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Aurélien Saghaï

Aurélien Saghai
I investigate the ecology and evolution of microbial communities involved in the nitrogen cycle. The main aim of my research is to harness soil N-cycling microorganisms to increase the nitrogen use efficiency in cropping systems and contribute to make agriculture more sustainable.


I study archaea and bacteria involved in various nitrogen transformations (i.e. nitrification, denitrification and nitrate ammonification [DNRA]) in agricultural soils and in the crop microbiome. Understanding the ecology and evolution of these microorganisms, in particular how they interact with crops, is central to the design of agricultural practices that increase nitrogen use efficiency and contribute to mitigate both climate change and environmental pollution. 

In my research I use a combination of field surveys and experimental studies, together with multivariate statistical tools, including machine learning, and phylogeny-based approaches.


I occasionaly teach at bachelor, master and PhD level. My lectures cover the ecology of archaea and bacteria in arable soils and in the rhizosphere, as well as an introduction to the protist world.

I am course leader for the bachelor course Molecular and Microbial Ecology (BI1438).


Ongoing research projects:

Harnessing plant traits to retain nitrogen in the rhizosphere. Swedish Research Council Formas. PI A. Saghaï (2022-2025).

Academia Network for RevIsing and Advancing the Assessment of the Soil Microbial TOxicity of Pesticides (ARISTO). MSCA – ITN – EID – H2020. (2020-2023).

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, SLU (2020-2023).

Past research projects:

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

Agroecosystem diversification: Digging Deeper. BiodivERsA. PIs F.T. Maestre (Universidad de Alicante, Spain), L. Philippot (INRAE, France), M. Rillig (Freie Universität Berlin, Germany), M. van der Heijden (Agroscope, Switzerland), S. Hallin (SLU)  (2017-2020).


I received a bachelor degree in Molecular Biology (2011) and a master degree in Microbiology (2013) from the University Paris-Sud (now Paris-Saclay). In December 2016 I completed my PhD on the phylogenetic and functional diversity of microbial mats in different environments under the supervision of Dr. Purificación López-García (Diversity, Ecology and Evolution of Microbes Group, Paris-Saclay University). I joined the Soil Microbiology Group led by Pr. Sara Hallin at the Dept. of Forest Mycology and Plant Pathology at SLU in 2017 as a post-doc to give a more applied perspective to my research. I have a researcher position in this group since March 2021.


PhD students

Laura J Müller (co-supervisor; 2021-): Ecotoxicity of pesticides ​on nitrifiers in soil ​under a climate change scenario​.

Master students

Elin Almén (main supervisor; 2021)

Frida Lindvall (main supervisor; 2022): Controls of the partitioning of nitrate between DNRA and denitrifiers.

Selected publications

The full list of peer-reviewed publications can be found here.

Saghaï A, Pold G, Jones CM, Hallin S (2023). Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes. Nat Commun 14, 8249 (2023).

Hallin S, Saghaï A (2023). Can nitrate-reducing ammonifiers increase nitrogen retention in soil and support ammonium-based cropping systems?  J Sustain Agric Environ. 2023; 2: 541–545.

Saghaï A, Almén E, Hallin S, Glinwood R (2023). Seed treatment with plant-defense elicitors decreases the abundance of ammonia oxidizers associated with winter wheat roots. Soil Biol Biochem 180:109016.

Saghaï A,  Banjeree S,  Degrune F,  Edlinger A,  García‐Palacios P,  Garland G, Heijden MGA,  Herzog H,  Maestre FT,  Pescador DS, Philippot L,  Rillig MC, Romdhane S,  Hallin S (2022). Diversity of archaea and niche preferences among putative ammonia‐oxidizing Nitrososphaeria dominating across European arable soils. Environ Microbiol, 24: 341-356.

Saghaï A, Wittorf L, Philippot L, Hallin S (2022). Loss in soil microbial diversity constrains microbiome selection and alters the abundance of N-cycling guilds in barley rhizosphere. Applied Soil Ecology 169: 104224.

Edlinger E, Saghaï A, Herzog C, Degrune F and Garland G (2020). Towards a multidimensional view of biodiversity and ecosystem functioning in a changing world. New Phytol 228: 820-822.

Graf DRH, Saghaï A, Zhao M, Carlsson G, Jones CM and Hallin S (2019). Lucerne (Medicago sativa) alters N2O-reducing communities associated with cocksfoot (Dactylis glomerata) roots and promotes N2O production in intercropping in a greenhouse experiment. Soil Biol and Biochem 137:107547.


Researcher at the Department of Forest Mycology and Plant Pathology; Markmikrobiologi
Telephone: +4618-671575
Postal address:
Skoglig mykologi och växtpatologi
Box 7026
750 07 Uppsala
Visiting address: Almas Allé 5, Uppsala