Aurélien Saghaï

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 multifaceted approach combining comparative (meta)genomics, greenhouse experiments, field surveys and phylogenetics.

I was appointed associate professor (docent) in October 2024.

I am course leader for the bachelor course Molecular and Microbial Ecology (BI1438) and occasionaly teach in different courses at bachelor, master and PhD level.

Funded grant applications:

• UnderPressure - Metal impacts on deep-sea microbial diversity and
  nitrogen cycling potential. Portuguese Research Council FCT. PI. Miguel Semedo, Interdisciplinary Centre of Marine and Environmental Research, Portugal (2025-2028).
• 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 VR. PI S. Hallin, SLU (2024-2027).
• Harnessing plant traits to retain nitrogen in the rhizosphere. Swedish Research Council Formas. PI A. Saghaï (2022-2025).

Appointments
2024     Associate Prof., Swedish University of Agricultural Sciences, Uppsala
2021     Researcher, Swedish University of Agricultural Sciences, Uppsala
2017     Post-doc, Swedish University of Agricultural Sciences, Uppsala

Education
2016  PhD in Microbiology, University of Paris-Saclay, France
2013  M.Sc. in Microbiology, University of Paris-Sud, France
2011   B.Sc. in Molecular Biology, University of Paris-Sud, France

Post-docs
Oliver Moore (main supervisor together with Sara Hallin; 2023-2025)

PhD students
Laura J Müller (co-supervisor; 2021-present)

Master students
Yuyan Teng (30 ECTS, main supervisor; 2025)
Frida Lindvall (30 ECTS; main supervisor; 2022)
Elin Almén (30 ECTS; main supervisor; 2021)

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

Müller LJ, Alicke M, Romdhane S, Pold G, Jones CM, Saghaï A, Hallin S (2025).
Resistance and resilience of co-occurring nitrifying microbial guilds to drying-rewetting stress in soil. Soil Biol Biochem, 208:109846.

Saghaï A, Hallin S (2024). Diversity and ecology of NrfA-dependent ammonifying microorganisms. Trends Microbiol, 32: 602-613.

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.

Google Scholar

ORCID