Research Project: Discovery of Plant Genetic Mechanisms Controlling Microbial Recruitment to the Root Microbiome

Location: Plant Gene Expression Center

Publications (Clicking on the reprint icon will take you to the publication reprint.)

High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration - (Peer Reviewed Journal)
Elmore, J., Dexter, G., Baldino, H., Huenemann, J., Francis, R., Peabody, G.L., Martinez-Baird, J., Riley, L.A., Simmons, T., Coleman-Derr, D.A., Guss, A., Egbert, R. 2023. High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration. Science Advances. 9(10). Article eade1285. https://doi.org/10.1126/sciadv.ade1285.

Photosynthesis in rice is increased by CRISPR/Cas9-mediated transformation of two truncated light-harvesting antenna - (Peer Reviewed Journal)
Caddell, D.F., Langenfeld, N.J., Zhen, S., Eckels, M., Zhen, S., Klaras, R., Mishra, L., Bugbee, B., Coleman-Derr, D.A. 2023. Photosynthesis in rice is increased by CRISPR/Cas9-mediated transformation of two truncated light-harvesting antenna. Frontiers in Plant Science. 14. Article 1050483. https://doi.org/10.3389/fpls.2023.1050483.

Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities - (Peer Reviewed Journal)
Gao, C., Xu, L., Montoya, L., Madera, M., Hollingsworth, J., Chen, L., Purdom, E., Singan, V., Vogel, J., Hutmacher, R., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P., Taylor, J. 2022. Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities. Nature Communications. 13. Article 3867. https://doi.org/10.1038/s41467-022-31343-y.

Plant microbiome-based genome-wide association studies - (Book / Chapter)
Deng, S., Meier, M., Caddell, D., Yang, J., Coleman-Derr, D.A. 2022. Plant microbiome-based genome-wide association studies. In: Torkamaneh, D., Belzile, F., editors. Genome-Wide Association Studies. Methods in Molecular Biology. New York, NY: Humana. p. 353-367. https://doi.org/10.1007/978-1-0716-2237-7_20.

Plant immunity suppression via PHR1-RALF-FERONIA shapes the root microbiome to alleviate phosphate starvation - (Peer Reviewed Journal)
Tang, J., Wu, D., Li, X., Wang, L., Xu, L., Zhang, Y., Xu, F., Liu, H., Xie, Q., Dai, S., Coleman-Derr, D.A., Yu, F. 2022. Plant immunity suppression via PHR1-RALF-FERONIA shapes the root microbiome to alleviate phosphate starvation. EMBO Journal. 41(6). Article e109102. https://doi.org/10.15252/embj.2021109102.

Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression - (Peer Reviewed Journal)
Gao, C., Courty, P., Varoquaux, N., Cole, B., Montoya, L., Xu, L., Purdom, E., Vogel, J., Hutmacher, R., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P., Taylor, J. 2022. Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression. Molecular Ecology. https://doi.org/10.1111/mec.16343.

Keep your friends close: Host compartmentalisation of microbial communities facilitates decoupling from effects of habitat fragmentation - (Peer Reviewed Journal)
Willing, C., Pierroz, G., Guzman, A., Anderegg, L., Gao, C., Coleman-Derr, D.A., Taylor, J., Bruns, T., Dawson, T. 2021. Keep your friends close: Host compartmentalisation of microbial communities facilitates decoupling from effects of habitat fragmentation. Ecology Letters. 24(12):2674–2686. https://doi.org/10.1111/ele.13886.

Plant single-cell solutions for energy and the environment - (Peer Reviewed Journal)
Cole, B., Bergmann, D., Blaby-Haas, C., Blaby, I., Bouchard, K., Brady, S., Ciobanu, D., Coleman-Derr, D.A., Leiboff, S., Mortimer, J., Nobori, T., Rhee, S., Schmutz, J., Simmons, B., Singh, A., Sinha, N., Vogel, J., O'Malley, R., Visel, A., Dickel, D. 2021. Plant single-cell solutions for energy and the environment. Communications Biology. 4. Article 962. https://doi.org/10.1038/s42003-021-02477-4.

Towards a biomanufactory on Mars - (Peer Reviewed Journal)
Berliner, A., Hilzinger, A., Abel, A., McNulty, M., Makrygiorgos, G., Averesch, N., Gupta, S., Benvenuti, A., Caddell, A., Coleman-Derr, D.A., et al. 2021. Towards a biomanufactory on Mars. Frontiers in Astronomy and Space Sciences. 8. Article 711550. https://doi.org/10.3389/fspas.2021.711550.

The plastid-localized AtFtsHi3 pseudo-protease of Arabidopsis thaliana has an impact on plant growth and drought tolerance - (Peer Reviewed Journal)
Mishra, L., Mishra, S., Caddell, D.F., Coleman-Derr, D.A., Funk, C. 2021. The plastid-localized AtFtsHi3 pseudo-protease of Arabidopsis thaliana has an impact on plant growth and drought tolerance. Frontiers in Plant Science. 12. Article 694727. https://doi.org/10.3389/fpls.2021.694727.

Genome resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics - (Peer Reviewed Journal)
Xu, L., Dong, Z., Chiniquy, D., Pierroz, G., Deng, S., Gao, C., Diamond, S., Simmons, T., Wipf, H.M., Caddell, D.F., Varoquaux, N., Madera, M.A., Hutmacher, R., Deutschbauer, A., Dahlberg, J., Guerinot, M., Purdom, E., Banfield, J.F., Taylor, J.W., Lemaux, P.G., Coleman-Derr, D.A. 2021. Genome resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nature Communications. 12. Article 3209. https://doi.org/10.1038/s41467-021-23553-7.

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome - (Peer Reviewed Journal)
Deng, S., Caddell, D.F., Xu, G., Dahlen, L., Washington, L., Wang, J., Coleman-Derr, D.A. 2021. Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. Available: https://doi.org/10.1038/s41396-021-00993-z.

Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome - (Peer Reviewed Journal)
Wipf, H., Coleman-Derr, D.A. 2021. Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome. PLoS ONE. 16(3). Article e0248030. https://doi.org/10.1371/journal.pone.0248030.

Holo-omics for deciphering plant-microbiome interactions - (Peer Reviewed Journal)
Xu, L., Pierroz, G., Wipf, E., Gao, C., Taylor, J., Lemaux, P., Coleman-Derr, D.A. 2021. Holo-omics for deciphering plant-microbiome interactions. Microbiome. 9:69. https://doi.org/10.1186/s40168-021-01014-z.

Agricultural soil management practices differentially shape the bacterial and fungal microbiome of Sorghum bicolor - (Peer Reviewed Journal)
Wipf, H., Xu, L., Gao, C., Spinner, H., Taylor, J., Lemaux, P., Mitchell, J., Coleman-Derr, D.A. 2021. Agricultural soil management practices differentially shape the bacterial and fungal microbiome of Sorghum bicolor. Applied and Environmental Microbiology. 87(5). https://doi.org/10.1128/AEM.02345-20.

Loss of Arabidopsis matrix metalloproteinase-5 affects root development and root bacterial communities during drought stress - (Peer Reviewed Journal)
Mishra, L., Kim, S., Caddell, D.F., Coleman-Derr, D.A., Funk, C. 2021. Loss of Arabidopsis matrix metalloproteinase-5 affects root development and root bacterial communities during drought stress. Physiologia Plantarum. 172(2):1045-1058. https://doi.org/10.1111/ppl.13299.

Distinguishing between the impacts of heat and drought stress on the root microbiome of Sorghum bicolor - (Peer Reviewed Journal)
Wipf, H., Bui, T., Coleman-Derr, D.A. 2021. Distinguishing between the impacts of heat and drought stress on the root microbiome of Sorghum bicolor. Applied and Environmental Microbiology. 5(2):2471-2906. https://doi.org/10.1094/PBIOMES-07-20-0052-R.

The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots - (Peer Reviewed Journal)
Willing, C., Pierroz, G., Coleman-Derr, D.A., Dawson, T. 2020. The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots. Molecular Ecology. 29:4721–4734. https://doi.org/10.1111/mec.15666.

Nematode-encoded RALF Peptide Mimics Facilitate Parasitism of Plants through the FERONIA Receptor Kinase - (Peer Reviewed Journal)
Zhang, X., Peng, H., Zhu, S., Xing, J., Li, X., Zhu, Z., Zheng, J., Wang, L., Wang, B., Chen, J., Ming, Z., Yao, K., Jian, J., Luan, S., Coleman-Derr, D.A., Liao, H., Peng, Y., Peng, D., Yu, F. 2020. Nematode-encoded RALF Peptide Mimics Facilitate Parasitism of Plants through the FERONIA Receptor Kinase. Molecular Plant. https://doi.org/10.1016/j.molp.2020.08.014.

Nematode-encoded RALF peptide mimics facilitate parasitism of plants through the FERONIA receptor kinase - (Peer Reviewed Journal)
Zhang, X., Peng, H., Zhu, S., Xing, J., Li, X., Zhu, Z., Zheng, J., Wang, L., Wang, B., Chen, J., Ming, Z., Yao, K., Jian, J., Luan, S., Coleman-Derr, D.A., Liao, H., Peng, Y., Peng, D., Yu, F. 2020. Nematode-encoded RALF peptide mimics facilitate parasitism of plants through the FERONIA receptor kinase. Molecular Plant. 13:214-216. https://doi.org/10.1016/j.molp.2020.08.014.

Drought drives spatial variation in the millet root microbiome - (Peer Reviewed Journal)
Simmons, T., Styer, A., Pierroz, G., Goncalves, A., Pasicha, R., Hazra, A., Bubner, P., Coleman-Derr, D.A. 2020. Drought drives spatial variation in the millet root microbiome. Frontiers in Plant Science. 11. https://doi.org/10.3389/fpls.2020.00599.

Fungal community assembly in drought-stressed sorghum shows stochasticity, selection and universal ecological dynamics - (Peer Reviewed Journal)
Gao, C., Montoya, L., Xu, L., Purdom, E., Hollingsworth, J., Singan, V., Vogel, J., Hutmacher, R., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P., Taylor, J. 2020. Fungal community assembly in drought-stressed sorghum shows stochasticity, selection and universal ecological dynamics. Nature Communications. 11:34. https://doi.org/10.1038/s41467-019-13913-9.

Peanut plant growth was altered by monocropping-associated microbial enrichment of rhizosphere microbiome - (Peer Reviewed Journal)
Li, X., Panke-Buisse, K., Yao, X., Coleman-Derr, D.A., Ding, C., Wang, X., Ruan, H. 2019. Peanut plant growth was altered by monocropping-associated microbial enrichment of rhizosphere microbiome. Plant and Soil. 446:655–669. https://doi.org/10.1007/s11104-019-04379-1.

A plant growth-promoting microbial soil amendment dynamically alters the strawberry root bacterial microbiome - (Peer Reviewed Journal)
Deng, S., Wipf, H., Pierroz, G., Raab, T.K., Khanna, R., Coleman-Derr, D.A. 2019. A plant growth-promoting microbial soil amendment dynamically alters the strawberry root bacterial microbiome. Scientific Reports. 9:17677. https://doi.org/10.1038/s41598-019-53623-2.

Transcriptomic analysis of field-droughted sorghum from seeding to maturity reveals biotic and metabolic responses - (Peer Reviewed Journal)
Varoquaux, N., Cole, B., Gao, C., Pierroz, G., Baker, C., Patel, D., Madera, M., Jeffers, T., Hollingsworth, J., Sievert, J., Yoshinaga, Y., Owiti, J., Singan, V., Degraaf, S., Xu, L., Blow, M., Harrison, M., Visel, A., Jansson, C., Niyogi, K., Hutmacher, R., Coleman-Derr, D.A., O'Malley, R., Taylor, J., Dahlberg, J., Vogel, J., Lemaux, P., Purdom, E. 2019. Transcriptomic analysis of field-droughted sorghum from seeding to maturity reveals biotic and metabolic responses. Proceedings of the National Academy of Sciences. 116(52):27124–27132. https://doi.org/10.1073/pnas.1907500116.

Causes and consequences of a conserved bacterial root microbiome resposnse to drought stress - (Peer Reviewed Journal)
Xu, L., Coleman-Derr, D.A. 2019. Causes and consequences of a conserved bacterial root microbiome resposnse to drought stress. Current Opinion in Microbiology. 49:1-6.

Role of the plant root microbiome in abiotic stress tolerance - (Book / Chapter)
Caddell, D., Deng, S., Coleman-Derr, D. 2019. Role of the plant root microbiome in abiotic stress tolerance. In: Verma, S. and White, J. editors. Seed Endophytes 1st Edition. Sham, Switzerland: Springer Verlag. p. 273-311.

Strong succession in arbuscular mycorrhizal fungul communities - (Peer Reviewed Journal)
Gao, C., Montoya, L., Xu, L., Madera, M., Hollingsworth, J., Purdom, E., Hutmacher, R., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P.G., Taylor, J.W. 2018. Strong succession in arbuscular mycorrhizal fungul communities. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 13:214-226. https://doi.org/10.1038/s41396-018-0264-0.

Strong succession in arbuscular mycorrhizal fungal communities - (Peer Reviewed Journal)
Gao, C., Montoya, L., Xu, L., Madera, M., Hollingsworth, J., Sievert, J.A., Purdom, E., Dahlberg, J., Coleman-Derr, D.A., Lemaux, P.G., Taylor, J.W. 2018. Strong succession in arbuscular mycorrhizal fungal communities. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 13:214-226. https://doi.org/10.1038/s41396-018-0264-0.

Exploring the root microbiome: extracting bacterial community data for the soil, rhizosphere, and root endosphere - (Peer Reviewed Journal)
Simmons, T., Caddell, D., Deng, S., Coleman-Derr, D.A. 2018. Exploring the root microbiome: extracting bacterial community data for the soil, rhizosphere, and root endosphere. Journal of Visualized Experiments. 135:1-10.

Drought stress and root-associated bacterial communities - (Review Article)
Naylor, D., Coleman-Derr, D.A. 2018. Drought stress and root-associated bacterial communities. Frontiers in Plant Science. 8(2223):1-16. https://doi.org/10.3389/fpls.2017.02223.

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria - (Peer Reviewed Journal)
Xu, L., Naylor, D., Dong, Z., Simmons, T., Pierroz, G., Hixson, K., Young, M., Zink, E.M., Engbrecht, K., Wang, Y., Gao, C., Degraff, S., Madera, M., Sievert, J.A., Hollingsworth, J., Birdseye, D., Scheller, H., Hutmacher, R., Dahlberg, J., Jansson, C., Taylor, J., Lemaux, P., Coleman-Derr, D.A. 2018. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proceedings of the National Academy of Sciences. 115(18):E4284-E4293.