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PhD in Engineering: Profiling active nitrifiers in coastal sediments with single cell approaches and metagenomics.


Project Description

Microorganisms within coastal sediments are the engines of these ecosystems driving essential biogeochemical cycles that underpin ecosystem functioning. Of particular importance are those that transform nitrogen and in doing so mediate nutrient loads entering coastal ecosystems. Central to this process is nitrification conducted by organisms that oxidise ammonia to nitrate and then nitrite. Recently there have been a number of exciting revelations that have turned current understanding of this ‘simple’ process on its head, including the discovery of comammox, complete nitrification within a single organism1,2,3.
However, a major hindrance to expanding our understanding of these organisms, beyond their detection, is linking activity and identify of the active nitrifiers within complex environmental samples based on DNA approaches alone. Therefore, in this project we are proposing a novel approach to identify active nitrifiers within coastal sediments. This approach is based on our state-of-the-art microfluidics platform that couples Stable Isotope Probing (SIP) to Resonance Raman and Raman Activated Cell Sorting (RR-RACS)4,5,6 to label and sort actively nitrifying cells. Subsequently the identify of active sorted cells can be achieved by high-throughput sequencing approaches. This method is truly innovative and will enable unparalleled insights into the ecophysiology and underpinning molecular diversity of individual nitrifiers within mixed microbial communities. Using this approach will address fundamental ecological questions on the distribution and activity of nitrifiers within coastal sediments6.
We are looking for a highly-motivated, excellent student, preferably with a first class honours undergraduate degree and a MSc in microbiology, marine science, molecular biology/ecology or a related subject area to undertake this exciting project. The applicant will join a highly dynamic interdisciplinary research team at the University of Glasgow and undergo training in all the necessary approaches in environmental microbiology (including stable isotope probing, DNA extraction, qPCR and metagenomics), Raman spectroscopy and bioinformatics. They will also have the opportunity to work with Prof Tom Curtis at Newcastle University to further develop expertise in FiSH-Flow cytometry.

Further project details available at:
https://www.iapetus2.ac.uk/studentships/profiling-active-nitrifiers-in-coastal-sediments-with-single-cell-approaches-and-metagenomics/

Funding Notes

Start date: October 2020
Funding is available to cover tuition fees for UK and EU as well as paying a stipend at the Research Council rate (estimated £15,009 for Session 2019-20).

IAPETUS 2: View Website

References

References
1. Daims H et al 2015 Nature 528: 504–509. 2. van Kessel MA et al 2015 Nature 528: 555– 559. 3. Pinto A et al 2015 mSphere 1 e00054. 4. Mcllvanna, D et al 2016 Lab on a Chip 16:1420-1429. 5. Song Y et al 2017 Microbial Biotechnology 10: 125-137. 6. Yuan X et al (2018) Applied and Environmental Microbiology 8: e02508-17. 7. Zhang LM et al (2018) Environmental Microbiology 20: 2834-2853.

How good is research at University of Glasgow in General Engineering?

FTE Category A staff submitted: 84.00

Research output data provided by the Research Excellence Framework (REF)

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