Imperial College London Featured PhD Programmes
Gdansk University of Technology Featured PhD Programmes
Queen’s University Belfast Featured PhD Programmes

EASTBIO Microbiome-mediated carbon sequestration in soil

   School of Biological Sciences

This project is no longer listed on and may not be available.

Click here to search for PhD studentship opportunities
  Dr A Malik, Dr T Freitag  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project


Dr Ashish Malik (University of Aberdeen)

Dr Thomas Freitag (The James Hutton Institute)

Increasing food and energy needs have led to intensive land use practices that deplete soil organic carbon (SOC) stores. This necessitates developing more sustainable soil management practices that balance agricultural productivity and soil health, including functions such as SOC storage. Soil microbes are critical because they control the fate of recent plant carbon inputs and determine the stability of assimilated carbon. The balance between the rate of microbial decomposition and stabilisation of organic carbon can shift under altered environmental conditions.

Recent research has led to a growing consensus that most soil organic matter (SOM) consists of microbial necromass that interacts with the mineral matrix, creating stable organo-mineral complexes1. Therefore, microbiome-mediated solutions offer the potential to accumulate SOM and improve soil health. This potential is limited by lack of mechanistic understanding of SOC accumulation and underlying microbial ecophysiology.

Our work has shown that higher microbial growth yield, with a greater proportion of substrate allocated to biosynthesis, increases the ability of communities to store carbon in soils2. The results suggest that by improving microhabitat conditions (thereby reducing stress), and increasing plant-derived resource inputs in degraded soils, microbial growth yield can be increased, leading to greater carbon sequestration. However, it is not clear whether the high yield strategy is inherent and genome-encoded (in which case inoculating high yield microbes to soils will increase carbon sequestration) or a result of emergent traits reflecting microhabitat conditions (in which case creating the correct microenvironment will lead to carbon sequestration)3.

Project aims:

The PhD project aims to determine how land use change impacts microbial traits that influence substrate transformations and ultimately soil carbon sequestration. Key objective will be to understand the feedbacks of microbial traits and abiotic microhabitat conditions on soil carbon sequestration. Experiments will test the hypothesis that ecosystem-relevant genomic and phenotypic traits are emergent and influenced by soil microhabitat conditions.

Research methods and training:

The project will benefit from access to soils from field sites across Britain differing in land use intensity. Targeted experiments will be performed on these soils involving reciprocal microbial transplants using sterilised soils. Changes in microbial community structure and functions in field and experimental soils will be measured using shotgun metagenomic sequencing. Functional classification will be performed using established pipelines. Centre for Genome Enabled Biology and Medicine at University of Aberdeen (UoA) has in-house DNA sequencing platforms. Bioinformatics support will be available to the student though them as well as through the supervisors.

Microbial phenotypic traits such as growth yield and respiration rate will be quantified by 13C tracing2. 13C-labelled plant organic matter will be used as a tracer and 13C in microbial DNA and respired CO2 will be measured on mass spectrometers (available at UoA). Statistical approaches such as differential gene abundance analysis, PERMANOVA and variation partition analysis will be used to assess trait variations across gradients and impact on soil carbon3. Such a combination of metagenomic sequencing and stable isotope tracing approaches in field and lab experiments will allow the student gain unique technical skills across disciplines.

Application Procedure:

Please send your completed EASTBIO application form, along with academic transcripts to Alison McLeod at [Email Address Removed]. Two references should be provided by the deadline using the EASTBIO reference form. Please advise your referees to return the reference form to [Email Address Removed].

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition (limited funding is available to provide international tuition fees). Please refer to UKRI website and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria.

Candidates should have (or expect to achieve) a minimum of a 2:1 UK Honours degree, or the equivalent qualifications gained outside the UK, in a relevant subject.


1. Kallenbach, C. M., Frey, S. D. & Grandy, A. S. Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls. Nat. Commun. 7, 13630 (2016).
2. Malik, A. A. et al. Land use driven change in soil pH affects microbial carbon cycling processes. Nat. Commun. 9, 3591 (2018).
3. Malik, A. A. et al. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. ISME J. 14, 1–9 (2020).
PhD saved successfully
View saved PhDs