Developing Sustainable Soil Ecosystems: Microbial Ecology and Biogeochemistry of Nitrogen Cycling in Artificial Soils

Apply now. ARIES PhD project opportunities October 2020

Project description: 

Healthy soils are the basis for sustainable agriculture, but they are threatened by erosion, nutrient loss, and climate change. The use of artificial soils - mixtures of waste materials - would drastically increase the availability of soil for developments (ecotowns, agricultural land), however, this practice is not yet sustainable. Application of nitrogen (N)-rich fertilisers is common practice when artificial soils are deployed, but this is likely an oversupply that can result in negative environmental impacts, such as oxygen-poor marine environments. Microplastics from the waste materials could also be problematic. In this exciting PhD project, you will characterise 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 and is applied to regenerate sites in the UK, Canada, and China. There, you will have the opportunity to apply your findings, and make a lasting impact in line with the Eden global mission. 

Objectives: 

1. Create and maintain experiments using artificial soil prototypes. 

2. Identify sources and pathways of nutrient cycling. 

3. Use molecular approaches to identify N-cycling organisms and communities. 

4. Collaborate with Eden Project sites to test findings in an applied setting. 

Supervisory team:

You will be based at the UoP (Dr Lengger, Prof Fitzsimons) where you will conduct experiments and analyses, and analyse the microbiome at the UoE (Dr Dumbrell). You will collaborate with the Eden Project for field work and internships (Dr Warmington). 

Training:

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 science communication. 

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 ENV.

Supplementary information: 

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 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 Nlosses 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. 

Training 

The student will receive expert training in stable isotope techniques (Lengger), Nanalysis (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.

References: 

1. Galloway, J. N. et al. Transformation of the Nitrogen Cycle: Recent Trends,Questions, and Potential Solutions. Science 320, 889–892 (2008) 

2. Kendall, C. Chapter 16 - Tracing Nitrogen Sources and Cycling inCatchments. in Isotope Tracers in Catchment Hydrology (eds. Kendall, C. &McDONNELL, J. J.) 519–576 (Elsevier, 1998). 

3. Schofield, H. K., Pettitt, T. R., Tappin, A. D., Rollinson, G. K. & Fitzsimons, M.F. Does carbon limitation reduce nitrogen retention in soil? Environ. Chem. Lett. 16,623–630 (2018). 

4. S. K. Lengger, Y. A. Lipsewers, H. de Haas, J. S. Sinninghe Damsté, S.Schouten, Lack of 13C-label incorporation suggests low turnover rates ofthaumarchaeal intact polar tetraether lipids in sediments from the Iceland shelf.Biogeosciences. 11, 201–216 (2014) 

5. Dumbrell, A. J., Nelson, M., Helgason, T., Dytham, C. & Fitter, A. H. Relativeroles of niche and neutral processes in structuring a soil microbial community. ISMEJ. 4, 337–345 (2010).