Sustainable innovation of microbiome applications in food system

Project Information

SIMBA

Grant agreement ID: 818431

DOI 10.3030/818431

Project closed

EC signature date 5 October 2018

Start date 1 November 2018

End date 31 October 2023

Funded under

• SOCIETAL CHALLENGES - Food security, sustainable agriculture and forestry, marine, maritime and inland water research, and the bioeconomy

Total cost € 10 373 931,62

EU contribution € 9 999 999,77

Coordinated by

LUONNONVARAKESKUS
Finland

Deliverables

Documents, reports (24)

Description of fermentation product effects on fish health

xx

Taxonomic & functional description of salt tolerant potato associated microbiome during a full growth season

x

Microbial starter culture for amendment to micro-algal cultivation

xx

Report on the economic impacts

Report or scientific publication describing the calculations of indicators of the economic dimension and related results for each of four case study scenarios

Protocol describing maintenance of coastal marine microbiomes

xx

Producing a database containing genome information (gene prediction, annotation and species identification) of approximately 200 to 250 bacterial isolates and approximately 50 mobilome samples
Description of growth characteristics of selected micro- and macro-algae

x

Report on the overall sustainability

Report or scientific publication describing the integration of environmental economic and social indicators for the assessment of the overall sustainability of using the new microbial processproduct for each of four case study scenarios

Practical manual for stakeholders

xx

Selection of 15 microbial strains from the NORCCA and ISCaR collection for use in fish food

xx

Taxonomic & functional description of macro-algae associated microbiome during a full growth season

x

Description of an initial coastal marine microbiome

xxx

Description of biofilm forming properties of selected microbial consortia tested in the field

xx

Description of artificial microbiome for enhancing crop growth

xx

Release of the marketing plan

xx

Selection of 5 microalgal strains with increased lipid productivity and 5 strains with increased astaxanthin productivity

xx

Protocols for analysis of biofilm formation in water and soil substrates

xx

Microalgae-boosted fish food assessed for growth of salmon, seabass and seebream

xx

Taxonomic & functional description of micro-algae associated microbiome during a full growth season

x

Microbial starter culture for amendment to macro-algal cultivation

xx

Portfolio of communication material

xx

Identification of ‘high risk' conditions for the development of fish pathogens

xx

Protocol for optimized and up-scaled cultivation of selected algae

xxx

Three training courses

xx

Other (4)

Nomination of members of Scientific Advisory Board, Innovation Management Board and Ethical Advisory Board

xx

Final update of the Dissemination and Exploitation Plan

Update of the protocols as there is an obligation for partners to carry out exploitation for another four years after the project. The Knowledge Output Pathways and Knowledge Transfer Plans are included. An update of the Horizon Results Platform and information about that in the DEP.

Final event

xx

Dissemination and Exploitation Plan

xx

Websites, patent fillings, videos etc. (3)

Video

xx

Publicly accessible database platform and web interface released

A validated public access platform will be made openly available to the general public. The open beta platform will be validated using case studies from all WP1 participating partners. The platform will have the ability to accept new submissions and support all functionality analysis and all prototype bugs will be addressed.

Project intranet operational

xx

Demonstrators, pilots, prototypes (1)

Open beta platform opened

The platform will be based on the prototype from D12 The data analysis platform is open for public access New users are able to log in and provide new data

Publications

Peer reviewed articles (26)

Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis

Author(s): Johanna Nelkner, Liren Huang, Timo W. Lin, Alexander Schulz, Benedikt Osterholz, Christian Henke, Jochen Blom, Alfred Pühler, Alexander Sczyrba & Andreas Schlüter
Published in: Environmental Microbiome, 2023, ISSN 2524-6372
Publisher: Springer Nature
DOI: 10.1186/s40793-023-00479-9

Investigating the relationship between knowledge and the adoption of sustainable agricultural practices: The case of Dutch arable farmers

Author(s): Thomas Slijper Annika F. Tensi Frederic Ang Beshir M. Ali H.J. van der Fels-Klerx
Published in: Journal of Cleaner Production, 2023, ISSN 0959-6526
Publisher: Elsevier BV
DOI: 10.1016/j.jclepro.2023.138011

Ultra-high Performance Liquid Chromatography–Ion Mobility–High-Resolution Mass Spectrometry to Evaluate the Metabolomic Response of Durum Wheat to Sustainable Treatments

Author(s): Nicolò Riboni; Federica Bianchi; Monica Mattarozzi; Marina Caldara; Mariolina Gullì; Sara Graziano; Elena Maestri; Nelson Marmiroli; Maria Careri
Published in: Journal of Agricultural and Food Chemistry, Issue 4, 2023, ISSN 0021-8561
Publisher: American Chemical Society
DOI: 10.1021/acs.jafc.3c04532

Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter

Author(s): Julia Hassa, Daniel Wibberg, Irena Maus, Alfred Pühler, Andreas Schlüter
Published in: Microorganisms, Issue 8/1, 2020, Page(s) 13, ISSN 2076-2607
Publisher: Microorganisms
DOI: 10.3390/microorganisms8010013

Impact of microbial consortia on organic maize in a temperate climate varies with environment but not with fertilization

Author(s): Jonas Hett Thomas F. Döring Annamaria Bevivino Daniel Neuhoff
Published in: European Journal of Agronomy, Issue Volume 144, March 2023, 126743, 2023, ISSN 1161-0301
Publisher: Elsevier BV
DOI: 10.1016/j.eja.2023.126743

Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture

Author(s): Silvia Tabacchioni, Stefania Passato, Patrizia Ambrosino, Liren Huang, Marina Caldara, Cristina Cantale, Jonas Hett, Antonella Del Fiore, Alessia Fiore, Andreas Schlüter, Alexander Sczyrba, Elena Maestri, Nelson Marmiroli, Daniel Neuhoff, Joseph Nesme, Søren Johannes Sørensen, Giuseppe Aprea, Chiara Nobili, Ombretta Presenti, Giusto Giovannetti, Caterina Giovannetti, Anne Pihlanto, Andrea Bruno
Published in: Microorganisms, Issue 9/2, 2021, Page(s) 426, ISSN 2076-2607
Publisher: Microorganisms
DOI: 10.3390/microorganisms9020426

A Metagenomic and Gene Expression Analysis in Wheat (T. durum) and Maize (Z. mays) Biofertilized with PGPM and Biochar

Author(s): Sara Graziano, Marina Caldara, Mariolina Gullì, Annamaria Bevivino, Elena Maestri and Nelson Marmiroli
Published in: International Journal of Molecular Sciences; Volume 23; Issue 18; Pages: 10376, Issue 1, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms231810376

Stimulating risk averse farmers to adopt microbial applications

Author(s): Annika Francesca Tensi, Frederic Ang
Published in: Q Open, Volume 3, Issue 1, 2023,, 2023, ISSN 2633-9048
Publisher: Oxford Academic
DOI: 10.1093/qopen/qoad011

Designing a Waste-Based Culture Medium for the Production of Plant Growth Promoting Microorganisms Based on Cladodes Juice from Opuntia ficus-indica Pruning

Author(s): Rosaria Alessandra Magarelli Mario Trupo Alfredo Ambrico Vincenzo Larocca Maria Martino Salvatore Palazzo Roberto Balducchi Vesa Joutsjoki Anne Pihlanto Annamaria Bevivino
Published in: Fermentation, 2022, ISSN 2311-5637
Publisher: MDPI
DOI: 10.3390/fermentation8050225

Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics

Author(s): Julia Hassa Tom Jonas Tubbesing Irena Maus Robert Heyer Dirk Benndorf, Mathias Effenberger Christian Henke Benedikt Osterholz Michael Beckstette Alfred Pühler Alexander Sczyrba Andreas Schlüter
Published in: Microorganisms, 2023, ISSN 2076-2607
Publisher: MDPI
DOI: 10.3390/microorganisms11102412

Behavioural drivers and barriers for adopting microbial applications in arable farms: Evidence from the Netherlands and Germany

Author(s): Annika Tensi; Frederic Ang; H.J. van der Fels-Klerx
Published in: Technological Forecasting and Social Change, Issue 7, 2022, ISSN 0040-1625
Publisher: Elsevier BV
DOI: 10.5281/zenodo.6821262

Immunomodulatory peptides—A promising source for novel functional food production and drug discovery

Author(s): Milica Pavlicevica Nelson Marmiroli Elena Maestri
Published in: Peptides, Issue 148, 2021, ISSN 0196-9781
Publisher: Elsevier BV
DOI: 10.1016/j.peptides.2021.170696

Building a risk matrix for the safety assessment of wood derived biochars

Author(s): Marta Marmiroli; Marina Caldara; Serena Pantalone; Alessio Malcevschi; Elena Maestri; Arturo A. Keller; Nelson Marmiroli
Published in: Science of The Total Environment, Issue 1, 2023, ISSN 0048-9697
Publisher: Elsevier BV
DOI: 10.1016/j.scitotenv.2022.156265

Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants

Author(s): Hassa, J.; Klang, J.; Benndorf, D.; Pohl, M.; Hülsemann, B.; Mächtig, T.; Effenberger, M.; Pühler, A.; Schlüter, A.; Theuerl, S.
Published in: Microorganisms, Vol 9, Iss 1457, p1457 (2021), Issue 1, 2021, ISSN 2076-2607
Publisher: Microorganisms
DOI: 10.3390/microorganisms9071457

The Impact of Soil-Applied Biochars From Different Vegetal Feedstocks on Durum Wheat Plant Performance and Rhizospheric Bacterial Microbiota in Low Metal-Contaminated Soil

Author(s): Arianna Latini, Giovanni Bacci, Manuel Teodoro, Daniele Mirabile Gattia, Annamaria Bevivino, Lukáš Trakal
Published in: Frontiers in Microbiology, Issue 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.02694

Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes

Author(s): Johanna Nelkner, Christian Henke, Timo Wentong Lin, Wiebke Pätzold, Julia Hassa, Sebastian Jaenicke, Rita Grosch, Alfred Pühler, Alexander Sczyrba, Andreas Schlüter
Published in: Genes, Issue 10/6, 2019, Page(s) 424, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes10060424

Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics

Author(s): Johanna Nelkner, Gonzalo Torres Tejerizo, Julia Hassa, Timo Wentong Lin, Julian Witte, Bart Verwaaijen, Anika Winkler, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Rita Grosch, Alfred Pühler, and Andreas Schlüter
Published in: Genes, Issue 10/8, 2019, Page(s) 601, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes10080601

Transcriptome and Metabolome Reprogramming in Tomato Plants by Trichoderma harzianum strain T22 Primes and Enhances Defense Responses Against Aphids

Author(s): Mariangela Coppola, Gianfranco Diretto, Maria Cristina Digilio, Sheridan Lois Woo, Giovanni Giuliano, Donata Molisso, Francesco Pennacchio, Matteo Lorito, Rosa Rao
Published in: Frontiers in Physiology, Issue 10, 2019, ISSN 1664-042X
Publisher: Frontiers Research Foundation
DOI: 10.3389/fphys.2019.00745

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

Author(s): Irena Maus, Michael Klocke, Jaqueline Derenkó, Yvonne Stolze, Michael Beckstette, Carsten Jost, Daniel Wibberg, Jochen Blom, Christian Henke, Katharina Willenbücher, Madis Rumming, Antje Rademacher, Alfred Pühler, Alexander Sczyrba, Andreas Schlüter
Published in: Environmental Microbiome, Issue 15/1, 2020, ISSN 2524-6372
Publisher: BioMed Central Ltd, Springer Nature
DOI: 10.1186/s40793-020-00354-x

The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses

Author(s): Irena Maus1,2, Daniel Wibberg1,2, Peter Belmann2,3, Sarah Hahnke4, Liren Huang3, Cathrin Spröer5, Boyke Bunk5, Jochen Blom6, Alexander Sczyrba2,3, Alfred Pühler1, Michael Klocke7 and Andreas Schlüter1*
Published in: Frontiers in Microbiology, 2023, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2022.1032515

Consumer willingness to pay for plant-based foods produced using microbial applications to replace synthetic chemical inputs

Author(s): Beshir M. Ali ,Frederic Ang,H. J. van der Fels-Klerx
Published in: PLOS ONE, Issue 16(12), 2021, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0260488

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis

Author(s): Nan Yang, Joseph Nesme, Henriette Lyng Røder, Xuanji Li, Zhangli Zuo, Morten Petersen, Mette Burmølle & Søren Johannes Sørensen
Published in: npj Biofilms and Microbiomes, 2021, ISSN 2055-5008
Publisher: Nature Portfolio
DOI: 10.1038/s41522-021-00253-0

The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses

Author(s): Irena Maus, Tom Tubbesing, Daniel Wibberg, Robert Heyer, Julia Hassa, Geizecler Tomazetto, Liren Huang, Boyke Bunk, Cathrin Spröer, Dirk Benndorf, Vladimir Zverlov, Alfred Pühler, Michael Klocke, Alexander Sczyrba, Andreas Schlüter
Published in: Microorganisms, Issue 8/12, 2020, Page(s) 2024, ISSN 2076-2607
Publisher: Microorganisms
DOI: 10.3390/microorganisms8122024

Nanomaterials biotransformation: In planta mechanisms of action

Author(s): Luca Pagano, Riccardo Rossi, Jason C. White, Nelson Marmiroli, Marta Marmiroli
Published in: Environmental Pollution, 2023, ISSN 0269-7491
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.envpol.2022.120834

Effects of Multi-Species Microbial Inoculants on Early Wheat Growth and Litterbag Microbial Activity

Author(s): Jonas Hett; Daniel Neuhoff; Thomas F. Doring; Giorgio Masoero; Enrico Ercole; Annamaria Bevivino
Published in: Agronomy, Issue 5, 2022, Page(s) 0734395, ISSN 2073-4395
Publisher: MDPI
DOI: 10.3390/agronomy12040899

Engineered Nanoparticles, Natural Nanoclay and Biochar, as Carriers of Plant-Growth Promoting Bacteria

Author(s): Milica Pavlicevic; Wael Abdelraheem; Nubia Zuverza-Mena; Tana O'Keefe; Salma Mukhtar; Gale Ridge; John Ranciato; Christy Haynes; Wade Elmer; Joseph Pignatello; Luca Pagano; Marina Caldara; Marta Marmiroli; Elena Maestri; Nelson Marmiroli; Jason C. White
Published in: Nanomaterials, Issue 1, 2022, ISSN 2079-4991
Publisher: MDPI
DOI: 10.3390/nano12244474