Booklet of IWIM Presentations Abstracts

92 Pages·2017·2.08 MB·English

by  Nejma Garnier

Booklet of IWIM
Presentations
Abstracts
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Table des matières
INRA Meta-Programs: a tool for transdisciplinary Research ................................................................... 1
Introduction to IWIM workshop ......................................................................................................... 2
METASCREEN High-throughput functional exploration of microbial diversity ................................... 4
Eternal Rice: a case study of sustainable management of plant resistance ....................................... 7
LACCAVE: Wine industry and climate change, a systemic approach .................................................. 9
R2D2: a research network for analysing the efficiency of genomic selection .................................. 12
Towards sustainable diets: benefit-cost assessment of dietary recommendations ......................... 15
R2A2 network – A think tank dedicated to the antimicrobial crisis .................................................. 18
The CompAg project: Achieving agroecological transition through ecological compensation ........ 20
Governing by models: Land use models as tools for governing food security (GOSAMO) ............... 23
On “TRACKS”... 10 years after “Multidimensional analysis & support to Trajectories of conversion
to Organics” ....................................................................................................................................... 26
Findings from the synthesis report on metaprograms ..................................................................... 29
Findings from the IWIM Scientific Committee .................................................................................. 33
Agriculture and Agrifood Canada’s approach to interdisciplinary research programs ..................... 35
CAAS and its inter-displinary programs ............................................................................................. 38
Interdisciplinary @ Wageningen University & Research .................................................................. 39
Interdisciplinary @ UK ....................................................................................................................... 40
Sharing our understanding of research programs addressing grand challenges .................................. 41
Land sustainability and global change............................................................................................... 42
Towards a foresight on SDG compatible European food systems .................................................... 45
Rethinking the Meta-program tool ....................................................................................................... 48
From Meta- Programmes to Mission-Oriented Programmes? ......................................................... 49
Rethinking the MP tool: From Meta-programs to International programs? .................................... 51
From meta-programs to open innovation and participatory research ............................................. 53
New frontiers and new visions .............................................................................................................. 56
Bioeconomy and Circular Economy: transformation of agriculture and industries toward
sustainability ..................................................................................................................................... 57
Towards a Zero Plastic Bio-Economy ................................................................................................ 60
Innovations to integrate the environment and health in agri-food systems .................................... 62
Healthier and more sustainable food systems. From diagnosis to participatory design .................. 65
Knowledge-based agricultural and food policies .............................................................................. 68
Digital agriculture and emerging technologies ................................................................................. 71
Modeling future landscapes of adaptation to climatic and sanitary risks in European agriculture . 74
New frontiers and new visions through Meta-Programs ...................................................................... 76
New frontiers and new visions on adaptation of agriculture and forest to climate change,
ecosystem services and organic farming........................................................................................... 77
NEW FRONTIERS AND NEW VISIONS THROUGH META-PROGRAMs: GISA- and SMaCH-MP
perspective ........................................................................................................................................ 80
Roundtable on « Diets, Health and Food Security” ........................................................................... 82
NEW FRONTIERS AND NEW VISIONS THROUGH MP Selgen and MEM ............................................ 84
Findings from IWIM 2018 .................................................................................................................. 86
INRA Meta-Programs: a tool for transdisciplinary
Research

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Introduction to IWIM workshop

Jean-François Soussana

INRA, Vice-Chair for international affairs, Paris, France.

As a public targeted research organisation, INRA mobilises a wide spectrum of disciplinary research
ranging from biological and ecological sciences, economic and social sciences, to the engineering
sciences and biotechnologies.
This broad range of disciplines is an opportunity to address the complex social and scientific challenges
facing food systems and bioeconomy at the start of the 21st century: achieving global food security in a
context of nutritional transition; transforming agricultural production systems to base performance on
agro-ecological solutions and digital farming; ensuring the provision of food that is healthy, sustainable
and accessible to all; developing the sustainable management of ecosystem services by adapting to
climate change; mastering new ‘-omic’ tools and their applications in biology.
This opportunity is contingent upon a skilful combination of disciplinary dynamics and interdisciplinary
approaches. This requires an epistemological effort to build common research goals, such as agro-
ecosystem services, or adaptation to climate change. INRA took up this challenge in 2010 with the
creation of its metaprograms: cross-cutting, cross-disciplinary programmes in synergy with discipline-
based initiatives led by the Institute’s research divisions. Through the MPs, collaborations between
social sciences divisions, the applied mathematics division and the natural sciences divisions have led
to interdisciplinary projects. Moreover, collaborations across natural science divisions were markedly
strengthened, e.g., between plant and animal genetics, plant and animal health, and agronomy and animal
husbandry.
The total number of papers published by INRA within the thematic fields of the MPs has increased by
250% over 2010-2016, whereas this increase was of 160% in the global scientific literature for the same
fields. Beyond scientific production, 8 categories of outputs by the MPs are identified: i)
interdisciplinary scientific community building; ii) benchmarking existing research and identifying
novel research directions; iii) expertise and foresight; iv) knowledge transfer and innovation; v) evidence
base for public policies; vi) international collaborations; vii) communication; and viii) training. Some
MPs were relatively more oriented towards knowledge transfer and innovation (e.g., GISA – Integrated
animal health management), others towards international collaborations (e.g., AAFCC – Adaptation of
agriculture and forest to climate change), or national expertise and stakeholder’s interaction (e.g.,
EcoServ – Practices and services of anthropized ecosystems). Several large collaborative research
projects supported by external funding from various sources (European Commission, French national
agency for research, foundations, private sector) were launched after being incubated by the MPs.
9 MPs were launched successively in 2011 (3 MPs), 2013 (3 MPs), 2015 (2 MPs) and 2018 (by
transforming an existing program, OF&F – Organic Food and Farming, into an MP) and one MP
(GloFoodS, on Global Food Security) is shared with CIRAD. In total, MPs have benefited from a total
direct funding by INRA of 400-500 k€ per year and per MP, which translates in 2 to 2.5 M€ per year
and per MP in terms of full costs (salaries of permanent staff included), including co-funding for up to
100 PhD grants. In addition, since 2011, 86 junior scientists and engineers were recruited by INRA as
permanent staff (23% of the total tenure-track recruitments) based on profiles initially provided by the
MPs. INRA’s MPs have launched close to 300 research projects. These projects are estimated to have
published so far ca. 2,000 indexed peer-reviewed papers, including a significant number in high-impact
multidisciplinary journals. Despite some limitations, MPs have allowed INRA to strengthen
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interdisciplinary research and pathways to impact in highly relevant fields for major societal challenges,
while fostering international collaborations.
After several years of operation, INRA has launched a process of review and revision of this approach
to bring it the necessary evolutions. The 2018 International Workshop on INRA’s Meta-Programs
(IWIM), held in Versailles on February 1-2, has been prepared through a review process by an
international panel of invited scientific experts. This review was based on self-assessment reports
prepared by each MP and on a synthesis of the individual reports. 130 participants from 15 countries
attended IWIM 2018, most of them being scientific experts from disciplines supporting INRA MPs.
During IWIM 2018, after an introduction by the French ministry for research, a review of the
advancement of INRA’s MPs was provided by presenting: i) highlights from each MP, ii) a summary
of the self-assessment reports and iii) the conclusions of the international assessment panel. These
presentations helped to share the results of the meta-programs and parallel sessions allowed to reflect
on developments and perspectives on various aspects such as internationalization, innovation and
stakeholder dialog.
This international workshop allowed to reflect on similar initiatives taken by large research
organizations in other countries (Canada, China, the Netherlands and UK) and to discuss new research
needs to face the global challenges of agriculture, the environment and food. A series of key-note
lectures by international experts allowed to introduce some of the main challenges ahead and to provide
some novel research perspectives on how to answer these challenges. The main perspectives for
European and for international research and impact in these fields were addressed by the European
Commission and by the FAO before a conclusive address by the President and CEO of INRA.

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METASCREEN
High-throughput functional exploration of microbial diversity

Sophie Bozonnet1, Roland Marmeisse2, Diego Morgavi3, Marion Leclerc4, Stephane Uroz5, Alain
Brauman6, Guillermina Hernandez-Raquet1, Muriel Mercier-Bonin4, Claire Dumon1, Elisabeth Laville1,
Sandra Pizzut-Serin1, Sophie Duquesne1, Sandrine Laguerre1, Simon Ladevèze1, Lisa Ufarté1,
Alexandre David4, Gregory Arnal1, Adèle Lazuka1, Laurence Tarquis1, Marie-Pierre Duviau1, Joël
Doré4, Patricia Luis2, Laetitia Bernard6, and Gabrielle Potocki-Veronese*1.

1 LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
2 UMR INRA, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
3INRA, UMR 1213 Herbivores, Saint-Genès Champanelle, France
4 Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
5 UMR1136 INRA/University of Lorraine “Tree-Microbe Interactions” (IAM), Labex ARBRE,
Champenoux, France
6 Laboratoire de Microbiologie ORSTOM, Université de Provence, Marseille, France
*[email protected]

Microbial communities are ubiquitous in the biosphere, and play key roles in plant and animal health,
food security and quality, and ecosystem remediation. However, most of the microbial species which
compose these ecosystems are uncultured and, thus, difficult to study. In the MEM
metaprogram_Metascreen project, we circumvented the barrier of cultivation by using metagenomics
and metatranscriptomics (the genomic/transcriptomic analysis of a population of microbes), in order to
explore the hidden prokaryotic and eukaryotic fractions of various microbial communities. The targeted
microbiota are representative of enzyme-rich and relevant environments, i.e. human gut, bovine rumen,
insect gut and soil microbial communities. The Metascreen objectives were to decipher the functions of
specific microorganisms, from the ecosystemic to the molecular levels, and to create a large collection
of catalytic tools of biotechnological interest. The goal was, ultimately, to understand how ecosystems
operate and also to exploit interesting microbial functions ex vivo, for the development of enzyme-based
processes and synthetic biology. In order to meet these challenges, the Metascreen consortium combined
the expertise of biochemists, microbiologists and microbial ecologists from six INRA divisions, who
received in total 270 k€.

Metascreen allowed a steep increase in activity-based functional metagenomics. A very large battery of
functional screens (Larraufie et al., 2015; Ufarté et al., 2015a, 2015b; Tauzin et al., 2017) was developed
on our high-throughput screening platform ICEO, which is now part of the European infrastructure
IBISBA project (H2020 INFRAIA). We also created and organized metagenomic libraries from the four
targeted ecosystems, covering 6 Gbp of DNA (the equivalent of 2,000 bacterial genomes), and
evidenced important differences in the screening effort required depending on the considered
environment.

These developments led to the discovery of a battery of new tools for biorefineries, synthetic biology,
environmental and health industries. We indeed designed new microbial consortia (Lazuka et al., 2015,
2017) and enzymatic cocktails (Arnal et al., 2015) to improve plant cell wall degradation for the
biorefinery industry. This was done by combining different metabolic pathways, issued from insect and
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bovine rumen gut bacteria, or from soil fungi (Bragalini et al., 2014; Yadav et al., 2016; Marmeisse et
al., 2017). We also discovered new families of enzymes that can be used for bioremediation, in particular
for the degradation of pesticides and polyurethane foams (Ufarté et al., 2015c, 2017). From soil bacteria,
we identified a novel mechanism of quorum sensing signal communication and degradation (Torres et
al., 2017). In addition, we deciphered the mechanisms of biofilm formation and mucin adhesion in the
human gut microbiota, and discovered a novel enzyme family involved in the degradation of the
intestinal mucus, which could contribute to the alteration of the intestinal barrier for patients suffering
from inflammatory bowel diseases (Ladevèze et al., 2013, 2015, 2016). By exploiting this enzymatic
function in vitro, we also developed a new process of conversion of plant cell wall substrates into human
oligosaccharides, of which the price exceeds 10 k€/mg (Potocki-Veronese et al., 2013).

Overall this project led to one European patent and to 17 collaborative papers published in high-ranked
journals. Thanks to this increased visibility, we expanded our network in functional metagenomics,
especially in Europe, Canada and Australia. A direct consequence of Metascreen is the participation, as
workpackage leaders or coordinators, in 12 new industrial, national and international projects (for a total
of 3.2 M€ for INRA partners), in which we are exploiting our generic functional screening assays, and/or
the collection of Metascreen enzymes for biotechnological applications.

Thanks to the developments made in Metascreen and in two running H2020 projects (Catsys-H2020-
MSCA-IF-2015 and Metafluidics-H2020-LEIT-BIO-2015, obtained thanks to the expertise acquired in
Metascreen), we open a new area in functional metagenomics. We integrated microfluidics to
metagenomics, and designed several ultra-high-throughput workflows allowing us to suppress the limits
in terms of throughput, cost and library size (Colin et al., 2015, Dagkesamanskaya et al., 2018). We are
now able to explore, extremely quickly, the vast world of still unknown bacterial, fungal and viral
functions to boost the development of bioeconomy.

References

Arnal G, Bastien G, Monties N, Abot A, Leberre V, Bozonnet S, O’Donohue M and Dumon C (2015) Investigating
the function of an arabinan utilization locus isolated from a termite gut community. Applied and environmental
microbiology 81(1), 31-39.

Bragalini C, Ribière C, Parisot N, Vallon L, Prudent E, Peyretaillade E, Girlanda M, Peyret P, Marmeisse R, Luis
P (2014) Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from
complex environmental samples. DNA Research 21(6), 685-694.

Colin PY, Kintses B, Gielen F, Miton CM, Fischer G, Mohamed MF, Hyvönen M, Morgavi DP, Janssen DB,
Hollfelder F (2015) Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional
metagenomics. Nature communications 6, 10008.

Dagkesamanskaya A, Langer K, Tauzin A, Rouzeau C, Lestrade D, Potocki-Veronese G, Boitard L, Bibette J,
Baudry J, Pompon D, Anton-Leberre V (2018) Use of photoswitchable Fluorescent Proteins for droplet-based
microfluidic screening. Journal of Microbiological Methods. In press.

Larraufie P, de Wouters T, Potocki-Veronese G, Blottière HM, Doré J (2014). Functional metagenomics to
decipher food-microbe-host crosstalk. Proceedings of the Nutrition Society 74 (1), 14.

Ladeveze S, Tarquis L, Cecchini D, Bercovici J, Andre I, Topham C, Morel S, Laville E, Monsan P, Lombard V,
Henrissat B, Potocki-Veronese G (2013) Role of Glycoside Phosphorylases in Mannose Foraging by Human Gut
Bacteria. Journal of Biological Chemistry 288 (45), 32370-32383.
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Ladeveze S, Cioci G, Roblin P, Mourey L, Tranier S, Potocki-Veronese G (2015) Structural bases for N-glycan
processing by mannoside phosphorylase. Acta Crystallographica Section D Biological Crystallography 71 (6),
1335-46.

Ladeveze S, Laville E, Despres J, Mosoni P, Potocki Veronese G (2016) Mannoside recognition and degradation
by bacteria. Biological Reviews 92(4), 1969-1990.

Lazuka A, Auer L, Bozonnet S, Morgavi DP, O’Donohue MJ, Hernandez-Raquet G (2015). Efficient anaerobic
transformation of raw wheat straw by a robust cow rumen-derived microbial consortium. Bioresource Technology
196, 241-249.

Lazuka A, Roland C, Barakat A, Guillon F, O'Donohue M, Hernandez Raquet G (2017) Ecofriendly lignocellulose
pretreatment to enhance the carboxylate production of a rumen-derived microbial consortium. Bioresource
Technology 236, 225-233.

Marmeisse R, Kellner H, Fraissinet-Tachet L, Luis P (2017) Discovering Protein-Coding Genes from the
Environment: Time for the Eukaryotes? Trends in Biotechnology 35:824-835.

Potocki-Veronese G, Ladeveze S, Tarquis L, Henrissat B, Monsan P, Laville E (2013) Use of specific glycoside
phosphorylases for the implementation of phosphorolysis or reverse phosphorolysis reactions. European patent
filed by Toulouse Tech Transfert, N° EP 13306108.5. Mondial extension in 2014, N° PCT/EP2014/066565.

Tauzin A, Laville E, Cecchini D, Blottiere H, Leclerc M, Dore J, Potocki-Veronese G (2017) Human gut
metagenomics: success and limits of the activity-based approaches. In ‘Functional Metagenomics: Tools and
Applications’, (Ed. Springer, Cham) pp. 161-178.

Torres M, Uroz S, Salto R, Fauchery L, Quesada E, Llamas I (2017) HqiA, a novel quorum-quenching enzyme
which expands the AHL lactonase family. Scientific reports, 7(1), 943.

Ufarté L, Potocki-Veronese G, Laville E (2015a). Discovery of new protein families and functions: new challenges
in functional metagenomics for biotechnologies and microbial ecology. Frontiers in Microbiology 6, 563.

Ufarté L, Bozonnet S, Laville E, Cecchini DA, Pizzut-Serin S, Jacquiod S, Demanèche S, Simonet P, Franqueville
L, Potocki-Veronese G (2015b) Functional metagenomics: construction and high-throughput screening of fosmid
libraries for discovery of novel carbohydrate-active enzymes. In ‘Microbial Environmental Genomics (Methods
in Molecular Biology)’ pp. 257-271 (Humana Press, New York, NY).

Ufarté L, Laville E, Duquesne S, Potocki-Véronèse G (2015c) Metagenomics for the discovery of pollutant
degrading enzymes. Biotechnology advances 33(8), 1845-1854.

Ufarté L, Laville E, Duquesne S, Morgavi D, Robe P, Klopp C, Rizzo A, Pizzut-Serin S, Potocki-Veronese G
(2017) Discovery of carbamate degrading enzymes by functional metagenomics. PloS one 12(12), e0189201.

Yadav RK, Bragalini C, Fraissinet-Tachet L, Marmeisse R, Luis P (2016) Metatranscriptomics of Soil Eukaryotic
Communities. Methods in Molecular Biology 1399, 273-287.

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