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Fiona Brennan

Research Officer

Research Interests

I am a senior Research Officer in Soil Microbiology at the department of Environment, Soils and Landuse in Johnstown Castle, where I lead a research group focused on the soil and plant microbiome.  Our research group aims to harness knowledge of the soil and plant microbiome towards the development of sustainable, resilient agricultural systems. We are currently assessing the impact of agricultural practice on soil health, microbial-soil-plant interactions and microbial functioning, particularly with respect to the role of microbial communities in soil nutrient cycles, greenhouse gas emissions and plant health. We have an interest in the development of indicators and tools for assessment of soil health and biological functioning. We also investigate the impact of climate stressors on microbial function, the role of microbial communities in supporting climate resilient agricultural systems, and the ecology of enteropathogens in the environment. As part of my role I hold an adjunct lecturer position in NUI Galway and am a researcher within Vistamilk and APC Microbiome Ireland research centres. I am a currently an associate editor with the European journal of Soil Science and on the editorial board of the European Journal of Soil Biology.

Research group details 

Research Team


Post-doctoral Researchers:

  • Natalie Oram
  • Israel Ikoyi
  • Aaron Fox
  • Arne Schwelm

PhD students

  • Aisling Moffat
  • Kerry Ryan
  • Katie Martin
  • Niranjana Rose Edwin
  • Yahaya Jebril Amanor

Current Projects

  • Soilguard: Understanding the effects of soil management and climate change stressors on soil biodiversity & ecosystem services across biomes to deliver evidence-based conservation strategies)
  • Master: Microbiome Applications for Sustainable food systems through Technologies and EnteRprise
  • Root2 Resilience: Root phenotyping and genetic improvement for rotational crops resilient to environmental change
  • Grassmicro: Function follows diversity: Consequences of altered plant or soil microbial diversity for nutrient turnover in grasslands
  • FASTEN: Farm Sustainability Tools for Efficient Nutrient management
  • SoilMems: Remembering the drought: How soil memories affect grassland resilience
  • Species Mixtures: Understanding the effect of legume-based mixtures on the soil microbiome for improving resource use efficiency and yield stability
  • Leatherjacket Biocontrol
  • i-SoMPE: Innovative Soil Management Practices across Europeand their suitability for European farming systems
  • SIREN: Stocktaking for Agricultural Soil Quality and Ecosystem Services Indicators and their Reference Values
  • PLASOBINU: Plant infection by plasmodiophorids and their influence on soil biodiversity and nutrient flow
  • Minotaur: Modelling and mapping soil biodiversity patterns and functions across
  • Triple A: Abating Ammonia in Agriculture


  • 2019 - Managing People, Management Development Programme, QQI 6
  • 2010 - D Soil Microbiology, National University of Ireland, Galway
  • 2005 - BSc (Hons) Environmental Biology, University College, Dublin

Dr. Brennan has published many peer reviewed scientific journals.  A full list of Fiona's publications are available on:
Fiona's Google Scholar account
Fiona's ResearchGate account
Fiona's Publons account
Fiona's ORCID account

Martin, K.A., Brennan, F.P., Schmidt, O., Tracy, S., 2022. Comparison of two image analysis software for root trait analysis of single and mixed species grasslands. The Plant Phenome Journal 5, e20034.

Gebremichael, A.W., Wall, D.P., O’Neill, R.M., Krol, D.J., Brennan, F., Lanigan, G., Richards, K.G., 2022. Effect of contrasting phosphorus levels on nitrous oxide and carbon dioxide emissions from temperate grassland soils. Scientific Reports 12, 2602.

Zurovec O, Wall D, Brennan F.P, Krol DJ, Forrestal P, Richards K. Increasing soil pH reduces fertiliser derived N2O emissions in intensively managed temperate grassland. Agriculture, Ecosystems and Environment. 2021;311:107319.

Waters N, Abram F, Brennan F, Holmes A, Pritchard L. Easily phylotyping E. coli via the EzClermont web app and command-line tool. Access Microbiology. 2020:DOI 10.1099/acmi.0.000143.

Randall KC, Brennan F, Clipson N, Creamer RE, Griffiths BS, Storey S, et al. An Assessment of Climate Induced Increase in Soil Water Availability for Soil Bacterial Communities Exposed to Long-Term Differential Phosphorus Fertilization. Frontiers in microbiology. 2020;11:682-.

O'Neill RM, Girkin NT, Krol DJ, Wall DP, Brennan FP, Lanigan GJ, et al. The effect of carbon availability on N2O emissions is moderated by soil phosphorus. Soil Biology and Biochemistry. 2020;142:107726.

Merget B, Dobrindt U, Forbes KJ, Strachan NJC, Brennan F, Holden NJ. Variability in growth responses of non-O157 EHEC isolates in leafy vegetables, sprouted seeds and soil extracts occurs at the isolate level. FEMS Microbiology Letters. 2020;367.

Masters-Clark E, Shone E, Paradelo M, Hirsch PR, Clark IM, Otten W, et al. Development of a defined compost system for the study of plant-microbe interactions. Scientific Reports. 2020;10:7521.

Dundore-Arias JP, Eloe-Fadrosh EA, Schriml LM, Beattie GA, Brennan FP, Busby PE, et al. Community-driven Metadata Standards for Agricultural Microbiome Research. Phytobiomes Journal. 2020:https://doi.org/10.1094/PBIOMES-09-19-0051-P.

des Roseaux MD, Shi S, Duff AM, Brennan FP, Condron L, Finn JA, et al. Impacts of pasture species and ruminant urine on N2O emissions and nitrogen transforming microbial communities in soil mesocosms. New Zealand Journal of Agricultural Research. 2020:1-21.

Tyrrell C, Burgess C, Brennan FP, Walsh F. Antibiotic resistance in grass and soil. Biochemical Society Transactions. 2019:1-10.

Thorn CE, Bergesch C, Joyce A, Sambrano G, McDonnell K, Brennan F, et al. A robust, cost‐effective method for DNA, RNA and protein co‐extraction from soil, other complex microbiomes, and pure cultures. Molecular Ecology Resources. 2019;19:439-55.

Randall K, Brennan F, Clipson N, Creamer R, Griffiths B, Storey S, et al. Soil bacterial community structure and functional responses across a long-term mineral phosphorus (Pi) fertilisation gradient differ in grazed and cut grasslands. Applied Soil Ecology. 2019;138:134-43.

Merget B, Forbes K, Brennan FP, McAteer S, Shepherd T, Strachan N, et al. The influence of plant species, tissue type and temperature on the capacity of Shigatoxigenic Escherichia coli to colonise, grow and internalise into plants. Appl Environ Microbiol. 2019;85:e00123-19.

Machado-Moreira B, Richards K, Brennan F, Abram F, Burgess C. Microbial Contamination of Fresh Produce: What, Where, and How? Comprehensive reviews in food science and food safety. 2019;18:1727 -50.

Somorin Y, Vollmerhausen T, Waters N, Pritchard L, Abram F, Brennan F, et al. Absence of Curli in Soil-Persistent Escherichia coli is Mediated by a C-di-GMP Signalling Defect and suggests Evidence of Biofilm Independent Niche Specialisation. Frontiers in Microbiology 2018 9:1340.

Waters NR, Abram F, Brennan F, Holmes A, Pritchard L. riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions. Nucleic Acids Research. 2018;46:e68.

Nolan S, Waters NR, Brennan F, Auer A, Fenton O, Richards K, et al. Toward Assessing Farm-Based Anaerobic Digestate Public Health Risks: Comparative Investigation With Slurry, Effect of Pasteurization Treatments, and Use of Miniature Bioreactors as Proxies for Pathogen Spiking Trials. Frontiers in Sustainable Food Systems. 2018 2018-July-20;2.