Taking viral ecology of anaerobic digestion to the next level – VIRALSONG

In a context of energy transition, the European Union has set the target of producing 35 billion m3 of biomethane per year by 2030. Achieving this ambitious target will require not only the installation of new anaerobic digestion plants, but also a major optimization of the performance and stability of existing ones. Anaerobic digestion is catalyzed by complex microbial consortia. One of the most promising ways of improving process performance is therefore to develop a process operation based on microbial communities. However, this remains a major scientific challenge. Thanks to the development of technologies for characterizing microbial consortia, such as high-throughput sequencing, a great deal of research is currently led to make progress on this front. However, the viral ecology of anaerobic digestion has long been overlooked, and has only recently emerged as an important topic for improving anaerobic digestion performance: host-virus dynamics could influence process performance through various mechanisms, and in particular through their effect on elemental fluxes. It is therefore important to identify the operational parameters that could influence host-virus dynamics, offering the possibility of acting directly on this component. Another important question is to determine the possible role of viruses in yet-unexplained process dysfunctions.
For the interdisciplinary VIRALSONG project, we hypothesize that various abiotic factors directly influence host-virus dynamics in anaerobic digesters, affecting the process, and we will specifically focus on the effect of water content and ionic strength. These two parameters are expected to affect virion diffusion and adsorption, respectively. They are moreover relevant from an industrial standpoint. We will work at different complementary scales: microcosm, pilot and semi-industrial. In the laboratory, in microcosms or pilots, the effect of water content and ionic strength on host-virus dynamics will be finely assessed through the application of well-controlled and replicated conditions. On a semi-industrial scale, we will conduct a longitudinal monitoring of a micro anaerobic digester processing biowaste, located on the site of one of the project partners. At this scale, conditions will be less adjustable than in the laboratory, but will offer a more realistic setting. They will also feature a certain variability, linked to the ongoing optimization of the digester's operation: this will enable us to identify more widely the operating parameters influencing host-virus dynamics within anaerobic digesters. In the meantime, we will isolate and characterize viruses infecting methanogenic archaea. Those are key components of microbial communities in anaerobic digestion and they have been little studied. During the project, the biological knowledge generated on these methanogenic archaeal viruses will directly feed the interpretations made in the more complex context of the process. For VIRALSONG, we will be applying state-of-the-art techniques in molecular microbial ecology, including high-throughput sequencing.
VIRALSONG will be organized into 5 interconnected work packages. It will be led by a consortium of 3 funded French partners (INRAE PROSE, INRAE LBE, Institut Pasteur ARVIR) and one unfunded Italian partner (University of Padova). This consortium brings together acknowledged specialists in virology, microbial ecology, metagenomics and anaerobic digestion process engineering. Scientific integration will be a high priority throughout the project. The results of VIRALSONG will provide important scientific bases for the future integration of viral ecology into operating strategies, to support further optimization of anaerobic digestion processes.