Offre de stage de M2 en écologie microbienne

Post-doctoral position in Environmental Microbiology

EFFECT OF URBANIZATION ON THE DIVERSITY, VIRULENCE AND RESISTANCE OF ENVIRONMENTAL AMOEBAE AND THEIR ENDOSYMBIONTS

Keywords

• Free-living amoebae
• associated bacteria
• diversity
• virulence
• resistance

Qualifications

PhD with a strong background in environmental microbiology and molecular biology. Skills of cellular biology would be appreciated.

Project description

Free-living amoebae (FLA) are eukaryotic microorganisms found in a wide range of environments such as lakes, rivers, soil, and occasionally in swimming pools or drinking water. During their life cycle they can switch between a vegetative, mobile stage called the trophozoite and a non-mobile, resistant stage called the cyst. Due to their phagotrophic mode of nutrition, FLA can act as a reservoir for diverse potentially pathogenic intracellular organisms, particularly bacteria that can resist phagocytosis. Several studies have shown that FLA can serve as a “training field” for these bacteria, called amoeba‑resistant bacteria (ARB), increasing their virulence for mammalian hosts. Furthermore, antibacterial resistant bacteria have been identified within the microbiome of some FLA. In addition to this Trojan horse role, some FLA can develop a direct pathogenicity to mammals, leading to severe ocular (keratitis) or cerebral (encephalitis or meningoencephalitis) infections, as seen with the genera Acanthamoeba, Balamuthia mandrillaris, or Naegleria fowleri. Treatments for these infections are often empiric and non‑specific, so FLA and their endosymbionts represent a potential public‑health risk that must be anticipated and controlled, especially in natural environments that interface with urban settings.

Objectives

The present project aims to determine how urbanization impacts the diversity of FLA and their endosymbionts, as well as their virulence and resistance to antimicrobials.

Methods

• Surface water sampling (river, ponds, etc.) at various distances from urban areas.
• Determination of total diversity of FLA and their endosymbionts at the molecular level by PCR and sequencing.
• Culture of FLA and their endosymbionts from water samples.
• Determination of cultivable diversity of FLA and their endosymbionts by PCR and sequencing.
• Development/optimization of a protocol for endosymbiont isolation.
• Analysis of amoebae–endosymbiont relationships with co‑cultures of FLA and their endosymbionts.
• Analysis of virulence of isolated FLA and endosymbionts on mammalian cells in vitro.
• Analysis of antimicrobial resistance of isolated FLA and endosymbionts.

Funding

Région Île de France (DIM1HEALTH 2.0) for 2 years from November 2026 to November 2028.

Salary

Details to be discussed.

How to apply

Send a CV, a motivation letter, and the name and contact information of three references to Sébastien POMEL ( ). For additional information, contact Ludwig (email omitted for brevity).