Context and objective

Anaerobic digestion is frequently considered an environmentally friendly bioprocess for generating methane as renewable energy carrier. One rarely considered drawback of anaerobic digestion are methane emissions from the treated water after leaving the digesters. The newly installed equilibrium leads to methane degassing. While this loss may be economically acceptable, from an environmental point of view, the release of the potent greenhouse gas methane limits the environmental benefit of anaerobic digestion.

Dissolved methane can be removed biologically, as we recently demonstrated by ecologically engineering a methanotrophic microbiome. The biocatalysts are bacterial aggregate with an approximate diameter of 5 mm. These so-called photogranules are composed of cyanobacteria and heterotrophic bacteria interacting syntrophically with each other: cyanobacteria produce oxygen by photosynthesis and organic matter; the heterotrophic bacteria convert organic matter (including methane) into CO2, which is again assimilated as phototrophic biomass by the cyanobacteria. The produced biomass has captured the interest in bioprocess engineering as it may be the valorization of this biomass that turns a photogranule-based process into an environmentally and economically feasible biotechnological solution for methane removal. Extracts from the produced biomass may be used as additives of construction materials, in green chemistry or as animal feed, since the carbon source is “clean”.

To push our methane-converting system further towards higher technology readiness levels (TRL), we need to demonstrate the stability of our ecologically engineered industrial microbiome and determine how it behaves under relevant industrial conditions. Exposed to real wastewater, the microbiome will be constantly challenged by an influx of allochthonous microorganisms and a diverse range of organic substrates. These conditions favor the installation of other bacteria in the photogranules that compete with methanotrophs for common resources, for example O2. If methanotrophs are less competitive, they may be gradually displaced from the photogranules and their function is lost.

Our main objective is to identify levers that enable us to maintain the putative fragile ecosystem function of methane oxidation in an open ecosystem facing selection pressure from invading microorganisms. The work in this thesis will contribute to the industrialization of this novel bioprocess as it will lead to recommendations for process operation.

Methods and program of the work

The PhD student will monitor the performance of photobioreactors containing methanotrophic photogranules. Our recently developed photoreactor can be fed with the most extreme feedstock for culturing methanotrophic photogranules, consisting of methane (as sole source of organic carbon) in equilibrium with a headspace of 100% methane. The feed solution can be complexified at will (quantity and quality of organic matter; presence/absence of allochthonous microbes). The PhD student will conduct experiments varying the properties of the feed solution and light conditions. These environmental conditions will be related to the physical properties of the resulting photogranules, because exposure to light, organic carbon and allochthonous microbes may shape its microbiome structure and the stability of the methanotroph population.

The PhD student will analyze the observed photogranule microbiomes in the light of community coalescence, photogranule phenotype and environmental conditions. For this, time-series of sequenced amplicons and quantitative PCR for cyanobacteria, methanotrophs and overall bacteria will be regularly acquired to describe community dynamics. The PhD student will describe the distribution of light within the reactor environment (intensity, spectrum) as a function of biomass density and.

In collaboration with Elie Le Quéméner in our laboratory, the PhD student will assist in coupling the experimental data to mathematical modelling. In a comprehensive analysis, we will then relate methane oxidation, granule phenotype, micro-environmental conditions to the microbiome of individual photogranules. As a consequence, the PhD student will be able to suggest operating conditions (e.g., illumination, biomass harvesting) favoring the development and maintenance of methanogenic photogranules.

The PhD student will work in a multidisciplinary project, exposed to methods in microbial ecology, process engineering and mathematical modeling. This kind of mixed profile will enable the PhD student to integrate easily into the challenging professional environment of the environmental biorefinery and the circular economy.


We are seeking for a microbial ecologist by training, with a strong interest in biotechnological processes. An affinity for practical problem solving, e.g., during reactor operation, is required for successful experimental work with lab-scale bioreactors.

English proficiency (oral and written) is required. French proficiency is an advantage but can be acquired during the stay.


The PhD student will be based at the INRAE Laboratoire de Biotechnologie de l’Environnement (LBE) in Narbonne (, a city with about 50000 inhabitants situated in the south of France on the Mediterranean cost.

The LBE is staffed with 16 tenured researchers, 20 technicians and support staff, about 8 postdocs and 20 PhD students. Activities at LBE cover a wide range of scientific disciplines: microbiology, microbial ecology, microbial engineering, process engineering, modelling, control, life cycle assessment and technology transfer. Research at LBE focuses on the development of new solutions for pollution removal and the generation of value-added products from waste in the framework of the Environmental Biorefinery concept.

The LBE maintains a strong national and international network of academic and industrial partnerships from which the future PhD student will greatly benefit.

Timeline and review of application

50% of the PhD scholarship will be provided by the INRAE division MICA. This funding is already acquired. A project financing the remaining 50% of the PhD scholarship is submitted and currently reviewed by the Région Occitanie, one of the 13 large-scale administrative units in France. We expect a positive reply in July 2021.

Since not all of the funding is yet confirmed, we cannot start the hiring process. However, we encourage interested candidates to get in touch with us so that hiring can be quickly finalized when the budget is acquired.

Please send a curriculum vitae, a meaningful letter of motivation, and marks & rank obtained during the Master program. Incomplete applications will not be considered.

The start date for the PhD project will be in September-October 2021.


Jérôme Hamelin (

Kim Milferstedt (

Application deadline:
Start date:
Location: Narbonne, France