Raman microspectroscopy to characterize the physiological state of marine bacteria at the single-cell scale (M/F)

Job Description

Thesis Subject

Context
Functional characterization of marine microbial communities is a major challenge for improving our understanding of the state of ocean ecosystems. Conventional approaches based on culture, qPCR or sequencing provide information on the presence of microorganisms, but do not describe their physiological state. However, distinguishing active, stressed or dormant bacteria is essential for interpreting the dynamics of microbial communities in marine environments.

The SEACAM PhD project (Single-cell Optical Characterization of Marine Microorganisms) aims to develop an innovative approach combining Raman microspectroscopy, deuterium isotope labelling, optical trapping and data analysis to characterize the metabolic activity of marine bacteria at the single-cell scale. This non-destructive approach, which does not require fluorescent labelling, will make it possible to build a database of spectral signatures and to develop classification models capable of linking Raman spectra to the physiological state of bacteria.

Missions
You will be hosted at ANSES in Boulogne-sur-Mer, within the Food Safety Laboratory. Travel to Villeneuve-d'Ascq (UMR UMET, PIHM team) and Grenoble (CEA, DTIS and SiNaPS teams) will be required.

As part of the PhD project, you will be responsible for:
- Building a spectral reference database of marine bacteria.
You will work on bacterial strains isolated from the marine environment and preserved in the ANSES strain collection. You will culture these strains under controlled conditions and then analyze them by Raman microspectroscopy. You will preprocess and annotate the spectra obtained, then integrate them into a database for the development of machine learning models.

- Characterizing the physiological state of bacteria using Raman-DIP.
You will apply stress conditions representative of marine environments to bacteria in order to induce different physiological states. You will assess the responses using classical microbiology, qPCR and Raman analyses coupled with deuterium isotope labelling. The objective will be to identify spectral signatures associated with the physiological state of microorganisms.

- Analyzing planktonic cells and evaluating model performance.
You will first test the acquisition of Raman spectra on optically trapped planktonic cells in microcavities. You will then perform analyses in monoculture and subsequently in coculture, in order to assess the performance of the system and the robustness of the models. Finally, you will use environmental samples, including coastal waters, to test the transferability and predictive capacity of the models under near-real-world conditions.

Desired profile
Engineer, Master's degree or equivalent qualification with a background mainly in physics, instrumentation or data processing applied to biology. Skills, or a strong interest, in optical instrumentation and methodological development will be considered assets. Specific skills in microbiology may be acquired during the PhD.

Your Work Environment

The Aquatic Products Health Safety Unit (SANAQUA) is part of the Food Safety Laboratory and is located in Boulogne-sur-Mer, Pas-de-Calais. SANAQUA is a multidisciplinary unit, with activities in bacteriology, physico-chemistry, algology and parasitology. It conducts research, reference, surveillance and expert appraisal work in these four areas, mainly in the field of the health safety of aquatic products. Through its own projects and national and international collaborations, it contributes to the detection, identification and characterization of biological and chemical hazards associated with the consumption of aquatic products. More specifically, it carries out studies on bacterial hazards (Vibrio, Listeria, antimicrobial resistance), parasitic hazards (Cryptocotyle, Clinostomum complanatum) and the characterization of hazards associated with the consumption of algae.

You will work within the “Bacteriology” theme, under the hierarchical authority of the head of the SANAQUA unit. The work will be organized and carried out in consultation with the person in charge of the “Bacteriology” theme.

Constraints and risks

Travel to Villeneuve-d'Ascq (UMR UMET, PIHM team) and Grenoble (CEA, DTIS and SiNaPS teams) will be required.

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

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