Project Description

Compared to monocultures, the enhanced biodiversity of crop mixtures can improve the sustainability of agricultural systems. Crop mixtures provide within-crop phenotypic diversity, with stems, leaves and roots occupying more ‘resource space’, and producing more biomass to build organic matter in soil, an underpinning premise supported by numerous experiments including a recent study across multiple cereal-legume trials in Scotland conducted by the James Hutton Institute. This study, however, detected a novel and surprising result of decreased soil carbon in mixture plots, compared to plots containing the components in monocultures.  Carbon cycling under mixtures might be affected by changes in soil physical and biochemical properties and decomposition rates. These properties are rarely monitored in crop mixture studies and are not incorporated in current soil process-based models, so it is difficult to predict crop mixture impacts on carbon cycling. Furthermore the previous study only examined topsoil (5-10 cm), so effects of crop mixtures on carbon stored deeper in soils have been missed.

In this PhD project, you will explore drivers of carbon dynamics under crop mixtures that could affect the distribution of carbon in soils and wider soil health. To address these gaps in knowledge and to disentangle the surprising result of decreased topsoil carbon (C) under mixtures, the PhD project will explore the follow questions:

  1. Do cereal-legume crop mixtures drive a redistribution of C across the soil profile (i.e. less higher up, more lower down)?
  2. Does enhanced crop diversity in crop mixtures – or associated changes in management (i.e. reduced inputs) or both – improve soil functioning which reduces soil C? How is C turnover affected by other changes in soil properties under mixtures (soil moisture, N/P availability, porosity etc)?
  3. What are the implications of growing cereal-legume mixtures for soil carbon sequestration and GHG emissions?

A combination of field and laboratory research will produce data to improve soil carbon models so that mixture impacts can be better understood and predicted. At the James Hutton Institute mixture trials are underway, and further field experiments could be established to directly address some research questions and parameterise models. Some process-based simulation models have been adapted to simulate two crop species growing simultaneously (e.g., DayCent, APSIM, STICS). However, these models do not estimate soil carbon dynamics explicitly. On the other end, soil process-based models simulate soil carbon cycling under monocrops, but there is novelty and also challenges in developing such models for mixed crops.

We envisage the project beginning with a meta-analysis to inform modelling and experimental design.  A farm-scale study, complementing ongoing James Hutton Institute research, will then explore how mixtures impact soil carbon and biophysical properties across the soil profile.  Further research with field experiments or mesocosm studies will explore mixture impacts in more controlled conditions, with the research building on Annette Raffan’s QUADRAT PhD exploring grassland mixtures.  Finally, the data will be brought together to improve soil carbon modelling of crop mixtures vs. monocultures, with an emphasis on environmental impacts such as greenhouse gas emissions and carbon sequestration.


There is considerable scope for the PhD student to adapt this project to their expertise and interest. Applicants could have a background in environmental science, ecology or plant science, with numeracy skills essential to develop the environmental models. Programming skills are desirable, but not essential, for modelling purposes.

Photo by Ant Rozetsky on Unsplash


Paul Hallett

Primary Supervisor:

Profile: Paul Hallett
Institution: University of Aberdeen
Department/School: School of Biological Sciences

Mark Emmerson

Secondary Supervisor:

Profile: Mark Emmerson
Institution: Queen's University, Belfast
Department/School: School of Biological Sciences

Additional Supervisor:

Dr Marta Dondini

University of Aberdeen, School of Biological Sciences


Additional Supervisor:

Prof. Rob Brooker, The James Hutton Institute



Dr Alison Karley, The James Hutton Institute



Brooker, RW, George, TS, Homulle, Z, et al. Facilitation and biodiversity–ecosystem function relationships in crop production systems and their role in sustainable farming. J Ecol. 2021; 109: 2054–2067.

Hallett, P.D., Marin, M., Bending, G.D., George, T.S., Collins, C.D. & Otten, W. 2022. Building soil sustainability from root–soil interface traits. Trends in Plant Science. 27.

Brooker, R.W., Bennett, A.E., Cong, W.F., Daniell, T.J., George, T.S., Hallett, P.D., Hawes, C., Iannetta, P.P.M., Jones, H.G., Karley, A.J., Li, L., McKenzie, B.M., Pakeman, R.J., Paterson, E., Schöb, C., Shen, J., Squire, G., Watson, C.A., Zhang, C., Zhang, F., Zhang, J., and White, P.J. 2015. Improving intercropping: A synthesis of research in agronomy, plant physiology and ecology. New Phytologist, 206, 107-117.


  • biodiversity
  • environmental-management


The James Hutton Institute will be a contributing partner on this project.

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