Decoding the Rhizobiota Interactome for Improved Crop Resilience (INTERACT)

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). 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:

• 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 https://doi.org/10.1101/2022.01.23.477386
• Lozano-Andrade CN, Nogueira CG, Wibowo M, Kovács ÁT (2022) Establishment of a transparent soil system to study Bacillus subtilis chemical ecology. bioRxiv https://doi.org/10.1101/2022.01.10.475645
• 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: https://doi.org/10.1101/2021.03.29.437612 
• 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:
  doi: https://doi.org/10.1101/2020.05.05.078766 
  https://www.biorxiv.org/content/10.1101/2020.05.05.078766v2.full