Luke Fountain

Investigating links between plant nitrogen preference, root exudation and microbial nitrogen cycling

About me

 I completed my integrated master’s degree (MBiolSci) in molecular biology at The University of Sheffield in June 2018. During my final year, I carried out a research project in the lab of Professor Julie Gray, characterising mutants of Arabidopsis thaliana with altered numbers of stomata (small pores on the surface of the leaf that regulate CO2 uptake for photosynthesis and water loss via transpiration) and defective stomatal regulation and developing a thermal imaging technique to characterise stomatal responses to abscisic acid (ABA) dynamically. The technique allows stomatal responses to be monitored in real-time in a whole-plant context, in a higher-throughput manner than most current methods. I presented my thermal imaging work at the International Workshop on Image Analysis Methods for the Plant Sciences at The University of Nottingham in January 2018.

After completing my degree, I continued to work in the Gray lab as a laboratory assistant, working on investigating how the manipulation of stomatal density in rice can improve drought tolerance, being acknowledged in a paper published from the lab during this time (Caine et al. (2019). Rice with reduced stomatal density conserves water and has improved drought tolerance under future climate conditions. New Phytologist

I am now applying my work with stomata and rice to investigate how variation in the number of stomata affects key plant and soil microbe interactions, starting my PhD at The University of Sheffield in October 2018, co-supervised by Professor Tim Daniell, Professor Julie Gray and Professor Duncan Cameron. The main aim of my PhD is to dissect the mechanisms by which plants can manipulate microbial nitrogen cycling in agricultural soils, using the stomatal mutants as a model system.

My project

Plants are capable of manipulating the microbial nitrogen cycling processes of nitrification and denitrification through exudation of low molecular weight carbon compounds like amino acids, sugars and secondary metabolites into the rhizosphere, the region of soil around the roots of plants. This manipulation of nitrogen cycling can affect the forms of nitrogen that are available to plants, either through direct inhibition of the enzymes involved in these N transformation processes, or through affecting the nitrifying/denitrifying microbial community dynamics by changing the carbon substrates available to them.

Plants primarily take up nitrogen from soil in the form of either ammonium (NH4+) or nitrate (NO3), with some plant species showing a preference for one form over the other. Many crop species prefer NO3 although some are known to prefer NH4+, notably Oryza sativa (rice). Environment plays a considerable role in determining plant N preference (among other factors), particularly in rice, with lowland varieties grown in flooded, largely anaerobic paddy soils preferring NH4+, and upland rice varieties grown in dryer, more aerobic soils preferring NO3.

It is not known whether the nitrogen preference of plants has an impact on root exudation and N cycling, but it is possible that this is the case, encouraging the maintenance or generation of the form of nitrogen the plant prefers in the soil. Investigation of differences in exudate composition and effects on N cycling between plants with different N preference could therefore provide a route to dissect the drivers of plant manipulation of soil N cycling.

This could be investigated by studying different species or cultivars with known differences in nitrogen preference, for example by comparing upland and lowland varieties of rice. However, these cultivars will likely inherently have differences in exudate composition due to the fact they are not genetically identical.

Carbon and nitrogen metabolism are tightly linked, and consequently photosynthesis directly affects the nitrogen demand of the plant. Therefore, by manipulating photosynthesis, there is the potential for altering the nitrogen demand and potentially the nitrogen preference of the plant. Mutants of the rice cultivar IR64 with altered numbers of stomata may allow more or less carbon to enter the plant (as CO2), and as a consequence may show differences in their N preference, therefore offering a potential route for investigation of links between N preference, plant root exudation and effects on soil N cycling, without any interference that may be observed if comparing between different species/cultivars.

Main objectives of the PhD

  • To assess whether the number of stomata affects the nitrogen preference of rice
  • To collect and analyse root exudates to identify the active compounds driving biological nitrification inhibition and or alteration of denitrification (i.e. manipulating soil nitrogen cycling processes)
  • Dissect if the mechanism for alteration in activity is driven by manipulation of the soil community structure or changes in the activity of a stable community