Profile – Sara Hallin

, ,


Sara Hallin

Job Title:



Phone Number:



Google Scholar Profile


MSc in Agronomy 1992, PhD in Microbiology 1998, Associate Professor in Microbiology 2005, Professor in Microbial Ecology 2011, Professor in Soil Microbiology 2012

My research area is ecology of functional communities in the nitrogen cycle. The work ranges from theoretical studies examining genomes, fundamental questions in community ecology based on experiments or natural gradients and applied research with relevance for agriculture, climate, and the environment. The aim is to understand relationships between the ecology of the microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions.

Research Areas:

  • Microbial ecology
  • Nitrogen cycling

Current N-related Projects:

  • Accelerated water purification during artificial recharge of aqui-fers – a tool to restore drinking water resources (ACWAPUR) Fungal denitrification


Hallin, S, Philippot, L, Löffler, F., Sanford, R.A. and Jones, C.M. Genomics and ecology of novel N2O reducing microorganisms. Trends in Microbiology, in press, doi: 10.1016/j.tim.2017.07.003

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

Zhao, M., Jones, C.M., Meijer, J., Lundquist, P.-O., Fransson, P., Carlsson, G. and Hallin, S. 2017. Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata. Applied Soil Ecology, 119:260-266.

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.

Bonilla-Rosso, G., Wittorf, L., Jones, C.M. and Hallin, S. 2016. Design and evaluation of primers targeting genes encoding NO-forming nitrate reductases: implications for ecological inference of denitrifying communities. Scientific Reports, 6:39208.

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, 8:836-836. Corrigendum.This article corrects: Habitat partitioning of marine benthic denitrifier communities in response to oxygen availability. 2016. 8:486–492.

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.

Graf, D.R.H., Zhao, M., Jones, C.M., and Hallin, S. 2016. Soil type overrides plant effect on genetic and enzymatic N2O production potential in arable soils. Soil Biology and Biochemistry, 100:125-128.

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.

Graham E.B., Knelman, J.E., Schindlbacher, A., Siciliano, S., Breulmann, M., Yannarell, A., Beman, J.M., Abell, G., Philippot, L., Prosser, J., Foulquier, A., Yuste, J.C., Glanville, H.C., Jones, D.L., Angel, R., Salminen, J., Newton, R.J., Bürgmann, H., Ingram, L.J., Hamer, U., Siljanen, H.M.P., Peltoniemi, K., Potthast, Bañeras, L., Hartmann, M., Banerjee, S., Yu, R.-Q., Nogaro, G., Richter, A., Koranda, M., Castle, S.C., Goberna, M., Song, B., Chatterjee, A., Nunes, O., Lopes, R., Cao, Y., Kaisermann, A., Hallin, S., Strickland, M., Garcia-Pausas, J., Barba, J., Kang, H., Isobe, K., Papaspyrou, S., Celussi, M., Pastorelli, R., Lagomarsino, A., Lindström, E.S., Basiliko, N. and Nemergut, D.R. 2016. Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes? Frontiers in microbiology, 7:214.

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.

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.

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.

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.

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.

Herbert Jr, R. B., Winbjörk, H., Hellman, M. and Hallin, S. 2014. Nitrogen removal and spatial distribution of denitrifier and anammox communities in a bioreactor for mine drainage treatment. Water Research, 66:350-360.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 farm related to ecosystem functioning. ISME J, 5:1213-1225.

Wessén, E. and Hallin, S. 2011. Abundance of archaeal and bacterial ammonia oxidizers – possible indicator for soil monitoring. Ecological Indicators, 11:1696-1698.

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.

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.

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.

Jones, C. M. and Hallin, S. 2010. Ecological and evolutionary factors underlying global and local assembly of denitrifier communities. ISME Journal 4: 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.

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.

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.

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.

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.

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.

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.

Jones, C.M., Stres, B., Rosenquist, M. and Hallin, S. 2008. Evolutionary history of denitrification as assessed by phylogenetic analysis of nitrite, nitric oxide and nitrous oxide respiratory enzymes. Molecular Biology and Evolution 25: 1955-1966.

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.

Philippot, L., Hallin, S. and Schloter, M. 2007. Ecology of denitrifying prokaryotes in agricultural soil. Advances in Agronomy, 96: 249-305.

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.

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.

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.

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.

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.

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. Front cover JAM 100 (1) 2006.

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.

Throbäck, I., Enwall, K., Jarvis, Å. and Hallin, S. 2004. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiology Ecology, 49:401-417. The second most cited article in FEMS Microbiol. Ecol. since 2004.

Hallin, S and Lindgren, P.-E. 1999. PCR detection of genes encoding nitrite reductase in denitrifying bacteria. Applied and Environmental Microbiology, 65:1652-1657.

Pell, M., Stenberg, B. and Hallin, S. 1998. Bacterial structure of biofilms in wastewater infiltration systems. Water Science and Technology, 37 (4-5):203-206.

Hallin, S. and Pell, M. 1998. Metabolic properties of denitrifying bacteria adapting to methanol and ethanol in activated sludge. Water Research, 32:13-18.

Hasselblad, S. and Hallin, S. 1998. Intermittent addition of external carbon to enhance denitrification in activated sludge. Water Science and Technology, 37 (9):227-233.

Hallin, S., Rothman, M. and Pell, M. 1996. Adaptation of denitrifying bacteria to acetate and methanol in activated sludge. Water Research, 30:1445-1450.

Hallin, S. Lindberg, C.-F., Carlsson, B., Plaza, E. and Pell, M. 1996. Microbial adaptation, process performance and a suggested control strategy in a pre-denitrifying system with ethanol dosage. Water Science and Technology, 34 (1-2):91-99.

Hasselblad, S. and Hallin, S. 1996. Intermittent dosage of ethanol in a pre-denitrifying activated sludge process. Water Science and Technology, 34 (1-2): 387-389.

Hallin, S. and Pell, M. 1994. Acetylene inhibition for measuring denitrification rates in activated sludge. Water Science and Technology, 30 (6):161-167.