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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.


  • Taylor, Andy F. S.; Freitag, T.; Robinson, Lucinda J.; White, Duncan (2021) Advances in measuring soil health, Book chapter entitled "Characterisation of fungal communities and functions in agricultural soils"

Printed from /staff/thomas-freitag on 08/02/23 01:36:19 PM

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.