Senior Research Fellow


Contact Details

work +44 (0)1224 273662
The University of Aberdeen Institute of Biological & Environmental Sciences Cruickshank Building University of Aberdeen St Machar Drive Aberdeen AB24 3UU Scotland, United Kingdom


2016-2021: Royal Society University Research Fellowship in evolutionary microbial ecology, University of Aberdeen 

2012-2015: Early-career NERC Fellowship in evolutionary microbial ecology, University of Aberdeen.

2009-2012: Post-doctoral researcher in microbial ecology, University of Aberdeen, JI Prosser and GW Nicol group.

2005-2008: PhD student in bacterial population genetics, University of Montpellier (France), under the supervision of G Béna and JC Cleyet-Marel.


Research Interests

My research is directed toward understanding ecological adaptation of microorganism populations. My work interest is orientated on microbial diversity and ecological function for microbes playing fundamental processes in the global biogeochemical cycling of nitrogen. I am currently more focused on microorganisms (both archaea and bacteria) implicated in the ammonia oxidation process. My fundamental aims are to determine the environmental factors controlling their community structure and diversity and to understand their physiological and evolutionary adaptation.

Current Research

Research Areas

  • Long-term evolution of Thaumarchaeota
  • Ecology and physiology of archaeal nitrifiers
  • Single-cell genomics of uncultivated archaea
  • Cultivation of microorganisms

Research Group

From left to right: Lewis Cowie, Lloyd Potts, William Williams, Angus Meng, Marcus Bello, Heather Richmond, Jun Zhao, Keir Hugues, Axel Aigle, Cecile Gubry-Rangin and Manolya Balbay.


Current members

  • Dr Axel AIGLE (postdoctoral researcher): Functional redundancy in ammonia oxidiser communities.
  • Dr Jun Zhao (postdoctoral researcher): Ammonia oxidiers in tropical soils.
  • Miss Heather RICHMOND (Research technician): Cultivation of nitrifiers.
  • Dr Yiyu (Angus) Meng (Research technician): Genomics of non-ammonia oxidising archaea.
  • Mr Marcus BELLO (PhD student). co-I. Ecological implications of ammonia affinity for archaeal and bacterial ammonia ecology in soil.
  • Mr Lloyd POTTS (PhD student). co-I. Site-specific DNA- and RNA- based biomarkers to monitor low-level oil pollution and test the effectiveness of bioremediation approaches.
  • Miss Manolya BALBAY (PhD student). Evolutionary adaptation of acidophilic terrestrial Thaumarchaeota.
  • Mr William WILIAMS (PhD student). Unravelling the metabolic versatility and diversity of abundant but unexplored terrestrial Thaumarchaeota.
  • Mr Lewis Cowie (Undergraduate). Phylogenetic reconstruction of ancestral ammonia oxidation.
  • Mr Keir Hugues (Undergraduate). Acidophilic Thaumarchaeota in soils.

Past members

  • Dr Eva WEBER (PhD student). 2013-2017. Unravelling the unknown function of an under-explored but abundant archaeal group using single-cell genomics.
  • Dr Linda HINK (PhD student). co-I. 2013-2017. Influence of archaeal and bacterial ammonia oxidisers on nitrous oxide emissions in soils.
  • Mr Emmanuel Langst (MSc ERASMUS-Germany). 2017. Physiological and genomic characterisation of acidophilic nitrite oxidizer.
  • Miss Maria SPULER (PhD student). 2016. Visiting student from Chile. Effect of pre and post-emergent herbicides on N mineralization process in urea fertilized volcanic soils to improve wheat production.
  • Dr Cecile-Elodie THION (postdoctoral researcher). 2014-2015. Functional redundancy in ammonia oxidiser communities.
  • Mr Eduard VICO OTON (MSc student). 2015. Phylogenetic coherence and congruence in Thaumarchaeota.
  • Miss Noemie HAUSS (Msc, ERASMUS-France). 2015. Influence of oxygen on ecology of Group 1.1c Thaumarchaeota.
  • Mr Michael LUKUMBUZYA (Msc). 2015. Ecological importance of a novel acidophilic nitrite-oxidizing bacterium
  • Miss Anja STANJKO (Msc, ERASMUS - Slovenia). 2014. Single-cell sorting of alkalinophilic Thaumarchaeota
  • Miss Linda HINK (Msc, ERASMUS - Germany). 2013. Physiology of a novel acidophilic nitrite-oxidizing bacterium
  • Miss Urse KRUGER (Msc, ERASMUS -Denmark). 2013. Effect of pH, temperature and organic substrates on Thaumarchaeota
  • Miss Eva WEBER (Msc, ERASMUS -Slovenia). 2012. Ammonium sources for archaeal and bacterial ammonia-oxidisers
  • Miss Laura SANGUINO (Msc). 2011. Effect of methane on terrestrial ammonia oxidizing Thaumarchaea
  • Miss Breda NOVOTNIK (Msc, ERASMUS -Slovenia). 2010. Temperature affects thaumarchaeotal communities


Research Grants

Awarded as PI

  • Royal Society PhD studentship (2018-2022): "Experimental evolution of Thaumarchaeota". 
  • Post-doctoral NERC standard grant (2017- 2021): "Evolution of thaumarchaeotal metabolism under contrasting oxygen conditions". 
  • Royal Society PhD studentship (2017-2021): "Unravelling the metabolic versatility and diversity of abundant but unexplored terrestrial Thaumarchaeota". 
  • University of Aberdeen PhD studentship (2017-2021): "Adaptation of Thaumarchaeota in terrestrial environments". 
  • NERC postdoctoral grant (2017-2018): "Greenhouse gas emissions by soil microbes in tropical forest". 
  • Royal Society University Research Fellowship (2016-2021): "Adaptation in Thaumarchaeota: the interplay between ecology and evolution".
  • NERC Biomolecular Analysis Facility Application (2015): "Single-cell comparative genomics of Thaumarchaeota". 
  • Early career NERC Independent Fellowship (2012-2016): “Evolutionary adaptation in archaea”.  
  • PhD studentship (2013-2016) funded by the Centre for Genome-Enabled Biology and Medicine: “Unravelling the unknown function of an under-explored but abundant archaeal group using single-cell genomics”. 
  • NERC Biomolecular Analysis Facility Application (2013): “Phylogenetic resolution and coherence in thaumarchaea”.  
  • NERC Biomolecular Analysis Facility Application (2013): “Evolutionary adaptation in archaea- community sequencing”.  
  • MRT (French Research Ministry) Postgraduate Scholarship (2005-2008)
  • European ERASMUS Traineeship Grant (2004)
  • ESA (European Space Agency) Traineeship Grant (2003)


Awarded as coI

  • Post-doctoral NERC standard grant (2014-2018): “Soil ammonia oxidisers: an embarrassment of richness?” with JI Prosser (PI) and GW Nicol (CoI). 

Teaching Responsibilities


2013-2016: Supervision of 4 PhD students.

2009-2015: Supervision of 9 Masters project students, University of Aberdeen.

2005-2008: Supervision of 3 Masters and undergraduate project students , University of Montpellier 2, France.




Lectures at Master and undergraduate level: Environmental Microbiology (MC5507), Ocean Biology (BI25Z4), Diversity of life (BI2008)

Assessements:  Research Publications (MC5506)


Undergraduate instructor (70 hours per year): Department of Microbiology and Department of Plant Physiology

Further Info

External Responsibilities

Referee for several journals: ISME J, MBE, Microb Ecol, Plos One, BFSO and AMAB.

Membership of professional bodies: SGM (Society of General Microbiology), SMBE (Society of Molecular Biology and Evolution), ISME (International Society of Microbial Ecology), Nitrification network

Mentor as a senior scientist in the laboratory for post-doctoral researchers, visiting researchers, PhD students, master and undergraduate students.

Conference communications

List of oral presentations:

Invited conference talks:

  • Role of lateral gene exchange in acidophilic ammonia-oxidising archaea adaptation. Microbiology Society Annual Conference 2018 (Birmingham, UK) April 2018.
  • Adaptation of acidophilic ammonia-oxidising archaea: Insights from comparative genomics, metatranscriptomics and proteomics. 2nd Gobal Soil Diversity Conference (Nanjing, China) October 2017.
  • Eco-evo in Thaumarchaeota. GRC archaea (Waterville, USA) July 2017.
  • Rocky road to targeted single-cell genomics. NextgenBUG (Aberdeen, UK) May 2017.
  • Ecological insights from soil single-cell genomics. 3rd Thuenen Soil Metagenomics Symposium (Braunschweig, Germany) Dec 2016.
  •  Interplay between ecology and evolution on thaumarchaeotal adaptation: from community to single-cell level. Molecular Biology of Archaea 5 (London, UK) Aug 2016.
  •  Genomics to unravel microbial ecology and evolution. 2nd annual College of Life Sciences and Medicine symposium (Aberdeen, UK) Dec 2015.
  • The key role of pH adaptation in terrestrial Thaumarchaeota. 1st Frontiers on Soil Microbiology Conference (Beijing, China) Oct 2015. – Last minute cancellation due to unforeseen conditions.
  • Ecology and evolution of terrestrial Thaumarchaeota. 20th European Nitrogen Cycle Conference (Aberdeen, United Kingdom) Sept 2015.
  • From ecosystem functioning to single-cell genomic in ammonia-oxidising archaea. Institute of Biological and Environmental Sciences Day (Aberdeen, UK) Dec 2012.

Invited department seminars:

  • Frontiers of microbial adaptation: a multifaceted analysis. (Nottingham, UK) November 2017.
  • Ammonia oxidising archaea living in acidic soils. (Beijing, China) October 2017.
  • Why analysis of thaumarchaeotal adaptation is trendy?(Aberdeen, UK) Dec 2016.
  • Understanding the ecological function of non-abundant soil microorganisms using targeted single-cell genomics and cultivation.(Uppsala, Sweden) Nov 2016.

Selected oral presentations:

  • Single-cell genomics-driven isolation of a non-ammonia oxidising Thaumarchaeon from soil. 14th Bacterial Genetics and Ecology Conference (Aberdeen, UK) June 2017.
  • Reconstructing the role of pH adaptation in thaumarchaeal evolution. 15th International Symposium on Microbial Ecology (Seoul, South Korea) August 2014.
  • Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Modern Phylogenetic Comparative Methods (Sevilla, Spain) November 2014.
  • The role of selection in terrestrial thaumarchaeal evolution and adaptation to pH. Workshop on Linking microbial ecology and evolution (Berlin,Germany) June 2013.
  • Ecological and evolutionary adaptation of terrestrial thaumarchaea. GT archaea 2013 (Brest, France) June 2013.
  • How have terrestrial thaumarchaea really evolved? 12th Bacterial Genetics and Ecology Conference (Ljubljana, Slovenia) June 2013.
  • From ecosystem functioning to single-cell genomic in ammonia-oxidising archaea. Institute of Biological and Environmental Sciences Day (Aberdeen, UK) December 2012.
  • Importance of pH for terrestrial ammonia-oxidizing archaea. GT archaea 2012 (Paris, France) December 2011.
  • Adaptation and ecological significance of terrestrial ammonia oxidising archaea in soils. Integrative Ecological Genomics meeting (Roscoff, France) October 2011.
  • Niche specialization of terrestrial thaumarchaea. 2nd International Conference on Nitrification (Nijmegen, The Netherlands) July 2011.
  • Ecological significance and niche specialization of terrestrial thaumarchaea. Biological Interactions in Soil (Aberdeen, UK) March 2011.
  • Activity and ecological distribution of ammonia-oxidizing archaea in acidic soils. Ecology Research Day (Aberdeen, UK) March 2010.
  • Phylogeography, population dynamic and speciation of Sinorhizobium meliloti and Sinorhizobium medicae. 12th International Symposium on Microbial Ecology (Cairns, Australia) August 2008.
  • How does Medicago truncatula influence the population pattern of its favourite symbiotic bacteria, Sinorhizobium spp.? 2nd International Symposium on Rhizosphere (Montpellier, France) August 2007.
  • Experimental evolution of symbiotic bacteria under plant-host pressure. Francophone Association on Microbial Ecology (La Grande-Motte, France) October 2007.


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