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Aoife M. Duff

Soil Biotechnologist

Research Interests

My main research interests lie in the field of molecular microbial ecology, with particular focus on microbial community structure and functioning within agricultural habitats such as soil, plants and slurry.  Specifically, my research focuses on the microorganisms who mediate the nitrogen cycle and disentangling the complex interactions between microbes and their environment. Subsequently, findings from our research will contribute to finding the best management strategies for farmers to obtain the most out of their soil or organic fertiliser in a sustainable way.

Current Projects

I am currently working under the supervison of Dr. Fiona Brennan as a soil biotechnologist.  I am the lab manager of the Soil and Environmental Microbiology research group specialising in a range of molecular techniques such as DNA and RNA extraction from environmental samples, quantitative PCR, functional assays, library preparation for amplicon or whole genome sequencing.

I am involved in the following research projects :

  • Protected Urea and its impact on soil microbes
  • Antimicrobial Resistance and the Environment (AREST)
  • Microbiome Applications for Sustainable Food Systems through Technologies and Enterprise (MASTER)
  • Manipulation and Integration of Nitrogen Emissions (MINE)
  • Mitigating Agricultural greenhouse gas emissions (MAGGE)
  • Sustainable soil management to unleash soil biodiversity potential and increase environmental, economic and social wellbeing (SOILGUARD)


  • 2019   -  Crop Nutrition Management, Fetac level 6
  • 2017   -  Postdoc, University of Glasgow
  • 2016   -  PhD in Environmental Microbiology, NUI Galway
  • 2012   -  BSc in Microbiology, NUI Galway

Professional Membership

  • Member of the Microbiology Society

Dr. Duff has published peer reviewed scientific papers.  Her full publication list is available on:

Aoife's Google Scholar account

Tatti E, Duff AM, Kostrysia A, Cholet F, Ijaz UZ, Smith CJ (2022) Potential nitrification activity reflects ammonia oxidising bacteria but not archaea activity across a soil-sediment gradient. Estuarine, Coastal and Shelf Science 264

O’Neill RM, Duff AM, Brennan FP, Gebremichael AW, Girkin NT, Lanigan GJ, Krol DJ, Wall DP, Renou-Wilson, F, Müller, C, Richards, KG, Deveautour C (2022) Linking long-term soil phosphorus management to microbial communities involved in nitrogen reaction.  Biology and Fertility of soils inpress

Delacoux des Roseaux M, Shi S, Duff AM, Brennan FP, Condron L, Finn JA, Richards KG, O’Callaghan M, Clough T.J (2020) Impacts of pasture species and ruminant urine on N2O emissions and nitrogen transforming microbial communities in soil mesocosms. New Zealand Journal of Agricultural Research

Zhang LM, Duff AM, Smith CJ (2018) Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems Environmental microbiology 20 (8)

Duff AM, Zhang LM, Smith CJ (2017) Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts. Scientific reports 7 (1)

View media presentations by Aoife here.

  • Soil Microbiome conference Thunen Poster presentation (2019): Assessing the impact of urease and nitrification inhibitors on microbial community composition, diversity and function in grassland
  • Soil Microbiome conference Thunen Poster presentation (2019): Quantitative PCR: the importance of choosing the correct taq polymerase for environmental samples
  • Microbiology society Cork Poster presentation(2018): Quantitative PCR: the importance of choosing the correct taq polymerase for environmental samples
  • ENC Córdoba Oral Presentation (2017): Growth and activity response of ammonia oxidisers along a natural salinity gradient
  • Microbiology Society Young Microbiologist of the Year Nomination (2016): Growth and activity response of ammonia oxidisers along an estuarine salinity gradient in sediment microcosms
  • SGM Oral presentation (2015): Temporal and spatial trends in nitrification activity, ammonia oxidiser abundance and gene expression within the intertidal sediments of two coastal bays.
  • ENC Aberdeen Oral Presentation (2015): Seasonal and spatial variability of nitrification in intertidal sediments where ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts dominate
  • ISME Poster presentation (2014): Temporal and spatial variability in potential nitrification rates and abundance of ammonia-oxidising bacteria and archaea within intertidal sediments of two coastal bays 
  • Environ Oral presentation (2013): Molecular Ecology of Ammonia oxidation in coastal bay sediments