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Manipulation of the soil microbial community in stabilising SOM to improve soil function


Project Description

Sustainable food production is top of the global policy agenda. This requires that soil functions are optimized (Rojas et al., 2016; Schulte et al., 2014) to sustainably meet increased agricultural productivity (provision of food, fibre and fuel), and other necessary soil functions such as carbon sequestration, climate regulation and nutrient cycling. Soil organic carbon (SOC) is strongly linked to these soil functions and is recognized as a keystone indicator of soil quality (Koch et al., 2013), but the relationship between SOC and specific soil functions has not yet been quantitatively determined. Carbon:nutrient stiochiometry has recently been shown to limit the stabilised SOC pool (Kirkby et al., 2016; 2013). This research will investigate the mechanisms for soil organic matter (SOM) stabilization and determine how improved soil function can be controlled by macroscale manipulation of nutrients. The research project objectives are to advance mechanistic understanding of fine fraction soil organic matter (FF-SOM) stabilization by supplementary nutrients focusing on:
(i) the processes involved in increasing the SOC content with supplementary nutrients
(ii) the role of the soil microbial community in stabilising SOM
(iii) quantitatively linking SOC to specific soil functions

This PhD is funded as part of a project ’Carbon-nutrient stoichiometry to stabilise soil organic matter and improve soil function’ (Cfunction). This work will be completed in laboratory, greenhouse and field phases based at University College Dublin and the UCD Research Farm. The research team is the research team leader (Dr. Sharon O’Rourke) and the PhD student, and each will have dual involvement in each experiment phase.

This work of the PhD will focus most strongly on objective (ii), unravelling the role of the microbial community as a driver of SOM stabilisation and as a pool of SOM itself, through manipulation of C substrate and supplementary nutrients to investigate ‘microbial metabolism’. State-of-the-Art stable isotope ratio analysis and 13C Nuclear Magnetic Resonance (NMR) analysis will be used to measure δ13C in SOM fractions (Amelung et al., 2008) and describe the molecular characteristics of microbial biomass and SOM (Courtier-Murias et al., 2014) following isotopic enrichment of the C input (crop residues). These techniques allow (i) the quantitative measurement of the proportion of C residue assimilated in to the FF-SOM and (ii) will identify classes of chemical compounds so that FF-OM can be characterized as plant derived, of microbial origin, or from different biological sources. Quantitative PCR (qPCR), amplification of DNA with a polymerase chain reaction to examine microbial diversity (Fierer et al., 2005), and the relatively new cDNA metattranscriptomics, sequencing of mRNAs to monitor gene expression (Carvalhais & Schenk, 2013), will be employed to examine microbial diversity and function (i.e. decomposer, mineralization, nitrification) to better understand how macronutrients regulate microbial control of SOC stabilisation. Two academic advisors who are experts in NMR and microbiology (Dr. Evelyn Doyle – UCD & Dr. Brian Kelleher – DCU) will assist in the microbiology aspects of the PhD project.

A suite of soil physical, chemical and microbiological data will be collected throughout the project and will be used to relate SOC to overall soil function.

The candidate should have a primary degree in microbiology, or a science based degree with microbiology as a major component, and/or masters in the same. Experience of microbiology techniques listed would be an advantage.

Funding Notes

Funding received from the Irish Research Council Laureate Awards 2017/2018.

References

Amelung W et al. (2008) Combining biomarker with stable isotope analyses for assessing the transformation and turnover of soil organic matter. Adv Agron, 100, 155-250.
Carvalhais LC, Schenk PM (2013) Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities. Methods Enzymol, 531, 251-267.
Courtier-Murias D et al. (2014) Cross-polarization-single pulse/magic angle spinning (CPSP/MAS): A robust technique for routine soil analysis by solid-state NMR. Geoderma, 226-227, 405-414.
Fierer N et al. (2005) Assessment of soil microbial community structure by use of taxon specific quantitative PCR assays. Appl Environ Microbiol, 71, 4117-4120.
Kirkby CA et al. (2016) Inorganic nutrients increase humification efficiency and C sequestration in an annually cropped soil. PLoS ONE 11: e0153698.
Kirkby CA et al. (2013) Carbon-nutrient stoichiometry to increase soil carbon sequestration. Soil Biol Biochem, 60, 77-86.
Koch A et al. (2013) Soil Security: Solving the Global Soil Crisis. Global Policy, 4, 434-441.
Rojas RV et al. (2016). Healthy soils: a prerequisite for sustainable food security. Environ Earth Sci, 75,180.
Schulte RPO et al. (2014) Functional land management: A framework for managing soil based ecosystem services for the sustainable intensification of agriculture. Environ Sci Policy, 38, 45-58.

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