C3AnaeroBi - Carbon Capture and Conversion via Anaerobic Biosystems for a sustainable biorefinery

Abstract

Biological carbon capture and utilization technologies hold transformative potential for achieving sustainable decarbonization while advancing the development of a sustainable biorefinery. Anaerobic microbiota capable of converting gaseous carbon emissions into biofuels and platform chemicals remain underexplored, representing an immense latent resource. C3AnaeroBio proposes a multimodal approach that integrates systems biology with model-driven culturomics to: 1) deepen our understanding of the interplay between environmental factors and microbial dynamics, 2) uncover molecular drivers of anaerobic pathways, and 3) unlock efficient carbon bioconversion systems. High-throughput single-cell technologies will enable the isolation and characterization of yet-uncultivated anaerobes, providing critical insights into microbe-prophage interactions and metabolic niche overlaps. By combining metabolic flux balance modeling with biochemical validation, exchanged metabolites, microbial interactions, and metabolic networks will be systematically mapped. Custom inocula will be developed to optimize gaseous carbon bioconversion into biomethane and platform chemicals such as acetate and butyrate through targeted biosynthesis pathways. C3AnaeroBio will create predictive tools for designing specialized anaerobic consortia at the strain level. To further enhance precision, phages capable of selectively eliminating undesirable community members will be identified and tested. These data-driven strategies will enable the ad hoc assembly of consortia to streamline carbon capture processes, accelerating the transition to a sustainable biorefinery. Preliminary data suggest that C3AnaeroBio can achieve at least a 10% improvement in gaseous carbon fixation compared to current technologies. The insights gained are poised to propel innovations in the capture and bioconversion of industrial waste streams, serving as a pivotal milestone towards a circular bioeconomy.

Project Details

Principal Investigator Laura Treu

Type of Grant FIS3

Current position at UNIPD Associate Professor

Project acronym C3AnaeroBi

Project title Carbon Capture and Conversion via Anaerobic Biosystems for a sustainable biorefinery

Host Department Department of Biology

Research budget € 1.598.000

Start date of the project 15/03/2026

Duration of the project 60 months

People

Eric Olo Ndela

Postdoc

Nicola De Bernardini

Postdoc

Filippo Savio

PhD student

Flavio Agostini

PhD student

Research plan

WP1. Establishment of single-cell resolution data acquisition systems
DNA/RNA-seq probes and SC-culturomics will enable metabolic profiling at single-cell resolution. Inocula will be adapted to gaseous feedstocks to direct bioconversion toward CH4, acetate, and butyrate (T1.1). Single cells will be encapsulated in gel droplets for sc-DNAseq (SAGs) and sc-RNAseq (expression heterogeneity) (T1.2). A Microbe-seq-based bioinformatic toolbox will build a species-level reference collection and virome analysis pipeline, validated against MAGs (T1.3). A fluorescence-based single-cell dispenser (B.SIGHT, Cytena) will isolate single species and syntrophic co-cultures (T1.4).
WP2. Investigation of host-phage associations, microbial interactions and exchanged compounds
Single-cell-resolution screening will target individuals, pairs, and host-phage couples. Nutrient preferences and C source utilization will be profiled via mass spectrometry metabolomics (T2.1). Microbe-microbe pairings will assess trophic niches, resource allocation, syntrophy, and competitive exclusion (T2.2). Prophage identification and viral susceptibility assays will inform phage-therapy-like microbiome manipulation (T2.3). Gas conditions will be tuned to adapt consortia to C1 substrates, with growth and metabolite exchange (amino acids, peptides) tracked by GC/LC-MS (T2.4).
WP3. Reconstruction of community exchange networks to identify molecular drivers
GEMs will be built for isolates, co-cultures, and consortia, with SAG models via pan-Draft, and CoCo-GEMs refined using transcriptomics and carbon niche overlap data from WP2 (T3.1). Dynamic FBA and FBA will integrate single-cell multi-omic data, iteratively refined through in vivo testing of model predictions (T3.2). Machine-learning (deep learning) approaches will generate predictions from metabolic networks, integrating all data to design controlled consortia (T3.3).
WP4. Validation of community exchange networks through lab-scale fed-batch setup
Approximately 30 in vitro growth assays will be run on controlled consortia (ideally 5–10 species) (T4.1). Co-cultures will be scaled up in fed-batch bioreactors with online monitoring (T4.2). Controlled vs. spontaneous consortia will be compared for conversion efficiency, including targeted viral induction to eliminate competitors like homoacetogens (T4.3). Long-term preservation testing will evaluate the stability of bioconversion capabilities in controlled consortia (T4.4).

International Conferences Contributes

30th Research in Computational Molecular Biology (RECOMB), May 26th-29th 2026, Thessaloniki, Greece. INTERNATIONAL CONGRESS, POSTER: Agostini F, Savio F, De Bernardini N, Treu L, Campanaro S. From droplets to genomes: evaluating lysis methods and assembly approaches for prokaryotic single-cell sequencing.

Deliverables and Milestones

The Deliverables and Milestones reported here are provided as a summary, more detailed information may be made available upon request (PI, laura.treu @ unipd.it), subject to data sensitivity and publication constraints.

WP1

D1.1 Report on anoxic microfluidic droplet method setup (Month 36).

D1.2 Characterization plan via multi-omics approaches (Month 36).

M1 Strain-specific isolation strategy release (Month 36).

WP2

D2.1 Microbial functional potential from SC culturomics (Month 48).

D2.2 Carbon utilization, microbe interactions, and prophage induction (Month 48).

M2 Microbial growth patterns, metabolic profiles, and viral manipulation strategy (Month 48).

WP3

D3.1 Metabolic interaction patterns in consortia (Month 60).

D3.2 Reliable FBA predictions from strain-level GEMs (Month 60).

M3 Compendium of SAG-based CoCo-GEMs and strategy for controlled consortia (Month 60).