Selected papers about our work with microbiomes and ecological genomics

Preprint

Garrett, K. A., E. E. Frank, S. P.  Dendy, J. F. Leslie, and A. Saleh. 2017. Microbiome engineers: Grazers, browsers, and the phytobiome stampede. bioRxiv: http://dx.doi.org/10.1101/087494.

Published Journal Articles

Alcalá-Briseño, R. I., K. Casarrubias-Castillo, D. López-Ley, K. A. Garrett, L. Silva-Rosales. 2019. Network analysis of the papaya orchard virome from two agroecological regions of Chiapas, Mexico. mSystems, accepted. [open access link to preprint in bioRxiv]

Ascunce, M. S., Keumchul Shin, J. C. Huguet-Tapia, R. PoudelK. 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. DendyE. E. FrankM. 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.