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Sara Hallin

Sara Hallin
My research focuses on the ecology of nitrogen cycling communities with emphasis on denitrifying organisms.


Most of the work concerns nitrogen cycling communities in terrestrial environments, but aquatic ecosystems and engineered systems are also investigated. 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.

In the group, we charcterize size, composition and activity of functional microbial communities to understand  relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. We also want to understand how diversity and distribution of functional or taxonomic genes at different levels of resolution relates to ecological processes. For this purpose, we use phylogeny-based measures of community diversity to infer potentially important ecological factors involved in structuring microbial biodiversity in terrestrial and aquatic ecosystems.

Research group members

Chris Jones (researcher), Jaanis Juhanson (postdoc), Germán Bonilla Rosso (postdoc), Robert Almstrand (postdoc), Daniel Graf (postdoc), Lea Wittorf (PhD student), Martina Putz (PhD student), Ming Zhao (PhD student) and Maria Hellman (research engineer and PhD student) work in my research group and we are the Soil Microbiology Group.

Currently funded projects

  1. Promoting ecosystem services by diversification to enhance biomass production on agricultural land in a bio-basd economy. The Swedish Research Council Formas. 2016.
  2. APPLICERA: Applicable site-specific environmental risk assessment of contaminted soils.(Coordinator: K. Wiberg) The Swedish Research Council Formas. 2015-2017.
  3. Linking directional changes in vegetation induced by climate warming to microbial communities across the arctic tundra – implications for nitrogen cycling and carbon balance. The Swedish Research Council Formas. 2014-2016.
  4. The unaccounted nitrous oxide-reducing microbial community: a nitrous oxide sink in agricultural soils.The Swedish Research Council Formas. 2014-2016.
  5. Reduction of nitrogen discharges in mining processes and mitigating its environmental impact – miNing.  (Coordinator: F. Ecke) VINNOVA. 2013-2017.
  6. Marie Curie ITN "NORA"-Nitrous Oxide Research Alliance. 2013-2016.
  7. Ecotypes in a trait based microbial community. The Swedish Research Council. 2012-2016.

Supervision of PhD students and postdocs

  1. Dr. Robert Almstrand, PhD Univ. Gothenburg, Postdoc at SLU Jan 2016-Dec 2016, main advisor.
  2. Martina Putz, SLU, admitted Nov 2013 – presently, main advisor.
  3. Lea Wittorf, SLU, admitted Jan 2013  – presently, main advisor.
  4. Dr. Germán Bonilla Rosso, PhD Univ. Nacional Autónoma de México, Mexico. Postdoc at SLU Jan 2013–Jan 2017, main advisor.
  5. Dr. Maren Emmerich, PhD Univ. Tübingen, Germany. Postdoc at SLU Jan 2013–June 2014, main advisor.
  6. Dr. Jaanis Juhanson, PhD Univ. Tartu, Estonia. Postdoc at SLU Sept 2012–Dec 2016, main advisor.
  7. Daniel Graf, SLU, PhD degree Oct 2015, main advisor. 
  8. Dr. Christopher Jones, Postdoc period April 2011–March 2013, main advisor.
  9. Ming Zhao, Plant biology, SLU, admitted June 2010 – presently, main advisor.
  10. Dr. Allana Welsh, PhD from Texas State University-San Marcos, USA. Postdoc period at SLU Aug 2009–Aug 2011, main advisor.
  11. Ella Wessén, PhD degree April 2011, main advisor.
  12. Christopher Jones, PhD degree Dec 3, 2010, main advisor.
  13. Dr. Karin Enwall. Postdoc period Nov 2008–Oct 2010, main advisor.
  14. Dr. Janet Andert, PhD MPI, Marburg, Germany. Postdoc period at SLU March 2008– March 2010, main advisor.
  15. Karin Enwall, PhD degree October 2008, main advisor.
  16. Johan Kjellin, KTH Royal Institute of Technology, licenciate thesis May 2007, assistant advisor.
  17. Karin Nyberg, PhD degree March 2006, assistant advisor.
  18. Ingela N. Throbäck, PhD degree May 2006, main advisor.




Current teaching at the undergraduate level:

  • Soil Biology, advanced level (MSc level), SLU. Currently 5 hp.  Covers the basis in soil biology and introduces the biotic components (bacteria, archaea, fungi, soil fauna) in terrestrial ecosystems 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

Publications in refereed journals since 2005

  1. Levén, L., Wijnbladh, E., Tuvesson, M., Kragelund, C. and Hallin, S. Control of Microthrix parvicella and sludge bulking by ozone in a full-scale WWTP. Water Science and Technology, in press.
  2. 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.
  3. 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.
  4. Kolseth, A.-K., D’Hertefeldt, T., Emmerich, M., Forabosco, F., Marklund, S., Cheeke, T.E., Hallin, S., Weih, M. 2015. Influence of genetically modified organisms on agro-ecosystem processes. Agriculture, Ecosystems & Environment, 2014:96-106.
  5. Powell, J.R., Welsh, A. and Hallin, S. Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties. Ecology, 96:1985-1993.
  6. Hossain, S., Bergkvist, G., Glinwood, R., Berglund, K., Mårtensson, A., Hallin, S. and Persson, P. 2015. Brassicaceae cover crops reduce Aphanomyces pea root rot without suppressing genetic potential of microbial nitrogen cycling. Plant and Soil, 392:227-238.
  7. Iribar, A., Hallin, S., Sánchez Pérez, J.M., Enwall, K., Poulet, N. and Garabétian, F. 2015. Potential denitrification rates correlation with nosZ genotypes colonization patterns in an alluvial wetland. Ecological Engineering, 80:101-197.
  8. 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.
  9. Andersson, B., Sundbäck, K., Hellman, M., Hallin, S. and Alsterberg, C. 2014. Nitrogen fixation in shallow-water sediment systems – spatial variation and controlling factors. Limnology and Oceanography, 59:1932-1944.
  10. Herbert Jr, R. B., Winbjörk, H., Hellman, M. and Hallin, S. 2014. Nitrogen removal and spatial distribution of denitrifier and anammox community abundances in pilot-scale bioreactor for mine drainage treatment. Water Research, 66:350-360.
  11. 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.
  12. Cederlund, H. Wessén, E., Enwall, K., Jones, C., 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
  13. Jones, C.M., Jones, C.M., Graf, D., Bru, D., Philippot, L. and Hallin, S. The unaccounted yet abundant nitrous oxide reducing microbial community - a potential nitrous oxide sink. TheISME J, 7:417-426
  14. Leutey, E., Hallin, S., Teissier, S., Iribar, A., Compin, A. Philippot, L. and Garabetian, F.  2013. Abundance, activity and structure of denitrifier communities in phototrophic river biofilms (River Garonne, France). Hydrobiologia, 716:177-187.
  15. 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.
  16. Andert, J., Börjesson, G. and Hallin S. 2012. Temporal changes in methane oxidizing and denitrifying communities and their activities in a drained and forested peat soil. Wetlands, 32:1047-1055.
  17. Philippot, L., Ritz, K., Pandard, P., Hallin, S. and Martin-Laurent, F. 2012. Standardisation of methods in soil microbiology: progress and challenges. FEMS Microbiology Ecology, 82:1-10.
  18. Trias, R., Ruiz-Rueda, O., García-Lledó, A., Vilar-Sanz, A., Hallin, S. and Bañeras, L. 2012. Emergent macrophytes act selectively on ammonia oxidizing bacteria and archaea. Applied and Environmental Microbiology, 78:6352-6356.
  19. Bañeras, L., Ruiz-Rueda, O., López-Flores, R., Quintan, X. D. and Hallin, S. 2012. Plant type and salinity selects for the denitrifying community structure in the rhizosphere of wetland vegetation. International Microbiology, 15:89-99.
  20. Nyberg, K. A., Enwall, K., Schnürer, A., Sundh, I. and Hallin, S. 2012. Response of induced perturbation on replicating β-proteobacterial ammonia oxidizing populations in soil. Microbial Ecology, 63:701-709
  21. Trias, R., García-Lledó, A., Sánchez, N., López-Jurado, J.-L., Hallin, S. and Bañeras, L. 2012. Abundance and composition of epiphytic bacterial and archaeal ammonia oxidizers of marine red and brown macroalgae. Applied and Environmental Microbiology,78:318-325.
  22. Rodriguez Caballero, A., Hallin, S. Påhlson, C., Odlare, M. and Dahlquist, E. 2012. Ammonia oxidizing bacterial community composition relates to process performance in wastewater treatment plants under low temperature conditions. Water Science and Technology, 65:197-204.
  23. Andert, J., Wessén, E., Börjesson, G. and Hallin S. 2011. Temporal changes in abundance and composition of ammonia oxidizing bacterial and archaeal communities in a drained peat soil in relation to N2O emissions. Journal of Soils and Sediments, 11:1399-1407.
  24. Philippot, L. and Hallin, S. 2011. Towards food, feed and energy crops mitigating climate change. Trends in Plant Science, 16:476-480.
  25. 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.
  26. Hellman, M., Berg, K., Brandt, K. K. and Hallin, S. 2011. Survey of bromodeoxyuridine uptake among environmental bacteria and variation in uptake rates in a taxonomically diverse set of bacterial isolates. Journal of Microbiological Methods, 86:376–378.
  27. Wessén, E. and Hallin, S. 2011. Abundance of archaeal and bacterial ammonia oxidizers – possible indicator for soil monitoring. Ecological Indicators 11:1696-1698.
  28. 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 farm related to ecosystem functioning. The ISME Journal 5:1213-1225.
  29. Jones, C.M., Welsh, A., Throbäck, I.N., Dörsch, P., Bakken, L.R. and Hallin, S. 2011. Phenotypic and genotypic heterogeneity among closely related soil-borne N2- and N2O-producing Bacillus isolates harboring the nosZ gene. FEMS Microbiology Ecology 76: 541-552.
  30. Petric, I., Philippot, L., Abbate, C., Bispo, A., Chesnot, T., Hallin, S., Jourdain, M.J., Laval, K., Lebeau, T., Lemanceau, P., Leyval, C., Lindström, K., Pandard, P., Romero, E., Sarr, A., Schloter, M., Simonet, P., Smalla, K., Wilke, B-M., Martin-Laurent, F. 2011. Inter-laboratory evaluation of the ISO standard 11063 “Soil quality - method to directly extract DNA from soil samples”. Journal of Microbiological Methods 84:454-460.
  31. Gärdenäs, A.I., Ågren, G.I., Bird, J.A., Clarholm, M., Hallin, S., Ineson, P., Kätterer, T., Knicker, H., Nilsson, S.I., Näsholm, T., Ogle, S., Paustian, K., Persson, T., Stendahl, J. 2011. Knowledge gaps in soil carbon and nitrogen interactions - From molecular to global scale. Soil Biology and Biochemistry 43:702-717.
  32. 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.
  33. Beier, S., Jones, C. M., Mohit, V., Hallin, S. and Bertilsson, S. 2011. Global phylogeography of chitinase genes in aquatic metagenomes. Applied and Environmental Microbiology, 77: 1101-1106.
  34. 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 Microbiology 8:523-529.
  35. Wessén, E., Nyberg., K., Jansson, J.K. and Hallin, S. 2010. Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management. Applied Soil Ecology 45:193-200.
  36. Jones, C. M. and Hallin, S. 2010. Ecological and evolutionary factors underlying global and local assembly of denitrifier communities. The ISME Journal 4:633-641.
  37. 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.
  38. Wessén, E., Hallin, S. and Philippot, L. 2010. Differential responses of bacterial and archaeal groups at high taxonomical ranks to fertilization. Soil Biology and Biochemistry 42:1759-1765.
  39. Philippot, L., Abbate, C., Bispo, A., Chesnot, T., Hallin, S., Lemanceau, P., Lindstöm, K., Pandard, P., Romero, E., Schloter, M., Simonet, P., Smalla, K., Wilke, B-M. and Martin-Laurent F. 2010. Soil microbial diversity: An ISO standard for soil DNA extraction. Journal of Soils and Sediments 10:1344-1345.
  40. Granhall, U., Welsh, A., Throbäck, I.N., Hjort, K., Hansson, M. and Hallin, S. 2010. Bacterial community diversity in a paper mill processing recycled paper pulp. The Journal of Industrial Microbiology and Biotechnology 37:1061-1069.
  41. 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.
  42. Philippot, L., Hallin, S., Börjesson, G. and Baggs, E. M. 2009. Biochemical cycling in the rhizosphere having an impact on global change. Plant and Soil 321:61-81.
  43. Hallin S., Jones, C., Schloter, M. and Philippot, L. 2009. Relationship between N-cycling communities and ecosystem functioning in a 50 years old fertilization experiment. The ISME Journal, 3:597-605.
  44. Jarvis, Å., Sundberg, C., Milenkovski, S., Pell, M., Smårs, S., Lindgren, P.-E., Hallin, S. 2009. Activity and composition of ammonia oxidizing bacterial communities and emissions dynamics of NH3 and N2O in a compost reactor treating organic household waste. Journal of Applied Microbiology 106:1502-1511.
  45. Enwall, K. and Hallin, S. 2009. Comparison of T-RFLP and DGGE techniques to assess denitrifier community composition. Letters of Applied Microbiology 48:145-148.
  46. Ruiz-Rueda, O., Hallin, S. and Bañeras, L. 2009. Structure and function of denitrifying and nitrifying bacterial communities in relation to plant species in a constructed wetland. FEMS Microbiology and Ecology 2:308-319.
  47. Jones, C., Stres, B., Rosenquist, M. and Hallin, S. 2008. Evolutionary history of denitrification as assessed by phylogenetic analyis of nitrite, nitric oxide and nitrous oxide respiratory enzymes. Molecular Biology and Evolution 25:1955-1966.
  48. Kjellin, J., Hallin, S. and Wörman, A. 2007. Spatial variations in denitrification activity in wetland sediments explained by hydrology and denitrifying community structure. Water Research 41: 4710-4720.
  49. Philippot, L., Hallin, S. and Schloter, M. 2007. Ecology of denitrifying prokaryotes in agricultural soil. Advances in Agronomy 96:249-305.
  50. Throbäck, I. N., Johansson, M., Rosenquist, M., Hansson, M. Pell, M. and Hallin, S. 2007. Silver (Ag+) reduces denitrification and induces enrichment of novel nirK genotypes in soil. FEMS Microbiology Letters 270:189-194.
  51. Enwall, K., Nyberg, K. Bertilsson, S., Cederlund, H., Stenström, J. and Hallin, S. 2007. Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil. Soil Biology and Biochemistry 39: 106-115.
  52. Hallin, S., Throbäck, I. N., Dicksved, J., and Pell, M. 2006. Metabolic profiles and genetic diversity of denitrifying communities in activated sludge processes after addition of methanol or ethanol. Applied and Environmental Microbiology, 72:5445-5452.
  53. Nyberg, K., Schnürer, A., Sundh, I., Jarvis, Å. and Hallin, S. 2006. Ammonia oxidising communities in agricultural soil incubated with organic waste residues. Biology and Fertility of Soils, 42:315-323.
  54. Enwall, K., Philippot, L. and Hallin, S. 2005. Activity and composition of the denitrifying community respond differently to long-term fertilization. Applied and Environmental Microbiology, 71:8335-8343.
  55. Hallin, S., Lydmark, P., Kokalj, S., Hermansson, M., Sörensson, F., Jarvis, Å. and Lindgren, P.-E. 2005. Community survey of ammonia oxidizing bacteria in full-scale activated sludge processes with different solids retention time. Journal of Applied Microbiology, 99:629-640.
  56. Philippot, L. and Hallin, S. 2005. Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community. Current Opinion in Microbiology, 8:234-239.

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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