating.

Funding Notes

This is a joint studentship between the School of Biological Sciences & the School of Geosciences. This studentship provides stipend, Home/EU Fees & a £1K p.a. RTSG (Research Training & Support Grant).

References

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 112:9370-5.

Lin X, Handley KM, Gilbert JA, Kostka JE (2015) Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. ISME J 1: 1-5.

McClymont EL, Mauquoy D, Yeloff D, Broekens P, van Geel B, Charman DJ, Pancost RD (2008) The disappearance of Sphagnum imbricatum from Butterburn Flow, UK. The Holocene 18; 991. Eds Chambers FM and Evershed RP.

Vico Oton E, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C. (2015) Ecological coherence and phylogenetic congruence in Thaumarchaeota. ISME J 10:85-96.

Weber E, Lethovirta-Morley LE, Prosser JI, Gubry-Rangin C. (2015) Ammonia oxidation is not required for growth of Group 1.1c soil Thaumarchaeota. FEMS Microbiol Ecol 91(3): pii :fiv001.



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