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  Where has all of the carbon gone? Understanding the molecular mechanisms of long-term soil carbon capture

   Department of Earth and Environmental Sciences

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  Prof Duncan Cameron, Dr Sophie Nixon  Applications accepted all year round  Funded PhD Project (UK Students Only)

About the Project

Soils, while unglamorous, form the basis of the terrestrial biosphere and are ultimately the source of the majority of the food that we eat, yet fundamental aspects of how soils form and how they store carbon are poorly understood. Despite the importance of soil, modern farming approaches and industrial pollution mean we have lost half of our agricultural soils over the past 40 years. We are now facing a soils crisis, where our rapidly degrading soils represent one of, if not the, biggest threat to global food security. Soils are becoming depleted in organic carbon and consequently, the structural complexity generated the incorporation of organic carbon and that defines a healthy soil, is lost. Despite the importance of soil carbon, the mechanistic biology of long-term carbon storage in soils is poorly resolved.

An unhealthy, poorly structured soil is unable to provide the ecosystem services on which we depend such as water and carbon storage as well as food production. As soils continue to degrade, we increase the external inputs required to maintain crop yield such as fertilisation, irrigation and pesticide applications; the extreme endpoint being soils reduced to their bare mineral components essentially turning soil-based agriculture into in-field hydroponics.

The processes that form soil, collectively termed pedogenisis, are complex and occur over lengthy timescales, with the rates of soil loss far out stripping the rates of soil formation in an agricultural setting and as a result, some soils are release more carbon than they capture, becoming net sources of CO2 rather than carbon sinks. Given there is currently around twice as much carbon stored in soils than there is in the atmosphere, increasing rates of loss of soil carbon is a very real contributor to the climate crisis as well as a threat to food security.

Pedogenisis is defined by five so called “pillars”; parent material, weathering, climate, topography and biology and it is the biological dimension that is least understood. What we do understand is that biological secretions and necromass represent the ‘glue’ that drives the accretion of mineral particles forming micro aggregates and that the continuous accretion of micro aggregates into macro aggregates that in turn leads to soil structure. The complex spatial structure of soils not only supports the development of complex ecosystems but also makes soils resilient to perturbation. Moreover, it is the carbon at the core of these soil micro and macro aggregates that is protected and therefore stored, potentially over geological timescales. This is unless these soil aggregates are disturbed and broken down, by ploughing for example, exposing the protected carbon where it can be mineralised into CO2.

This PhD will use a novel combination of biogeochemistry, environmental microbiology and bioinformatic interrogation of microbial genomes to understand:

1.        What are the organic compounds exuded by microorganisms that act as the ‘glue’ in pedogenisis;

2.        What are the organisms that produce these compounds and what is the underlying chemistry;

3.        What genes encode the biochemistry of these exudates and what organisms have the capability of producing soil/stabilising exudates?

Through an environmental biotechnology lens, this project will also consider potential applications of soil-stabilising exudates in the context of enhancing rates of pedogenisis and will also investigate potential of harnessing this chemistry for other industrial processes? 


You will join leading laboratories working at the cutting edge of soil biology and chemistry. This project will offer an exceptionally broad multidisciplinary training, including soil science and biology, biochemistry, genetics, microbiology. In addition, the student will gain experience of multi-omics techniques (including genomics, transcriptomics, proteomics, metabolomics) and associated bioinformatics and training in experimental design and statistics. You will also have the opportunity to work closely with real-world practitioners including land managers, farmers and our industrial and third sector collaborators. You will be based at the Manchester institute of Biotechnology, one of the leading institutes for biotechnology in the UK. We are home to over 40 research groups who lead a portfolio of pioneering research projects that continue to advance our knowledge and uses of biotechnology. Our biomolecular analytical facilities are truly World-class with dedicated technical specialists supporting a range of technology platforms, examples include bioanalytical techniques, directed evolution and molecular design through to synthetic genomics and modelling and data science.

Our academics actively work with businesses to solve real-world problems and our research is used to support strategies for the future as well as in today's manufacturing processes for everything from flavourings, to new drugs to tackle illness, to fuel for our factories, homes and vehicles. In short, we are helping to feed, fuel and heal the world.

The supervisors are: Prof. Duncan Cameron, Dr Janice Lake and Dr Sophie Nixon (Manchester Institute of Biotechnology & Department of Earth & Environmental Sciences); Dr Helen Glanville, (Geography and Environmental Science, Loughborough University).

The PhD is 3.5 years long and the proposed start date is September 2023.

Entry requirements:

Applicants should have or expect to achieve at least a 2.1 honours degree in Microbiology, Ecology, Biology, Biochemistry.

How to apply:

You will need to submit an online application through our website here:

You must contact the main supervisor to discuss the application before you apply. The email address for Professor Duncan Cameron is [Email Address Removed].

Equality, diversity and inclusion is fundamental to the success of The University of Manchester, and is at the heart of all of our activities. We know that diversity strengthens our research community, leading to enhanced research creativity, productivity and quality, and societal and economic impact. We actively encourage applicants from diverse career paths and backgrounds and from all sections of the community, regardless of age, disability, ethnicity, gender, gender expression, sexual orientation and transgender status.

We also support applications from those returning from a career break or other roles. We consider offering flexible study arrangements (including part-time:

50%, 60% or 80%, depending on the project/funder). 

Agriculture (1) Biological Sciences (4) Chemistry (6) Environmental Sciences (13)

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 About the Project