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                    U.S. DEPARTMENT OF AGRICULTURE
 Plant Gene Expression Center: Albany, CA
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ARS Home Pacific West Area Albany, California Plant Gene Expression Center People & Locations







Devin  Coleman-Derr
                        Plant Gene Expression Center

                        




                        
                        Director
                        Phone: (510) 559-5911
                        
                        
                        Fax: (510) 559-5678(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsMolecular Causes and Phenotypic Consequences of Bacterial Enrichment Patterns in the Root Endospheres of Drought-Stressed Crop Systems
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 436643Molecular Causes and Phenotypic Consequences of Bacterial Enrichment Patterns in the Root Endospheres of Drought-Stressed Crop Systems
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 437351Enhancing Crop Resilience to Biotic and Abiotic Stress Through Understanding the Microbiome and Immune Signaling Mechanisms
                                                    In-House Appropriated
                                                                    (D)Accession Number: 444646Non-funded Cooperative Agreement Between University of Calfornia, Berkeley and U.S. Department of Agriculture, Agricultural Research Service
                                                    Non-Funded Cooperative Agreement
                                                                    (N)Accession Number: 442938Regulatory Mechanisms Controlling Plant Development, Biotic and Abiotic Stress Responses, and Microbiome Interactions
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 440675**Publications**
                                                (Clicking on the reprint icon
                                                    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. 13:214-216. 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. 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.OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species
                                                        

- (Peer Reviewed Journal)Xu, L., Dong, Z., Fang, L., Luo, Y., Wei, Z., Guo, H., Zhang, G., Gu, Y.Q., Coleman-Derr, D.A., Xia, Q., Wang, Y. 2019. OrthoVenn2: a web server for the whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 47(W1):W52-W58. https://doi.org/10.1093/nar/gkz333.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 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.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.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 and host selection influence microbial community dynamics in the grass root microbiome
                                                        

- (Peer Reviewed Journal)Naylor, D., Degraaf, S., Purdom, E., Coleman-Derr, D.A. 2017. Drought and host selection influence microbial community dynamics in the grass root microbiome. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. 11:2691-2704. https://doi.org/10.1038/ismej.2017.118.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.PIECE 2.0: an update for the plant gene structure comparison and evolution database
                                                        

- (Peer Reviewed Journal)Wang, Y., Xu, L., Thilmony, R.L., You, F., Gu, Y.Q., Coleman-Derr, D.A. 2016. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Research. 45(D1):1015-1020. https://doi.org/10.1093/nar/gkw935.Piece2.0: an update for the pant gene structure comparison and evolution database

- (Peer Reviewed Journal)Wang, Y., Ling, X., Thilmony, R., You, F., Gu, Y., Coleman-Derr, D.A. 2016. Piece2.0: an update for the pant gene structure comparison and evolution database. Nucleic Acids Research. 45:1015-1020.Drought-induced shifts in the root microbiome

- (Abstract Only)Naylor, D., Deng, S., Xu, L., Coleman-Derr, D.A. 2016. Drought-induced shifts in the root microbiome. Meeting Abstract. Plant Microbial Interactions Symposium, Joint Genome InstituteGSP: A web-based platform for designing genome-specific primers in polyploids

- (Peer Reviewed Journal)Wang, Y., Tiwari, T., Coleman-Derr, D.A., Rawda, N., Gill, B., Huo, N., You, F., Gu, Y.Q. 2016. GSP: A web-based platform for designing genome-specific primers in polyploids. Bioinformatics. doi: 10.1093/bioinformatics/btw/34.MetaCoMET: a web platform for discovery and visualization of the core microbiome

- (Peer Reviewed Journal)Wang, Y., Xu, L., Gu, Y.Q., Coleman-Derr, D.A. 2016. MetaCoMET: a web platform for discovery and visualization of the core microbiome. Bioinformatics. 32(22):3469-3470. doi:10.1093/bioinformatics/btw507.GSP: a web-based platform for designing genome-specific primers in polyploids

- (Peer Reviewed Journal)Wang, Y., Tiwari, V.K., Rawat, N., Gill, B.S., Huo, N., You, F.M., Coleman-Derr, D.A., Gu, Y.Q. 2016. GSP: a web-based platform for designing genome-specific primers in polyploids. Bioinformatics. 32(15):2382-2383.The Cacti microbiome: interplay between habitat-filtering and host-specificity

- (Peer Reviewed Journal)Fonseca-Garcia, C., Coleman-Derr, D.A., Garrido, E., Visel, A., Tringe, S., Partida-Martinez, L. 2016. The Cacti microbiome: interplay between habitat-filtering and host-specificity. Frontiers in Microbiology. 7:1-16.High-resolution phylogenic microbial community profiling

- (Peer Reviewed Journal)Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species.

- (Peer Reviewed Journal)OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

- (Peer Reviewed Journal)Wang, Y., Coleman-Derr, D.A., Chen, G., Gu, Y.Q. 2015. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 43(W1):W78-W84. doi: 10.1093/nar/gkv487.Inferring geographic origin of barley accessions using molecular markers

- (Peer Reviewed Journal)Bonman, J.M., Gu, Y.Q., Coleman Derr, D., Jackson, E.W., Bockelman, H.E. 2010. Inferring geographic origin of barley accessions using molecular markers. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-010-9574-4.Origin of barley accessions with multiple disease resistance determined by SSR analysis.

- (Abstract Only)Bonman, J.M., Gu, Y., Coleman Derr, D., Jackson, E.W., Chao, S., Bockelman, H.E. 2008. Origin of barley accessions with multiple disease resistance determined by SSR analysis.. International Congress of Plant Pathology Abstracts and Proceedings.HYBSWEEPER:  A RESOURCE FOR DETECTING HIGH-DENSITY PLATE COORDINATES

- (Peer Reviewed Journal)Lazo, G.R., Lui, N., Gu, Y.Q., Kong, X., Coleman Derr, D., Anderson, O.D. 2005. Hybsweeper:  a resource for detecting high-density plate coordinates. Biotechniques.  39:320-324.GENOMIC ORGANIZATION OF THE COMPLEX A-GLIADIN GENE LOCI IN WHEAT

- (Peer Reviewed Journal)Gu, Y.Q., Crossman, C.C., Kong, X., Luo, M., You, F.M., Coleman Derr, D., Dubcovsky, J., Anderson, O.D. 2004. Genomic organization of the complex a-gliadin gene loci in wheat. Theoretical and Applied Genetics.  109:648-657.Rapid genome evolution as revealed by comparative sequence analysis of orthologous regions from four triticeae genomes

- (Peer Reviewed Journal)Gu, Y.Q., Coleman-Derr, D., Kong, X., Anderson, O.D. 2004. Dynamics and rapid genome evolution in allopolyploid wheat as revealed by comparative sequence analysis of the complex hmw-glutenin locus regions. Plant Physiology.  135:459-470.
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