Graeme Nicol Environmental Microbial Genomics Group

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Laboratoire Ampere
Ecole Centrale de Lyon . France
(33) 472 18 65 14


Education | Research Interests | Publications | Curriculum Vitae | More...

   
  Graeme Nicol
 

Environmental Microbial Genomics Group
Laboratoire Ampère, UMR CNRS 5005
Ecole Centrale de Lyon
Université de Lyon
36 avenue Guy de Collongue
69134 Ecully cedex
France

 

graeme.nicol@ec-lyon.fr

  Phone: (33) 4 72 18 62 37
Fax: (33) 4 78 43 37 17

 

top EDUCATION

1997 - 2001 Ph.D. , Department of Molecular and Cell Biology, University of Aberdeen, Thesis title: A molecular analysis of archaeal community structure and activity in grassland rhizosphere soil
1993 – 1997 University of Strathclyde, Glasgow, B.Sc. Honours (2i) - Environmental Biology

top RESEARCH INTERESTS

Graeme

  • Nitrogen cycling in soil
    • influence of pH on activity
    • ecology of nitrifying archaea and bacteria
  • Physiology, ecology and genomics of cultivated soil Archaea

topPUBLICATIONS

60. Elling, F.J., Könneke, M., Nicol, G.W., Stieglmeier, M., Bayer, B., Spieck, E., de la Torre, J.R., Becker, K.W., Thomm, M., Prosser, J.I., Herndl, G.J., Schleper, C. and Hinrichs, K.-U. (2017) Chemotaxonomic characterization of the thaumarchaeal lipidome. Environmental Microbiology. In press.
59. Hink, L., Nicol, G.W., and Prosser, J.I. (2016). Archaea produce lower yields of N2O than bacteria during aerobic ammonia oxidation in soil. Environmental Microbiology. In press.
58. Gubry-Rangin, C., Novotnik, B., Mandič-Mulec, I., Nicol, G.W., and Prosser, J.I. (2017) Temperature responses of soil ammonia-oxidising archaea depend on pH. Soil Biology and Biochemistry. 106: 61-68.
57. Lehtovirta-Morley, L.E., Sayavedra-Soto, L.A., Gallois, N., Schouten, S., Stein, L.Y., Prosser, J.I., and Nicol, G.W. (2016) Identifying potential mechanisms enabling acidophily in the ammonia-oxidising archaeon ‘Candidatus Nitrosotalea devanaterra’. Applied and Environmental Microbiology. 82: 2608-2619.
56. Bao, Q., Huang, Y., Wang, F., Nie, S., Nicol, G.W., Yao, H., and Ding, L. (2016) Effect of nitrogen fertilizer and/or rice straw amendment on methanogenic archaeal communities and methane production from a rice paddy soil. Applied Microbiology and Biotechnology. 100: 5989–5998.
55. Lehtovirta-Morley, L.E., Ross, J., Hink, L, Weber, E.B., Gubry-Rangin, C., Thion, C., Prosser, J.I., and Nicol, G.W. (2016) Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiology Ecology. 92: fiw057.
54. Nicol, G.W., and Prosser, J.I. (2016). Ecology of Archaea. Oxford Bibliographies. Oxford University Press. DOI: 10.1093/obo/9780199363445-0041
53. Prosser, J.I. and Nicol, G.W. (2016) Candidatus Nitrosotaleales. Bergey’s Manual of Systematics of Archaea and Bacteria. Editor Whitman, P.W.B. Wiley-Blackwell.
52. Prosser, J.I. and Nicol, G.W. (2016) Candidatus Nitrosotaleaceae. Bergey’s Manual of Systematics of Archaea and Bacteria. Editor Whitman, P.W.B. Wiley-Blackwell.
51. Prosser, J.I. and Nicol, G.W. (2016) Candidatus Nitrosotalea. Bergey’s Manual of Systematics of Archaea and Bacteria. Editor Whitman, P.W.B. Wiley-Blackwell.
50. Oton, E.V., Quince, C., Nicol, G.W., Prosser, J.I. and Gubry-Rangin, C. (2015) Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. The ISME Journal. 10: 85–96.
49. Stempfhuber, B.,  Engel, M., Fischer, D., Neskovic-Prit, G., Wubet, T., Schöning, I., Gubry-Rangin, C.,  Kublik, S., Schloter-Hai, B., Rattei, T., Welzl, G., Nicol, G.W., Schrumpf, M., Buscot, F., Prosser, J.I., and Schloter., M. (2015) pH as a driver for ammonia-oxidizing archaea in forest soils. Microbial Ecology. 69: 879-883.
48. Lehtovirta-Morley, L.E., Ge, C., Ross, J., Yao, H., Nicol, G.W., and Prosser, J.I. (2014) Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds. FEMS Microbiology Ecology. 89: 442-452.
47. Bartram, A.K., Jiang, X., Lynch, M.D.J., Masella, A.P., Nicol, G.W., Dushoff, J., and Neufeld, J.D. (2014) Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm. FEMS Microbiology Ecology. 87: 403-415.
46. Yao, H., Campbell, C.D., Chapman, S.J., Freitag, T.E., Nicol, G.W., and Singh, B.K. (2013) Multi-factorial drivers of ammonia oxidizer communities: evidence from a national soil survey. Environmental Microbiology. 15: 2545-2556.
45. Lehtovirta-Morley, L.E., Verhamme, D.T., Nicol, G.W., and Prosser, J.I. (2013) Effect of nitrification inhibitors on the growth and activity of Nitrosotalea devanaterra in culture and soil. Soil Biology and Biochemistry. 62: 129-133.
44. Ruyters, S., Nicol, G.W., Prosser, J.I., Lievens, B., and Smolders, E. (2013) Activity of the ammonia oxidising bacteria induces zinc tolerance development of the ammonia oxidising community in soil: a stable isotope probing study. Soil Biology and Biochemistry. 58: 244-247.
43. Prosser, J.I., and Nicol, G.W. (2012). Archaeal and bacterial ammonia oxidisers in soil: the quest for niche specialisation and differentation. Trends in Microbiology. 20: 523-531.
42. Mayor, D.J, Thornton, B., Hay, S., Zuur, A.F., Nicol, G.W., McWilliam, J.M., and Witte, U.F.M. (2012) Resource quality affects carbon cycling in deep-sea sediments. The ISME Journal. 6: 1740-1748.
41. Levicnik Hofferle, S., Nicol, G.W., Ausec, L., Mandic-Mulec, I., and Prosser, J.I. (2012) Stimulation of thaumarchaeal ammonia oxidation by mineralised organic nitrogen, but not inorganic nitrogen. FEMS Microbiology Ecology. 80: 114-123.
40. Gubry-Rangin, C., Hai, B., Quince, C., Engel, M., Thomson, B.C., James, P., Schloter, M., Griffiths, R.I., Prosser, J.I., and Nicol, G.W. (2011) Niche specialization of terrestrial archaeal ammonia oxidizers. Proceedings of the National Academy of Sciences USA. 108: 21206-2111.
39. Lehtovirta-Morley, L.E., Stoecker, K., Vilcinskas, A., Prosser, J.I., and Nicol, G.W. (2011) Cultivation of an obligate acidophilic ammonia oxidiser from a nitrifying acid soil. Proceedings of the National Academy of Sciences USA. 108: 15892-15897.
38. Merbt, S., Stahl, D.A., Casamayor, E.O., Eugenia, M, Nicol, G.W., and Prosser, J.I. (2011) Differential photoinhibition of bacterial and archaeal ammonia oxidation. FEMS Microbiology Letters. 327: 41-46.
37. Huaiying, Y., Gao, Y, Nicol, G.W., Campbell, C.D., Prosser, J.I., Zhang, L., Han, W., and Singh, B.K. (2011) Links between ammonia oxidizer community structure, abundance and nitrification potential in acidic soils. Applied and Environmental Microbiology. 77: 4618-4625.
36. Stein, L.Y., and Nicol, G.W. (2011) Grand challenges in terrestrial microbiology. Frontiers in Microbiology. 2: 1-2.
35. Nicol, G.W., and Prosser, J.I. (2011) Strategies to determine diversity, growth and activity of ammonia oxidising archaea in soil. Methods in Enzymology. 496: 3-34.
34. Verhamme, D.T., Prosser, J.I., and Nicol, G.W. (2011) Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms. The ISME Journal. 5: 1067-1071.
33. Offre, P. O., Nicol, G.W., and Prosser, J.I. (2010) Autotrophic community profiling and quantification of putative autotrophic thuamarchaeal communities in environmental samples. Environmental Microbiology Reports. 3: 245-253.
32. Zhang, L., Offre, P.O., He, J.-Z., Verhamme, D.T., Nicol, G.W., and Prosser, J.I. (2010) Autotrophic ammonia oxidation by soil thaumarchaea. Proceedings of the National Academy of Sciences USA. 107: 17240-17245.
31. Stopnisek, N., Gubry-Rangin, C., Hofferle, S., Nicol, G.W., Mandic-Mulec, I., and Prosser, J.I. (2010) Thaumarchaeal ammonia oxidation in an acidic forest peat soil is not influenced by ammonia amendment. Applied and Environmental Microbiology. 76: 7626-7634.
30. Gubry-Rangin, C., Nicol, G.W., and Prosser, J.I. (2010) Archaea rather than bacteria control nitrification in two agricultural acidic soils. FEMS Microbiology Ecology. 74: 566-574.
29. Hofferle, S., Nicol, G.W., Pal, G.W., Hacin, J., Prosser, J.I., and Mandic-Mulec, I. (2010) Nature of the ammonium supply is selective for ammonia-oxidising archaea and bacteria in a wetland soil vertical profile. FEMS Microbiology Ecology. 74: 302-315.
28. Peterse, F., Nicol, G.W., Schouten, S., and Sinninghe Damste, J.S. (2010) Influence of soil pH on the abundance and distribution of core and intact polar lipid-derived branched GDGTs in soil. Organic Geochemistry. 41: 1171-1175.
27. Schleper, C. and Nicol, G.W. (2010) Ammonia Oxidizing Archaea: Genomes, Physiology and Ecology. Advances in Microbial Physiology. 57: 1-41.
26. Coci, M., Nicol, G.W., Pilloni, G.N., Schmid, M., Kamst-van Agterveld, M.P., Bodelier, P.L.E., and Laanbroek, H.J. (2010) Quantitative assessment of ammonia-oxidizing bacterial communities in the epiphyton of submerged macrophytes in shallow lakes. Applied and Environmental Microbiology. 76: 1813-1821.
25. Ross, J.L., Ivanova, E.S., Spiridonov, S.E., Waeyenberge, L., Moens, M., Nicol, G.W., and Wilson, M. (2010) Molecular phylogeny of slug-parasitic nematodes inferred from 18S rRNA gene sequences. Molecular Phylogenetics and Evolution. 55: 738-743.
24. Nicol, G.W., Leininger, S., and Schleper, C. (2010) Distribution and Activity of Ammonia-Oxidising Archaea in Natural Environments. Nitrification. Editors Ward, B.B., Klotz, M.G., and Arp, D.J. ASM Press.
23. Bartossek, R., Nicol, G.W., Lanzen, A., Klenk, H.-P., and Schleper, C. (2010) Homologues of Nitrite Reductases in Ammonia-Oxidizing Archaea: Diversity and Genomic Context. Environmental Microbiology. 12: 1075-1088.
22. Baker, K.L., Marshall, S., Nicol, G.W., Campbell, C.D., Nicollier, G., Ricketts, D., Killham, K., and Prosser, J.I. (2010) Degradation of metalaxyl-M in contrasting soils is influenced more by differences in physicochemical characteristics than in microbial community composition after re-inoculation of sterilised soils. Soil Biology and Biochemistry. 42: 1123-1131.
21. Baker, K.L., Langenheder, S., Nicol, G.W., Ricketts, D., Killham, K.S., Campbell, C.D. and Prosser, J.I. (2009) Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies. Soil Biology and Biochemistry. 41: 2292-2298.
20. Lehtovirta, L.E., Prosser, J.I., and Nicol, G.W. (2009) Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota. FEMS Microbiology Ecology. 70: 367-376.
19. Offre, P., Prosser, J.I., and Nicol, G.W. (2009) Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene. FEMS Microbiology Ecology. 70: 99-108.
18. Watkins, A., Nicol, G.W., and Shaw, L.J. (2009) Use of an artificial root to examine the influence of 8-hydroxyquinoline on soil microbial activity and bacterial community structure. Soil Biology and Biochemistry. 41: 580-585.
17. Prosser, J.I. and Nicol, G.W. (2008) Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environmental Microbiology.10: 2931-2941.
16. Nicol, G.W., Leininger, S., Schleper, C., and Prosser, J.I. (2008) The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidising archaea and bacteria. Environmental Microbiology. 10: 2966-2978.
15. Tourna, M., Freitag, T.E., Nicol, G.W., and Prosser, J.I. (2008) Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environmental Microbiology. 10: 1357-1364.
14. Le Roux, X., Poly, F., Currey, P., Commeaux, C., Hai, B., Nicol, G.W., Prosser, J.I., Schloter, M., Attard, E.O., and Klumpp, K. (2008). Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure. The ISME Journal. 2: 221?232.
13. Watson-Craik, I., Nitayapat, N., and Nicol, G.W. (2008) Toxicity, fate and impacts of phenolic compounds in anaerobic municipal solid waste. Management of Pollutant Emission from Landfills and Sludge. Editors Pawlowska, M. and Pawlowski, L. Taylor and Francis. pp. 65-73.
12. Aitkenhead, M., Pickles, B., Norton, G., Macmillan, K., and Nicol G.W. (2007) Skill-based optimised aiming in darts. Mathematics Today. 2: 212-214.
11. Nicol, G.W., Campbell, C.D., Chapman S.J., and Prosser, J.I. (2007) Afforestation of moorland leads to changes in crenarchaeal community structure. FEMS Microbiology Ecology. 60: 51-59.
10. Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G.W., Prosser, J.I., Schuster, S.C., and Schleper C. (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature. 442: 806-809.
9.    Nicol, G.W., and Schleper, C. (2006) Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? Trends in Microbiology.14: 207-212.
8.    Shaw, L.J., Nicol, G.W., Smith, Z., Fear, J., Prosser, J.I., and Baggs, E.M. (2006) Nitrosospira spp. can produce nitrous oxide via a nitrifier denitrification pathway. Environmental Microbiology. 8: 214-222
7.    Nicol, G.W., Tscherko, D., Chang, L., Hammesfahr, U., and Prosser, J.I. (2006) Crenarchaeal community assembly and microdiversity in developing soils at two sites associated with deglaciation. Environmental Microbiology. 8: 1382-1393.
6.    Nicol, G.W., Tscherko, D., Embley, T.M., and Prosser, J.I. (2005) Primary succession of soil Crenarchaeota across a receding glacier foreland. Environmental Microbiology. 7: 337-347.
5.    Rangel-Castro, J.I., Killham, K., Ostle, N., Nicol, G.W., Anderson, I.C., and Scrimgeour, C.M., et al. (2005) Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. Environmental Microbiology. 7: 828-838.
4.    Nicol, G.W., Webster, G., Glover, L.A., and Prosser, J.I. (2004) Differential response of archaeal and bacterial communities to nitrogen inputs and pH changes in upland pasture rhizosphere soil. Environmental Microbiology.6: 861-867.
3.    Nicol, G.W., Glover, L.A., and Prosser, J.I. (2003) The impact of grassland management on archaeal community structure in upland pasture rhizosphere soil. Environmental Microbiology.5: 152-162.
2.    Nicol, G.W., Glover, L.A., and Prosser, J.I. (2003) Molecular analysis of methanogenic archaeal communities in managed and natural upland pasture soils. Global Change Biology. 9: 1451-1457.
1.    Nicol, G.W., Glover, L.A., and Prosser, J.I. (2003) Spatial Analysis of Archaeal Community Structure in Grassland Soil. Applied and Environmental Microbiology. 69: 7420-7429.

 

 

top CURRICULUM VITAE

Aug 2011 - 2014 Lecturer, Senior Lecturer, Reader, Professor, University of Aberdeen

Sept 2006 - Aug 2011 Natural Environment Research Council (NERC) Advanced Research Fellow, School of Biological Sciences, University of Aberdeen

July 2001 - Aug 2006 Postdoctoral research fellow, Department of Molecular and Cell Biology, University of Aberdeen

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Research Grants

  • AXA Research Fund: AXA Professor in Ecosystem Engineering and Microbial Ecology. €550 000. 2015-2020 (PI)
  • Le Programme Avenir Lyon Saint-Etienne (PALSE): Understanding microbial networks driving nitrogen cycling in soil. 2015-2017. €500,000 (PI)
  • NERC Consortium Grant (NE/K016342/1): Biodiversity, ecosystem functions and policy across a tropical forest modification gradient. 2016-2018. £261,000 (of £2.1 million total). (PI)
  • NERC Standard Grant (NE/L006286/1): Soil ammonia oxidisers: an embarrassment of richness?  2014-2017. £379,000. (Co-I)
  • NERC Capital Award: PolyExESS: PolyEXtremophile Environment Simulation System. 2014-2015. £150,000. (Co-I)
  • Marie Curie International Training Network: Nitrous oxide research alliance. 2013-2016. £120,000 (Co-I)
  • Royal Society International Exchange: Reduced fertiliser loss by inhibition of bacterial and archaeal nitrifiers. 2012-2014. £12,000 (Co-I)
  • NERC Standard Grant (NE/I027835/1): Do novel acidophilic archaeal ammonia oxidisers solve the paradox of nitrification in acid soils? 2011-2015. £440,000 (PI)
  • NERC Standard Grant (NE/F021909/1): Are archaea responsible for ammonia oxidation in acid soils? 2009-2012. £355,860 (PI)
  • NERC small grant (NE/G010404/1): Unravelling the functional diversity of fungi in ericaceous hair roots. 2009-2010. £42,000 (Co-I)
  • BBSRC Standard Grant (BB/F022646/1): Are bacteria or archaea the major players in nitrogen fertiliser loss in agricultural soils? 2008-2011. £411,483 (PI)
  • Royal Society International Joint Project: Investigating the role of soil archaea in nitrogen cycling. 2007-2010. £11,800 (PI)
  • NERC Advanced Research Fellowship (NE/D010195/1): Linking crenarchaeal activity to global nitrogen cycling in soil. 2006-2011. £446,412 (PI)
  • EMBO Short-term Fellowship (University of Bergen, Norway): Genomic analysis of soil archaea in glacier forefields. 2005. £5,000 (PI

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External Responsibilities

  • Editorial Board Member of Environmental Microbiology
  • Editorial Board Member of FEMS Microbiology Ecology
  • Editorial Board Member of The ISME Journal
  • Editorial Board Member of Frontiers in Terrestrial Microbiology
  • NERC Peer Review College (2011-)
  • Society of General Microbiology - Prokaryotic Division Member (2011-)

Invited International Conference Speaker

  • Society for Molecular Biology and Evolution, Vienna. July 2015. Plenary speaker.
  • 4th International Conference on Nitrification, Edmonton, Canada. July 2015.
  • Isaac Newton Institute, University of Cambridge. Structure, Function and Dynamics in Microbial Communities. October 2014. Plenary speaker.
  • Gordon Research Conference on Archaea: Ecology, Metabolism and Molecular Biology. Barga, Italy. July 2013.
  • 11th Dahlia Greidinger Memorial Symposium. Haifa, Israel. March 2013. Keynote speaker.
  • 'Microbial diversity in environmental signal response' symposium. Marburg, Germany. November 2012.
  • 17th Nitrogen Cycle Conference, Oslo, Norway. September 2012. Plenary speaker.
  • Society of General Microbiology General Meeting, Dublin, Ireland. March 2012.
  • 2nd International Conference on Nitrification, Nijmegen, The Netherlands. July 2011. Plenary speaker
  • FEMS Microbiology Congress, Geneva, Switzerland. June 2011.
  • Nordic Archaeal Conference, Tuusula, Finland. May 2011. Keynote speaker.
  • ESF-funded soil microbiology workshop, Breukelen, The Netherlands. December 2010.
  • 2nd Soil microbial ecology workshop, Changsha, China. October 2009.
  • 1st International Conference on Nitrification, Louisville, Kentucky. July 2009.
  • 1st Soil microbial ecology workshop, Beijing, China. October 2008.
  • GRC Archaea: Ecology, Metabolism and molecular Ecology, New Hampshire, USA. August 2007.
  • American Society of Microbiology, Toronto, Canada. May 2007.

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Invited University & Institute Seminar Speaker

  • INRA, Dijon. May 2017
  • University of California, Davis. August 2015.
  • University of California, Berkeley. August 2015.
  • University of Utrecht. September 2014.
  • NIOO, The Netherlands. September 2014.
  • University of Lyon. May 2013.
  • John Innes Centre, Norwich. April 2013.
  • Max Planck Institute, Marburg. November 2012.
  • Research Centre for Eco-Environmental Sciences, Beijing. October 2012.
  • Institute of Urban Environment, Xiamen. October 2012.
  • University of Glasgow. October 2012.
  • University of Cardiff. December 2011.
  • Max Plank Institute, Bremen. November 2011.
  • University of Warwick. October 2011.
  • Centre for Ecology & Hydrology, Wallingford. October 2011
  • School of Medical Sciences, University of Aberdeen. November 2010.
  • NIOO, The Netherlands. December 2009.
  • Chinese Academy of Sciences, Beijing. October 2009.
  • Helmholtz Institute, Munich. September 2009.
  • Department of Soil Science, University of Reading. October 2008.
  • University of Innsbruck. October 2007.
  • University of Hohenheim, October 2007.
  • SCRI, Dundee. November 2005.
  • Department of Microbiology, University of Darmstadt. July 2004.
British use the term " University of Lyons " in some of their references to our institution.
   

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