Climate warming and microbial carbon-use in tropical soils


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. However, 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 and their carbon-use (Melillo et al., 2017; Wieder et al., 2013). Despite this, we have scarce information on the nature of these responses in tropical forests (Nottingham et al., 2020).


In this PhD project, the student will investigate how microbial carbon-use determines the vulnerability of soil carbon stocks to warming in tropical forests. Microbial carbon-use has a huge influence on soil carbon stabilisation (Buckeridge et al., 2020) and on the magnitude of carbon release under warming (Wieder et al., 2013). However, our understanding is limited by lack of critical assessment of the methods used for its quantification (Hagerty et al., 2018, Spohn et al., 2016).

The student will address the following specific research questions: i) How does soil microbial community functioning and metabolism in tropical lowland and montane forests change under warming? ii) Are these changes linear or non-linear across ranges of warming and over time? iii) How are these functional responses related to the composition of the microbial community? iv) How is soil microbial ‘carbon-use efficiency’ related to the isotopic and molecular methods used to describe it? The student will address these questions by using existing soil-warming experiments in lowland and montane tropical forests, laboratory experiments and biogeochemical and stable isotope techniques.

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 University of Vienna and the UK Centre for Ecology & Hydrology, 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.

Methods and training:

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 to examine 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 receive comprehensive training at the University of Leeds and 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 stoichiometric methods by measurements of microbial biomass carbon and soil enzymes. The field work components, including laboratory facilities for incubation studies, 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 University of Vienna (Dr 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 Masters Degree or equivalent. The candidate will demonstrate interest or research in fundamental ecological and biogeochemical questions. In addition, the candidate will have a background in the natural sciences (biological or Earth), especially biogeochemistry, ecology, molecular sciences and soil science. The successful candidate will have a proficiency in statistical methods (R software), be highly self-motivated and able to work independently, including remote tropical forest fieldwork. Spanish skills are helpful but not essential.

Key references:

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.