Selected papers about our work with microbiomes and ecological genomics
Published Journal Articles
Alcalá Briseño, R. I., O. Batuman, J. Brawner, W. J. Cuellar, E. Delaquis, B. A. Etherton, R. D. French-Monar, J. F. Kreuze, I. Navarrete, K. Ogero, A. I. Plex Sulá, S. Yilmaz, and K. A. Garrett. 2023. Translating virome analyses to support biosecurity, on-farm management, and crop breeding. Frontiers in Plant Science 14:1056603. [open access link]
Martins, S. J., J. Pasche, H. A. O. Silva, G. Selten, N. Savastano, L. M. Abreu, H. Bais, K. A. Garrett, N. Kraisitudomsook, C. M. J. Pieterse, and T. Cernava. 2023. The use of synthetic microbial communities (SynComs) for plant health. Phytopathology 113:1369-1379. [open access link]
Poudel, R., A. Jumpponen, M. M. Kennelly, C. Rivard, L. Gomez-Montano, and K. A. Garrett. 2023. Integration of phenotypes in microbiome networks for designing synthetic communities: a study of mycobiomes in the grafted tomato system. Applied and Environmental Microbiology 89:e01843-22. [open access link]
Saleh*, A. A., N. Kraisitudomsook*, E. E. Frank, S. P. Dendy, J. F. Leslie, and K. A. Garrett. 2023. Phytobiome stampede: Bison as potential dispersal agents for the tallgrass prairie microbiome. PhytoFrontiers 3:512-517. [open access link]
Poudel, M., R. Mendes, L. A. S. Costa, C. G. Bueno, Y. Meng, S. Y. Folimonova, K. A. Garrett and S. J. Martins. 2021. The role of plant-associated bacteria, fungi, and viruses in drought stress mitigation. Frontiers in Microbiology 12:743512. [open access link]
Alcalá-Briseño, R. I., K. Casarrubias-Castillo, D. López-Ley, K. A. Garrett, L. Silva-Rosales. 2020. Network analysis of the papaya orchard virome from two agroecological regions of Chiapas, Mexico. mSystems 5:e00423-19. [open access link]
Ascunce, M. S., Keumchul Shin, J. C. Huguet-Tapia, R. Poudel, K. A. Garrett, A. H. C. van Bruggen, E. M. Goss. 2019. Penicillin trunk injection affects bacterial community structure in citrus trees. Microbial Ecology 78:457-469. [link]
Bell, T. H., K. Hockett, R. I. Alcalá-Briseño, M. Barbercheck, G. A. Beattie, M. A. Bruns, J. Carlson, T. Chung, A. Collins, B. Emmett, P. Esker, K. A. Garrett, L. Glenna, B. K. Gugino, M. d. M. Jimenez Gasco, L. Kinkel, J. Kovac, K. Kowalski, G. Kuldau, J. Leveau, M. Michalska-Smith, J. Myrick, K. Peter, M. V. Salazar, A. Shade, N. Stopnisek, X. Tan, A. Welty, K. Wickings, and E. Yergeau. 2019. Manipulating wild and tamed phytobiomes: challenges and opportunities. Phytobiomes 3:3-21. [open access link]
Bennett, A. E., K. Preedy, A. Golubski, J. Umbanhowar, S. R. Borrett, L. Byrne, K. Apostol, J. D. Bever, L. Biederman, A. T. Classen, K. Cuddington, M.-A. de Graaff, K. A. Garrett, L. Gross, A. Hastings, J. D. Hoeksema, V. Hrynkiv, J. Karst, M. Kummel, C. T. Lee, C. Liang, W. Liao, K. Mack, L. Miller, B. Ownley, C. Rojas, E. L. Simms, V. K. Walsh, M. Warren and J. Zhu. 2019. Beyond the black box: promoting mathematical collaborations for elucidating interactions in soil ecology. Ecosphere 10:e02799. [open access link]
Poudel, R., A. Jumpponen, M. M. Kennelly, C. Rivard, L. Gomez-Montano and K. A. Garrett. 2019. Rootstocks shape the rhizobiome: Rhizosphere and endosphere bacterial communities in the grafted tomato system. Applied and Environmental Microbiology 85:e01765-18. [link]
Garrett, K. A., R. I. Alcalá-Briseño, K. F. Andersen, C. E. Buddenhagen, R. A. Choudhury, J. C. Fulton, J. F. Hernandez Nopsa, R. Poudel, and Y. Xing. 2018. Network analysis: A systems framework to address grand challenges in plant pathology. Annual Review of Phytopathology 56: 559-580. [open access link]
Poudel, R., A. Jumpponen, D. C. Schlatter, T. C. Paulitz, B. McSpadden Gardener, L. L. Kinkel, and K. A. Garrett. 2016. Microbiome networks: A systems framework for identifying candidate microbial assemblages for disease management. Phytopathology 106:1083-1096. [open access link] [one of the most downloaded papers in Phytopathology]
Gomez-Montano, L., A. Jumpponen, M. A. Gonzales, J. Cusicanqui, C. Valdivia, P. Motavalli, M. Herman, and K. A. Garrett. 2013. Do bacterial and fungal communities in soils of the Bolivian Altiplano change under shorter fallow periods? Soil Biology & Biochemistry 65:50-59. [link] [Supplemental materials, including beautiful photos] [Associated R scripts]
Garrett, K. A. 2012. Information networks for plant disease: Commonalities in human management networks and within-host signaling networks. [Invited] European Journal of Plant Pathology 133:75-88. [link]
Garrett, K. A., A. Jumpponen, C. Toomajian, and L. Gomez-Montano. 2012. Climate change and plant health: Designing research spillover from plant genomics for understanding the role of microbial communities. [Invited] Canadian Journal of Plant Pathology 34:349-361. [link]
Saleh, A. A., H. U. Ahmed, T. C. Todd, S. E. Travers, K. A. Zeller, J. F. Leslie, and K. A. Garrett. 2010. Relatedness of Macrophomina phaseolina isolates from tallgrass prairie, maize, soybean, and sorghum. Molecular Ecology 19:79-91. [link]
Travers, S. E., Z. Tang, D. Caragea, K. A. Garrett, S. H. Hulbert, J. E. Leach, J. Bai, A. Saleh, A. K. Knapp, P. A. Fay, J. Nippert, P. S. Schnable, and M. D. Smith. 2010. Variation in gene expression of Andropogon gerardii in response to altered environmental conditions associated with climate change. Journal of Ecology 98:374-383. [Editor’s choice]
Yin, C., K. L. Jones, D. E. Peterson, K. A. Garrett, S. H. Hulbert, and T. C. Paulitz. 2010. Members of soil bacterial communities sensitive to tillage and crop rotation. Soil Biology & Biochemistry 42:2111-2118. [link]
Milliken, G. A., K. A. Garrett, and S. E. Travers. 2007. Experimental design for two-color microarrays applied in a pre-existing split-plot experiment. Statistical Applications in Genetics and Molecular Biology 6, Article 20. [link]
Travers, S. E., M. D. Smith, J. Bai, S. H. Hulbert, J. E. Leach, P. S. Schnable, A. K. Knapp, G. Milliken, P. Fay, A. Saleh, and K. A. Garrett. 2007. Ecological genomics: making the leap from model systems in the lab to native populations in the field. Frontiers in Ecology and the Environment 5:19-24. [link]
Garrett, K. A., S. P. Dendy, E. E. Frank, M. N. Rouse, and S. E. Travers. 2006. Climate change effects on plant disease: Genomes to ecosystems. Annual Review of Phytopathology 44:489-509. [link]
Garrett, K. A., S. H. Hulbert, J. E. Leach, and S. E. Travers. 2006. Ecological genomics and epidemiology. European Journal of Plant Pathology 115:35-51. [link]
Al-Naimi, F. A., K. A. Garrett, and W. W. Bockus. 2005. Competition, facilitation, and niche differentiation in two foliar pathogens. Oecologia 143:449-457. [link]
BOOK CHAPTERS
Beed, F., A. Benedetti, G. Cardinali, S. Chakraborty, T. Dubois, K. Garrett and M. Halewood. 2015. Climate change and micro-organism genetic resources for food and agriculture: State of knowledge, risks and opportunities. In Food and Agriculture Organization of the United Nations, and available at http://www.fao.org/docrep/meeting/022/mb392e.pdf.
Gadbury, G. L., K. A. Garrett, and D. B. Allison. 2009. Challenges and approaches to statistical design and inference in high dimensional investigations. Pages 181-206 in Plant Systems Biology, Methods in Molecular Biology Series. D. A. Belostotsky, editor. Humana Press, Totowa, New Jersey.