STARS@ UNIPD

SIGMA project

SIGMA - SIngle-cell Genomics and Metabolic modeling for tailored microbial consortiA design

ABSTRACT

Studying the microbiome of anaerobic digestion (AD) and biogas upgrading (BU) is critical to achieving a more sustainable energy production system. The microbial communities involved in AD and carbon dioxide (CO₂) fixation are complex and play a crucial role in the success of the processes. To advance our understanding of BU microbiota and how microbes can be harnessed for more effective and efficient biogas production and biomethanation, SIGMA proposes a composite approach of advanced bioinformatics analyses and culturomics. High-throughput single-cell technologies will be used to isolate new unculturable anaerobes from the microbiome, characterize their genome and transcriptome and interaction with prophages; at the same time, prediction of exchanged metabolites through metabolic modeling and verification with metabolic measurements will identify syntrophic relationships. Acquired knowledge on the interaction between microbes and the effects of phages on them will constitute a powerful tool to shape the microbiota towards the desired productivity. Overall, SIGMA will provide insight and instruments to design and create specialized microbial consortia with increased efficiency in biotechnological processes, in particular BU. Additionally, the newly developed innovative computational tools will enhance the accuracy of identifying and predicting biosynthetic gene clusters responsible for carbon fixation and product biosynthesis. The knowledge produced by SIGMA will lead to increased bioconversion of carbon-based materials and CO₂ into biofuels, important for circular bioeconomy.

Project Details

Type of Grant CoG

Current position at UNIPD Associate Professor

Project acronym SIGMA

Project title SIngle-cell Genomics and Metabolic modeling for tailored microbial consortiA design

Host Department Department of Biology

Research cost € 175.000,00

Start date of the project 01/02/2024

Duration of the project 30 months

PEOPLE

Filippo Savio

PhD student

Flavio Agostini

PhD student

Nicola De Bernardini

Postdoc

Gabriele Ghiotto

Postdoc

RESEARCH PLAN

WP1. Single-cell technology applied to AD and BU communities T1.1 Single or few cells will be captured in gel droplets, forming microreactors to support growth of (co)isolated cells. To analyze single-cell sequencing data, a bioinformatics toolbox will be developed using genome-centric metagenomics strategies (T1.2) to reconstruct draft genomes by pooling sequences from cells of the same species. Genome-centric metatranscriptomics will integrate DNA/RNA-seq and bioinformatics to infer microbial functions and activity (T1.3). D&M: D1.1 Report on a microfluidic droplet method for anaerobic microorganisms; D1.2 Multi-omics characterization plan (genomics, transcriptomics); M1 Release of new pipelines to analyze target species in communities.

WP2. Recognition of phage-host interaction DNA from samples in WP1 and WP3 (T2.1) will be used to study interactions between phages, microbiomes, and free-living phages. Integrated prophages and free viruses will be analyzed to define infection mechanisms and microbial defenses (e.g., CRISPR-Cas). Phage-driven community dynamics will be characterized (T2.2). Environmental conditions inducing phages targeting unwanted bacteria will be selected to shape communities (T2.3). D&M: D2.1 Global map of microbial–viral interactions; D2.2 Phages and conditions for microbiota control; M2 Strategy to control microbial–phage dynamics in AD microbiomes.

WP3. Reconstruction of community exchange networks Gas composition, pressure, and carbon sources will be experimentally tested (T3.1). Growth rate, gases, and VFAs will be monitored by GC, flow cytometry, and microscopy. Microbiome evolution will be tracked by time-series single-cell genomics and transcriptomics to validate syntrophic interactions (T3.2). Flux balance analysis and condition-specific genome-scale metabolic models will be optimized for primary CO₂ consumers (T3.3). D&M: D3.1 Report on selected strains and syntrophic consortia; D3.2 Metabolic models integrating metabolomics and transcriptomics; M3 Strategy to obtain optimized microbial consortia.

WP4. Innovation outreach, dissemination, and exploitation. Results will be disseminated through high-impact journals (T4.1), international conferences (T4.2), and outreach to young researchers via social media and congresses (T4.3). D&M: Three high-impact publications (e.g., Environmental Science & Technology, Microbiome, The ISME Journal); D4.2 Conference dissemination; M4 Report on communication activities.

Biological BU process based on hydrogen methanation for CCU.

Schematic illustration of the experimental plan of BU community exploration

International Conferences Contributes

19th International Symposium on Microbial Ecology (ISME19), August 18th-23th 2024, Cape Town, South Africa. INTERNATIONAL CONGRESS, POSTER: De Bernardini N, Giangeri G, Savio F, Ling M, Fraulini S, Orellana E, Ji M, Campanaro S, Treu L. Genetic variability in a carbon dioxide reducing microbial community: a comparison between metagenomics and single-cell sequencing.
19th International Symposium on Microbial Ecology (ISME19), August 18th-23th 2024, Cape Town, South Africa. INTERNATIONAL CONGRESS, POSTER: Orellana E., De Bernandini N., Zampieri G., Serna R., Jalali F., Campanaro S., Treu L. Syntrophy in anaerobic microbial communities: amino acids as key players in CO2 methanation.
EMBO | EMBL Symposium. New approaches and concepts in microbiology, June 24th-27th 2025, Heidelberg, Germany. INTERNATIONAL SYMPOSIUM, POSTER: De Bernardini N., Savio F., Orellana E., Campanaro S., Treu L. The hidden influence of phage-host interactions on carbon dioxide methanation
5th International conference on biogas microbiology (ICBM-5), May 26th-29th 2025, Galway, Ireland. INTERNATIONAL CONGRESS, SELECTED ORAL PRESENTATION: Savio F., De Bernardini N., Orellana E., Ji M., Campanaro S., Treu L. Integrating single-cell DNA sequencing and metagenomics to uncover overlooked genetic features in a CO₂-fixing microbiome for biogas upgrading.

Deliverables and Milestones

WP1

D1.1: Report on a microfluidic droplet method for anaerobic microorganisms (Month 4)
D1.2: Multi-omics characterization plan (Month 8)
M1: Strategy to analyze target species at community-level (Month 8)

WP2

D2.1: Global map of the microbial-viral interactions (Month 12)
D2.2: Phages-mediated condition for microbiota composition (Month 16)
M2: Strategy to control microbial-phages dynamics (Month 18)

WP3

D3.1: Report on selected strains and syntrophic consortia (Month 25)
D3.2: Report on condition-specific metabolic model (Month 28)
M3: Strategy to control microbial-phages dynamics (Month 28)

WP4

D4.1: Manuscript publication (Month 28)
D4.2: Dissemination in Conferences (Month 28)
M4: Report on dissemination and communication activities (Month 28)

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