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Sara Hallin

Sara Hallin
My research focuses on the ecology of microbial communities in terrestrial environments, including wetlands. I have a special interest in microbes involved in cycling of inorganic nitrogen.


I address fundamental questions regarding their ecology, and also do applied research related to agricultural and environmental issues, such as nutrient cycling, greenhouse gas emissions, nitrogen leaching and water treatment.


Research group members

Chris Jones (researcher), Jaanis Juhanson (researcher), Lea Wittorf (postdoc), Aurélien Saghaï (postdoc), Valerie Hubalek (postdoc), Yvonne Bösch (PhD student), Arpita Maheshwari  (PhD student) and Maria Hellman (research engineer and PhD student) work in my research group. We work in the Soil Microbiology Group, wich also includes Karina Clemmensen (Associate Senior Lecturer), Carles Castaño Soler (postdoc) and Louis Mielke (PhD student).



Current teaching at the undergraduate level:

  • Soil Biology and biogeochemistry, advanced level (MSc level), SLU, 15 hp.  Covers the basis in soil biology  and the major biogeochemical cycles. Runs yearly since 1993.
  • Municipal and industrial wastewater treatment, Department of Technology, Uppsala University, 5hp. Mechanical, chemical and biological processes in wastewater treatment. New course since fall 2010.

Selected publications

Full list: Google Scholar; Research Gate

Selected publications:

Jones, C.M. and Hallin, S. 2019. Geospatial variation in co-occurrence networks of nitrifying microbial guilds. Molecular Ecology, 28:293-306

de Vries, F.T., Griffiths, R.I., Bailey, M., Craig, H., Girlanda, M., Gweon, H.S., Hallin, S., Kaisermann, A., Keith, A., Kretzschmar, M., Lemanceau, P., Lumini, E., Mason, K.E., Oliver, A., Ostle, N., Prosser, J., Thion, C., Thomson, B. and Bardgett, R.D. 2018. Soil bacterial networks are less stable under drought than fungal networks.Nature Communications,9:3033

Putz, M., Schleusner, P., Rütting, T. and Hallin, S. 2018. Relative abundance of denitrifying and DNRA bacteria and their activity determine nitrogen retention or loss in agricultural soil. Soil Biology and Biochemistry, 123:97-104

Bommarco, R. Vico, G. and Hallin, S. 2018. Exploiting ecosystem services in agriculture for increased food security.Global Food Security, 17:57-63

Conthe, M., Wittorf, L., Kuenen, G., Kleerebezem, R., van Loosdrecht, M.C.M., Hallin, S. 2018. Life on N2O: deciphering the ecophysiology of N2O respiring bacterial communities in a continuous culture. ISME Journal,12:1142–1153

Hallin, S, Philippot, L, Löffler, F., Sanford, R.A. and Jones, C.M. 2018. Genomics and ecology of novel N2O reducing microorganisms. Trends in Microbiology, 26:43-55

Juhanson, J., Hallin, S., Stenberg, M., Söderström, M. and Jones, C.M. 2017.Spatial and phyloecological analyses of nosZgenes underscore niche differentiation amongst terrestrial N2O reducing communities. Soil Biology and Biochemistry, 115:82-91

Alsterberg, C., Roger, F., Sundbäck, K., Juhanson,J., Hulth, S., Hallin, S. and Gamfeldt, L. 2017. Habitat diversity and ecosystem multifunctionality - the importance of direct and indirect effects. Science Advances,3:e1601475.

Domeignoz-Horta, L.A., Putz M., Spor A., Bru D., Breuil M.C., Hallin S., Philippot, L. 2016. Non-denitrifying nitrous oxide-reducing bacteria - an effective N2O sink in soil. Soil Biology and Biochemistry, 103:376-378.

Wittorf, L., Bonilla-Rosso, G., Jones, C.M., Bäckman, O., Hulth, S. and Hallin, S. 2016. Habitat partitioning of marine benthic denitrifier communities in response to oxygen availability.Environmental Microbiology Reports, 8:486-492.

Sterngren, A.E., Hallin, S. and Bengtson, P. 2015. Archaeal ammonia oxidizers dominate in numbers, but bacteria drive gross nitrification in N-amended grassland soil. Frontiers in microbiology, 6:1350.

Hallin, S., Hellman, M., Choudhury, M.I. and Ecke, F.2015.Relative importance of plant uptake and denitrification for nitrogen removal by macrophytes in sub-arctic wetlands treating mine drainage. Water Research, 85:377-383.

Powell, J.R., Welsh, A. and Hallin, S. 2015. Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties. Ecology, 96:1985–1993.

Graf, D.R.H, Jones, C.M. and Hallin, S. 2014. Intergenomic comparisons highlight modularity of the denitrification pathway and underpin the importance of community structure for N2O emissions. PLoS ONE, 9(12):e114118.

Jones, C. M., Spor, A., Brennan, F. P., Breuil, M.-C., Bru, D., Lemanceau, P., Griffiths, B., Hallin, S. and Philippot, L. 2014. Recently identified microbial guild mediates soil N2O sink capacity. Nature Climate Change,4:801-805.

Cederlund, H. Wessén, E., Enwall, K., Jones, C.M., Juhanson, J., Pell, M., Philippot, L. and Hallin, S. 2014. Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla. Applied Soil Ecology,84:62-88.

Jones, C.M., Graf, D.R.H, Bru, D., Philippot, L. and Hallin, S. 2013. The unaccounted yet abundant nitrous oxide reducing microbial community - a potential nitrous oxide sink. ISME J, 7:417-426.

Hallin, S., Welsh, A., Stenström, J., Hallet, S., Enwall, K., Bru, D. and Philippot, L. 2012. Soil functional operating range linked to microbial biodiversity and community composition using denitrifiers as model guild. PLoS ONE, 7:e51962.

Philippot, L., Ritz, K., Pandard, P., Hallin, S. and Martin-Laurent, F. 2012. Standardisationof methodsin soil microbiology:progressand challenges. FEMS Microbiology Ecology, 82:1-10.

Philippot, L. and Hallin, S. 2011.Towards food, feed and energy crops mitigating climate change. Trends in Plant Science, 16:476-480.

García-Lledó, A., Vilar-Sanz, A., Trias, R., Hallin, S. and Bañeras, L. 2011.Genetic potential for N2O emissions from the sediment of a free water surface constructed wetland. Water Research,45:5621-5632.

Wessén. E, Söderström, M., Stenberg, M., Bru, D., Hellman, M., Welsh, A., Thomson,F., Klemedtsson, L., Philippot, L.and Hallin, S. 2011. Spatial distribution of ammonia oxidizing bacteria and archaea across a 44-hectare farmrelated to ecosystem functioning. ISME J, 5:1213-1225.

Philippot, L., Andert, J., Jones, C.M. and Hallin, S. 2011. Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil. Global Change Biology, 17: 1497-1504.

Philippot,L., Andersson, S.G.E., Battin,T.J., Prosser, J.I., Schimel, J.P.,  Whitman, W.B. and Hallin, S. 2010. The ecological coherence of higher bacterial taxonomic ranks. Nature Reviews Microbiology8:523-529.

Jones, C. M. and Hallin, S. 2010. Ecological and evolutionary factors underlying global and local assembly of denitrifier communities. ISME Journal4: 633-641.

Enwall, K., Throbäck, I.N., Stenberg, M., Söderström, M. and Hallin, S. 2010. Soil resources influence spatial patterns of denitrifying communities at scales compatible with land management. Applied and Environmental Microbiology, 76: 2243-2250.

Philippot, L., Bru, D, Saby, N.P.M., Cuhel, J., Arrouays, D., Simek, M. and Hallin, S. 2009. Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree. Environmental Microbiology, 11: 3096–3104.

Hallin S., Jones, C.M., Schloter, M. and Philippot, L. 2009. Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment. ISME Journal, 3: 597-605.


Professor at the Department of Forest Mycology and Plant Pathology; Markmikrobiologi
Telephone: 018-673209
Postal address:
Skoglig mykologi och växtpatologi
Box 7026
750 07 Uppsala
Visiting address: Almas Allé 5, Uppsala
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