Forskningsprojekter

Aktuelle projekter

Afsluttede projekter

Period: 1 April 2016 - 15 July 2020.

In the LIFER project, supported by Villum Fonden, we are aiming at finding which proteins interact with and regulate plant lipid flippases involved in responses to stress conditions.

As a model, we are using ALA10, and Arabidopsis flippase important for stress responses to phosphate deficiency. This is a major issue in agricultural production as it results in the use of enormous amount of phosphate-containing fertilizers and the pollution of ground-water sources.

Background

Many members of the P-type ATPase family, that includes the lipid-transporting P4-ATPases (also known lipid flippases), are involved in relevant physiological functions, such as the generation of electrochemical gradients across membranes or cell detoxification. In accordance to their relevance, P-type ATPases are subjected to several regulatory mechanisms (phosphorylation/dephosphorylation, presence of autoinhibitory domains, interaction with activating proteins).

In yeast, several flippases of the P4 family are known to be regulated by interaction with proteins involved in vesicle production. Due to the higher complexity of plants and mammals with respect to yeast, flippases in these organisms are also expected to have interaction partners relevant for the fulfilment of their physiological roles.

Selected publications

  • Davis, JA, Pares RB, Bernstein T, McDowell SC, Brown E, Stubrich J, Rosenberg A, Cahoon E.B, Cahoon RE, Poulsen LR, Palmgren M, López-Marqués RL, Harper JF. Two lipid flippases, ALA4 and ALA5, are critical to cell expansion and plant growth in Arabidopsis. Plant Physiology (2019), accepted
  • Nintemann SJ, Palmgren M, López-Marqués RL. Catch You on the Flip Side: A Critical Review of Flippase Mutant Phenotypes. Trends Plant Sci., 24 (2019) 468-478.
  • Palmgren M, Østerberg JT, Nintemann SJ, Poulsen LR, López-Marqués RL. Evolution and a revised nomenclature of P4 ATPases, a eukaryotic family of lipid flippases. Biochim Biophys Acta Biomembr. 1861 (2019) 1135-1151.

Project leader: Rosa López-Marqués

Project participants: Rosa López-Marqués & Sebastian J Kjeldgaard-Nintemann

Funding: The project is funded by Villum Fonden.

Period: 2015-2019

BestPass project was an Innovative Training Network (ITN) funded by the European Union’s Horizon 2020 research and innovation programme. The project focused producing knowledge about the use of endophytes to improve plant productivity in a sustainable way.

Plant endophytic microorganisms can improve plant yield and enhance plant tolerance to abiotic stress as well as to pathogens under experimental conditions, but these effects are often not sufficiently stable for practical application. BestPass addressed these concerns and successfully trained a new generation of bright researchers who gained a profound understanding of the potential for endophytes in contributing to the next green revolution.

BestPass provided a unique opportunity for 15 Early Stage researchers (ESRs) to obtain the knowledge and skills needed to develop and utilize new technologies for understanding and using endophytes to improve plant productivity in a sustainability way. 

About the project

Societal challenges addressed in BestPass

Global food production is facing a number of major challenges over the coming century. The global population is growing and becoming increasingly urban and sophisticated in their diet. The climate is changing and becoming more unpredictable. To meet these and other challenges we need to increase crop yields while reducing pesticide input and use of inorganic fertiliser. Plant endophytic microorganisms can contribute to these goals by improving plant yield and enhancing plant tolerance to abiotic stress as well as to pathogens under experimental conditions, but these effects are often not sufficiently stable for practical application.

The effects of endophytes on plants

We need to understand the genetic basis of beneficial interactions between crops and endophytes and extend this basic knowledge of phenotypic plasticity to all interaction levels from the cellular to the field environment. This requires research into the molecular mechanisms underlying the effects of endophytes, including intra and inter-kingdom exchange and distribution of resources (nutrients). The genetic variation and its plasticity in host and microbe will be exploited in order to establish crop breeding and inoculum production processes for boosting the establishment and stability of plant-microbe mutualisms to benefit crop development, stress tolerance, pathogen resistance and quality.

Overall objectives of BestPass:

  • To understand the genetic and mechanistic basis of plant – endophyte interactions.
  • To assess these interactions for improving plant yield and quality under abiotic and biotic stress conditions.
  • To boost the stability and reliability of the beneficial effects of endophytes or endophyte consortia on plants.
  • To provide the best possible training to support the career development of the Early Stage Researchers (ESRs) in the field of beneficial plant microbe interactions.

Participants

The BestPass project consisted of major research groups from leading universities, research institutes and key biotechnology companies. The highly innovative and multidisciplinary consortium entailed 6 European countries and New Zealand. BestPass was coordinated by the University of Copenhagen and consisted of the following 12 beneficiaries: 

Research outcomes

The BestPass project has made stable progress in its activities with contributions from the entire consortium throughout the project period. The main results achieved in the project includes:

  1. Phytohormones impact on fungal endophyte communities in tomato roots.
  2. Changes in plant hormone levels upon colonization of tomato by endophytic and/or pathogenic strains of F. oxysporum.
  3. Identification of P-solubilising bacteria and interaction with an AM fungus.
  4. Characterization of grass populations with improved endophyte compatibility.
  5. Detection and characterization of genotypic variation in Epichloë spp. using microsatellite markers. 

Approximately half of the papers expected from the project have been published (23 publications) at the time of project closure, therefore more publishable and disseminated results are still expected. Furthermore, one patent has been filled as an output from BestPass, as a joint invention between the Universities of Copenhagen and Michigan State.

The project has provided excellent training for the ESRs in the areas of genomics, bioinformatics, plant physiology, industrial production of microbial inoculants/products and endophyte performance.

Little was known in advance of the study about the microbes or molecules involved in the biological interactions under study. But BestPass has yielded new knowledge, which is exploitable and/or publishable, and has provided materials and techniques for improving crop plant productivity. BestPass has, moreover, formed a new generation of scientists with deep knowledge in basic research, and who possess the awareness of the challenge to bring this knowledge to practical applications. 

Publications

[1] Bedini, A., Mercy, L., Schneider, C., Franken, P. and Lucic-Mercy, E. (2018) Unraveling the Initial Plant Hormone Signaling, Metabolic Mechanisms and Plant Defense Triggering the Endomycorrhizal Symbiosis Behavior, Frontiers in Plant Science, 9, doi:10.3389/fpls.2018.01800 

[2] Di, X., Cao, L., Hughes, R. K., Tintor N., Banfield, M J. and Takken F. L. W. (2017) Structure-function analysis of the Fusarium oxysporum Avr2 effector allows uncoupling of its immune-suppressing activity from recognition, New Phytologist, 216/3, doi:10.1111/nph.14733 

[3] Di, X., Takken, F. L. W. and Tintor, N. (2016) How Phytohormones Shape Interactions between Plants and the Soil-Borne Fungus Fusarium oxysporum, Fron. in Plant Science, 7, doi:10.3389/fpls.2016.00170 

[4] Mülner, P., Bergna, A., Wagner, P., Sarajlic, D., Gstöttenmay, B., Dietel, K., Grosch, R., Cernava, T. and Berg, G. (2019) Microbiota Associated with Sclerotia of Soilborne Fungal Pathogens – A Novel Source of Biocontrol Agents Producing Bioactive Volatiles, Phytobiomes Journal, 3/2, doi:10.1094/pbiomes-11-18-0051-r 

[5] Bergna, A., Cernava, T., Rändler, M., Grosch, R., Zachow, C. and Berg, G. (2018) Tomato Seeds Preferably Transmit Plant Beneficial Endophytes, Phytobiomes Journal, 2/4, doi:10.1094/pbiomes-06-18-0029-r

[6] Franken, P., Takken, F. L. W. and rep, M. (2019) Transcript accumulation in a trifold interaction gives insight into mechanisms of biocontrol, New Phytologist, 224/2, doi:10.1111/nph.16141

[7] Furtado, B. U., Gołębiewski, M., Skorupa M., Hulisz, P., and Hrynkiewicz, K. (2019) Bacterial and Fungal Endophytic Microbiomes of Salicornia europaea, Applied and Env. Microbiology, 85/13, doi: 10.1128/aem.00305-19

[8] Furtado, B. U., Nagy, I., Asp, T., Jarosław Tyburski, J., Skorupa, M., Gołębiewski, M., Hulisz, P., and Hrynkiewicz, K. (2019) Transcriptome profiling and environmental linkage to salinity across Salicornia europaea vegetation, BMC Plant Biology, 19/1, doi:10.1186/s12870-019-2032-3 

[9] Pereira, E., Vázquez de Aldana, B. R., San Emeterio, L, and Zabalgogeazcoa, I. (2019) A Survey of Culturable Fungal Endophytes From Festuca rubra subsp. pruinosa, a Grass From Marine Cliffs, Reveals a Core Microbiome, Front. in Microbiology, 9, doi:10.3389/fmicb.2018.03321

[10] Cagnano, G., Roulund, N., Jensen, C. S., Forte F., Asp, T., and Leuchtmann, A. (2019) Large Scale Screening of Epichloë Endophytes Infecting Schedonorus pratensis and Other Forage Grasses Reveals a Relation Between Microsatellite-Based Haplotypes and Loline Alkaloid Levels, Front. in Plant Science, 10, doi:10.3389/fpls.2019.00765 

[11] Collinge, D. B., Jørgensen, H. J. L., Latz, M., Manzotti, A., Ntana, F., Rojas, E., and Jensen, B. (2019) Searching for Novel Fungal Biological Control Agents for Plant Disease Control Among Endophytes, 25-51, doi:10.1017/9781108607667.003

[12] Furtado, B. U., Szymańska, S., and Hrynkiewicz, K. (2019) A window into fungal endophytism in Salicornia europaea: deciphering fungal characteristics as plant growth promoting agents, Plant and Soil, 445/1-2, doi:10.1007/s11104-019-04315-3 

[13] Di, X., Gomila, J., Ma, L., van den Burg, H. A., and Takken, F. L. W. (2016) Uptake of the Fusarium Effector Avr2 by Tomato Is Not a Cell Autonomous Event, Front. in Plant Science, 7, doi: 10.3389/fpls.2016.01915

[14] Di, X., Gomila, J. and Takken, F. L. W. (2017) Involvement of salicylic acid, ethylene and jasmonic acid signalling pathways in the susceptibility of tomato to Fusarium oxysporum, Molecular Plant Pathology, 18/7, doi: 10.1111/mpp.12559 

[15] Cao, L., Blekemolen, M. C., Tintor, N., Cornelissen, B., and Takken, F. L. W. (2018) The Fusarium oxysporum Avr2-Six5 Effector Pair Alters Plasmodesmatal Exclusion Selectivity to Facilitate Cell-to-Cell Movement of Avr2, Molecular Plant, 11/5, doi: 10.1016/j.molp.2018.02.011 

[16] Acevedo-Garcia, J., Gruner, K., Reinstädler, A., Kemen, A., Kemen, E., Cao, L., Takken, F. L. W., Reitz, M., Schäfer, P., O’Connell, R., Kusch, S., Kuhn, H., and Panstruga, R. (2017) The powdery mildew-resistant Arabidopsis mlo2 mlo6 mlo12 triple mutant displays altered infection phenotypes with diverse types of phytopathogens, Scientific Reports, 7/1, doi: 10.1038/s41598-017-07188-7 

[17] Wróblewski, T., Spiridon, L., Martin, E. C., Petrescu, A-J., Cavanaugh, K., Truco, M. J., Xu, H., Gozdowski, D., Pawłowski, K., Michelmore, R. W., and Takken, F. L. W. (2018) Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity, PLOS Biology, 16/12, doi 10.1371/journal.pbio.2005821 

[18]  de Lamo, F., Constantin, M. E., Fresno, D. H., Boeren, S., Rep, M., and Takken, F. L. W. (2018) Xylem Sap Proteomics Reveals Distinct Differences Between R Gene- and Endophyte-Mediated Resistance Against Fusarium Wilt Disease in Tomato,Frontiers in Microbiology 9, doi 10.3389/fmicb.2018.02977

[19] Tintor, N., Paauw, M., Rep, M., and Takken F. L. W. (2020) The root-invading pathogen Fusarium oxysporum targets pattern-triggered immunity using both cytoplasmic and apoplastic effectors, New Phytol. doi: 10.1111/nph.16618. 

[20] Constantin, M. E., Vlieger B. V., Takken, F. L. W., and Rep, M (2020) Diminished Pathogen and Enhanced Endophyte Colonization upon CoInoculation of Endophytic and Pathogenic Fusarium Strains. Microorganisms, 8(4):544. doi: 10.3390/microorganisms8040544. 

[21] De Lamo, F. J. and Takken, F. L. W. (2020) Biocontrol by Fusarium oxysporum Using Endophyte-Mediated Resistance.  Front Plant Sci. 11: 37 2020. doi: 10.3389/fpls.2020.00037. 

[22] Constantin M. E., de Lamo, F. J., Vlieger, B. V., rep, M. and Takken F. L. W. (2019) Endophyte-Mediated Resistance in Tomato to Fusarium oxysporum Is Independent of ET, JA, and SA. Front Plant Sci. 10:979. eCollection 2019. doi: 10.3389/fpls.2019.00979. 

[23] Manzotti, A., Bergna, A., Burow, M., Jørgensen, H. J. L., Cernava, T., Berg, G., Collinge, D. B. and Jensen, B. (2020) Insight into the community structure and lifestyle of the fungal root endophytes of tomato by combining amplicon sequencing and isolation approaches with phytohormone profiling. FEMS Microbiology Ecology, 96:5, https://doi.org/10.1093/femsec/fiaa052. 

[24] De Lamo, F. J., Spijkers, S. B. and Takken, F. L. W. (2020) Protection to tomato wilt disease conferred by the non-pathogen Fusarium oxysporum Fo47 is more effective than that conferred by avirulent strains. Phytopathology 111: 253-257, https://pubmed.ncbi.nlm.nih.gov/32720878/

[25] Richard, M. M. S., Knip, M., Aalders, T. et al. (2020) Unlike many disease resistances , Rxl-Meditated immunity to potato virus X is not compromised at elevated temperatures. Frontiers in Genetics, 11:417, https://pubmed.ncbi.nlm.nih.gov/32391063/

[26] Forte FP, Schmid J, Dijkwel PP, et al., 2020. Fungal Endophyte Colonization Patterns Alter Over Time in the Novel Association Between Lolium perenne and Epichloë Endophyte AR37. Frontiers in Plant Science 11. https://www.frontiersin.org/articles/10.3389/fpls.2020.570026/full

[27] Ntana F, Bhat WW, Johnson SR, Jørgensen HJL, Collinge DB, Jensen B and Hamberger B. (2021) A sesquiterpene synthase from the endophytic fungus Serendipita indica catalyses formation of viridiflorol. Biomolecules 11: 898. doi:10.3390/biom11060898
https://www.mdpi.com/2218-273X/11/6/898/html

[28] Pereira EC, Vazquez de Aldana BR, Arellano JB, Zabalgogeazcoa I. 2021 The role of fungal microbiome components on the adaptation to salinity of Festuca rubra subsp. pruinosa. Frontiers in Plant Science 12: 695717. https://doi.org/10.3389/fpls.2021.695717

[29] Ntana F, Johnson SR, Hamberger B, Jensen B, Jørgensen HJL, Collinge DB. 2022 Regulation of Tomato Specialised Metabolism after Establishment of Symbiosis with the Endophytic Fungus Serendipita indica. Microorganisms 10: 194. https://doi.org/10.3390/microorganisms10010194

[30] Del Barrio-Duque A, Ley J, Samad A, Antonielli L, Sessitsch A, Compant S, 2019. Beneficial Endophytic Bacteria-Serendipita indica Interaction for Crop Enhancement and Resistance to Phytopathogens. Frontiers in Microbiology 10. https://doi.org/10.3389/fmicb.2019.02888

[31] Constantin ME, De Lamo FJ, Rep M, Takken FLW, 2020. From laboratory to field: applying the Fo47 biocontrol strain in potato fields. European Journal of Plant Pathology 158: 645-54. http://dx.doi.org/10.1007/s10658-020-02106-6 .

[32] Richard MMS, Knip M, Aalders T, Beijaert MS, Takken FLW, 2020. Unlike many disease resistances, Rx1-mediated immunity to Potato Virus X Is not compromised at elevated temperatures. Frontiers in Genetics 11. http://dx.doi.org/10.3389/fgene.2020.00417

[33] Del Barrio-Duque A, Samad A, Nybroe O, Antonielli L, Sessitsch A, Compant S, 2020. Interaction between endophytic Proteobacteria strains and Serendipita indica enhances biocontrol activity against fungal pathogens. Plant and Soil 451: 277-305. https://link.springer.com/article/10.1007%2Fs11104-020-04512-5

[35] Sharma S, Compant S, Ballhausen M-B, Ruppel S, Franken P, 2020. The interaction between Rhizoglomus irregulare and hyphae attached phosphate solubilizing bacteria increases plant biomass of Solanum lycopersicum. Microbiological Research 240, 126556. https://doi.org/10.1016/j.micres.2020.126556

[36] De Lamo FJ, Šimkovicová M, Fresno DH, et al., 2021. Pattern-triggered immunity restricts host colonization by endophytic Fusaria, but does not affect endophyte-mediated resistance. Molecular Plant Pathology 22, 204-15. http://dx.doi.org/10.1111/mpp.13018

[37] Richard MMS, Knip M, Schachtschabel J, Beijaert MS, Takken FLW, 2021. Perturbation of nuclear–cytosolic shuttling of Rx1 compromises extreme resistance and translational arrest of potato virus X transcripts. The Plant Journal 106, 468-79. http://dx.doi.org/10.1111/tpj.15179 .

[38] Constantin ME, Fokkens L, De Sain M, Takken FLW, Rep M, 2021. Number of candidate effector genes in accessory genomes differentiates pathogenic from endophytic Fusarium oxysporum strains. Frontiers in Plant Science 12. https://doi.org/10.3389/fpls.2021.761740

[39] Sharma S, Compant S, Franken P, Ruppel S, Ballhausen M-B, 2021. It takes two to tango: A bacterial biofilm provides protection against a fungus-feeding bacterial predator. Microorganisms 9: 1566. https://doi.org/10.3390/microorganisms9081566

[40] Cagnano G, Roulund N, Jensen CS, Lenk I, Cox MP and Asp T. 2020. Mycelial biomass and concentration of loline alkaloids driven by complex population structure in Epichloë uncinata and meadow fescue (Schedonorus pratensis). Mycologia, 112(3): 474–490.  https://doi.org/10.1080/00275514.2020.1746607

[41] Cagnano G, Vázquez-de-Aldana BR, Asp T, Roulund N, Jensen CS, Soto-Barajas MC. 2020 Determination of loline alkaloids and mycelial biomass in endophyte infected Schedonorus pratensis by near-infrared spectroscopy and chemometrics. Microorganisms, 8:776. https://doi.org/10.3390/microorganisms8050776https://www.mdpi.com/2076-2607/8/5/776

[42] Furtado BU, Hrynkiewicz K. Halophyte–Endophyte Interactions: Linking microbiome community distribution and functionality to salinity. InSymbiotic Soil Microorganisms 2021, Springer, Cham (pp. 363-377) https://doi.org/10.1007/978-3-030-51916-2_21

[43] Rändler-Kleine M., Wolfgang A., Dietel K., Junge H., Cernava T., Berg G. (2020) How Microbiome Approaches Can Assist Industrial Development of Biological Control Products. In: Gao Y., Hokkanen H., Menzler-Hokkanen I. (eds) Integrative Biological Control. Progress in Biological Control, vol 20. Springer, Cham. https://doi.org/10.1007/978-3-030-44838-7_13

[44] Mülner, P., Schwarz, E., Dietel, K., Junge, H., Herfort, S., Weydmann, M., Lasch, P., Cernava, T., Berg, G. & Vater, J. (2020). Profiling for bioactive peptides and volatiles of plant growth promoting strains of the bacillus subtilis complex of industrial relevance. Frontiers in Microbiology, 11, 1432. Doi: https://doi.org/10.3389/fmicb.2020.01432

[45] Mülner, P., Schwarz, E., Dietel, K., Herfort, S., Jähne, J., Lasch, P., Cernava, T., Berg, G. & Vater, J. (2021). Fusaricidins, Polymyxins and Volatiles Produced by Paenibacillus polymyxa Strains DSM 32871 and M1. Pathogens, 10, 1485. Doi: https://doi.org/10.3390/pathogens10111485

[46] Kusstatscher P, Wicaksono WA, Bergna A, et al., 2020. Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato. Environmental Microbiome 15, 17. https://doi.org/10.1186/s40793-020-00364-9

[47] Sarrocco S, Herrera-Estrella A, Collinge DB, 2020. Editorial: Plant Disease Management in the Post-genomic Era: From Functional Genomics to Genome Editing. Frontiers in Microbiology 11. DOI https://doi.org/10.3389/fmicb.2020.00107

[48] Taffner J, Bergna A, Cernava T, Berg G, 2020. Tomato-Associated Archaea Show a Cultivar-Specific Rhizosphere Effect but an Unspecific Transmission by Seeds. Phytobiomes Journal 4, 133-41.

[49] De Lamo FJ, Šimkovicová M, Fresno DH, et al., 2021. Pattern-triggered immunity restricts host colonization by endophytic fusaria, but does not affect endophyte-mediated resistance. Molecular Plant Pathology 22, 204-15.

[50] De Rocchis V, Roitsch T, Franken P, 2022. Extracellular Glycolytic Activities in Root Endophytic Serendipitaceae and Their Regulation by Plant Sugars. Microorganisms 10, 320. https://doi.org/10.3390/microorganisms10020320

[51] Pereira EC, Zabalgogeazcoa I, Arellano JB, Ugalde U and Vázquez de Aldana BR (2023) Diaporthe atlantica enhances tomato drought tolerance by improving photosynthesis, nutrient uptake and enzymatic antioxidant response. Front. Plant Sci. 14:1118698. doi: https://doi.org/10.3389/fpls.2023.1118698

[52] Collinge DB, Jensen B, Jørgensen HJL (2022) Fungal Endophytes in Plants and their Relationship to Plant Disease. Current Opinion in Microbiology 69: 102177 https://doi.org/10.1016/j.mib.2022.102177

[53] Forte, F. P., Malinowska, M., Nagy, I., Schmid, J., Dijkwel, P., Hume, D. E., Johnson, R. D., Simpson, W. R. & Asp, T. 2023. Methylome changes in lolium perenne associated with long-term colonisation by the endophytic fungus epichloë sp. Lptg-3 strain ar37. Frontiers in Plant Science, 14. 10.3389/fpls.2023.1258100

PhD fellows

BestPass recruited the following 15 PhD students:

  • ESR1 - Bliss Ursula Furtado: Nicolaus Copernicus University, Torun, Poland
  • ESR2 - Eric Carvalho Pereira: University of Salamanca, Spain
  • ESR3 - Flavia Pilar Forte: Aarhus University, Denmark
  • ESR4 - Alessandro Bergna: ACIB GmbH - TU Graz, Austria
  • ESR5 - Andrea Manzotti: University of Copenhagen, Denmark
  • ESR6 - Francisco J. de Lamo: University of Amsterdam, Netherlands
  • ESR7 - Maria E. Constantin: University of Amsterdam, Netherlands
  • ESR8 - Fani Ntana: University of Copenhagen, Denmark
  • ESR9 - Vincenzo De Rocchis: Humboldt University, Germany / University of Copenhagen, Denmark
  • ESR10 - Alejandro del Barrio: Austrian Institute of Technology (AIT), Austria
  • ESR11 - Giovanni Cagnano: DLF, Denmark
  • ESR12 - Pascal Muelner: ABiTEP GmbH, Germany
  • ESR13 - Manuela Randler- Kleine: Technical University of Graz, Austria
  • ESR14 - Shubhangi Sharma: Humbolt University, Germany
  • ESR15- Alberico Bedini: INOQ GmbH, Germany

Project coordinator: David B. Collinge

Project manager: Minttu Liuhto

Funding: The project has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Sklodowska-Curie grant agreement No 676480.

Period: 1 April 2020 - 31 March 2024.

The main goal of RadiBooster is to develop more robust and climate-secure wheat-, forage grass-, and potato varieties that can produce significantly higher yields under drought and take up more nitrogen than current varieties.

The ambition is to be world-leading in climate resilience breeding. The project builds on the unique RadiMax facility combined with multi-location field trials. A new multi-layered artificial intelligence system will be established for analysis of phenotypic and multiomics-based information.

Internal participants

  • Jesper Cairo Westergaard

  • Kristian Thorup-Kristensen

  • Tomke Susanne Wacker

External participants

  • Danespo A/S
  • DLF Seeds A/S
  • Nordic Seed A/S
  • Sejet Planteforædling A/S
  • Aalborg University
  • Aarhus University

Principal investigator: Kristian Thorup-Kristensen

Project manager: Marieke ten Hoeve

Funding: The project is funded by Innovation Fund Denmark - Grand Solutions.

Periode: 1. Januar 2022 - 31. December 2023

Projektets formål er at fremme fremtidig forædling af robuste, klima- og miljøvenlige græsmarksbælgplanter gennem viden om sortsforskelle i rodvækst og funktion. Målet er således at styrke præforædling, hvor sorter af græsmarksbælgplanter screenes for forskelle i rodvækst og –funktion, for at understøtte fremtidig forædling af mere robuste sorter. Et yderligere mål er at bestemme effekten på rodudviklingen ved samdyrkning med forskellige græsser.

Resultater

Projektleder: Dorte Bodin Dresbøll

Forskere: Dorte Bodin Dresbøll & Nawa Raj Dhamala

Finansieret af: Frøafgiftsfonden

Periode: 1. Januar til 31. December 2022

Projektet bidrager til en bedre forståelse af egenskaber hos græssers rodsystemer for mere effektiv og tørketolerant dyrkning og mere kulstoflagring i jorden

Med det store fokus på miljø og klimaforandringer bliver forbedret rodvækst et vigtigt konkurrenceparameter for salg af græsfrø. Projektets resultater skal fastlægge afgørende egenskaber (traits) i græssernes rodsystem, som skal bidrage til forædlingen af nye græssorter med bedre rodegenskaber.

Resultater: Resultater fra projektet Græsrodssystemer

Projektleder: Kristian Thorup-Kirstensen

Projektmanager: Marieke Ten Hoeve

Forskere: Kirsten Jørgensen, Kristian Thorup-Kristen & Kyriaki Adelais Boulata

Finansieret af: Frøafgiftsfonden 

Periode: 1. Januar 2022 - 31. December 2024

Projektets formål er at udvikle metoder til rodscreening, som kan gennemføres i almindelige markforsøg med græsser.

Med det store fokus på miljø og klimaforandringer bliver forbedret rodvækst et vigtigt konkurrenceparameter. Projektet skal udvikle metoder, der kan anvendes direkte i græsforædlingen, sikre effektiv forædling for forbedret rodvækst og at forbedringerne kan dokumenteres med målte effekter.

Projektleder: Kristian Thorup-Kristensen

Projektmanager: Marieke ten Hoeve

Finansieret af: Frøafgiftsfonden

Period: 1 January 2017 - 31 January 2020

Clean drinking water is crucial to human health and wellbeing. The ambition of the NaToxAq ETN network is to expand the research basis for EU’s leading role in securing high quality drinking waters for its citizens. Focus is on natural toxins – a large group of emerging contaminants with unknown impact on drinking water resources. Both known toxins, like cyanotoxins, cyanogenic glucosides and terpenes and not yet explored toxins will be investigated. Twenty leading universities, research institutions, and water enterprises will pioneer the field through joint training of 15 ESRs investigating natural toxin emission via water reservoirs to water works and consumers.

About the project

The natural toxin challenge is addressed by the concerted work of the ESRs within 4 scientific work packages comprising origin, distribution, fate and remediation. Priority toxins are selected using in silico approaches accompanied by novel non-targeted and targeted analyses to map natural toxins along vegetation and climatic gradients in Europe. Invasion of alien species, toxin emission, leaching and dissipation will be under strong influence of climate change.

Data collected for toxin emission, properties and fate will be used to model effects of climate, land use, and design of remediation actions. Special attention will be paid to toxin removal at water works including development of new technologies tailored to remove natural toxins. The results will contribute to strengthening of European policies and regulation of drinking water, while new business opportunities within the fields of water supply and treatment, chemical monitoring and sensing, and the consulting sector will arise from academia-indstry collaborations.

The urgency of the challenge, its eminent knowledge gaps, its multifaceted and multidisciplinary nature, and the need for scientific and public awareness to be communicated by ESRs in a balanced way makes the topic ideal for a European mobility and training network.

Participants

  • Hans Chr. Bruun Hansen

  • Bjarne W. Strobel

  • Jan H. Christensen

  • Nikoline Juul Nielsen

Research outcome

Great and highly interesting papers are being published and we can start to integrate the results and see patterns, and a first step was taken at the NaToxAq Conference. We have got to know many more and new natural toxins in natural waters thanks to intensive work with natural toxin prioritization, sample preparation and analytical work, and different monitoring strategies. We know more about toxin production, release, fate processes and transport, and first attempts to model natural toxin exposure are taken. We are getting insights into new ways of cyanotoxin exposure and on how we can remove natural toxins at water works, and the basis for risk assessment work is strongly improved.

Publications

[50] Hama, J.; Jørgensen, D.B.G.; Diamantopoulos, E.;  Bucheli, T.D.; Hansen, H.C.B.; Strobel, B.W. (2022) Indole and quinolizidine alkaloids from blue lupin leach to agricultural drainage water. Sci. Tot. Environ. 834: 155283

[49] Kisielius, V.; Drejer, M.; Dornhoff, J.K.; Skrbic, N.; Lindqvist, D.N.; Hansen, H.C.B.; Rasmussen, L.H. (2022) Occurence and stability of carcinogenic illudane glucosides from Bracken in surface waters. Environmental Science: Processes and Impacts. 24: 277.

[48] Jones, M.R.; Pinto, E.; Torres, M.A.; Dorr, F.; Mazur-Marzec, H.; Szubert, K.; Tartaglione, L.; Dell’Aversano, C.; Miles, C.O; Beach, D.G.; McCarron, P.; Sivonen, K.; Fewer, D.P.; Jokela, J.; Janssen, E.M.-L. (2021) CyanoMetCB, a comprehensive public database of secondary metabolites from cyanobacteria. Water Res. 196: 117017.

[47] Schneider, M., Grossi, M. F., Gadara, D., Spáčil, Z., Babica, P. & Bláha, L. (2021). Treatment of cylindrospermopsin by hydroxyl and sulfate radicals: Does degradation equal detoxification? Journal of Hazardous Materials. (in press)

[46] Gunthardt, B. F., Wettstein, F. E., Hollender, J., Singer, H., Harri, J., Scheringer, M., Hungerbuhler, K. & Bucheli, T. D. (2021). Retrospective HRMS Screening and Dedicated Target Analysis Reveal a Wide Exposure to Pyrrolizidine Alkaloids in Small Streams. Environmental Science & Technology, 55, 1036−1044

[45] Mrkajic, N. S., Hama, J. R., Strobel, B. W., Hansen, H. C. B., Rasmussen, L. H., Pedersen, A-K., Christensen, S. C.B. & Hedegaard, M. J. (2021). Removal of phytotoxins in filter sand used for drinking water treatment. Water Research, 205, 117610

[44] Hansen, H. C. B., Hilscherova, K.& Bucheli, T. D. (2021) Natural toxins: environmental contaminants calling for attention. Environmental Science Europe, 33(112)

[43] Hama, J. R., Kolpin, D. W., LeFevre, G. H., Hubbard, L. E., Powers, M. M. & Strobel, B. W. (2021). Exposure and Transport of Alkaloids and Phytoestrogens from Soybeans to Agricultural Soils and Streams in the Midwestern United States. Environmental Science & Technology. 55, 11029−11039

[42] Günthardt, B. F., Hollender, J., Scheringer, M., Hungerbühler, K., Nanusha, M. Y., Brack W. & Bucheli, T. D.(2021). Aquatic occurrence of phytotoxins in small streams triggered by biogeography, vegetation growth stage, and precipitation. Science of the Total Environment, 798

[41] Filatova, D., Jones, M.R., Haley, J.A.,  Núñez, O., Farré, M, Janssen, E.ML. (2021). Cyanobacteria and their secondary metabolites in three freshwater reservoirs in the United Kingdom. Environmental Science Europe, 33(29)

[40] Picardo, M., Núñez, O. & Farré, M. (2021). A data independent acquisition all ion fragmentation mode tool for the suspect screening of natural toxins in surface water. MethodsX, 8,101286

[39] Wu, J.S., Clauson-Kaas, F., Lindqvist, D. N., Rasmussen, L. H., Strobel, B. W. & Hansen, H. C. B. (2021). Does the natural carcinogen ptaquiloside
degrade readily in groundwater? Environmental Sciences Europe, 33(24)

[38] García-Jorgensen, D. B., Diamantopoulos, E., Kisielius V., Rosenfjeld, M., Rasmussen, L.H., Strobel B.W. & Hansen, H. C. B. (2021). Bracken growth, toxin production and transfer from plant to soil: a 2‑year monitoring study. Environmental Sciences Europe, 33(45)

[37] Skrbic, N., Kisielius V., Pedersen, A., Christensen, S. C. B., Hansen, H.C.B. & Rasmussen, L.H. (2021). Occurrence of carcinogenic illudane glycosides in drinking water wells. Environmental Sciences Europe, 33(44)

[36] Schönsee, C. D., Wettstein, F. E. & Bucheli, T.D. (2021). Disentangling Mechanisms in Natural Toxin Sorption to Soil Organic Carbon. Environmental Science and Technology, 55, 8, 4762–4771

[35] Schönsee, C. D., Wettstein, F. E. & Bucheli, T.D. (2021). Phytotoxin sorption to clay minerals. Environmental Sciences Europe, 33(36)

[34] Liang, X., Christensen, J. H. & Nielsen, N.P. (2021). Enhancing the power of liquid chromatography–Mass spectrometry for chemical fingerprinting of phytotoxins in the environment.  Journal of Chromatography A, 1642

[33] Nanusha, M. Y., Krauss, M., Strobel B.W., Sørensen, B.G., Schulze, T.,  & Brack, W. (2021) Occurrence of plant secondary metabolite fingerprints in river waters from Eastern Jutland, Denmark. Environmental Sciences Europe 33(25)

[32] Natumi, R., Marcotullio, S. & Janssen, E.ML. (2021). Phototransformation kinetics of cyanobacterial toxins and secondary metabolites in surface waters. Environmental Sciences Europe 33(26)

[31] Kubíčková, B., Ramwell, C., Hilscherová, K. & Jacobs M.N. (2021). Highlighting the gaps in hazard and risk assessment of unregulated Endocrine Active Substances in surface waters: retinoids as a European case study. Environmental Sciences Europe 33(20)

[30] Griffiths, M.R., Strobel, B.W., Hama, J.R. & Cedergreen, N. (2021). Toxicity and risk of plant-produced alkaloids to Daphnia magna. Environmental Sciences Europe, 33(1), pp.1-12.

[29] Picardo, M., Sanchís, J., Núñez, O. & Farré, M. (2020). Suspect screening of natural toxins in surface and drinking water by high-performance liquid chromatography / high-resolution mass spectrometry. Chemosphere, 261, 127888

[28]  Hama, J. R. & Strobel, B.W. (2021). Occurrence of pyrrolizidine alkaloids in ragwort plants, soils and surface waters at the field scale in grassland. Science of The Total Environment, 755(1), 142822; DOI

[27] Filatova, D., Picardo, M., Núñez, O. & Farré, M. (2020). Analysis, levels and seasonal variation of cyanotoxins in freshwater ecosystems. Trends in Environmental Analytical Chemistry, 26, e00091

[26]  Nanusha, M. Y., Krauss, M., Schönsee, C. D., Günthardt, B. F., Bucheli, T. D. & Brack, W. (2020). Target screening of plant secondary metabolites in river waters by liquid chromatography coupled to high-resolution mass spectrometry (LC–HRMS). Environmental Sciences Europe, 32,142

[25] Picardo, M., Núñez, O. & Farré, M. (2020). Suspect and Target Screening of Natural Toxins in the Ter River Catchment Area in NE Spain and Prioritisation by Their Toxicity. Toxins ,12(12), 752

[24] Kisielius V., Hama, J.R., Skrbic, N., Hansen, H.C.B., Strobel, B.W. & Rasmussen, L.H. (2020). The invasive butterbur contaminates stream and seepage water in groundwater wells with toxic pyrrolizidine alkaloids. Scientific Reports, 10, 19784

[23] Hama, J.R. & Strobel, B.W. (2020). Natural alkaloids from narrow-leaf and yellow lupins transfer to soil and soil solution in agricultural fields. Environmental Sciences Europe, 32, 126

[22] Skrbic, N., Pedersen, A., Christensen, S. C. B., Hansen, H. C. B. & Rasmussen, L. H. (2020). A novel method for determination of the natural toxin ptaquiloside in ground and drinking water. Water, 12(10), 2852

[21] Nanusha, M.Y., Krauss, M. & Brack, W. (2020). Non‑target screening for detecting the occurrence of plant metabolites in river waters. Environmental Sciences Europe, 32, 130

[20] García-Jorgensen, D. B., Hansen, H. C. B., Abrahamsen, P. & Diamantopoulos, E. (2020). A novel model concept for modelling the leaching of natural toxins: results for the case of ptaquiloside. Environmental Science: Processes & Impacts, 22(8), 1768-1779

[19] Schneider, M., Rataj, R., Kolb, J. F. & Bláha, L. (2020). Cylindrospermopsin is effectively degraded in water by pulsed corona-like and dielectric barrier discharges. Environmental Pollution, 266 (2), 115423

[18] Schneider, M. & Bláha, L. (2020). Advanced oxidation processes for the removal of cyanobacterial toxins from drinking water.  Environmental Sciences Europe, 32, 94

[17] Natumi, R. S. & Janssen, E. M.-L. (2020). Cyanopeptide co-production dynamics beyond microcystins and effects of growth stages and nutrient availability. Environmental Science & Technology, 54(10), 6063–6072

[16] Jones, M. R., Pinto, E., Torres, M. A., Dörr, F., Mazur-Marzec, H., Szubert, K., Tartaglione, L.,  Dell'Aversano, C., Miles, C. O., Beach, D. G., McCarron, P., Sivonen, K., Fewer, D. P.,  Jokela, J. & Janssen, E. M.-L. (2020). Comprehensive database of secondary metabolites from cyanobacteria. BioRxiv

[15] Filatova, D., Núñez, O. & Farré, M. (2020). Ultra-Trace Analysis of Cyanotoxins by Liquid Chromatography Coupled to High-Resolution Mass Spectrometry. Toxins, 12(4), 247

[14] Egli, C. M., Natumi, R. S., Jones, M. R. & Janssen, E. M.-L. (2020). Inhibition of Extracellular Enzymes Exposed to Cyanopeptides. Chimia (Aarau), 74(3), 122–128

[13] Günthardt, B. F., Schönsee, C. D., Hollender, J., Hungerbühler, K., Scheringer, M. & Bucheli, T. D. (2020). “Is there anybody else out there?” – First Insights from a Suspect Screening for Phytotoxins in Surface Water. CHIMIA, 74(3), 129–135

[12] Schönsee, C. D. & Bucheli, T.D. (2020). Experimental Determination of Octanol–Water Partition Coefficients of Selected Natural Toxins. Journal of Chemical & Engineering Data, 65(4), 1946-1953

[11]  Liang, X., Nielsen, N.P. & Christensen, J. H. (2020). Selective pressurized liquid extraction of plant secondary metabolites: Convallaria majalis L. as a case. Analytica Chimica Acta: X, 4, 100040

[10] Brozman, O., Kubíčková, B., Babica, P. & Labohá, P. (2020). Microcystin-LR does not alter cell survival and intracellular signaling in human bronchial epithelial cells. Toxins, 12(3), 165

[9] Schneider de Oliveira, L.G., Boabaid F.M., Kisielius V., Rasmussen L.H., Buroni F., Lucas M., Schild C.O., Lopez F., Machado M. & Riet-Correa F. (2020). Hemorrhagic diathesis in cattle due to consumption of Adiantopsis chlorophylla (Swartz) Fée (Pteridaceae). Toxicon: X, 5, 100024

[8] Kisielius, V., Lindqvist, D.N.,  Thygesen, M.B., Rodamer, M., Hansen, H.C.B. & Rasmussen, L.H. (2020). Fast LC-MS quantification of ptesculentoside, caudatoside, ptaquiloside and corresponding pterosins in bracken ferns. Journal of Chromatography B, 1138, 121966

[7] Hama, J.R. & Strobel B. W. (2019). Pyrrolizidine alkaloids quantified in soil and water using UPLC-MS/MS. RSC Advances, 9, 30350-57

[6] Aranha PCdR, Rasmussen L.H., Jensen HME, Hansen, H.C.B. & Friis C. (2019). Fate of ptaquiloside—A bracken fern toxin—In cattle. PLoS ONE 14(6): e0218628. 

[5] Kubíčková, B.; Babica, P.; Hilscherova, K. & Šindlerová, L. (2019). Effects of Cyanobacterial Toxins on the Human Gastrointestinal Tract and the Mucosal Innate Immune System. Environmental Sciences Europe, 31, 31

[4] Janssen, E.M.-L. (2019). Cyanobacterial peptides beyond microcystins – A review on co-occurrence, toxicity, and challenges for risk assessment, Water Research, 151, 488-499

[3] Kubíčková, B., Labohá, P., Hildebrandt, J.-P., Hilscherová, K. & Babica, P. (2019). Effects of cylindrospermopsin on cultured immortalized human airway epithelial cells. Chemosphere, 220, 620-628 

[2] Picardo, M., Filatova D., Núñez, O. & Farré, M. (2019). Recent advances in the detection of natural toxins in freshwater environments. Trend on Analytical Chemistry. 112, 75-86

[1] Bucheli, T.D., Strobel B.W. & Hansen H.C.B. (2018). Personal Care Products Are Only One of Many Exposure Routes of Natural Toxic Substances to Humans and the Environment. Cosmetics, 5(1), 10

Principal investigator: Hans Chr. Bruun Hansen

Funded by: Horizon 2020 - European Union Funding for Research & Innovation

Period: 1/11/2021 - 31/10/2025

We aim at deciphering the mechanism of lipid selection by P4 ATPases through structural and biochemical characterization of plant flippases with high sequence identity but different transport specificities. The project is a common effort between three groups at the University of Copenhagen (Rosa Lopez), Aarhus University (Joseph Lyons) and Ruhr University Bochum (Thomas Günther-Pomorski).

The mechanism by which lipid flippases transport their substrate is unclear. Recent structural studies have shed light on this subject in mammalian cells and yeast. However, most plant P4 ATPases have evolved independently of their yeast and mammalian counterparts, and many of the amino acid residues important for lipid recognition are not conserved in plants. Do plant P4 ATPases recognize lipids in the same way as flippases from other organisms?

Project number: 1026-00024B

Contact: Rosa Laura López Marqués

Funded by: Independent Research Fund Denmark

Period:  2022-2024

In this project we produce PGPPs and explore if these bio-friendly peptides have crop stimulating activity, that can promote sustainable production.

Previously, PGPPs have been synthesized by processes relying on expensive chemical components, providing low yields, only sufficient for research. For this reason, the many practical application prospects for crop production have not yet been explored in trial settings representing production conditions.

Project description

In the first year of the project, we have managed to establish a heterologous Escherichia coli expression system that allows for stable peptide production and activation by sulfonation. In these bacterial strains peptides are secreted, simplifying purification of stable preparations. An Arabidopsis plant-assay for determination of growth stimulation has been established and is currently optimized for better consistency.

In the second year of the project, 2024, we will conduct growth and nutrition uptake trials, and determine if treated tomato as well as barley crops become more productive. These results will be reported on this web site at the beginning of 2025 and published in a scientific journal.

Project leader: Anja Thoe Fuglsang

Project participants: Anja Thoe Fuglsang & Frederik Grønbæk Tidemand

Funded by: Promilleafgiftsfonden for landbrug

Period:  01/10/2020 to 30/09/2025

EcoSap will evaluate the efficacy and environmental safety of saponins as a novel green solution for sustainable food production. Saponins are a natural defense compound in plants that exhibit detergent-like properties that can disrupt the cell membranes of herbivore pests, causing cell death.

About the project

Herbivore insects are very damaging to world food production. It is estimated that they consume

20-30% of the potential production; therefore, there is a global need for more effective yet environmentally friendly pesticides. Plants and insects have interacted for millions of years with the former evolving specialized defense mechanisms against herbivore insects – providing an untapped opportunity to find and explore bioactive compounds in plants as sources for biopesticides. Saponins are a class of such underutilized defense compounds. They exhibit detergent-like properties that can disrupt the cell membranes of herbivore pests, causing cell death. In the EcoSap project, we will learn from nature and investigate the potential of saponins as biopesticides as Green Solutions for future insect pest management. However, to do so, we first need to find out how plants that produce saponins avoid intoxication by their own defense, where in the plant saponins are stored, and their actual mode of action. We assume that saponins target membrane systems, but surprisingly, we do not know the mode of action – yet this is key for their exploitation as insecticides.

A major bottleneck to utilizing plant compound as insecticides is their availability and ability to scale up. In EcoSap, we will screen a number of plants and biowastes for saponins that have the correct structures to be insecticides. In collaboration with a bio-refinery plant, we will address and evaluate the potential of saponins for upscaling. Finally, we will perform a thorough evaluation of the efficacy of selected saponin structures by studying their effect on target and non-target organisms to facilitate their ecotoxicological and environmental safety evaluation. In this way, EcoSap will fully assess the untapped potential of saponins as a novel green solution for sustainable food production going from mode-of-action, to upscaling, to evaluation of their efficacy and environmental safety.

Partners

The following partners are involved in the project

  • University of Copenhagen
  • University of Bochum, DE (links at bottom of page)
  • Rothamsted Research, UK
  • Dansk Bioindustri ApS

Internal participants:

  • Anja Thoe Fuglsang
  • Jincheng Shen
  • Malbor Dervishi
  • Nina Cerdergreen
  • Pablo D. Cárdenas
  • Søren Bak

External participants:

  • Linda M Field, Rothamsted Research
  • Thomas Günther-Pomorski, University of Borchum
  • Orla Møller Petersen, Dansk Bioindustri ApS

Contact: Søren Bak

Project manager: Katja Annette Willrodt 

Funded by: EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Period: 01/01/2021 - 01/01/2024

Crop for the Future will develop Chenopodium album to be reintroduced in modern agriculture by:
Establishing the technological platforms to accelerate the domestication of C. album. Characterizing the nutritional and anti-nutritional value of C. album. Elucidating the regulation and biosynthesis of anti-nutritional saponins in C. album.

About the project

THE CHALLENGE: We have to feed a growing population in a world with scarcity of land and water, over use of pesticides and fertilizers and climate emergency. Currently, just four crops (rice, wheat, maize and potato) out of 30.000 edible plants provide 60% of the world’s dietary energy intake. Our current food system is unnecessarily exposed and vulnerable to pests, diseases and climate change. Therefore, it is not enough to keep improving the current crops, but there is an urgent need to introduce new species to transition towards a more sustainable agriculture. New crops should 1)diversify our food system, 2)offer higher nutritional value and yields using fewer resources, 3) be more resilient to pests, diseases and climate change, and 4) be grown closer to the consumers to reduce the environmental impact of global transportation of food. Crop for the Future addresses these four major challenges.

A GREEN LOCAL SOLUTION:There are many wild and semi-domesticated plants with potential to be utilized as food crops. These plants are well adapted and thrive in local climate, and can be a unique and rich source of nutrients. However, many have anti-nutritional or unpleasant chemical compounds that harm their potential use as food and they are not suitable for large-scale agriculture because they have not been bred for traits of interest. Resolving these issues by traditional breeding is challenging due to the extended time required. Transgenic approaches are faster, but raise public concerns, limiting crop improvement.

This project has the potential of transforming a wild plant into a new sustainable food crop. In nature there are thousands of resilient plants with potential to be developed as new crops for future food security. However, many of them have anti-nutritional compounds and these need to be removed before we can use these plants for food and fodder. We hypothesize that, combining state- of-the-art technologies on speed breeding, gene editing, transcriptomics and metabolomics, it is possible to perform rapid domestication of wild plants. In the Crop for the Future project, we aim to develop a local Danish plant, Chenopodium album, as a potential nutritious food crop.

To achieve this, the objectives of the project are

  1. To establish the technological platforms to accelerate the domestication of C. album, using the novel Speed Breeding technology
  2. To characterize its nutritional and anti-nutritional value and
  3. To elucidate the regulation and biosynthesis of its Anti-nutritional saponins.

In the media

Partners

Participants: 

  • Søren Bak, UCPH
  • Pablo D. Cárdenas, UCPH
  • Thue Pavlo Hauser, UCPH
  • Poul Erik Jensen, UCPH
  • Brande Wulff, John Innes Institute

Contact: Søren Bak

Project manager: Katja Annette Willrodt

Funded by: Independent Research Fund Denmark

SAP-FATE: Saponins for sustainable agriculture - Fate, biological activity and environmental impact of saponins in soils

Period: 01/03/2022 to 31/12/2024

In SAP-FATE we aim to understand the properties, stability, activity and transformation of saponins in soil, and evaluate how saponins of known chemical structures affect soil microbial communities. SAP-FATE will provide answers that are pivotal for evaluation of the potential of saponins as future biopesticides and for their risk assessment.

About the project

Plant specialized metabolites have an untapped potential as biopesticides and can become part of the solution to secure sustainable food production and increase agricultural resilience. Saponins are one such class of plant specialized metabolites that work against above-ground insect herbivore pests. However, we know surprisingly little about what happens below-ground when they are introduced in agricultural pest management. In SAP-FATE we aim to understand the properties, stability, activity and transformation of saponins in soil, and evaluate how saponins of known chemical structures affect soil microbial communities. SAP-FATE will provide answers that are pivotal for evaluation of the potential of saponins as future biopesticides and for their risk assessment. The three researchers (Søren Bak, Mette Haubjerg Nicolaisen, and Hans Christian Bruun Hansen) bring the necessary and complementary competencies within plant specialized metabolites, soil environmental chemistry, and soil microbiota to achieve the ambitious aims. The project consists of three elements that comprise purification and isotopic labelling of saponins for fate studies, saponin mobility and degradation in soils, and their impact on microbial community structures and effects on element cycling.

Many of the new high protein crops to be introduced as part of the transition to a greener diet naturally contain saponins that inevitably will end up in the environment. We do not know if saponins will be released to the belowground from these plants. Therefore, SAP-FATE will also analyze the content, structural complexity and their ability for exudation to the soil.

SAP-FATE has a focus on saponins, but the knowledge gained and technologies implemented can directly be transferred to other classes of plant specialized metabolites and biopesticides. SAP-FATE is at the very forefront of the Green Transition agenda, and will contribute to positioning plant specialized metabolites as a logical approach to support to support productivity and resilience of agricultural production systems.

Aims

We must make agriculture more sustainable, productive, resilient and at the same time more environmentally friendly. Plant specialized metabolites like triterpenoid saponins can be part of this solution – but we need to understand their fate and environmental impact before we can unleash their potential.

In SAP-FATE we aim to understand the properties, stability and transformation of saponins in soil and evaluate how saponins of known chemical structures affect soil microbial communities and their responses towards saponins. 

Participants

  • Chen Wang
  • Hans Chr. Bruun Hansen
  • Malbor Dervishi
  • Mette Haubjerg Nicolaisen
  • Søren Bak

Contact: Søren Bak

Project manager: Katja Annette Willrodt

Funded by: ?

Period: 2016-2020

Construction and re-planning of urban land call for sound and adequate evaluation of potential negative health effects caused by pollution from former land use. This demands not only reliable chemical impact assessments but also cost-effective decision-making processes, to avoid unnecessary and costly delays.

The chemical impact assessment of soil and sediment contamination is today restricted to measuring concentrations of target organic and element contaminants covered by national quality criteria. Ignoring the presence of other contaminants and their combination in complex mixtures limits the reliability of this approach, and can increase construction costs.

We want to move towards a new paradigm where fingerprinting entire contaminant profiles will allow far more sound and reliable chemical impact assessments; appropriate visualization tools for larger areas makes this increased information easily accessible to public authorities, consultants and urban developers.

We will thus focus on two deliverables: new chemical analytical technologies for fingerprinting analysis of soil and sediments and GIS software add-on for visualization to integrate currently available contaminant data and the new chemical fingerprints.

The project is a public-private partnership between university, municipality and private companies, ensuring a strong position in the value chain from research to development and implementation.

Project partners

  • Eurofins Environment A/S

  • MOE | Seacon A/S

  • KMC-Nordhavn, The City of Copenhagen

  • Department of Computer Science, University of Copenhagen

  • Department of Plant and Environmental Sciences, University of Copenhagen

Acting Project Leader: Professor Jan H. Christensen

Deputy Project Leader: Customer Manager and Head of Innovation, Peter Mortensen, Eurofins Environment A/S

Project Manager: Environmental consultant, Nemanja Milosevic, MOE | Seacon A/S

Funded by: Innovation Fund Denmark

Period: 1 November 2019 - 1 November 2023.

Linking of Chemical and Toxicological Fingerprints: A new method to prioritize monitoring and regulation of pollutants in water.

Only a fraction of the toxicity (1-5%) of whole wastewater samples can be explained by standard monitored chemicals. VANDALF will develop and implement an innovative toxicology-driven risk assessment platform to identify Contaminants of Emerging Concern (CECs) in wastewater. With this it will be possible to focus monitoring programs, remediation strategies and regulatory measures on the chemicals causing the remaining 95-99% of toxicity in effluent water.

Approach

In VANDALF, the approach is to link technology-specific, but otherwise unbiased and non-targeted chemical detections (‘chemical fingerprints’) with sets of relevant toxicological endpoints (‘toxicological fingerprints’) to identify which chemicals or groups of chemicals that can explain the toxicity. This approach was put forward by Eide et al. in 2002 under the name virtual effect directed analysis (VEDA).

Research goals

  • To establish sampling, sample preparation, chemical analysis, and toxicology workflows that enable the identification of CECs in wastewater samples
  • To establish database-driven strategies for CEC identification using non-target chemical fingerprinting and toxicology data
  • To establish methods to quantify the fraction of toxicity explained by identified chemicals
  • To establish multivariate statistical models that relate chemical fingerprints to toxicological endpoints to identify unknown toxicants

News

Partners

Department of Plant and Environmental Sciences (PLEN), University of Copenhagen (UCPH) 

  • Jan H. Christensen
  • Nina Cedergreen
  • Peter E. Holm
  • Giorgio Tomasi
  • Nikoline J. Nielsen
  • Majbrit Dela Cruz

Eurofins: Peter Mortensen

VandCenterSyd (VCS): Per Henrik Nielsen

BIOFOS: Artur Mielczarek & Dines Thornberg

Department of Food Science (FOOD), UCPH: Rasmus Bro & Age Smilde

Danish Environmental Portal (DEP): Niels Høgsted

MSC, MSCi: Tore Vulpius

Copenhagen Municipality (KMC): Martin Jakobsen

Swiss Federal Institute of Aquatic Science and Technology (Eawag): Juliane Hollender

The Danish Environmental Protection Agency (Danish EPA):Helle Rüsz Hansen & Gudrun Frandsen Krog

Swedish University of Agricultural Sciences (SLU): Johan Lundqvist

Internal participants

  • Giorgio Tomasi
  • Jan H. Christensen
  • Majbrit Hansen Dela Cruz
  • Nikoline Juul Nielsen
  • Nina Cedergreen
  • Peter Engelund Holm
  • Selina Kornelia Tisler

Head of project: Jan H. Christensen

Funded by: The project is funded by Innovation Fund Denmark - Grand Solutions.

Period: 1 January 2020 - 23 December 2025

A Novo Nordisk Foundation Challenge project that aims to design barley and wheat resistance to powdery mildew and rust disease based on novel principles.

A recent study estimated that approximately 20% of the global crop production is lost to infectious plant diseases, despite use of pathogen control means, such as agrochemicals. Genes for disease resistance are commonly introduced into plant cultivars to activate efficient immunity upon pathogen attack. However, these resistances are generally not durable as new pathogen genotypes that overcome the resistances appear after a few years. This calls for smarter regulation of the plant immunity. Therefore, PlantsGoImmune aims to design resistance by following three overlapping strategies.

Research strategies

  • Effector-insensitive effector targets
    Make non-host-inspired “effector-insensitive effector targets” to prevent pathogen effectors from manipulating plant immunity and susceptibility.
  • Susceptibility mutants
    Eliminate susceptibility components that nourish the pathogens. This is likely to activate lesion formation, which we will “cure” by inactivating monitoring NLR-receptor proteins that trigger this undesired feature.
  • Effector decoy
    Exploit an NLR-monitored effector target, otherwise not targeted by fungal effectors, and turn it into a powdery mildew/rust effector decoy. This will make these pathogens activate this receptor and trigger immunity.

Research themes

  • Effector targets
    Selected barley powdery mildew and wheat stripe rust fungal effectors are being used in 1) yeast 2-hybrid screens for plant effector targets, and 2) in yeast growth retardation assays to search for interference of general eukaryotic cellular pathways. Based hereon effector/target sets will be selected, which have potential to contribute to resistance by making effector-insensitive effector targets.
    An opposite strategy will be followed as well. Here a known cereal NLR-monitored protein will be edited to become a powdery mildew/rust effector target (a decoy), and thereby immunity will be activated after attack.
  • Membrane trafficking in immunity
    Previous studies of membrane trafficking have shown that separate pathways control pre- and post-invasive immunity to the powdery mildew fungus. Interestingly, the pathways mediate secretion of two distinct classes of extracellular vesicles (EVs). Ongoing studies aim to identify more molecular details of these pathways, including how they diverge. EVs contain small RNAs and we are studying how these are loaded and potentially influencing the pathogens via RNA interference.
  • Susceptibility components
    Pathogens exploit plant mechanisms to their own benefit, including nutrient transfer and establishment of a membrane niche inside the host cell. Unlike immunity, susceptibility is poorly understood despite its potential importance as an avenue for disease resistance. The Mlo protein is being studied from this perspective. Powdery mildew and rust fungi develop haustorial structures inside the plant cells and stimulate the plant cell to generate extrahaustorial membranes (EHMs) as an essential susceptibility component. In PlantsGoImmune, we address how the EHM is formed based on our previous finding that barley powdery mildew EHM shares features with the endoplasmic reticulum (ER) membrane. 
    During the studies of effector targets, we will aim to select proteins involved in membrane processes controlling immunity and susceptibility. This will allow us to use our insight in these processes to assay the cellular impact of the effectors and how this is influenced by different versions of effector targets.

Partners

Internal partners:

  • Hans Thordal-Christensen, Dept. of Plant and Environmental Sciences, University of Copenhagen
  • Anja T. Fuglsang, Dept. of Plant and Environmental Sciences, University of Copenhagen

External partners:

Contact: Hans-Thordal Christensen

Project manager: Dorine Jeanne Mariëtte du Mee

Funded by: Novo Nordisk Fonden

Period: 2019-2025

In the MATRIX, we use new microbiome-assisted approaches combined with deep-learning and modelling to quantitatively and predictably improve crop resilience management strategies.

MATRIX is a part of the Collaborative Crop Resilience Program (CCRP), together with the projects INTERACT and InRoot, all funded by the Novo Nordic Foundation. We will zoom in on the taxonomic diversity and functional potential of the wheat flag leaf microbiome. Which key microbes are involved in plant protection against biotic and abiotic stress? Combined with machine learning, this allows us to predict microbiome-related changes and their effect on crop resilience and productivity under climate change scenarios.

Research questions

The following four Research Questions (RQ1-RQ4) will be addressed in the project:

RQ1: What is the microbiological and chemical diversity of the wheat phyllosphere (here encompassing the surface as well as the interior, the endosphere of the wheat flag leaf)?

RQ2: How can we best integrate multiple data types to develop a predictive model of microbiome-mediated wheat resilience to biotic and abiotic stress?

RQ3: What are the relationships between the leaf microbiota, phyllosphere chemistry, plant genetics, environmental factors, and stress resilience of wheat?

RQ4: How do we optimize use of the predictive model to engineer the wheat phyllosphere microbiome to improve resilience and productivity?

Work packages

MATRIX will address six scientific Work Packages (WP1-WP6). The experimental Tasks within each WP will contribute to answer the Research Questions

WP1:Field logistics, environmental and phenotype monitoring

This WP is responsible for the design of field experiments at UCPH and NCSU in order to investigate how the flag leaf microbiome of wheat is influenced by cropping factors, microclimate and wheat genotypes.

WP Lead: Svend Christensen (UCPH); Co-lead: Gina Brown-Guedira (NCSU)

  • Task 1.1 Establishment of field study infrastructure and field microbiome gradients.
  • Task 1.2 Optimize logistics for targeted sampling.
  • Task 1.3 Optimize logistics for basal environmental measurements.
  • Task 1.4 Design field intervention experiments.

WP2: Microbiomics & hub taxa

This WP is responsible for sequencing the wheat flag leaf phyllosphere metagenome and metatranscriptome from samples obtained from the different fields in the US and DK (see WP1). The sequencing data will together with the environmental metadata create the backbone of the initial data input into the MATRIX predictive model.

WP Lead: Jos Raaijmakers (NIOO-KNAW); Co-lead: Lars Hestbjerg Hansen (UCPH)

  • Task 2.1 Optimize protocols and pipelines.
  • Task 2.2 Sequence the wheat phyllosphere metagenome and metatranscriptome.
  • Task 2.3 Isolate, cultivate and identify phyllosphere microbes.
  • Task 2.4 Isolate bacteriophages with potential to regulate hub taxa and pathogens.
  • Task 2.5 Investigate microbe-microbe interactions and screening isolates for chemical signals.

     

WP3:Chemistry

This WP is responsible for providing the chemical profiling/characterization of the wheat flag leaf phyllosphere microbiome and in particular of hub microbial taxa that affect crop resilience. The targeted and untargeted analysis (metabolomics) performed in this WP covers finding carbohydrates, amino acids, organic acids as well as volatile organic compounds (VOCs) associated with the wheat phyllosphere microbiome.

WP Lead: Jan H. Christensen (UCPH); Co-lead: Jos Raaijmakers (NIOO-KNAW)

  • Task 3.1 Build a chemical database for targeted screening and suspect screening analysis of phyllosphere metabolites.
  • Task 3.2 Establish a pipeline for collection, handling and long-term storage of VOCs, semi-VOCs and non-VOCs in the phyllosphere.
  • Task 3.3 Targeted and untargeted metabolomics of organic compounds and elements in field and greenhouse samples.
  • Task 3.4 Metabolite profiling of isolated strains from flag leaves.
  • Task 3.5 Tentative and full identification of key metabolites.

WP4:Effect of plant-microbiome interactions on resilience

This WP is responsible for empirically testing, under controlled settings in greenhouse experiments, how the wheat phyllosphere microbiome and its members affect wheat growth, physiology, and yield under stress. Putative mechanisms underlying microbiome effects, as well as interactions within microbial consortia, will be identified by examining changes in gene expression and secondary metabolites. The WP serves as validation of the results obtained from field microbiomes (WP1-3), informatics analysis (WP5) and modelling (WP6).

WP Lead: Christine Hawkes (NCSU); Co-lead: Ross Sozzani (NCSU) 

  • Task 4.1 Optimize methods and select putative drivers of foliar microbiome effects on plant hosts.
  • Task 4.2 Identify minimal microbiomes needed to achieve resilient phenotypes.
  • Task 4.3 Identify putative mechanisms for how addition of hub taxa affects wheat phenotype resilience.
  • Task 4.4 Examine how consortia of hub taxa affect wheat resilience.
  • Task 4.5 Targeted microbiota manipulations by bacteriophage applications.
  • Task 4.6 Verify genetic mechanisms underlying microbiome effects on wheat resilience.
  • Task 4.7 Translate to real-world agriculture.

WP5:Informatics and data integration

This WP is responsible for establishing a common computational platform for handling major computational tasks related to storing, sharing and analysing large-scale data generated from the other WPs, such as metabolomics, environmental and microbiome data.

WP Lead: Simon Rasmussen (UCPH); Co-lead: Lars Hestbjerg Hansen (UCPH)

  • Task 5.1 Establish informatics infrastructure and accessible databases for chemical, environmental and microbial data, which can be used by all WPs.
  • Task 5.2 Preparation of microbiomics, metabolomics and environmental data for unsupervised learning and input to the deep learning model.
  • Task 5.3 Identify data manifolds for reconstruction of microbial genomes and metabolomic signatures.
  • Task 5.4 Network analysis and deep learning approaches for identification of microbial consortia, genes, and metabolites important for plant resilience.
  • Task 5.5 Determining the relationship between leaf, root, and seed microbiomes.
  • Task 5.6 Continuous update, validation and dissemination of data and results to the plant-microbiome experimental interactions (WP4) and the deep learning model (WP6).

WP6:Building a deep-learning model

This WP is responsible for the integration of all data and results produced in WP1-WP5, which will be based on deep neural networks. These networks will, by using representation learning, serve to integrate the environmental, microbial, metabolomics and network data in a single deep learning model that can be used to predict yield and crop resilience of the wheat system.

WP Lead: Mads Nielsen (UCPH); Co-lead: Simon Rasmussen (UCPH)  

  • Task 6.1 Determine the prerequisites for building an integrative deep learning model and identify existing mechanistic models of plant growth.
  • Task 6.2 Transform microbiome, chemical, environmental and imaging data to appropriate formats for feeding into the deep learning models.
  • Task 6.3 Identify resilience trajectories through representation learning of the diverse omics datasets.
  • Task 6.4 Create supervised deep learning models for prediction of phenotype membership.
  • Task 6.5 Develop time resolved deep learning models for prediction of resilience trajectories and for identifying possible interventions in a given field.
  • Task 6.6 Validating, refine and optimize the models after field trial data acquisition and test model transferability.

Partners

The following partners are involved in the project

  • University of Copenhagen, Denmark
  • North Carolina State University, United States
  • Netherlands Institute of Ecology, Netherlands
  • Technical University of Denmark, Denmark

External participants

Christine Hawkes, Professor, North Carolina State University

Ross Sozzani, Associate Professor, North Carolina State University

Gina Brown-Guedira, USDA Professor, North Carolina State University

Jos Raaijmakers, Professor, Netherlands Institute of Ecology (NIOO-KNAW)

Anders Bjorholm Dahl, Professor MSO, Technical University of Denmark

Rasmus Kjøller, Associate Professor, University of Copenhagen, Department of Biology

Mads Nielsen, Professor, University of Copenhagen, Department of Computer Science

Simon Rasmussen, Associate Professor, University of Copenhagen, Novo Nordisk Foundation Center for Protein Research

Publications

1. Hawkes, C. v et al. Extension of Plant Phenotypes by the Foliar Microbiome. Annu Rev Plant Biol 72, 823–846 (2021).

2. Gouka L, et al, Phenotypic and Metabolic Diversity of Yeasts From Wheat Flag Leaves. Front Plant Sci. 2022 Jul   7;13:908628. doi: 10.3389/fpls.2022.908628

3. Wacenius Skov Alanin, K. et al. Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and        Uncultured by Plaque Assay. Viruses (2021) doi:10.3390/v13060959.

4. Gobbi, A. et al. A global microbiome survey of vineyard soils highlights the microbial dimension of viticultural terroirs. Commun Biol (2022) doi:10.1038/s42003-022-03202-5.

5. Nielsen, T. K. et al. Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software. Mol Ecol (2022) doi:10.1111/mec.16679.

6. Gouka, L., Raaijmakers, J. M. & Cordovez, V. Ecology and functional potential of phyllosphere yeasts. Trends Plant Sci (2022) doi:10.1016/J.TPLANTS.2022.06.007.

7. Forero-Junco, L. M. et al. Bacteriophages Roam the Wheat Phyllosphere. Viruses (2022) doi:10.3390/v14020244.

8. Nielsen, T. K. et al. Complete Genome Sequence of the Cytokinin-Producing Biocontrol Strain Pseudomonas fluorescens G20-18. Microbiol Resour Announc 10, (2021).

9. Medina et al., Machine learning and deep learning applications in microbiome research.  ISME Communications,   Accepted)

Internal participants

  • Jan H. Christiansen
  • Jesper Cairo Westergaard
  • Lars Hestbjerg Hansen
  • Svend Christensen

Project leader: Lars Hestbjerg Hansen

Project manager: Katja Annette Willrodt

Scientific coordinator: Leise Riber

Funded by: This project is funded by the Novo Nordisk Foundation (Grant number: NNF19SA0059348).

Period:  01.01.2025 – 31.12.2025

We will explore the technological possibilities of generating marker-free NGT plants by cis-genesis through combining elements of our CRISPR breeding platform with traditional cis-genesis technology, in potato. If successful, this will enable introduction cis-genes into the genome of potato without the use of selection-markers.

We expect that results gathered throughout 2025 will enable us to assess the feasibility of the method by end 2025 or first half of 2026. Results will be published and appear on this homepage

Aim

We aimed to explore the possibility of expanding our CRISPR/Cas engineering platform in potato to encompass DNA free ribonucleoprotein (RNP) gene editing. 

Results

Results are published at Kartoffelafgiftsfonden webpage and our published paper can be found here: Strategies for Efficient Gene Editing in Protoplasts of Solanum tuberosum Theme: Determining gRNA Efficiency Design by Utilizing Protoplast (Research)

Project leader: Bent L. Petersen, Research Scientist KMC amba, with affiliation to PLEN-UCPH

Funded by: Kartoffelafgiftsfonden

Period: 2017-2022

Previous studies with administration of Trichuris suis eggs (TSO), the whipworm of pigs, have in a smaller number of volunteers, shown that this treatment can reduce inflammation in patients with intestinal bowel diseases (IBD) with few and mild side effects. It is known that TSO can re-program and normalize specific parts of the host immune defence that causes inflammation. The project also seeks to demonstrate a hypothesis that TSO will stimulate the natural gut microorganisms, in a way that they outcompete the bacteria known to be associated with the intestinal inflammation.

Patients are followed clinically for 24 weeks, during which period we will follow the immunological profile of the patients and perform detailed DNA mapping of the gut microbiome by next generation sequencing.

The TSO treatment is simply administered orally, and if the project is successful this probiotic treatment will represent a useful natural biological alternative to conventional treatment of IBD.

The project is approved by the Danish Medicinal Agency, The Danish Data Agency and Videnskabsetisk Komité (EUDRACT no. 2017-004772-65)

Internal participants: Christian Kapel & Lars Hestbjerg Hansen

External participants

  • Hvidovre Hospital
  • Herlev Hospital
  • Bispebjerg Hospital
  • Aleris-Hamlet Hospitals
  • Køge Hospital
  • Holbæk Hospital
  • Nordsjællands Hospital
  • Statens Serum Institutet
  • Dept of Food Science (KU)

Funded by: ParaTech A/S (And private investors)

Period: 1 April 2018 - 31 March 2023

The goal of GSTspecial is to advance our knowledge of a particularly challenging group of plant enzymes, glutathione transferases (GSTs), to help close a major gap in our understanding of plant metabolism and pave the way for optimizations of plant utilization strategies.

Plants are advanced chemists, producing a wealth of species specific molecules classified as specialized metabolites. They are important for plants in e.g. signaling, defense and climate adaptation, and used by humans as medicines and food ingredients, while our crop plants have been bred to reduce levels of toxic specialized metabolites. Understanding their biochemistry and physiology is therefore of general interest. The GST enzyme family is highly represented in plants, but poorly understood. It is characterized by low sequence similarities and differential localization patterns and in vitro activities. Physiological roles have been assigned to only few GSTs, but it is thought that several function in specialized metabolism. GSTspecial aims to elucidate such functions by a combination of state-of-the-art molecular techniques. The approach will alleviate the intrinsic problem in GST research of identifying substrates and products. The key technique is mass spectrometry imaging (MSI) which is new to plant science and rapidly advancing. With MSI, metabolite distributions in a sample such as a leaf cross-section can be visualized, and recent developments have pushed the spatial resolution of images to the single cell level. Liquid chromatography MS and MSI methods will be optimized for identification and distribution analyses of putative GST substrates and products, and the results will guide single cell-type transcriptome analyses to identify the associated GSTs. These will be characterized in vitro and in planta to identify their detailed physiological functions.

Participants: Nanna Bjarnholt & Mohammed Saddik Motawie

Collaborators

  • Associate Professor Christian Janfelt, Health Faculty, University of Copenhagen, Denmark
  • Professor Robert Edwards, Newcastle University, UK
  • Professor Ian Godwin, University of Queensland, Australia

Funded by: VILLUM Young Investigator grant, no. 19151, awarded by The VILLUM Foundation, Denmark

Period: 1.1.2023 - 31.03.2025 (year 3 of 3)

The purpose of the project is to create capacity for developing resilient forage mixtures with the ability to store more C in soil. To do so, we will identify the contribution of diverse mixtures and individual mixture components to soil C inputs, where this C ends up, and decomposition.

Results: Carbon sequestration in mixtures (2023-2025)

Project leader: Frederik van der Bom

Internal participants: Dorte Bodin Dresbøll

External participants: Carsten Müller, IGN

Funded by: Frøafgiftsfonden

Period: 2021-2025

The strategic objective in SUSWHEAT is to sustain grain yield and quality in view of increased frequency of drought and heat stresses and support the green transition into a more robust and sustainable agricultural production in the Northern European region.

SUSWHEAT, is a 4-year project granted by the Independent Research Fund Denmark in 2021 with 11 million DKK, and involves scientists from China, Wales and Denmark.

Central research questions / Focus area

SUSWHEAT aims at dissecting climate robustness for sustainable wheat production, focusing on multiple stresses, stress resilience, metabolites, yield, and quality.

Internal participants

  • Fulai Liu

  • Eva Rosenqvist

  • Theresa Pflüger

External participants

  • Carl-Otto Ottosen, Department of Food Science, Aarhus University

  • John Hugh Doonan, National Plant Phenomics Centre, IBERS, Aberystwyth University

  • Xiangnan Li, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences

Contact:Fulai Liu

Period: 1 Jan 2020 – 31 Dec 2023

New bio-based fertilisers from organic waste upcycling

The EU is heavily import dependent for more than 90% of the nonrenewable phosphorus and synthetic nitrogen fertilisers consumed. This has large economic cost (more than €15 billion/y) and negative environmental impacts from fertiliser production and use. European farmers and fertiliser industry therefore urgently need techniques for increasing substitution of synthetic with waste-derived nutrients formulated into high-quality, bio-based fertilisers to fulfill the EU action plan on circular economy. However, this requires research into new processing, application and assessment and more innovative and entrepreneurial scientists capable of meeting these future needs – FertiCycle aims to to fill this gap.

PhD Fellows

FertiCycle will train 15 PhD fellows (Early Stage Researchers) who are clustered in five work packages according to the focus of their research.

We want to be able to manage and process organic and nutrient containing societal waste streams much more intelligently, not just by recycling, but by upcycling their content of plant nutrients and organic matter, to create new, more valuable, bio-based fertilisers with higher benefits.  The new bio-based fertilisers should substitute fossil resources depletion (P) and energy consumption from conventional fertiliser production (industrial N-fixation), establish synergy with bioenergy production from the waste to substitute fossil fuels, and limit impacts on soil, air and water quality from traditional waste management.

All our developments should be based on the cradle-to-cradle concept that all nutrient containing products can be upcycled in a waste-free and circular economy, where their entire lifecycle is considered and dealt with, including consumer acceptability and market value.  We need a new generation of bio-based fertiliser experts to undertake this new development, and we consider the FertiCycle European Training Network (ETN) funded by the Marie Sklodowska-Curie Actions of H2020 an ideal engine for this!

Vision

We want to be able to manage and process organic and nutrient containing societal waste streams much more intelligently, not just by recycling, but by upcycling their content of plant nutrients and organic matter, to create new, more valuable, bio-based fertilisers with higher benefits.  The new bio-based fertilisers should substitute fossil resources depletion (P) and energy consumption from conventional fertiliser production (industrial N-fixation), establish synergy with bioenergy production from the waste to substitute fossil fuels, and limit impacts on soil, air and water quality from traditional waste management.

All our developments should be based on the cradle-to-cradle concept that all nutrient containing products can be upcycled in a waste-free and circular economy, where their entire lifecycle is considered and dealt with, including consumer acceptability and market value.  We need a new generation of bio-based fertiliser experts to undertake this new development, and we consider the FertiCycle European Training Network (ETN) funded by the Marie Sklodowska-Curie Actions of H2020 an ideal engine for this!

Beneficiaries and partners

Contact: Lars Stoumann Jensen

Funded by: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No.860127

Period: 2019-2025

INTERACT is a project under the Collaborative Crop Resiliency Program (CCRP), together with the projects MATRIX and InRoot, all funded by the Novo Nordisk Foundation. The INTERACT project will strive to unlock the enormous biotechnological potential of microbes, leading to sustainable crop productions systems.

About the project

The overall aim of the project is to decode microbial interactions in the complex soil matrix, in relation to soil biogeochemical status, water stress as well as pathogen attack, and establish the impact of these interactions on plant performance.

INTERACT will focus on the essential and mutually beneficial interactions between plants and microbes below ground. This project will go beyond a mere inventory of wheat plant microbiome community members, and will provide much needed insight into rhizosphere ecology and microbial communication, with a goal of establishing diagnostic chemical/biological signatures for agro-system stability. With this knowledge, we can rationally and strategically manipulate plant-associated microbial communities to support high plant productivity across challenging climatic and stress scenarios. These critical advances in our understanding of rhizosphere community structure and the chemical landscape that influences its formation and function will be achieved by using genomics, transcriptomics, metaproteomics, metabolomics, in-field and greenhouse plant phenotyping, and network analysis/model construction for evaluating rhizosphere interactions for wheat.

Research themes

INTERACT will address four Research Themes). The experimental Tasks within each Research Theme will contribute to answer the Research Questions raised in our application.

Research Theme 1: Indicator metabolites and microorganisms in relation to plant performance

Research Theme Lead: Amy Grunden (NCSU); Co-lead: Lars Stoumann Jensen (UCPH)

Research Theme 2: Isolation and metabolic profiling of rhizosphere microorganisms

Research Theme Lead: Carsten Suhr Jacobsen (AU); Co-leads: Mette Haubjerg Nicolaisen (UCPH), Oliver Baars (NCSU), Jens Frisvad (DTU)

Research Theme 3: Mechanistic understanding of signaling events driving microbiome assembly

Research Theme Lead: Mette H. Nicolaisen (AU); Co-leads: Ákos Kovács (DTU), Anne Winding (AU)

Research Theme 4: Development of models predictive for plant resiliency

Research Theme Lead: Bjarne Ersbøll (DTU); Co-leads: Lars Stoumann Jensen (UCPH), Ignazio Carbone (NCSU)

Publications

  • Ahmad J, Zervas A, Ellegaard-Jensen L, Hennessy RC, Carbone I, Cornish V, Müller-Stöver DS, Grunden A, Jacobsen CS, Nicolaisen MH. (2022) Microbial diversity in four rhizocompartments (bulk soil, rhizosphere, rhizoplane and endosphere) of four winter wheat varieties at the fully emerged flag leaf growth stage. Microbiol Resour Announc. In Press.
  • Athanasios Zervas, Lea Ellegaard-Jensen, Rosanna C. Hennessy, Frederik Bak, Ying Guan, Courtney Horn Herms, Kitzia Yashvelt Molina Zamudio, Dorthe Thybo Ganzhorn, Dorette Sophie Müller-Stöver, Jabeen Ahmad, Amy Grunden, Carsten S. Jacobsen, Mette Haubjerg Nicolaisen (2022) Diversity and Structure of Bacterial Communities in Different Rhizocompartments (Rhizoplane, Rhizosphere, and Bulk) at Flag Leaf Emergence in Four Winter Wheat Varieties. American Society for Microbiology, Vol 11(5). https://journals.asm.org/doi/full/10.1128/mra.00222-22
  • Salvato F, Vintila S, Finkel OM, Dangl J, and Kleiner M (2022) Evaluation of protein extraction methods for metaproteomic analyses of root-associated microbes. Molecular Plant-Microbe Interactions. https://doi.org/10.1094/MPMI-05-22-0116-TA 
  • Nordgaard M, Blake C, Maróti G, Strube ML, Kovács ÁT (2022) Experimental evolution of Bacillus subtilis on Arabidopsis thaliana roots reveals fast adaptation and improved root colonization. iScience 25(6): 104406 (https://doi.org/10.1016/j.isci.2022.104406)
  • Nunes I, Hansen V, Bak F, Bonnichsen L, Su J, Hao X, Raymond NS, Nicolaisen MH, Jensen LS, Nybroe O (2022) Succession of the wheat seed-associated microbiome as affected by soil fertility level and introduction of Penicillium and Bacillus inoculants in the field. FEMS microbiology ecology, Volume 98, Issue 3, March 2022, fiac028, https://doi.org/10.1093/femsec/fiac028 
  • Courtney Horn Herms , Rosanna Catherine Hennessy , Frederik Bak , Dorte Bodin Dresbøll and Mette Haubjerg Nicolaisen (2022). Minireview - Back to our roots: exploring the role of root morphology as a mediator of beneficial plant–microbe interactions. Environmental Biology. doi:10.1111/1462-2920.15926. https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.15926 
  • Wagner, M. R., C. Tang, F. Salvato, K. M. Clouse, A. Bartlett, S. Sermons, M. Hoffmann, P. J. Balint-Kurti and M. Kleiner (2021). Microbe-dependent heterosis in maize. Proceedings of the National Academy of Sciences 118(30): e2021965118. https://doi.org/10.1073/pnas.2021965118
  • Visagie, C.M., Frisvad, J.C., Visagie, A., Houbraken, J., Seifert, K.A., Samson, R.A., Jacobs, K. (2021). A re-evaluation of Penicillium section Canescentia, including the description of five new species. Persoonia 46: 163-187.
    doi: 10.3767/persoonia.2021.46.06 
  • Salvato F, Hettich RL, Kleiner M (2021) Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes. PLoS Pathog 17(2): e1009245. doi:10.1371/journal.ppat.1009245
    https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009245 
  • Blake C, Nordgaard Christensen M, Kovács ÁT (2020) Molecular aspects of plant growth promotion and protection by Bacillus subtilis. Molecular Plant-Microbe Interactions (https://doi.org/10.1094/MPMI-08-20-0225-CR)

Preprints

Partners

  • University of Copenhagen
  • Aarhus University
  • North Carolina State University
  • Technical University of Denmark
  • National Institute of Agricultural Botany, UK

Internal participants

  • Mette Haubjerg Nicolaisen
  • Lars Stoumann Jensen
  • Dorette Müller-Stöver
  • Rosanna Hennessy
  • Klara Cecilia Gunnarsen
  • Frederik Bak
  • Dorthe Thybo Ganzhorn
  • Courtney Horn Hermes
  • Jakob Klinge Meier
  • Xingyun Yi

External participants

  • Carsten Suhr Jacobsen, Aarhus University
  • Anne Winding, Aarhus University
  • Peter Stougaard, Aarhus University
  • Rumakanta Sapokota, Aarhus University
  • Lea Ellegaard-Jensen, Aarhus University
  • Athanasios (Thanassis) Zervas, Aarhus University
  • Christine Lorenzen Elberg, Aarhus University
  • Julie Egelund Andersen, Aarhus University
  • Tina Thane, Aarhus University
  • Tanja Begovic, Aarhus University
  • Amy Grunden, North Caroline State University
  • Ignazio Carbone, North Caroline State University
  • Marc Cubeta, North Caroline State University
  • Manuel Kleiner, North Caroline State University
  • Clara Tang, North Caroline State University
  • Juliet Ochola, North Caroline State University
  • James (Jim) White, North Caroline State University
  • Jens Christian Frisvad, Technical University of Denmark
  • Ákos T. Kovács, Leiden University (also affiliated to Technical University of Denmark)
  • Bjarne Kjær Ersbøll, Technical University of Denmark
  • Aaron John C. Andersen, Technical University of Denmark
  • Pietro Bortolozzo, Technical University of Denmark
  • Thomas Martini Jørgensen, Technical University of Denmark
  • Lisette Knoth-Nielsen, Technical University of Denmark
  • Caja Dinesen, Leiden University (also affiliated to Technical University of Denmark)
  • Adele Pioppi, Leiden University (also affiliated to Technical University of Denmark)
  • Manca Vertot, Technical University of Denmark)
  • Xiangming Xu, National Insitute of Agricultural Botany, UK
  • Netsai Mhlanga, National Institute of Agricultural Botany, UK 

Affiliated

  • Paolina Garbeva, The Netherlands Institute of Ecology
  • Efstathios Diamantopoulos, University of Bayreuth
  • Muhammed Zohaib Anwar, University of British Columbia, Vancouver CA (Previously Aarhus University)

Project leader: Mette H. Nicolaisen

Project manager: Kristine Kirkensgaard

Funded by: This project is funded by the Novo Nordisk Foundation (Grant number: NNF19SA0059360)

Period: 2024-2025

We are demonstrating that plant peptide hormones (PPHs) can increase agricultural yields.

We have already demonstrated the PPHs can affect growth of maize root; now we want to extend the plant growth trials to other crops, for the first time showcasing the immense possibilities of these peptides. We have engineered a special bacterial strain that allows mass-production of these complex peptides that enhance root growth, a trait which allows the plant to increase the nutrient and water uptake. In addition, they are highly specific towards a specific plant receptor family, meaning that there are no non-plant targets, making the peptides safe for the environment. Previously, the bottleneck in using these peptides was a modified amino acid that hindered mass production.

Project leader: Frederik Grønbæk Tidemand

Funded by: Innovation Fund Denmark

Period:  2024-2025

The increasing population on earth sets high demands for a parallel increase in food production. However, free hectares of arable land are scarce, and consequently development of novel tools to increase crop yields are essential.

Project description

We aim to develop the use of native plant peptide growth hormones to improve agricultural use of marginal-yielding fields and generally improve crop yields in a sustainable manner. In planta, peptide hormones are involved in traits like root-branching and root elongation. Root branching is important for uptake of non-mobile ions in the soil, such as phosphate, whereas the length of roots is essential for plants growing in dry areas as it enables increased water uptake. Until now, these peptide hormones have been chemically synthesized, which is hampered by the presence of an essential modification on the active peptides. This means that small quantities for lab-scale experiments are available, but large-scale experiments and potential agricultural use have thus far been out of reach due to peptide shortage. Recent developments in our lab have allowed us to recombinantly produce these peptide hormones in a scalable and cost-efficient manner.

The proposed project aims to further optimize our production strain as well as to perform a thorough characterization of the effect on plants. The final stage of the project will be performed at the Phenolab in Taastrup where a state-of-the-art growth facility will allow daily monitoring of phenotypic effects of the peptides on relevant crops. Such data will reveal the potential of these peptide hormones as biologicals for the future of a more sustainable agricultural sector.

Project leader: Anja Thoe Fuglsang

Participants: Anja Thoe Fuglsang & Frederik Grønbæk Tidemand

Funded by: Novo Nordisk Foundation

Period: 2019-2025

Dette projekt har derfor til formål at kvantificere potentialet for at anvende efterafgrøder som et virkemiddel at lagre kulstof og reducere lattergas udledning fra dansk landbrug.

Formål

Efterafgrøder er et effektivt virkemiddel til at reducere kvælstofudvaskning, men hvad er potentialet som klimavirkemiddel?

Det er netop det, projektet har til formål at undersøge ved at kvantificere potentialet for at anvende efterafgrøder som et virkemiddel at lagre kulstof og reducere lattergas udledning fra dansk landbrug. 

Projektet vil kortlægge variationen i biomasseproduktivitet for en række efterafgrødearter i almen landbrugspraksis, og hvad jordtype, frugtbarhedsniveau og dyrkningshistorie betyder. Dernæst vil vi for relevante efterafgrøder måle kulstofproduktion og -afsætning over og under jorden (inklusiv. dybe rødder), og deres nedbrydning, kulstoflagring og risiko for øget lattergas-emission, samt betydningen af en række dyrkningsfaktorer. Dernæst vil projektet analysere en række dyrkningsscenarier under forskellige klima, jordtype og landbrugspraksis. Og endeligt vil vi udvikle en satellit-baseret metode til at verificere deres klima-effekt.

Samarbejdspartnere

Aarhus Universitet, Institut for Agroøkologi

Lars Elsgaard, Lektor
Jørgen E. Olesen, Professor
Jim Rasmussen, Seniorforsker
Zhi Liang, Postdoc

SEGES

Leif Knudsen Titel, Chefkonsulent
Nanna Hellum Kristensen, Specialkonsulent
Stinna Susgaard Filsø, Konsulent
Mikkel Møller Østerhaab, Konsulent
Rita Hørfarter, Specialkonsulent

Forskere

  • Veronika Hansen

  • Jakob Magid

  • Tine Engedal

  • Sander Bruun

Projektleder: Lars Stoumann Jensen

Projektmanager: Angelika Rasmussen 

Funded by: CatCap has received a three year funding from Danish Min. for Food, Agriculture and Environment, Climate proram.

Period:  2021-2023

We will amend coarse sandy subsoils with biochar, using different application rates and particle size distributions, and investigate the effects on plant available water and root growth. Positive results will contribute to a more resilient crop production, a more efficient utilization of water and nutrients and an increased soil carbon storage.

Coarse sandy soil comprises approximately 24 % of the classified area in Denmark. The subsoil is characterized by a low water holding capacity and a strong mechanical resistance to root growth resulting in low yields, high nitrate leaching and a restricted crop choice. These problems are expected to even increase in a future more extreme climate. Previous investigations showed a great potential to improve these subsoils by amendment with biochar from thermal conversion of biomass. In the transition process of the agricultural sector towards a climate-neutral production, pyrolysis is often mentioned as an important element, and it can be expected that biocharfrom pyrolysis processes will become available in large amounts in the future. In this project, we will amend coarse sandy subsoils with biochar derived from straw or wood, using different application rates and particle size distributions.

The effects on the soil’s physical, biological and chemical characteristics will be determined in the mixtures and in large soil column experiments over two growth seasons. Potential application methods are demonstrated at field-scale. We will use the Daisy model to calculate overall effects on crop production and environment based on the experimental results and relevant weather data. Positive results will contribute to a higher and more resilient crop production on coarse sandy soils, a more efficient utilization of water and nutrients and to an increased soil carbon storage.

External members

  • Ulrik Birk Henriksen (Senior Researcher) DTU

  • Zsuzsa Sárossy (Project Coordinator) DTU

  • Giulia Ravenni (Postdoc) DTU

  • Anne Winding (Senior Researcher) Aarhus University

  • Rumakanta Sapkota (Researcher) Aarhus University

  • Annette Vestergaard (Landskonsulent) SEGES

Project leader: Dorette Müller-Stöver

Funded by:BioAdapt has received a three year funding from LINK

Period: 2024 - ?

RECOPE aims to develop novel science-based management strategies by manipulating the rhizosphere environment using biochar combined with suitable plant beneficial microbes to enhance phosphorus (P) bioavailability and crop P use efficiency in wheat. In addition, biochar contributes to direct carbon sequestration while improving soil health and environmental sustainability.

Activities

Compatibility between biochar and soil in influencing soil P bioavailability to wheat will be evaluated. Three soil types with contrasting textures will be combined with three different biochars of varied pH. The effects of the biochar and soil mixtures on soil P bioavailability and P uptake of wheat grown in pots will be assessed at the tillering stage in greenhouse. Bulk soil and rhizosphere soil will be collected to assess plant available P, soil microbial structure and enzyme activity. Root exudates will be collected for the analyses of sugars and organic acids. Root morphology will be determined by root imaging. Trichoderma sp. and Bacillus sp. are selected to study the synergistic effect of biochar and plant beneficial microbes on P dynamics in rhizosphere. Wheat seedlings will be inoculated with different microbial strains and hereafter will be planted into their respective soil with and without biochar. The abundance of microbes involved in inorganic P solubilization will be determined. P forms will be extracted and identified to examine the effect of microbes on P transformation. Lifestyles of microbes interacting with plants and biochar will be determined through microscopic, molecular and HPLC methods to identify treatments that positively impact on plant growth and P uptake.

Effects

Applying certain biochar on specific soil type in combination with suitable plant beneficial microbial will modulate the rhizosphere bio-physiochemical environments and root activity for better P acquisition, which will limit the global dependence on non-renewable P rock and reduce the risk of P loss by leaching and erosion. The knowledge gained from this project will support a stable, effective and green transition towards sustainable agriculture.

Preliminary results

Information on the preliminary results can be found in this document

Contact: Fulai Liu

Funded by: RECOPE is funded by the Planteafgiftsfonden with a budget of 0.78 DKK for the first year (2024).

Project period: 07.04.2022 - 30.04.2024

The aim is to establish the foundation for developing superior plant-based food products for the future, and exploit the potential for Denmark to become a leader in the increasing global market for plant-based foods, while at the same time contribute significantly to reducing global greenhouse gas emissions, minimizing pressures on the environment and improving biodiversity. This will require a coordinated effort focused on increasing the quality of raw materials and ingredients through advanced plant breeding, crop management and processing technologies while at the same time ensuring sustainability, supply and demand.

Unmet need

The project addresses an urgent unmet need for high-quality plant-based raw materials and ingredients. This will be essential for developing superior plant-based food products made from oat, pea and faba bean cultivated by Danish farmers, and crucial for giving Danish food sector companies a competitive advantage on the rapidly increasing global market for plant-based food. Currently, the raw materials and ingredients used for plant-based food products are almost exclusively made from unspecified cultivars of imported soy as well as oat, pea and faba bean that are either imported or domestically produced and traded as bulk commodities primarily used for feed. This is the case both nationally and internationally. Therefore, it will be a substantial business opportunity for Denmark if Danish food sector companies could get access to raw materials and ingredients that are made from cultivars selected and bred for meeting the specific quality requirements relevant for making superior plant-based food products.

Project structure

It is envisioned that the AQRIFood project will be structured in three phases:

  • Phase I: Raw materials and derived ingredients (funded by Innovation Fund Denmark)
  • Phase II: Ferments (funding TBD)
  • Phase III: Breeding, supply and demand (funding TBD)
    AQRIFood Phase I will provide detailed knowledge about the most important nutritional, functional and sensory characteristics of raw materials and derived ingredients from the selected cultivars of oat, pea and faba bean that are needed for making high-quality plant-based food products. This will make it possible for the partnering food sector companies to develop extracts, isolates and extrudates with higher quality than before. In AQRIFood Phase II the focus will be on improving food processing technologies and optimising protein bioavailability, functionality, digestibility and flavour generation via microbial fermentation and enzymatic treatments. In AQRIFood Phase III, which is planned to run in parallel with Phase II, the focus will be on improving the quality even further and unlock the potential for Denmark to become a global leader in plant-based food production by applying advanced plant breeding and crop management while at the same time ensuring sustainability, supply and demand. Phase III will be composed of a matrix of key elements and key pins that can be combined in different ways and in different projects depending on the current and future funding landscape. 

Phase I objectives

  • Select and grow relevant cultivars of oats, pea and faba bean that are potentially suitable for large scale production of high quality plant-based food products
  • Assess how the combination of selected cultivars and processing technologies affect the quality of raw materials, extracts, concentrates, isolates and extrudates (NB: Ferments and microbial cultures will be assessed in Phase II)
  • Determine the most important quality parameters that need to be improved in Phase III for increasing the nutritional, sensorial and functional characteristics of raw materials and ingredients
  • Evaluate and prepare low-mutation density library of faba bean for subsequent rapid identification of pre‐targeted genetic variants in Phase III (NB: Low-mutation density library of pea is expected to be developed by Carlsberg by 2022 and prepared together with library of oats in Phase III)
  • Perform LCA pilot study including scoping and initial assessment of climate and biodiversity impact

Project partners

  • University of Copenhagen
  • Carlsberg A/S
  • Teknologisk Institut
  • Aalborg University
  • Aarhus University
  • SEGES
  • Innovationscenter for Økologisk Landbrug
  • Sejet Planteforædling
  • Aarhus Protein A/S
  • Sicca Dania
  • Arla Foods
  • DRYK
  • Crispy Food
  • Organic Plant Protein
  • DLG
  • DAKOFO
  • Chr Hansen
  • Novozymes
  • Danish Crown

Visit the project page here

Project coordinator: Christian Bugge Henriksen

Funded by: Innovation Fund Denmark through the Innomission 3 AgriFoodTure Partnership.

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