Towards sustainable land management: Improving microbial nitrogen-sequestration from artificial soils

Primary supervisor: Dr Sabine Lengger (University of Plymouth)

Secondary supervisor: Dr Mark Fitzsimmons (University of Plymouth)

Additional supervisors:

Dr Rachel Warmington/Mrs Katie Treseder (Eden Project). Email:

Dr Alex Dumbrell (University of Essex) Email:

Scientific background

Healthy soils are the basis for sustainable agriculture, but they are threatened by erosion and nutrient loss, worsened by climate change. The use of artificial soils - mixtures of waste materials – would drastically increase the availability of soil for developments (ecotowns, agricultural land). Application of nitrogen (N)-rich materials is common practice when artificial soils are deployed, but it is not known if they really lack nutrients. This oversupply can result in strongly negative environmental impacts.  

In this PhD project, you will characterise major N-sources and N-cycling microbial communities in artificial soils, and use this knowledge to improve the formulation and management of artificial soils. This will underpin their wider implementation (e.g. as a resource for agriculture). You will do this in collaboration with the Eden Project, where the use of artificial soils was pioneered through regeneration of a disused quarry in Cornwall using locally sourced waste. There, you will have the opportunity to apply your findings, and make a lasting impact in line with the Eden global mission.


  • Create and maintain soil experiments using artificial soil prototypes.
  • Apply isotope ratio-mass spectrometry (15N, 18O, 13C) to identify sources and pathways of nutrient cycling.
  • Use molecular approaches to identify N-cycling organisms and communities.
  • Characterise the mechanisms of N-sourcing using open source statistical tools.

Supervisory team

You will be based at the University of Plymouth (Drs Lengger, Fitzsimons, Tappin) where you will conduct experiments and analyses, and analyse the microbiome at the University of Essex (Dr Dumbrell). You will collaborate with the Eden Project for fieldwork and an internship (Mrs Treseder and Dr Warmington).


You will develop experimental, analytical, and transferable skills, through training from the supervisory team and the AERIES DTP. You will develop your skills in applied science, and communication with end-users.

Candidate profile

This project would suit a self-motivated student, with robust experimental experience. Relevant analytical skills, and an interest in hands-on, practical, soil science would be ideal. You should have or anticipate as a minimum a 1st or 2.1 BSc in the Biological, Chemical, or Environmental Sciences.

Scientific rationale

Securing the sustainability of soils is a priority for the UK government (1). The Eden Project in Cornwall was pioneering in its large-scale use of artificial soils; and tested the suitability of local waste materials to establish a soil and support large-scale growth of local and exotic plants (2). As the first of its kind, the Eden Project regenerated a former quarry by a deployment of to date > 85 kt of mixtures of waste material, namely clay, sand and green waste. A sustainable artificial soil could increase the availability of soil for large-scale developments, such as ecotowns, commercial sites, or agricultural land on a global basis. The common assumption that artificial soils are N-limited results in the application of N-rich material such as sludge(3), which often brings additional contamination problems. However, recent research suggests that N-sourcing in artificial soils is, in fact, poorly understood(4); it is mediated by different developing microbial communities(5, 6), in concert with the evolution of soil organic matter (7). The oversupply of reactive N and subsequent N-losses result in significant, negative environmental impact (8). Understanding of the major N-sources and involved microbial community is thus crucial to improve the formulation and management of artificial soils and to allow their wider implementation (e.g. as a resource for agriculture).

A powerful tool to unravel the nitrogen cycle are stable isotopes (13C, 15N, 18O) (9, 10). These vary naturally with sources (e.g. fertiliser vs manure, animal vs plant material) (11), and are affected by distinct fractionation processes of microbial metabolisms (12). In particular, paired stable isotopes of nitrate (15N, 18O) have been used extensively to disentangle N-dynamics in complex systems such as groundwater (13, 14). Changes in microbial communities across soil recipes and components will be characterised by Next Generation Sequencing of 16S rRNA genes. Shifts in specific functional groups of microbes involved in the N-cycle will be quantified via qPCR. Advanced isotope ecology models employing Bayesian statistics, will integrate data and use it to develop a clear concept of sources and processes.

Objectives and approach

Objective 1 will be achieved in collaboration with the Eden Project. Objectives 2 and 3 focus on the analysis of soil experiments, and objective 4 on the construction of a theoretical framework for pedogenesis and the nitrogen cycle in soils, in order to develop sustainable management of deployed artificial soils.


The student will receive expert training in stable isotope techniques (Lengger), N-analysis (Fitzsimons,Tappin), experimental design (Warmington/Treseder), and molecular quantification of microbial populations and communities (Dumbrell). Training in scientific, transferable and advanced research skills will include safe working practice, soil management, and data analysis using open source software (R). Fieldwork will develop organizational and interpersonal skills. The student will benefit from seminar series (UoP) and transferable skills courses at the University and DTP-level. They will present at national and international conferences, write peer-reviewed publications and a PhD thesis. The research training addresses numerical, statistical, fieldwork and laboratory skills, equipping the student for a career across a range of professions.


  • Sustainable Soils Alliance, (available at
  • K. Treseder, M. Pytel, M. Mappley, A. Griffiths, T. Pettitt, Evolution of Pest Management Strategies in the Rain-Forest Biome at the Eden Project, the First 10 Years. Outlooks on Pest Management. 22, 22–31 (2011).
  • O. Stabnikova, W.-K. Goh, H.-B. Ding, J.-H. Tay, J.-Y. Wang, The use of sewage sludge and horticultural waste to develop artificial soil for plant cultivation in Singapore. Bioresource Technology. 96, 1073–1080 (2005).
  • H. K. Schofield, T. R. Pettitt, A. D. Tappin, G. K. Rollinson, M. F. Fitzsimons, Does carbon limitation reduce nitrogen retention in soil? Environ Chem Lett. 16, 623–630 (2018).
  • G. J. Pronk et al., Interaction of minerals, organic matter, and microorganisms during biogeochemical interface formation as shown by a series of artificial soil experiments. Biol. Fertil. Soils. 53, 9–22 (2017).
  • J. A. Cox, R. J. Whelan, Soil development of an artificial soil mix: nutrient dynamics, plant growth, and initial physical changes. Aust. J. Soil Res. 38, 465–477 (2000).
  • C. M. Kallenbach, S. D. Frey, A. S. Grandy, Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls. Nat. Commun. 7, 13630 (2016).
  • J. N. Galloway et al., Transformation of the Nitrogen Cycle: Recent Trends, Questions, and Potential Solutions. Science. 320, 889–892 (2008).
  • Z. S. Venter, S. L. Scott, J. Strauss, K. Jacobs, H.-J. Hawkins, Increasing crop diversity increased soil microbial activity, nitrogen-sourcing and crop nitrogen, but not soil microbial diversity. South African Journal of Plant and Soil. 34, 371–378 (2017).
  • S. K. Lengger, Y. A. Lipsewers, H. de Haas, J. S. Sinninghe Damsté, S. Schouten, Lack of 13C-label incorporation suggests low turnover rates of thaumarchaeal intact polar tetraether lipids in sediments from the Iceland shelf. Biogeosciences. 11, 201–216 (2014).
  • C. Kendall, E. M. Elliott, S. D. Wankel, in Stable Isotopes in Ecology and Environmental Science (Wiley-Blackwell, 2008), pp. 375–449.
  • J. Böttcher, O. Strebel, S. Voerkelius, H.-L. Schmidt, Using isotope fractionation of nitrate-nitrogen and nitrate-oxygen for evaluation of microbial denitrification in a sandy aquifer. Journal of Hydrology. 114, 413–424 (1990).
  • C. Kendall, in Isotope Tracers in Catchment Hydrology, C. Kendall, J. J. McDONNELL, Eds. (Elsevier, Amsterdam, 1998), pp. 519–576.
  • A. Amberger, H.-L. Schmidt, Natürliche Isotopengehalte von Nitrat als Indikatoren für dessen Herkunft. Geochimica et Cosmochimica Acta. 51, 2699–2705 (1987).


This project has been shortlisted for funding by the ARIES NERC Doctoral Training Partnership. Undertaking a PhD with ARIES will involve attendance at training events.

ARIES is committed to equality & diversity, and inclusion of students of any and all backgrounds. All ARIES Universities have Athena Swan Bronze status as a minimum.  

Applicants from quantitative disciplines who may have limited environmental science experience may be considered for an additional three-month stipend to take appropriate advanced-level courses.

Usually, only UK and EU nationals who have been resident in the UK for three years are eligible for a stipend. Shortlisted applicants will be interviewed on 26/27 February 2019.

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