Publications

(* = contributed equally, † = corresponding author, OA = Open Access, PRE = preprint )

Other publications (book chapter, commentary, etc.


2022

Karasov T.L., Lundberg D.S. (2022). The changing influence of host genetics on the leaf fungal microbiome throughout plant development. PLoS Biol. doi:10.1371/journal.pbio.3001748 [OA, Commentary]


Saarenpää S., Shalev O., Ashkenazy H., de Oliveira-Carlos V., Lundberg D.S., Weigel D., Giacomello S. (2022). Spatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics. bioRxiv. doi:10.1101/2022.07.18.496977 [OA, PRE]


Karasov T.L., Neumann M, Shirsekar G, Monroe G, PATHODOPSIS Team (I am part of this team), Weigel D, Schwab R. (2022). Drought selection on Arabidopsis populations and their microbiomes. bioRxiv. doi:10.1101/2022.04.08.487684 [OA, PRE]


Shalev O., Karasov T.L., Lundberg D.S., Ashkenazy H., Pramoj Na Ayutthaya P., Weigel D. (2022). Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant. Nat Ecol Evol. https://doi.org/10.1038/s41559-022-01673-7 [OA]


2021

Lundberg D.S., Pramoj Na Ayutthaya P., Strauß A., Shirsekar G., Lo W-S, Lahaye T., Weigel D. (2021). Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition. eLife 10. https://doi.org/10.7554/eLife.66186 [OA]


Shirsekar G., Devos J., Latorre S.M., Blaha A., Queiroz Dias M., González Hernando A., Lundberg D.S., Burbano H.A., Fenster C.B., Weigel D. (2021). Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia. Mol Biol Evol 38:5328–5344. https://doi.org/10.1093/molbev/msab268 [OA]


Lundberg D.S., de Pedro Jové R., Pramoj Na Ayutthaya P., Karasov T.L., Shalev Skriptchak O., Ding W., Bollman-Giolai A., Bezrukov I., Weigel D. (2021). Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere. bioRxiv 10.1101/2021.04.06.438366. [OA, PRE]


2020

Cambiagno, D. A., Giudicatti, A. J., Arce, A. L., Gagliardi, D., Li, L., Yuan, W., Lundberg, D. S., Weigel, D., & Manavella, P. A. (2020). HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing. Molecular Plant. https://doi.org/10.1016/j.molp.2020.12.019


Regalado, J.*, Lundberg, D. S.*, Deusch, O., Kersten, S., Karasov, T., Poersch, K., Shirsekar, G., & Weigel, D. (2020). Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves. The ISME Journal, 14, 2116–2130. https://doi.org/10.1038/s41396-020-0665-8 [OA]

Co-first contribution: Planned study and wrote the manuscript with help from JR and DW. Collected samples and prepared libraries with help from SK and KP. Analyzed data with help from JR and OD, particularly amplicon data and the integration of amplicon and whole metagenome shotgun data.


Pramoj Na Ayutthaya, P., Lundberg, D. S., Weigel, D., & Li, L. (2020). Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) for the Analysis of Protein Oligomers in Plants. Current Protocols in Plant Biology, 5(2), e20107. https://doi.org/10.1002/cppb.20107 [OA, Protocol]


2019

Karasov, T. L., Neumann, M., Duque-Jaramillo, A., Kersten, S., Bezrukov, I., Schröppel, B., Symeonidi, E., Lundberg, D. S., Regalado, J., Shirsekar, G., Bergelson, J., & Weigel, D. (2019). The relationship between microbial biomass and disease in the Arabidopsis thaliana phyllosphere. In bioRxiv, 828814. https://doi.org/10.1101/828814 [OA, PRE]


Exposito-Alonso, M., 500 Genomes Field Experiment Team (I am part of this team of 38), Burbano, H. A., Bossdorf, O., Nielsen, R., & Weigel, D. (2019). Natural selection on the Arabidopsis thaliana genome in present and future climates. Nature 573, 126–129. https://doi.org/10.1038/s41586-019-1520-9 [OA]


2018

Karasov, T. L., Almario, J.*, Friedemann, C.*, Ding, W., Giolai, M., Heavens, D., Kersten, S., Lundberg, D. S., Neumann, M., Regalado, J., Neher, R. A., Kemen, E., & Weigel, D. (2018). Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host & Microbe, 24(1), 168–179.e4. https://doi.org/10.1016/j.chom.2018.06.011 [OA]


Lundberg, D. S., & Teixeira, P. J. P. L. (2018). Root-exuded coumarin shapes the root microbiome [Commentary on “MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health” by Stringlis et al. in the same issue]. Proceedings of the National Academy of Sciences of the United States of America, 115(22), 5629–5631. https://doi.org/10.1073/pnas.1805944115 [OA, Commentary]


Levy A.*, Salas Gonzalez I.*, Mittelviefhaus M., Clingenpeel S., Herrera Paredes S., Miao J., Wang K., Devescovi G., Stillman K., Monteiro F., Rangel Alvarez B., Lundberg D. S., Lu T-Y., Lebeis S., Jin Z., McDonald M., Klein A.P., Feltcher M.E., Glavina del Rio T., Grant S.R., Doty S.L., Ley R.E., Pelletier D.A., Vorholt J., Tringe S.G., Woyke T., and Dangl J.L. (2018). Genomic features of bacterial adaptation to plants. Nature Genetics, 50(1), 138–150. https://doi.org/10.1038/s41588-017-0012-9 [OA]


2017

Rowan, B. A., Seymour, D. K., Chae, E., Lundberg, D. S., & Weigel, D. (2017). Methods for Genotyping-by-Sequencing. Methods in Molecular Biology, 1492, 221–242. https://doi.org/10.1007/978-1-4939-6442-0_16 [Book chapter]


2016

Wagner, M. R., Lundberg, D. S., Del Rio, T. G., Tringe, S. G., Dangl, J. L., & Mitchell-Olds, T. (2016). Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nature Communications, 7, 12151. https://doi.org/10.1038/ncomms12151 [OA]


Biswas, S., Mcdonald, M., Lundberg, D. S., Dangl, J. L., & Jojic, V. (2016). Learning Microbial Interaction Networks from Metagenomic Count Data. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 23(6), 526–535. https://doi.org/10.1089/cmb.2016.0061


Johnston-Monje, D., Lundberg, D. S., Lazarovits, G., Reis, V. M., & Raizada, M. N. (2016). Bacterial populations in juvenile maize rhizospheres originate from both seed and soil. Plant and Soil, 405(1-2), 337–355. https://doi.org/10.1007/s11104-016-2826-0 [OA]


Tennessen, K., Andersen, E., Clingenpeel, S., Rinke, C., Lundberg, D. S., Han, J., Dangl, J. L., Ivanova, N., Woyke, T., Kyrpides, N., & Pati, A. (2016). ProDeGe: a computational protocol for fully automated decontamination of genomes. The ISME Journal, 10(1), 269–272. https://doi.org/10.1038/ismej.2015.100 [OA]


2015

Lebeis, S. L.*, Paredes, S. H.*, Lundberg, D. S.*, Breakfield, N., Gehring, J., McDonald, M., Malfatti, S., Glavina del Rio, T., Jones, C. D., Tringe, S. G., & Dangl, J. L. (2015). Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science, 349(6250), 860–864. https://doi.org/10.1126/science.aaa8764 [OA]

Co-first contribution: Helped plan study and collect samples. Isolated root bacteria for experiments and led the design and organization of the synthetic community, as well as the calcined-clay system in which it was applied. Developed the system for amplicon-based measurement of bacterial density. Edited manuscript.


2014

Argüeso, C., Huot, B., Kim, P., Lundberg, D. S., Halane, M., Serrano, I., Innes, R., & Mudgett, M. B. (2014). XVI Congress on Molecular Plant-Microbe Interactions Meeting Report. Molecular Plant-Microbe Interactions: MPMI, 27(11 Suppl), S1–S5. https://doi.org/10.1094/MPMI-27-11-S1 [OA, Meeting Report]


Yourstone, S. M., Lundberg, D. S., Dangl, J. L., & Jones, C. D. (2014). MT-Toolbox: improved amplicon sequencing using molecule tags. BMC Bioinformatics, 15, 284. https://doi.org/10.1186/1471-2105-15-284 [OA]


Wagner, M. R., Lundberg, D. S., Coleman-Derr, D., Tringe, S. G., Dangl, J. L., & Mitchell-Olds, T. (2014). Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecology Letters, 17(6), 717–726. https://doi.org/10.1111/ele.12276 [OA]


2013

Lundberg, D. S.*, Yourstone, S.*, Mieczkowski, P., Jones, C. D., & Dangl, J. L. (2013). Practical innovations for high-throughput amplicon sequencing. Nature Methods, 10(10), 999–1002. https://doi.org/10.1038/nmeth.2634

Co-first contribution: Conceived wet-bench methods with help from PM, CDJ and JLD. Designed and performed experiments with help from PM. Analyzed sequence data with help from SY. Wrote the manuscript with help from all authors.


2012

Lundberg, D. S.*, Lebeis, S. L.*, Paredes, S. H.*, Yourstone, S.*, Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Del Rio, T. G., Edgar, R. C., Eickhorst, T., Ley, R. E., Hugenholtz, P., Tringe, S. G., & Dangl, J. L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), 86–90. https://doi.org/10.1038/nature11237 [OA]

Co-first contribution: Designed the project with help from SLL and JLD. Set up experiments and organized construction of the sequencing libraries with help of SLL. Harvested samples and prepared DNA for sequencing with help of SLL, SHP and JG. Created and managed the data analysis pipeline with help from SHP, SY, and RE. Analyzed data and created figures with SLL, SHP, SY, JG, and JLD. Wrote the manuscript with SLL, SHP, and JLD.


2008

Goel, A. K., Lundberg, D. S., Torres, M. A., Matthews, R., Akimoto-Tomiyama, C., Farmer, L., Dangl, J. L., & Grant, S. R. (2008). The Pseudomonas syringae type III effector HopAM1 enhances virulence on water-stressed plants. Molecular Plant-Microbe Interactions: MPMI, 21(3), 361–370. https://doi.org/10.1094/MPMI-21-3-0361 [OA]