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Last update: May 2021

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METHADIAG - Development of fast diagnosis tools to monitor anaerobic digesters operation

Coordinator: Laurent Mazéas

STABILICS - Coupling statistics and multi-omics to gain new insights in the determinants of anaerobic microbial bioprocess stability

Coordinator: Olivier Chapleur

One of the major limitations of anaerobic digestion is the important susceptibility of the microbial communities to changes in operational conditions of the digesters. It can lead to unstable methane formation. Controlling AD microbial community stability, though, is not a trivial task. Knowledge on the determinants of anaerobic microbial process stability over time is still missing. Emerging omics high-throughput approaches can now lead to unprecedented data to portray AD microbiome at different levels (genes, gene expression, and metabolites production). Novel computational and statistical methods are progressively becoming available to fully harvest and integrate these complex datasets.

In this context, the aim of STABILICS is to conduct the first sets of high-throughput multi-omics longitudinal experiments, with an unprecedented sampling depth, in lab-scale semi-continuous anaerobic digesters under constant environmental parameters or subject to different model perturbations. Two levels of analysis will be applied. 1) A high frequency monitoring of different descriptors of microbiota activity, where non-targeted metabolomics and isotopic analyses will characterise the degradation pathways and metabarcoding of RNA and DNA will target both active and present microorganisms. 2) An in-depth monitoring of microbiota functioning with both metagenomics and metatranscriptomics on selected samples and conditions. These unprecedented sets of data will be thoroughly analysed and integrated using cutting-edge statistical methods.

BIOTUBA - Microbial electrochemical snorkel for optimization of wastewater treatment bioprocesses 

Coordinator: Yannick Fayolle

In urban areas, the amount of electrical energy expenditure for water treatment and supply could reach up to 18%. Within wastewater resource recovery facilities (WRRF), oxygen supply to microorganisms for carbon and nitrogen biological removal remains the main source of energy consumption (up to 75% of the overall power expenditure of the WRRF). Also, the development of alternatives to conventional processes is essential to reduce the environmental impact of these treatment units. Bio-electrochemical systems represent a technology in the making for the treatment and valorization of waste, based on catalysis of electrochemical reactions by microbial biofilms on electrode surfaces. Among these technologies, the bioelectrochemical snorkel (BIOTUBA) is original due to its simpler operation that allows to consider short-term implementation in existing WWTP bioreactors. This technology consists of a bio-anode and a (bio-)cathode connected in short-circuit. It ensures a maximal efficiency of the oxidation of organic matter and substantial energy savings can be considered. In addition, this technology could meet other issues of the water treatment (process control, reduction of the sludge production or metallic micro-pollutant treatment).

Several scientific and technical challenges must be raised before considering the implementation of such technologies at industrial scale. The cost of electrodes, due to the expensive materials used for their design, is a constraint on scale-up. In addition, researches shall be conducted to allow fundamental understanding and to optimize the bioelectochemical snorkel specifying both microbial and electrochemical processes governing its performance.

The BIOTUBA project aims to raise scientific and technical barriers to the implantation of the bioelectrochemical snorkel at industrial scale through a transdisciplinary and multiscale approach. The scientific program of the project is divided in different tasks: (i) Studies at laboratory scale to understand and optimize the operation of BIOTUBA by focusing on the use of low-cost recycled materials and application to real matrices (WP1); (ii) Development and use of models for electrode design and implementation in industrial bioreactors (WP2); (iii) Evaluation of energetic and environmental impacts of BIOTUBA on wastewater bioprocesses using an life cycle analysis coupled to experiments at semi-industrial scale (WP3).

The development of the BIOTUBA will be based on the precise knowledge of the electrochemical and biological mechanisms to optimize its operation and to maintain its performance over time. Experiments at a semi-industrial scale will allow to characterize its behavior and induced impacts at a representative scale and to validate the technological choices. The economic development will be supported a partner of the project (6TMIC).

The project involves five partners: an Institute for applied research (Irstea-HBAN), an academic laboratory (LGC), a public industrial enterprise for urban wastewater management and treatment of the Parisian area (SIAAP) and a private company SME specialized in the development of innovative processes and technology transfer (6TMIC). Coordination will be provided by Irstea-HBAN.

VIRAME - In situ characterization of the genomic content of viruses of methanogenic archaea in organic waste fermentation bioprocesses

Coordinator: Ariane Bize

Organic solid waste is emerging as an attractive resource for the production of biofuels and synthons through anaerobic bioprocesses. However, waste matrix is complex, heterogeneous, and temporally variable and such features contribute to the complexity of their valorization: organic waste biorefinery is currently in the exploratory research phase. To orientate fermentation pathways and establish stable processes, new sensitive operational levers are required. Viruses could thus serve as basis for the development of biocontrol tools specifically targeting certain functional microbial groups. In other sectors, including the medical field, agro-food-sector and waste water treatment, viruses and their components are indeed already used or considered for biocontrol applications. Regarding waste biorefinery, methanogens are particularly detrimental to the production of molecules more valuable than methane (e.g. ethanol, butanol) but viruses of methanogenic archaea are poorly characterized so that the development of such strategies is currently not possible. Project VIRAME thus aims at characterizing in situ the genomic content of viruses infecting methanogens within anaerobic bioprocesses for organic waste valorization.

THERMOMIC - A THERMOdynamic framework for modelling MICrobial growth and community dynamics

Coordinator: Théodore Bouchez

Microbes are the most abundant living forms on earth and constitute «the microbial engines that drives earth biogeochemical cycles«. However, existing ecosystem models have today exhibit only limited abilityies in to predicting microbial dynamics and require the calibration of multiple population specific empirical equations. In contrast, we build on a new kinetic "Microbial Transition State" (MTS) theory of growth derived from first physical principles.

THERMOMIC propose to build a theoretical framework for modelling microbial growth kinetics from first physical principles and to assess its potential for environmental engineering applications.

We therefore propose to combine skills in general and microbial ecology, statistical physics, applied mathematics and environmental engineering to (i) solidify the theoretical ground of thermodynamic growth models (WP1), (ii) to mathematically explore their characteristic features compared to current phenomenological approaches (WP2) and (iii) to assess their suitability for environmental engineering applications (WP3). The general THERMOMIC objective is to give rise to a comprehensive body of knowledge, relying on solid theoretical grounds, mathematically stated, supported by simulations and experiments, in order to renew our understanding of microbial dynamics and to propose new models featuring increased predictive abilities that could foster the emergence of sound engineering applications.

DIGESTOMIC - New operational strategies to overcome technical barriers in anaerobic digestion and extend its fields of application by using meta-omic approaches

Coordinator: Laurent Mazéas

Anaerobic digestion is a process of organic matter degradation which produces renewable energy. Experience has shown that digester operation relies on the know-how of the developer. Such a situation is mainly due to the limitations of microbial-based management of anaerobic reactors as the microbiome still remains largely unknown. Using meta-omics approaches it should be possible to propose new operational strategies to overcome technical barriers in anaerobic digestion.

The main scientific blockage to the development of operational strategies is the lack of knowledge concerning the functioning of the microbial communities responsible for anaerobic digestion. In this project we want to use an approach leading to a deeper characterization of the reactions of the microbial ecosystem during anaerobic digestion in the case of perturbations. The studied perturbations will be: (i) high ammonia concentration, (ii) co-substrate composition variation and (iii) temperature modification. The innovative approach we propose is based on the one hand on the use of meta-omics methodologies, to obtain information on the microorganisms present, the functions expressed and the metabolites produced, but also the variations of these indicators as a function of the operating conditions; and on the other hand on the application of powerful statistical methods of data integration.

N2OTrack - Analysis and mitigation of N2O emissions in biological wastewater treatment

Coordinator: Mathieu Spérandio - Toulouse Biotechnology Institute (TBI) - INSA Toulouse

PROSE partner: Ahlem Filali

Nitrogen protoxide (N2O) is a powerful greenhouse gas (GHG), with an impact 300 times higher than carbon dioxide, contributing significantly to global warming. Microbial processes (nitrification or denitrification) in soils or water contribute significantly to the production of N2O. To date, the contribution of wastewater management is still controversial as N2O emissions were poorly measured in wastewater treatment plants. Recent campaigns demonstrated however that the values assumed by the IPPC are much lower than reality. Moreover intensification of nitrogen removal in wastewater treatment and innovation for minimizing energy consumption can potentially increase the N2O emissions if nitrification and denitrification are insufficiently controlled with appropriate tools.

This project aims to quantify, model and reduce N2O emissions from wastewater treatment facilities. The ambition of the project is to evaluate solutions in intensive processes receiving domestic wastewater which are used for nutrient removal.

The project is divided in different tasks: (1) monitoring of full scale systems during long term campaigns, (2) tracking the main microbial pathways by innovative techniques (isotopes signature and NO:N2O ratio), (3) validation of a multiple pathway model for simulation and evaluation of mitigation strategies, (4) demonstration of innovative sensors and control tools for energy reduction and N2O mitigation.

N2OTRACK will provide representative and objective information on direct greenhouse gas emissions from depollution systems. The contribution of these systems to the national anthropogenic N2O emissions will be estimated. Special effort will be deployed on biofilters at full scale, systems poorly characterized so far.

The aim is also to provide an N2O modelling framework validated by lab-scale data with isotopic signature measurements and calibrated by full scale campaigns. Finally innovative control tools based on well-known and new sensors will be developed for both activated sludge processes and biofilters.


DeepOmics - Digital Environmental Engineering Platform for OMICS data

Coordinator: Ariane Bize

In order to better capitalize on meta-omics data from environmental biotechnology processes, we coordinate in INRAE the development of a data warehouse, DeepOmics (Digital Environmental Engineering Platform for OMICS data). This latter will enable to store and cross query environmental biotechnology data including: design and operating parameters, physico-chemical data from the process monitoring, and finally the meta-omics data characterizing the microbial communities involved in such processes.

This data warehouse aims at favoring the production of FAIR data and the development of operational tools based on meta-omics data, such as diagnosis biomarkers for environmental biotechnologies.

Anaerobic digestion and activated sludge have been selected as first process types to establish the proof-of-concept of the data warehouse. Similarly, gene amplicon sequencing (16S rRNA gene typically) has been considered to start with. The scope of DeepOmics should subsequently be broadened to bioelectrochemical processes and to shotgun metagenomics data.

Access to this tool will be extended progressively, in particular through scientific collaborations.

Easy16S - A user-friendly web application for statistical exploration of amplicon sequencing metagenomics data

Coordinator: Cédric Midoux

Easy16S is a user-friendly web application enabling to easily explore, visualize and analyze amplicon sequencing metagenomics data. Easy16S takes as input data in BIOM, tabulated or RData format. The data must have been processed beforehand by amplicon sequencing metagenomics pipelines such as FROGS or DADA2.

Within the application, it is possible to select samples of interest, and to numerically transform data (e.g. data normalization). Among others, barplots can be generated; multivariate analysis can be performed, with a dynamical mapping of co-variates of interest. R scripts and plots can be exported for further use. The Easy16S application is developed in R Shiny and it is based mainly on the phyloseq package.
It is hosted by the INRAE MIGALE bioinformatics facility and freely accessible: