Integrating physical and chemical techniques to characterise soil micro-sites

Lead Research Organisation: University of Abertay Dundee
Department Name: Sch of Contemporary Sciences


Many problems in environmental and soils research require techniques that quantify the soil micro-environment. It has become increasingly apparent that we need novel techniques to complement other techniques that often study soils at spatial scales that are too coarse. At the microscopic scale in a soil, bacteria and their food source or oxygen supply, for example, are spatially separated, even at relatively high densities of both. Fortunately, recent technological advances allow us to unravel the physical, chemical, and biological heterogeneity of soils, which combined with modelling techniques, enables us to make sense of the complexity of soil systems. Soil physics and soil chemistry are highly interdependent, with the spatial distribution of chemical species often heterogeneously distributed and intertwined with soil structure. Examples include the role of metal complexes, oxides and clay minerals in the formation and stabilization of aggregates, the soil organic mineral interactions in gley soils and gleyic features in poorly drained soils, or soils contaminated with metals. The opacity of soil has hampered progress in our understanding of physico-chemical processes in soils. To date, our understanding of the soil micro-environment relies heavily on the concept of soil aggregates. Advances in the use of X-ray CT, however, enable quantification of the internal structure of soils at microscopic scales without physical disruption. Similarly, chemical analyses often take place after homogenizing relatively large soil samples. Even studies with small samples of soils are effectively bulk analyses and a mechanistic understanding will remain lacking as long as techniques do not advance to microscopic scales. Recently, microscopic and micro-spectroscopic analyses have begun to address this. However, these techniques to date are restricted to small samples (a few mm in diameter) and often require access to synchrotron facilities. Rapid progress, however, may be possible if we are able to combine non-invasive and invasive techniques that operate at microscopic scales. In this proposal, we will make use of state of the art X-ray CT facilities to quantify the soil structure in situ at a resolution of 8 micrometres. We will then prepare soil sections to obtain 2-D spatial maps of the distribution of elements in the same soil samples using SEM-EDX. First we will make horizontal slices through soil to obtain sequential 2-D maps that are quantified with SEM-EDX. Then we will locate this surface within the 3-D physical structure characterised with X-ray CT, and use statistical modelling to integrate in between the 2-D planes. We will apply the techniques to soils amended with black carbon and kaolinte, keeping selected applications in mind during the development. The combination of these two techniques will add significantly to our understanding of the processes involved in C sequestration and soil structural dynamics and may provide means to test hypothesised theories on the formation of macro- and micro-aggregates in soil and the stability of biochar. This will be important for studies of C storage in soils and how this will be affected by climate change and soil management.
Description There is a considerable need to develop improved understanding of factors that control soil processes at micro-habitat scales. This requires integration of physical chemical and biological measurements of soil at microscopic scales that will allow for the production of 3D maps of related properties. To date, because of technical limitatiosn most biological and chemical measurements at this scale are obtained in 2D samples. This study develop a method to generate 3D maps of soil properties by combining 2S SEM-EDX data to determine the spatial distribution of chemical elements, with 3D Xray CT data, which visualise the soil physical structure and distribution of pores and solid-pore interfaces. A statistical approach using regression tree method and ordinary kriging applied to residuals was developed and applied to predict 3D spatial distribution of carbon, silicon, iron and oxygen at the microscale. This presents for the first time an integrated experimental and theoretical framework combining geostatistical methods with imaging techniques to unveil the 3D chemical structure of soils at scales relevant to bacteria.
Exploitation Route The method is available and can be used by other researchers in this field that are looking for ways to combine different imaging techniques in 3D
Sectors Agriculture, Food and Drink,Environment

Description One of the outputs of the project is visual representation of the soil microenvironment in the form of videos. A particular video (and still images) made during this grant has been used at various occasions to enhance public understanding, including presentation at BBC reporting Scotland (2014) and BBC radio (web-page) Shared Planet, Soil Science (2013) as well as café Science Presentations (2013, 2014). The acquired visualisation skills were also applied to produce a video of caries in teeth which has been used to promote a start-up company developing a novel way to remineralise teeth, led by partners at Dundee University.
First Year Of Impact 2010
Sector Agriculture, Food and Drink,Education,Environment,Healthcare
Impact Types Societal

Description Royal Society International Grant
Amount £2,668 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Description enabling fund
Amount £2,500 (GBP)
Organisation Scottish Alliance for Geoscience, Environment and Society (SAGES) 
Sector Academic/University
Country United Kingdom
Description international exchance program
Amount £1,755 (GBP)
Organisation Royal Society of Edinburgh (RSE) 
Sector Charity/Non Profit
Country United Kingdom
Description integrating biological and physical techniques to characterise soil micro-habitats 
Organisation University of Bremen
Country Germany 
Sector Academic/University 
PI Contribution The collaboration aimed to combine 3D physical characterisation of soil using Xray CT with biological thin sectioning. Our contribution included the Xray CT as well as the analyses and methodologies for aligning samples.
Collaborator Contribution Expertise in the preparation of biological thin sections and the use of a variety of staining techniques that are best used to visualise bacteria in thin sections and to integrate this with 3D data set obtained with Xray CT
Impact outputs in preparation
Start Year 2010
Description Farmers Weekly Soil in Practise 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact a Presentation was given to an audience mostly comprising farmers at a meeting held at a farm organised by Farmers Weekly as part of the soil in practise series. Presentation and focus of the meeting was on soil structure and knowledge and videos/images generated within the project were used as part of this meeting.
Year(s) Of Engagement Activity 2017