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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 (researcher), Grace Pold (postdoc), Yvonne Bösch (PhD student), Arpita Maheshwari  (PhD student), (Laura Müller (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 Castano (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.


Ongoing research projects:


ARISTO- The European Industry - Academia Network for Revising and Advancing the Assessment of the Soil Microbial Toxicity of Pesticides. Marie Sklodowska-Curie ITN, PI D. Karpoyzas, Greece, 2021-2024

Belowground biodiversity of grasslands – conservation needs and potential to promote sustainable agriculture. Swedish Research Council Formas. PI K. Clemmensen, SLU, 2021-2024

Biochar Integration in Small-Holder Cropping Systems – Economy, Food Product Value Chains, Climate Change Resilience and Soil Fertility. Swedish Research Council Formas. PI E. Karltun, SLU, 2021-2024

Microbial controls of the fate of nitrate via DNRA or denitrification is key for managing retention of soil nitrogen. Swedish Research Council Formas. PI S. Hallin, 2020-2023.

Mechanisms underlying TRAde-offs between Carbon sequestration,
greenhouse gas Emissions and nutrient losses in Soils under conservation
agriculture in Europe (TRACE-Soils). EJP Soil (European Joint Programme Cofund on Agricultural Soil Management). PI M. Goberna, 2021-2023.

Multifunctional chemical elicitors for sustainable crop protection and improved soil fertility. Swedish Research Council Formas, PI R. Glinwood, SLU 2019-2022.

Global distributions, ecological niches and assembly processes of N2O reducing microbes – keys to identifying the terrestrial N2O sink. Swedish Research Council, PI S. Hallin, 2017-2021

The unaccounted nitrous oxide reducing microbial community: a nitrous oxide sink in agricultural soils. Swedish Research Council Formas, PI S. Hallin, 2014-2021 (prolonged)

Fungal denitrification as a source of nitrous oxide in agricultural soils. Swedish Research Council Formas, PI S. Hallin, 2017-2021 (prolonged)

Arctic and boreal ecosystems

Year-round climate feedbacks of winter phenological (mis)matches of plants and microbes across the Arctic. Knut and Alice Wallenberg Foundation. PI E. Dorrepaal, Umeå university, Sweden, 2021-2025

The moss microbiome as mediator of forest nitrogen and carbon cycling. Swedish Research Council Formas. PI Fransson, SLU, 2021-2024

Aquatic research

Managed aquifer recharge: Addressing the risks of recharging regenerated water (MARadentro). Horizon 2020 JPI Water. PI S. Diaz Cruz CSIC, Spain, 2019-2023.


Selected publications

Full list: Google Scholar; Research Gate

Selected publications:

Hellman, M., Hubalek, V., Juhanson, J., Almstrand, R. Peura, S. and Hallin, S. 2021. Substrate type determines microbial activity and community composition in bioreactors for nitrate removal by denitrification at low temperature. Science of the Total Environment, 755:143023 

Garland, G., Edlinger, A., Banerjee, S., Degrune, F., García-Palacios, P., Pescador, D.S., Herzog, C., Romdhane, S., Saghaï, A., Spor, A., Wagg, C., Hallin, S., Maestre, F.T., Philippot, L., Rillig, M.C., van der Heijden, M.G.A. 2021. Crop cover is more important than rotational diversity for soil multifunctionality and cereal yields in European cropping systems. Nature Food, 2:28-37

Giovanni Tamburini, G., Bommarco, R., Wanger, T.C., Kremen, C., van der Heijden, M.G.A., Liebman, M. and Hallin, S. 2020. Agricultural diversification supports multiple ecosystem services without compromising yields. Science Advances 6:eaba1715

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

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

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

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.

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.

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.

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

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.

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: +4618-673209
Postal address:
Skoglig mykologi och växtpatologi
Box 7026
750 07 Uppsala
Visiting address: Almas Allé 5, Uppsala