Education and Appointments

MSc in Agricultural Sciences, SLU 1992; PhD in microbiology, SLU 1998; Assistant Professor in Microbiology, SLU 2002-2007; Associate Professor (Docent) in Microbiology 2005; Professor in Microbial Ecology 2011; Professor in Soil Microbiology 2012 (current position)

Research profile

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.

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, such as niche competition or differential distribution along environmental gradients. 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

Chris Jones (postdoc), Jaanis Juhanson (postdoc), Maren Emmerich (postdoc), Germán Bonilla Rosso (postdoc), Daniel Graf (PhD student) Lea Wittorf (PhD student) and Maria Hellman (research engineer) work in my research group and we are part of the Soil Microbiology Group.

Currently funded projects

1. Marie Curie ITN "NORA"-Nitrous Oxide Research Alliance. 2013-2016.
2. Ecotypes in a trait based microbial community. The Swedish Research Council. 2012-2015.
3. Minimizing nitrogen at LKAB mining site. LKAB. 2012.
4. COST Action ES1103: Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools. Coordinator: T.Curtis, UK. 2011-2015. 
5. Bio-indicators for increased risk of N2O production by denitrifying bacteria in the rhizosphere 2011-2014, Stiftelsen Oscar och Lili Lamms minne.
6. EcoFINDERS - Ecological Function and Biodiversity Indicators in European Soils. Coordinator: P. Lemanceau, INRA, France. 2011-2014, EU 7th Framework Program.
7. Predicting spatial patterns of nitrifying microorganisms for improved mitigation strategies for nitrate leaching from arable land. 2010-2012, The Swedish Research Council Formas.

Publications in refereed journals since 2005

1. 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. ISMEJ, in press.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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
8. 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.
9. 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.
10. 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.
11. Philippot, L. and Hallin, S. 2011. Towards food, feed and energy crops mitigating climate change. Trends in Plant Science, 16:476-480.
12. 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.
13. 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.
14. Wessén, E. and Hallin, S. 2011. Abundance of archaeal and bacterial ammonia oxidizers – possible indicator for soil monitoring. Ecological Indicators 11:1696-1698.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. 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.
33. 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.
34. 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.
35. 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.
36. Philippot, L., Hallin, S. and Schloter, M. 2007. Ecology of denitrifying prokaryotes in agricultural soil. Advances in Agronomy 96:249-305.
37. 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.
38. 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.
39. 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.
40. 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.
41. 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.
42. 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.
43. 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.

Supervision of PhD students and postdocs

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

Current teaching at the undergraduate level

Microbial Ecology, advanced level (MSc level), SLU, 5hp. On ecological theory and microbial ecology in terrestrial and aquatic ecosystems. Runs yearly since 2008.

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.

Microbial diversity, advanced level (MSc level), Uppsala University, 10 hp. Covers diversity and ecology of microorganisms in nature. Runs as an evening course, yearly since 2008.

Municipal and industrial wastewater treatment, Department of Technology, Uppsala University, 5hp. Mechanical, chemical and biological processes in wastewater treatment. New course since fall 2010.