NitrificationIt has been estimated that about 70% of N-fertiliser applied worldwide is lost to the environment, leading to economic losses, water pollution and increased greenhouse gas (GHG) emissions. When nitrogen is in the form of nitrate (NO3-), it is relatively mobile in soil and thus can easily be acquired by plants over distance through mass flow (Fig. 2). But nitrate is also subject to leaching and denitrification which, if incomplete, produces nitrous oxide emission, a gas with ca 300× the GHG effect of CO2. Ammonium (NH4+) is far less mobile in soil as it forms bonds with the soil particles so that losses by leaching are extremely low. Ammonium metabolism is also more favourable to plants since it requires 4 times less energy for assimilation.

Large amounts of N-fertilisers are therefore supplied in the form of ammonium. A major agronomic concern, however, is the nitrification of ammonium fertilisers by soil microorganisms where large amounts of nitrogen are transformed to nitrate and thus reduce soil pH, and become highly mobile and susceptible to leaching and conversion to GHG (N2O) via denitrification. 

Research in my group demonstrates that the physical and chemical structure of soils can be replicated using low refractive index (RI) solid particles that can adsorb nutrient and dyes and are suitable for image living organisms in situ. Our first generation of TS exhibits


 physical properties and growth conditions similar to those in sandy soils. Water retention can exceed that of sand (similar to vermiculite) and particle surface charge density is high and could be suitable to model clay particles (1). Mixtures of particles containing a range of size, surface charge 

density and compaction level could be used to mimic a natural soil. TS offers new opportunities to soil biology because they allow roots, microbes and soil particles to be imaged at resolutions not previously achievable. They are amenable to modern microscopy techniques, e.g. Laser Scanning Microscopy, Optical Projection Tomography or BioSpeckle Laser imaging (2,3). They can host numerous fluorescent markers and other dyes so that complex biological and chemical activity can be quantified non-destructively (4). Quantitative analysis of image data based on fluorescence imaging is greatly facilitated. Filters can be used to extract specific emission wavelengths and provide high contrast images that are suitable for computational processing of data (1).

Objective of the project

The broad aims of this project are therefore: 1) to build a multidisciplinary team to develop a model system for micro-scale quantitative imaging and tracking of roots, nitrogen and nitrifying/denitrifying bacteria in the rhizosphere; 2) engineer smart transparent soil technologies combining polymer chemistry, optics and soil physics; 3) to quantify nitrogen movement and transformation in soil; and 4) to discover how the rhizosphere is formed, how microbial activity, soil structure and root activity influence nitrogen movement in soil. 


Further Reading

(1) Downie, H., N. Holden, W. Otten, A.J. Spiers, T.A. Valentine and L.X. Dupuy. 2012. Transparent soil for imaging the rhizosphere. PLoS One 7: e44276.

(2) Yang, Z., H. Downie, E. Rozbicki, L.X. Dupuy and M.P. MacDonald. 2013. Light Sheet Tomography (LST) for in situ imaging of plant roots. Opt. Express 21: 16239-16247.

(3) Ribeiro, K.M., B. Barreto, M. Pasqual, P.J. White, R.A. Braga and L.X. Dupuy. 2014. Continuous, high-resolution biospeckle imaging reveals a discrete zone of activity at the root apex that responds to contact with obstacles. Ann. Bot. 113: 555-563.

(4) Downie, H., T.A. Valentine, W. Otten, A.J. Spiers and L.X. Dupuy. 2014. Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo. Plant Signaling and Behavior e29878.