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Thomas Freitag

Staff picture: Thomas Freitag
Ecological Sciences
Ecological Sciences
Molecular Microbiologist Metagenomics
+44 (0)1224 395326

The James Hutton Institute
Aberdeen AB15 8QH
Scotland UK


I am a molecular microbiologist in Ecological Sciences, having completed my doctoral degree and diploma in geomicrobiology at the University of Oldenburg, Germany. Through research positions at the University of Oldenburg and Prof. Prosser’s microbiology group at the University of Aberdeen prior to taking up my post at the Institute in 2011, I have worked across a broad range of fields investigating the relationships between biogeochemical cycling and microbial processes; covering microbial ecology in intertidal sand-flats to molecular ecology of ammonia and nitrite oxidising bacteria in soils and sediments and regulation of methane fluxes in peat soils by methanogen and methanotroph activity.

Current research interests

My general research interests are the relationships between biogeochemical cycling and microbial processes. I specialize in the molecular analysis of microbial DNA signatures (abundance and phylogeny) and their functional activity (mRNA expression) within soil and sediment ecosystems.  

Recent projects focus on the microbial processes and sources of respired carbon contributing to soil COemissions. In peatlands the contribution of CO2 produced by CH4 oxidising methanotrophs to total flux rates is largely unknown and may constitute a significant part of total soil respiration.

An other example of uncertainty in soil CO2 budget calculations is that of ‘priming’,

whereby inputs of labile C to soil from plants result in elevated rates of microbial mineralisation of existing soil organic matter (SOM). It is assumed that priming effects are mediated by the composition of soil microbial communities and we are attempting to demonstrate pathways of labile and SOM C-flux through components of these communities. 

I also have a long standing interest in the relationships and feed-back mechanisms between microbial functional and phylogenetic biodiversity and their ecological drivers.  We are currently analysing the existing NSIS II (national soils inventory of Scotland) DNA archive to investigate microbial habitat / community relationships on a national landscape scale.

Most recently I have developed interests in the application of comparative metagenomic and metatranscriptomic second generation sequencing approaches to investigate changes in microbial community metabolic capacity and pathways under environmental change scenarios. These approaches have been identified as most promising for understanding the regulation of microbial activities in response to environmental drivers and defined manipulations.

I collaborate with partners at the University of Western Australia as well as the Universities of Barcelona, Aberdeen and Glasgow. I am a review board member for Frontiers in Terrestrial Microbiology and a research associate of the University of Aberdeen and contribute to the “Marine Benthic Ecology” and “Environmental Microbiology & Biotechnology” modules of the Masters course.

Past research

  • The mycorrhizal hyphosphere: a key driver of biogeochemical cycles?
  • BBSRC funded, 2010 – 2011, Universites of Aberdeen, York and Warwick, with Prof. E. Baggs, Prof. J.I. Prosser, Dr. A. Hodge, Dr. G. Bending.  
  • Links between methane flux and in situ transcriptional activities of methanogenic archaea and methane oxidising bacteria in peat soil. NERC funded, 2008-2009. Universities of Aberdeen and York, with Prof. J.I. Prosser & Prof. P. Ineson.
  • Development of a whole genome DNA microarray and analysis of nitrifier transcriptomic response to pH dependent ammonia availability. NERC funded, 2005-2007. Universities of Aberdeen and Newcastle, with Prof. J.I. Prosser & I. Head.
  • Impact of nitrogen fertiliser management regimes on nitrifier diversity and nitrification kinetics in agricultural grassland soils. BBSRC funded, 2002-2004, University of Aberdeen & IGER, North Wyke with Prof. J.I. Prosser & Dr. C. Clegg.
  • Development of molecular techniques for the detection of novel functional genes in unculturable microorganisms. Industry funded (NCIMB), 2002, University of Aberdeen, with Prof. J.I. Prosser.
  • Molecular analysis of nitrifier diversity and microbial recycling processes in anoxic marine sediments. Leverhulme Trust, 2000-2001, Universities of Aberdeen & Leeds and FRS Aberdeen, with Prof. J.I. Prosser, Dr. I. Davies & Dr. R. Mortimer.


  • Artz, R.R.E.; Freitag, T.; Pravia, A.; Littlewood, N. (2021) Case Study: Ecosystem resilience - peatland restoration., SEFARI Case Study.
  • Dawson, L.A.; Miller, D.R.; Freitag, T.; Brewer, M.; Robinson, L.; Ross, J. (2014) MiSAFE project mid term review report., Mid-Term Report to the EU Review Panel for the MiSAFE Project. Uploaded to the EU website.
  • Miller, D.R.; Dawson, L.A.; Morrice, J.; Ross, J.; Freitag, T.; Robinson, L. (2013) Knowledge exchange and dissemination strategy., Deliverable D7.1 (Knowledge Exchange Strategy), EU MiSAFE Project.
  • Brooker, R.; Aalders, I.H.; Ballingall, K.; Begg, G.; Birch, A.N.E.; Elliott, G.; Ellis, C.; Freitag, T.; Hawes, C.; Holland, J.; Holmes, B.; Hough, R.L.; Karley, A.; McCracken, D.; Mitchell, R.; Stockan, J.; Zadoks, R.; Albon, S.A.; Hester, A.J.; Pakeman, R.J. (2013) Biotic and biophysical underpinning of ecosystem services in the Scottish context: a review., Published online as an outputs from WP 1.1 of the Ecosystem Services Theme of the SRP.

  • Waibel, M.; Thornton, B.; Paterson, E.; Freitag, T. (2016) Interactions in labile C application to soil and soil organic matter mineralisation., 3rd Doctoral Researcher’s Conference, Signaling at the Plant-Soil Interface, Bad Salzdetfurth, Germany, 14-16 September 2016.
  • Dawson, L.A.; Freitag, T.; Ross, J.; Robinson, L.; Miller, D.R.; Pasternak, Z.; Habtom, H.J.C.; Robe, P.; Kahns, L.; Simonet, P.; Demaneche, S.; Gafny, R.; Cordero, J.C.; Jurkevitch, E. (2014) The development and validation of microbial soil Community analyses for forensic purposes (MiSAFE)., Forensics Geosciences Group, London, 2-4 December 2014. Proceedings.
  • Randerson, P.; Avery, L.M.; Hough, R.L.; Taylor, A.; Freitag, T.; Jefferson, B.; Tyrrel, S. (2012) Optimising wastewater irrigation of short rotation coppice for sustainable water and energy: a systems approach., Constructed Wetlands Association AGM, Slimbridge, UK.
  • Baggs, E.; Chadwick, K.; Giles, M.; Freitag, T.; Paterson, E. (2011) How strong is the coupling between plant C-flow and rhizosphere denitrification?, Rhizosphere 3 International Conference, Perth, Australia, 25-30 September 2011.

  • Britton, A.; Ewan, K.; Whyte, A.; Freitag, T.; Robinson, L.; White, D.; Morton, I.; Taylor, A. (2022) Going underground unleashing the power of citizen cience and eDNA to explore alpine soil biodiversity, International Mountain Conference 2022, 11 - 15 September 2022, Innsbruck, Austria.
  • Taylor, A. F. S.; Fielding, D.; Freitag, T.; Oddi, L.; Robinson, L.; van Paassen, J.; White, D.; Britton, A. J. (2022) Spatial congruity across six kingdoms of alpine biodiversity, International Mountain Conference 2022, 11 - 15 September 2022, Innsbruck, Austria.
  • Britton, A.J.; Freitag, T.; Oddi, L.; Fielding, D.; van Paassen, J.; White, D.; Robinson, L.; Taylor, A.F.S. (2019) Topography drives heterogeneity in alpine soil function., International Mountain Conference 2019, Innsbruck, 8-12 September 2019. (Poster)
  • Knapp, C.; Peshkur, T.; Graham, D.W.; McCann, C.; Cooke, R.; Hough, R.L.; Pagaling, E.; Avery, L.; Freitag, T.; Zhu, T.-G.; Su , J.Q. (2018) Antimicrobial resistance: soil-landscape conditions across NE England and Scotland., The Scottish Universities Life Science Alliance (SULSA) Antimicrobial Resistance Conference, Technology and Innovation Centre, Glasgow, 26-27 April 2018. (Poster)
  • Freitag, T.; Taylor;, A.; Black, H.I.J.; Campbell, C.D. (2017) Scotland's natural assets: the unseen majority - soil microbial communities., 40th T.B. Macaulay Lecture. Prosperity Without Growth: Foundations for the Economy of Tomorrow, Our Dynamic Earth, Edinburgh, 4 October 2018. (Poster)
  • Oddi, L.; Britton, A.J.; Freitag, T.; van Paassen, J.; Taylor, A.F.S. (2017) Microbial community activity along gradients of snow lie in the Scottish Highlands., British Ecological Society Winter Meeting 2017, Ghent, 11-14 December 2017, p60. (Poster)
  • Artz, R.R.E.; Smart, C.; Robertson, J.; Freitag, T. (2017) Indicators of peatland restoration success on former plantation forestry., Research in the ‘Flow Country’ IV: Thinking Big, Thurso, Caithness, 22-24 March 2017.
  • Artz, R.R.E.; Smart, C.; Bourne, E.; Robertson, J.; Freitag, T. (2016) Indicators of peatland restoration success on former plantation forestry., IUCN Peatland Programme Conference, Creating a Legacy for Peatlands, Shropshire Conference Centre, Shrewsbury, 29 November - 1 December 2016. 29th November – 1st December 2016
  • Zhang Z.L.; Lin H.; Osprey M.; Chapman S.J.; Freitag T.E.; Rhind S.M.; Kyle C.E.; Hamilton D. (2016) Occurrence and changes of classic and emerging contaminants in soils treated by organic wastes., ESPP (European Sustainable Phosphorus Platform) Workshop: Pharmaceuticals in Sewage Biosolids, Malmo, 27 November 2016.
  • Minet, E.P.; Rochford, N.; Brennan, F.P.; Breslin, C.; Freitag, T.; Lanigan, G.; Moynihan, E.; O'Carroll, C.; Rooney, A.D.; Richards, K. (2015) Environmental benefits of amending cow slurry with the nitrification inhibitor decyandiamide., RAMIRAN 2015, 16th International Conference, Rural-Urban Symbiosis, Hamburg, Germany, 8-10 September 2015.

Printed from /staff/thomas-freitag on 28/02/24 05:45:02 AM

The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.