Decoding the Rhizobiota Interactome for Improved Crop Resilience (INTERACT)

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.

Photo of wheat


















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)


    • 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).
    • 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. 
    • 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 (
    • 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, 
    • 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. 
    • 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.
    • 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 
    • Blake C, Nordgaard Christensen M, Kovács ÁT (2020) Molecular aspects of plant growth promotion and protection by Bacillus subtilis. Molecular Plant-Microbe Interactions (


    • Sun X, Xie J, Zheng D, Wang W, Xia R, Zhang R, Kovács ÁT, Zhihui Xu, Qirong Shen (2022) Keystone species determine the productivity of synthetic microbial biofilm communities. bioRxiv
    • Lozano-Andrade CN, Nogueira CG, Wibowo M, Kovács ÁT (2022) Establishment of a transparent soil system to study Bacillus subtilis chemical ecology. bioRxiv
    • Manuel Kleiner, Angela Kouris, Marlene Jensen, Yihua Liu, Janine McCalder, and Marc Strous (2021). Ultra-sensitive Protein-SIP to quantify activity and substrate uptake in microbiomes with stable isotopes. Available in bioRxiv. Doi: 
    • Maggie R. Wagner, Clara Tang, Fernanda Salvato, Kayla M. Clouse, Alexandria Bartlett, Shannon Sermons, Mark Hoffmann, Peter J. Balint-Kurti, Manuel Kleiner (2020). Microbe-dependent heterosis in maize. Available in bioRxiv:


















    Photo  Name Title  Affiliation E-mail
    Photo of Mette Nicolaisen Mette Haubjerg Nicolaisen Project Leader, Associate Professor University of Copenhagen meni@
    Photo of Lars Stoumann Jensen Lars Stoumann Jensen Professor University of Copenhagen lsj@
    Photo of Dorette Müller-Stöver Dorette Müller-Stöver Associate Professor University of Copenhagen dsst@
    Photo of Rosanna Hennessy Rosanna Hennessy Assistant Professor University of Copenhagen hennessy@
    Photo of Klara Cecilia Gunnarsen Klara Cecilia Gunnarsen Postdoc University of Copenhagen kcg@
    Photo of Frederik Bak Frederik Bak Assistant Professor University of Copenhagen f.bak@
    Photo of Dorthe Thybo Ganzhorn Dorthe Thybo Ganzhorn Laboratory Coordinator University of Copenhagen dtg@ 
    Photo of Courtney Horn Herms Courtney Horn Herms PhD Student University of Copenhagen chh@
    Photo of Jakob Klinge Meier Jakob Klinge Meier PhD Student University of Copenhagen jakob.klinge@
    Photo of Xingyun Yi Xingyun Yi PhD Student University of Copenhagen xingyun@
    Photo of Carsten Suhr Jacobsen Carsten Suhr Jacobsen Professor Aarhus University csj@
    Photo of Anne Winding Anne Winding Professor Aarhus University aw@
    Photo of Peter Stougaard Peter Stougaard Professor Aarhus University pst@
    Photo of Rumakanta Sapkota Rumakanta Sapkota Scientist Aarhus University rumakanta.sapkota@
    Photo of Lea Ellegaard-Jensen Lea Ellegaard-Jensen Scientist Aarhus University leael@
    Photo of Thanassis Zervas Athanasios (Thanassis) Zervas Assistant
    Aarhus University az@
    Photo of Ajay Sorty Ajay M. Sorty Postdoc Aarhus University amsorty@
    Photo of Christine Elberg Christine Lorenzen Elberg PhD Student Aarhus University cle@
    Photo of Julie Egelund Andersen Julie Egelund Andersen PhD Student Aarhus University jea@
    Photo of Tina Thane Tina Thane Laboratory Technician Aarhus University tth@
    Photo of Tanja Begovic Tanja Begovic Laboratory Technician Aarhus University tab@
    Photo of Amy Grunden Amy Grunden Professor North Carolina State University amgrunde@
    Photo of Ignazio Carbone Ignazio Carbone Professor North Carolina State University icarbon@
    Photo of Marc Cubeta Marc Cubeta Professor North Carolina State University


    Photo of Oliver Baars Oliver Baars Assistant Professor North Carolina State University obaars@
    Photo of Manuel Kleiner Manuel Kleiner Associate Professor North Carolina State University mkleine@
    Photo of Jabeen Ahmad Jabeen Ahmad PhD Student North Carolina State University jahmad2@
    Photo of Clara Tang Clara Tang PhD Student North Carolina State University cvtang@
    Photo of Jim White James (Jim) White Programmer and Bioinformaticist North Carolina State University jbwhite2@
    Photo of Jens Christian Frisvad Jens Christian Frisvad Professor Technical University of Denmark jcf@
    Photo of Akos Kovacs Ákos T. Kovács Professor Leiden University (also affiliated to Technical University of Denmark) a.t.kovacs@
    Photo of Bjarne Ersboell Bjarne Kjær Ersbøll Professor Technical University of Denmark bker@
    Photo of Aaron Andersen Aaron John C. Andersen Metabolomics Core Manager Technical University of Denmark ajca@
    Photo of Pietro Bortolozzo Pietro Bortolozzo IT Specialist & Coordinator Technical University of Denmark pbor@
    Photo of Thomas Martini Thomas Martini Jørgensen Senior Researcher Technical University of Denmark tmjq
    Photo of Lisette Knoth-Nielsen Lisette Knoth-Nielsen Laboratory Technician Technical University of Denmark lkn@
    Photo of Caja Dinesen Caja Dinesen PhD Student Leiden University (also affiliated to Technical University of Denmark) cajadin@
    Photo of Adele Piooi Adele Pioppi PhD Student Leiden University (also affiliated to Technical University of Denmark) adepio@
    Photo of Manca Vertot Manca Vertot PhD Student Technical University of Denmark mavert@
    Photo of Xiangming Xu Xiangming Xu Senior Scientist National Institute of Agricultural Botany, UK


    Photo of Netsai Mhlanga Netsai Mhlanga Postdoc National Institute of Agricultural Botany, UK



    Photo of Paolina Garbeva Paolina Garbeva  Senior Scientist  The Netherlands Institute of Ecology  P.Garbeva@
    Photo of Efstathios Diamantopoulos Efstathios Diamantopoulos Professor University of Bayreuth Efstathios.Diamantopoulos
    Photo of Zohaib Muhammad Zohaib Anwar Postdoc University of British Columbia, Vancouver CA (Previously Aarhus University)




    Project leader
    Mette H. Nicolaisen
    Ph: +45 35 33 26 49

    Project manager
    Kristine Kirkensgaard
    Ph: +45 30 69 53 46


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

    Project Start: 1 Oct 2019
    Duration: 6 years