Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).
NITRO DIALOGUE – Interactions between nitrogen fixers and nitrifiers and their impact of agricultural soil emissions
Secondary Supervisor(s): Professor Miriam Gifford
University of Registration: University of Warwick
BBSRC Research Themes:
Project Outline
Potential Research Questions and Objectives
How do spatial and temporal dynamics of nitrogen-fixing and nitrifying microbial communities influence each other and subsequently affect GHG and trace gas emissions? This project will map the distribution and activity of both microbial groups at various soil aggregate scales using advanced spatial multi-omics techniques. The doctoral researcher (DR) will develop and employ novel in-situ sensors for real-time monitoring of microbial activity and associated N2O and NO emissions.
What are the molecular mechanisms mediating the interactions between nitrogen fixers and nitrifiers, and how do these interactions modulate gas emissions? Utilising single-cell RNA sequencing, the DR will uncover gene expression patterns in key microbial players during different interaction stages. This will be coupled to identification of signalling molecules, metabolites, and other compounds facilitating cross-talk between the two microbial groups.
How do environmental factors and agricultural practices influence the nitrogen fixer-nitrifier relationship and subsequent gas emissions? The DR will conduct manipulative experiments in controlled mesocosms to simulate various environmental conditions and agricultural practices. From these parameters, we will develop predictive models to understand how different factors affect microbial interactions and resulting emissions.
Can we leverage our understanding of nitrogen fixer-nitrifier interactions to design microbial consortia for reduced GHG emissions while maintaining soil fertility? The DR will design and test synthetic microbial communities with optimised nitrogen cycling capabilities. Explore the potential of plant growth-promoting rhizobacteria to enhance beneficial interactions between nitrogen fixers and nitrifiers.
Potential Methodology
The project will leverage Warwick’s technical capability to employ a multi-faceted approach, combining advanced field experimentation, cutting-edge molecular and analytical techniques, and innovative modelling.
Field Experiments. The DR will utilise established agricultural plots with continuous monitoring of soil parameters and gas fluxes. Simultaneously, we will implement isotope pool dilution techniques using 15N and 18O to trace nitrogen transformations mediated by both microbial groups in situ.
Advanced Molecular and Analytical Techniques. The DR will apply spatial transcriptomics and metabolomics to map microbial interactions at the microscale, utilising Raman spectroscopy for high-resolution spatial analysis of isotope incorporation in nitrogen-fixing and nitrifying cells. This will be coupled to metaproteomics to characterise the functional interactions between the two microbial groups.
Microbial Interaction Studies. The DR will develop microfluidic devices to study direct cell-to-cell interactions between nitrogen fixers and nitrifiers. A potential focus of this will be to define the role of extracellular vesicles in mediating information exchange between the two microbial groups.
Modelling and Data Integration. The DR will develop multi-scale models integrating molecular interactions, microbial community dynamics, and ecosystem-level processes. This will exploit machine learning algorithms to identify key drivers of microbial interactions and predict their impact on emission patterns.
Applied Aspects. The DR will test bioinoculants combining nitrogen-fixing and nitrifying microbes for enhanced nitrogen use efficiency and reduced soil emissions. Explore precision agriculture techniques for managing microbial interactions, including site-specific application of microbial consortia.
Expected Outcomes and Impact
This project will provide unprecedented insights into the intricate interactions between nitrogen-fixing and nitrifying microorganisms in agricultural soils. By elucidating the molecular dialogue between these key players, we aim to develop novel strategies for manipulating soil microbial communities to reduce GHG emissions while maintaining agricultural productivity. The findings will inform the development of next-generation bioinoculants and precision agriculture practices, contributing to more sustainable and climate-smart farming systems.
Key References
Kuypers M. et al. (2018). The microbial nitrogen-cycling network. Nature Reviews Microbiology, 16(5), 263-276.
Stein, L. et al. (2016). The nitrogen cycle. Current Biology, 26(3), R94-R98.
Butterbach-Bahl, K. et al. (2013). Nitrous oxide emissions from soils: how well do we understand the processes and their controls? Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1621), 20130122.
Orr, C. et al. (2011). Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils. Applied and Environmental Microbiology, 77(3), 911-919.
Ouyang, Y., et al. (2016). Ammonia-oxidizing bacteria are more responsive than archaea to nitrogen source in an agricultural soil. Soil Biology and Biochemistry 96, 4-15.
