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Sara Hallin

Sara Hallin
My research focuses on the ecology of microbial communities in terrestrial environments, with 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.
Hiring PhD student in compuational microbial ecology. More info and how to apply.


Research group members

I lead the Soil Microbiology Group, wich currently includes Karina Clemmensen (Associate Senior Lecturer), Chris Jones (researcher), Jaanis Juhanson (researcher), Aurélien Saghaï (researcher), Carles Castano (researcher), Stephanie Turner (postdoc),  Oliver Moore (postdoc), Juan José Rodriguez Serrano (postdoc), (Laura Müller (PhD student), and Maria Hellman (research engineer).



Current teaching at the undergraduate level:

  • Soil Biology and biogeochemistry, (MSc level, SLU, 15 hp).  Covers the basis in soil biology and the major biogeochemical cycles.
  • Mikrobiom - en introduktion till mikroorganismernas fascinerande värld (BSc level, SLU, 7.5 hp). Introductory course in microbiology.
  • Molecular and microbial ecology, (BSc level, SLU, 15 hp).
  • Sustainable Plant Production - from Molecular to Field Scale (MSc level, SLU, 15 hp). On the basic principles of sustainable production in agriculture.


Ongoing research projects:

Basic research on nitrogen cycling

  1. The many faces of nitrate ammonifying bacteria – Unraveling their role in nitrogen retention and loss, and nitrous oxide emissions in terrestrial ecosystems. Swedish Research Council. PI S. Hallin, 2024-2027
  2. Ecological processes underpinning N-transformations in soil SLU. (career grant). PI S. Hallin, 2019-2024


  1. The capacity of crops for enhanced carbon allocation to soil in a changing climate - synergies and trade-offs. Swedish Research Council Formas. PI T. Keller, SLU, 2022-2026
  2. Harnessing plant traits to retain nitrogen in the rhizosphere. Swedish Research Council Formas. PI A. Saghaï, SLU, 2022-2025
  3. 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
  4. Belowground biodiversity of grasslands – conservation needs and potential to promote sustainable agriculture. Swedish Research Council Formas. PI K. Clemmensen, SLU, 2021-2024
  5. 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
  6. 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 (extended to 2024).
  7. 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, 2021-2024.

Arctic and boreal ecosystems

  1. 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
  2. The moss microbiome as mediator of forest nitrogen and carbon cycling. Swedish Research Council Formas. PI Fransson, SLU, 2021-2024

Environmental engineering

  1. Sulfate removal from mine leachate (SULFREM). Vinnova. PI R. Herbert, Uppsala univerity, 2022-2025
  2. Treatment of low-contaminated soil with biochar produced from organic waste for sustainable resource use and circular economy (BALANCE). PI A. Enell, Swedish Geotechnical Institute SGI, 2022-2025

Selected publications

Full list: Google Scholar; Research Gate

Selected publications:

Saghaï, A, Pold, G, Jones, CM, Hallin, S. 2023. Phyloecology of nitrate ammonifiers and their importance relative todenitrifiers in global terrestrial biomes. Nature Communications, 14:8249

Hallin, S., Saghaï, A. 2023. Can nitrate reducing ammonifiers increase nitrogen retention in soil and support ammonium-based cropping systems? Journal of Sustainable Agriculture and Environment, 2:541-545

Bösch, Y., Pold, G., Saghaï, A., Karlsson, M., Jones, C.M., Hallin, S. 2023. Distribution and environmental drivers of fungal denitrifiers in global soils. Microbiolgy Spectrum, 11: e00061-23

Jones, C.M., Putz, M., Emmerich, M., Hallin, S. 2022. Reactive nitrogen restructures and weakens microbial controls of soil N2O emissions. Communications Biology, 5:273

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. The 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.

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. The ISME J, 7:417-426.

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

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.



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