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Linking Microbial Physiology with Carbon Transformations in Peatlands Under Land Use Change

School of Biological Sciences

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Dr A Malik , Dr R Andersen , Dr Rebekka Artz , Prof J Smith No more applications being accepted Funded PhD Project (European/UK Students Only)

About the Project

Significant amount of carbon is stored in soils, particularly in peatlands. Increasing food and energy needs have led to intensive land use practices that deplete soil organic carbon (SOC) stores. In Scotland, drainage for agriculture and commercial forestry in its vast swathes of peatlands has caused their degradation with significant loss of carbon. Their recent restoration has led to the return of SOC sequestration, and associated climate benefits, but the underlying carbon cycling mechanisms have not been clearly understood. This mechanistic understanding is required to better predict and manage soil processes to maintain or even enhance SOC storage in peatlands while economising land-use.

Microorganisms are critical in this regard because their growth and activity largely control the fate of recent plant carbon inputs, as well as the stability of assimilated microbial carbon. The balance between the rate of microbial decomposition and stabilisation of organic carbon in soil can shift under altered environmental conditions. In peatlands, water-logged conditions, anaerobiosis and acidity limit microbial growth and decomposition that consequently causes preservation of organic carbon. Peatland degradation through drainage removes the factors causing organic carbon preservation thus leading to SOC loss through microbial decomposition. Restorative approaches aim at reversing these effects thereby limiting the loss of SOC; however, the exact hydrological, chemical and biotic mechanisms and their inter-dependencies are poorly understood.

This project aims at understanding the effects of peatland degradation and subsequent restoration on microbial physiological processes and their consequences on soil carbon transformations. Project will rigorously test the hypotheses that microbial growth, activity and decomposition is limited by acidity and anaerobiosis in peatlands; and that peatland degradation causes increased microbial growth and consequently decomposition of peat organic matter. We will have access to multiple peatland sites under various land use types across Scotland to test the hypotheses. The goal is to assess microbial carbon cycling functions like growth rate, carbon use efficiency, resource breakdown and uptake, maintenance and stress tolerance. These community traits will be quantified using a combination of stable isotope tracing and shot-gun metagenomics, and their fingerprints in driving changes in SOC will be assessed using chemical molecular tools like FTIR.

Using stable isotope tracers, we will measure microbial incorporation of carbon into biomass and loss through respiration to quantify community-level traits like carbon use efficiency, growth rate and specific respiration across land use types. Analytical facilities for gas, solid, soil solution and compound-specific 13C isotope ratio mass spectrometry (IRMS) including cavity ring-down spectrometry (CRDS) at University of Aberdeen (UoA) and James Hutton Institute (JHI) are unique and training will be provided by the supervisory team. Whole genome shot-gun metagenomics will be used to investigate functions of peatland microbial communities under different land use. The goal here will be to extract physiological traits of microbes that are dominant in soils under different land use.

The Centre for Genome Enabled Biology and Medicine ( at UoA houses DNA sequencing platforms like Illumina NextSeq500 and Oxford Nanopore GridION which will be available to the project including training in molecular methods and bioinformatics. Chemical analysis of the extant organic matter will be used to characterise peatland organic matter at the molecular level using FTIR. Once we are able to form a link between microbial traits and carbon cycling processes, we will be able to use the combined knowledge to ascertain the efficacy of restorative practices in changing microbial physiology aimed at regaining and sequestering carbon in peatlands. The student will primarily be based at UoA with access to lab, facilities and field sites through co-supervisors at University of Highlands and Islands and JHI.

Ashish Malik (University of Aberdeen)

Roxane Andersen (University of Highlands and Islands)

Rebekka Artz (James Hutton Institute)

Jo Smith (University of Aberdeen)

Funding Notes

This project is funded by the SUPER-DTP and is available to UK/EU nationals who meet the RCUK eligibility criteria. The studentship provides funding for tuition fees, stipend and a research training and support grant- subject to eligibility.

Candidates should have (or expect to achieve) a minimum of a 2.1 Honours degree in a relevant subject.


• Apply for Degree of Doctor of Philosophy in Soil Science
• State the name of the lead supervisor on your application (found above)
• State ‘SUPER DTP’ as Scholarship/Studentship Title
• Select 'Visit Website' to apply now


Malik, A.A., Martiny, J.B.H., Brodie, E.L., Martiny, A.C., Treseder, K.K., Allison, S.D. (2019) Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. The ISME Journal.

Malik, A.A., Puissant, J., Buckeridge, K.M., Goodall, T., Jehmlich, N., Chowdhury, S., Gweon, H.S., Peyton, J.M., Mason, K.E., van Agtmaal, M., Blaud, A., Clark, I.M., Whitaker, J., Pywell, R.F., Ostle, N., Gleixner, G., Griffiths, R.I. (2018) Land use driven change in soil pH affects microbial carbon cycling processes. Nature Communications, 9:3591.

Hermans, R., Zahn, N., Andersen, R., Teh, Y.A., Cowie N. & Subke, J.-A. (2019) An incubation study of GHG flux responses to a changing water table linked to biochemical parameters across a peatland restoration chronosequence. Mires and Peat, 23(08), 1–18.

Lees, K.J.; Artz, R.R.E.; Quaife, T.; Khomik, M.; Clark, J.M. (in press) Changes in carbon flux and spectral reflectance of Sphagnum mosses as a result of simulated drought. Ecohydrology.

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