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EASTBIO: Microbial carbon cycling traits in soils across land use gradients.

School of Biological Sciences

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Dr A Malik , Prof E Paterson , Dr C Gubry-Rangin No more applications being accepted Competition Funded PhD Project (European/UK Students Only)

About the Project


Dr Ashish A Malik (University of Aberdeen)

Professor Eric Paterson (The James Hutton Institute)

Dr Cecile Gubry-Rangin (University of Aberdeen)

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 microorganisms are critical because they control the fate of recent plant C inputs and determine the stability of assimilated C (reference 1,2). The balance between the rate of microbial decomposition and stabilisation of organic C can shift under altered environmental conditions. However, we lack a detailed mechanistic understanding of these microbial processes.

Technological innovations like next generation sequencing have massively improved our understanding of the taxonomic and physiological diversity of soil microbial communities and their shifts in response to anthropogenic influences. However, integration of these large datasets with process rate measurements remains a challenge, thereby making it difficult to link microbial function with ecosystem processes like SOC storage (reference 3).

The project aims to determine how microbial genomic information translates into phenotypic characteristics or traits that influence substrate transformations and ultimately carbon cycling rates in ecosystems. Key objectives are: 1) to define traits-based life history strategies of soil microbes, 2) to identify populations that favour higher SOC storage and 3) to assess the distribution of these populations and their strategies across land use types. The project will test the hypothesis that individual taxa with higher growth yield or efficiency cause higher organic matter formation and therefore lead to higher SOC storage.

Research methods:
The project will benefit from access to soils from field sites across Britain based on land use and SOC content. Access will be facilitated through links at University of Aberdeen (UoA), James Hutton Institute (JHI), and Centre for Ecology & Hydrology. The student will aim to culture taxonomically diverse bacteria and fungi from the sampled soils across land use types. The genomes of isolates will be sequenced to characterise the genetic details of population-level traits such growth rate, carbon use efficiency, resource acquisition, stress tolerance, etc from genomic features. Centre for Genome Enabled Biology and Medicine ( at UoA has in-house DNA sequencing platforms like Illumina MiSeq, Illumina NextSeq500 and Oxford Nanopore GridION and also provides bioinformatics support which will be available for the project.

In addition, the student will quantify traits like growth yield and growth rate for individual isolates using stable isotope tracers. This will allow linking phenotypic traits of individual isolates with their genome-derived properties. Analytical facilities for gas and compound-specific 13C isotope ratio mass spectrometry such as cavity ring-down spectrometry at UoA and JHI are unique and will be accessible for the student. Routine chemical analysis of soils to measure carbon concertation, pH, redox potential, soil moisture, etc will also be performed. Ultimately, traits of isolates and their distribution across soils and land use types will be used to form statistical linkages between dominant microbial traits and soil carbon transformations. Such a combination of microbiological culturing, population genomics and stable isotope tracing approaches will allow the student to gain unique technical skills across disciplines

Application Procedure:

Please send your completed EASTBIO application form, along with academic transcripts and CV 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 only open to UK nationals (or EU students who have been resident in the UK for 3+ years immediately prior to the programme start date) due to restrictions imposed by the funding body. Queries on eligibility? Email Alison McLeod ([Email Address Removed]).

Candidates should have (or expect to achieve) a minimum of a First Class Honours degree in a relevant subject. Applicants with a minimum of a 2:1 Honours degree may be considered provided they have a Distinction at Masters level.


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. Schimel, J. P. & Schaeffer, S. M. Microbial control over carbon cycling in soil. Front. Microbiol. 3, 1–11 (2012).

3. Malik, A.A., Martiny, J.B.H., Brodie, E.L. et al. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. ISME J (2019) doi:10.1038/s41396-019-0510-0
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