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Climate warming and microbial carbon-use in tropical soils

Faculty of Environment

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Dr A Nottingham , Prof Oliver Phillips No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

This project provides an exciting opportunity to investigate how soil microbial communities determine the vulnerability of soil carbon stocks to warming in tropical forests.


Tropical forests play a dominant role in the terrestrial carbon cycle. They cycle more carbon between the land and the atmosphere than any other terrestrial ecosystem, and contain huge stores of carbon in their plants and soils. Yet, this vital ecosystem service is under threat in a warming world. Climate warming is predicted to destabilise large stocks of soil carbon in terrestrial ecosystems by increasing rates of decomposition in soil. Consequently, this could significantly accelerate climate change through increased emissions of carbon dioxide to the atmosphere (Crowther et al., 2016, Davidson & Janssens, 2006).

Models and experiments performed outside the tropics show that the size of this feedback is strongly affected by the response of microbial communities (Melillo et al., 2017; Wieder et al., 2013). The efficiency of carbon-use among microbial communities, in particular, is known to have a huge influence on both soil carbon stabilisation (Buckeridge et al., 2020) and soil carbon release under warming (Wieder et al., 2013). Despite this, our understanding is limited by a lack of census among methods to quantify microbial carbon-use (Hagerty et al., 2018, Spohn et al., 2016) and by a lack of information for tropical forests (Nottingham et al., 2020).


The student will address the following specific research questions:
• What is the effect of warming on the function and carbon-use of the tropical forest soil microbial community?
• Are these effects linear or non-linear across ranges of warming and over time?
• How are these functional responses related to the composition of the microbial community?
• How is soil microbial ‘carbon-use efficiency’ related to the isotopic and molecular methods used to describe it?

According to the student’s research interests, the studentship could be expanded to address further related questions on global change impacts in tropical forest soils, including gas-exchange, rhizosphere processes, nutrient cycling and soil-microbial models.

The project provides a timely and globally-unique opportunity to address critical questions on the relationships between soil microbial ecology and biogeochemical cycling in tropical forests. A major strength of the project is the combination of analytical training and expertise in molecular analytical methods at The UK Centre for Ecology & Hydrology and The University of Vienna, and novel experimental study systems in tropical forest. The work will deliver new understanding on soil microbial carbon cycle feedbacks on the climate under future global change scenarios.


The student will employ cutting-edge techniques in biogeochemistry and microbiology and use two study systems that deliver short-term and long-term responses of microbial carbon-use to temperature. First, a soil warming experiment in lowland tropical forest will deliver novel mechanistic understanding of short-term warming responses (Nottingham et al., 2020). Second, a network of transects along lowland-to-montane tropical forests will be used as natural temperature ‘manipulations’, delivering insight across longer time-scales and wider biogeographical-scales (Nottingham et al., 2015). These study systems will be complemented by laboratory incubation studies to understand the temperature response of microbial carbon-use. There will also be an opportunity to use experimental outputs for the development of microbial-soil models.

The student will join the Ecology and Global Change research cluster in the School of Geography, a vibrant group of researchers studying global change impacts on ecosystems and biogeochemical cycles. The student will receive comprehensive training at the University of Leeds, UKCEH in biogeochemical analyses including molecular and isotopic methods: 13C-substrate utilisation and 13C tracing into biomarkers (e.g. phospholipid fatty acids), 18O labelling followed by DNA extraction, and soil enzymes. The field work components, including laboratory facilities, will be hosted by the Smithsonian Tropical Research Institute in Panama. Further isotopic work will be performed at UKCEH using the state-of-the-art isotopic facilities including Picarro CRDMS (Dr J. Whitaker) and at the terrestrial ecosystem research group at the University of Vienna (Prof W. Wanek). Training in generic transferable and professional skills will also be provided by The University of Leeds and the NERC DTP.


The successful candidate will have a very good first degree, Masters Degree or equivalent in the Natural Sciences (environmental, biological or Earth) or related disciplines, especially biogeochemical, molecular and soil science. Proficiency in statistical methods (e.g. R software) is essential, as is a demonstrated interest in fundamental ecological and biogeochemical questions. The successful candidate will be highly self-motivated and able to work independently, including during periods of remote tropical forest fieldwork. Spanish skills are helpful but not essential.

Funding Notes

We offer 3.5 years fully funded studentships including full tuition fees for all successful applicants, and stipend at the UKRI rate plus a training grant.


Buckeridge, K.M., Mason, K.E., McNamara, N.P. et al.(2020) Environmental and microbial controls on microbial necromass recycling, an important precursor for soil carbon stabilization. Nature Commun Earth Environ 1, 36.
Crowther TW, Todd-Brown KEO, Rowe CWet al.(2016) Quantifying global soil carbon losses in response to warming. Nature,540, 104-108.
Davidson EA, Janssens IA (2006) Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature,440, 165-173.
Hagerty SB, Allison SD, Schimel JP (2018) Evaluating soil microbial carbon use efficiency explicitly as a function of cellular processes: implications for measurements and models. Biogeochemistry,140, 269-283.
Melillo JM, Frey SD, Deangelis KMet al.(2017) Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world. Science,358, 101-104.
Nottingham AT, Meir P, Velasquez E, Turner BL (2020) Soil carbon loss by experimental warming in a tropical forest. Nature,584, 234-237.
Nottingham AT, Whitaker J, Turner BL, Salinas N, Zimmermann M, Malhi Y, Meir P (2015) Climate warming and soil carbon in tropical forests: insights from an elevation gradient in the Peruvian Andes. Bioscience,65, 906-921.
Spohn M, Klaus K, Wanek W, Richter A (2016) Microbial carbon use efficiency and biomass turnover times depending on soil depth – Implications for carbon cycling. Soil Biology & Biochemistry,96, 74-81.
Wieder WR, Bonan GB, Allison SD (2013) Global soil carbon projections are improved by modelling microbial processes. Nature Climate Change,3, 909-912.

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