Aurélien Saghai

My research focuses on the ecology and evolution of nitrogen-cycling archaea and bacteria—particularly those driving nitrification, denitrification, and nitrite ammonification (DNRA)—in cropping systems. These microbial processes are key regulators of nitrogen availability for plants, greenhouse gas emissions, and nutrient losses.

A central theme of my work is understanding how interactions between plants and microbial communities mediate nitrogen transformations. I explore how plant traits, root exudates, and rhizosphere dynamics shape microbial activity and nutrient cycling, and conversely, how microbial communities influence plant nutrient acquisition and productivity.

The goal is to guide the design of sustainable and resilient agroecosystems that leverage plant-microbial partnerships and microbial nitrogen processes to reduce inputs and minimize environmental losses.

Funded grant applications as PI:

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

Funded grant applications as co-PI:

• 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, Swedish University of Agricultural Sciences (2024-2027).

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

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)

Appointments
2024  Associate Prof., Dept. Forest Mycology and Plant Pathology
          Swedish University of Agricultural Sciences, Uppsala
2021  Researcher, Dept. Forest Mycology and Plant Pathology
          Swedish University of Agricultural Sciences, Uppsala
2017  Post-doc, Dept. Forest Mycology and Plant Pathology
          Swedish University of Agricultural Sciences, Uppsala

Education
2016  Ph.D. 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

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, 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.