bioRxiv preprint.
Des Marais, D.L., Hernandez, K.M. & Juenger, T.E. (2013). Genotype-by-environment interaction and plasticity: exploring genomic responses of plants to the abiotic environment. Annu. Rev. Ecol. Evol. Syst. , 44, 5–29.
Des Marais, D.L., Lasky, J.R., Verslues, P.E., Chang, T.Z., Juenger, T.E. & Des Marais, D.L. (2016). Interactive effects of water limitation and elevated temperature on the physiology, development and fitness of diverse accessions of Brachypodium distachyon. New Phyt ., 214: 132–144.
De Souza, R.S.C., Armanhi, J.S., & Arruda, P. (2020). From microbiome to traits: designing synthetic microbial communities for improved crop resiliency. Front. Plant Sci., 11, 1–7.
Edwards, J., Santos-Medellín, C., Nguyen, B., Kilmer, J., Liechty, Z., Veliz, E., et al. (2019). Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota.Genome Bio. , 20, 1–14.
Edwards, J., Johnson, C., Santos-medellín, C., Lurie, E. & Kumar, N. (2014). Structure, variation, and assembly of the root-associated microbiomes of rice. Proc. Natl. Acad. Sci. , 112, E911-E920.
Egamberdieva, D., Wirth, S.J., Shurigin, V. V & Hashem, A. (2017). Endophytic bacteria improve plant growth, symbiotic performance of chickpea (Cicer arietinum L .) and induce suppression of root rot caused by Fusarium solani under salt stress. Front. Microbiol., 8, 1–13.
Fierer, N. (2017). Embracing the unknown: disentangling the complexities of the soil microbiome. Nat. Publ. Gr. , 15, 579–590.
Finkel, O.M., Salas-González, I., Castrillo, G. & Conway, J.M. (2020). A single bacterial genus maintains root growth in a complex microbiome.Nature , 587, 103-108.
Friesen, M.L., Porter, S.S., Stark, S.C., Wettberg, E.J. Von & Sachs, J.L. (2011). Microbially mediated plant functional traits. Annu. Rev. Ecol. Evol. Syst. , 42, 23–46.
Gray, M.M., Amand, P.S.T., Bello, N.M., Galliart, M.B., Knapp, M., Garrett, K.A., et al. (2014). Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii ) exhibit genetic divergence across the U. S. Midwest grasslands’ environmental gradient.Molec. Ecol., 23, 6011–6028.
Jaremo, J., Tuomi, J., Nilsson, P. & Lennartsson, T. (1999). Plant adaptations to herbivory: mutualistic versus antagonistic coevolution.Oikos , 84, 313–320.
Hartman, K. & Tringe, S.G. (2019). Interactions between plants and soil shaping the root microbiome under abiotic stress. Biochemical J.,476, 2705–2724.
Jeuken, M.J., Zhang, N.W., McHale, L.K., Pelgrom, K., den Boer, E., Lindhout, P., et al. (2009). Rin4 causes hybrid necrosis and race-specific resistance in an interspecific lettuce hybrid. Plant Cell , 21, 3368–3378.
Jones, P., Garcia, B.J., Furches, A., Tuskan, G.A., Jacobson, D. & Jacobson, D. (2019). Plant host-associated mechanisms for microbial selection. Front. Plant Sci., 10, 1–14.
Khasanova, A., Lovell, J.T., Bonnette, J., Weng, X., Jenkins, J., Yoshinaga, Y., et al. (2019). The genetic architecture of shoot and root trait divergence between mesic and xeric ecotypes of a perennial grass. Front. Plant Sci., 10, 1–10.
Lau, J.A. & Lennon, J.T. (2012). Rapid responses of soil microorganisms improve plant fitness in novel environments. Proc. Natl. Acad. Sci. , 109, 14058–14062.
Leimu, R. & Fischer, M. (2008). A meta-analysis of local adaptation in plants. PLoS One , 3, 1–8.
Li, Y., Wu, X., Chen, T., Wang, W., Liu, G. & Zhang, W. (2018). Plant phenotypic traits eventually shape its microbiota: A common garden test.Front. Microbiol., 9, 1–13.
Littell, R.C., Milliken, G.A., Stroup, W.W. & Wolfinger, R.D. (1996).SAS system for mixed models. New York. USA: SAS Institute Inc.
Love, M.I., Huber, W. &Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol.,15, 550.
Lovell, J.T., Jenkins, J., Lowry, D.B., Mamidi, S., Sreedasyam, A., Weng, X., et al. (2018). The genomic landscape of molecular responses to natural drought stress in Panicum hallii .Nature Commun., 9, 1-10.
Lowry, D.B., Hernandez, K., Taylor, S.H., Meyer, E., Logan, T.L., Barry, K.W., et al. (2014). The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii . New Phyt.,205, 402-414.
Lundberg, D.S., Lebeis, S.L., Paredes, S.H., Yourstone, S., Gehring, J., Malfatti, S., et al. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature , 488, 86–90.
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J., 17, 10-12.
Mendes, R., Garbeva, P. & Raaijmakers, J.M. (2013). The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev. , 37, 634–663.
Midolo, G. & Wellstein, C. (2020). Plant performance and survival across transplant experiments depend upon temperature and precipitation change along elevation. J. Ecol. , 108, 2107–2120.
Müller, L.M. & Harrison, M.J. (2019). Phytohormones, miRNAs, and peptide signals integrate plant phosphorus status with arbuscular mycorrhizal symbiosis. Cur. Opin, in Pl. Bio., 50, 132–139.
Oksanen, J., Blanchet, F.G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., et al . (2020). vegan: Community Ecology Package . R package version 2.5-7. https://CRAN.R-project.org/package=vegan
Palacio-Mejía, J.D., Grabowski, P.P., Ortiz, E.M., Silva-Arias, G.A., Haque, T., Des Marais, D.L., et al. (2021). Geographic patterns of genomic diversity and structure in the C4 grassPanicum hallii across its natural distribution. AoB Pants , 13, 1-19.
Paredes, S.H., Gao, T., Law, T.F., Finkel, O.M., Teixeira, P.L., Gonza, S., et al. (2018). Design of synthetic bacterial communities for predictable plant phenotypes. PLoS Biol., 16, 1-41.
Pérez-Jaramillo, J.E., Carrión, V.J., Bosse, M., Ferrão, L.F. V, Hollander, M. De, Garcia, A.A.F., et al. (2017). Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME J., 11, 2244–2257.
Petipas, R.H., Geber, M.A. & Lau, J.A. (2021). Mediated adaptation in plants. Ecology Letters, 24, 1302–1317.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Glo, F.O.,et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41, 590–596.
R Core Team. (2020). R: A language and environment for statistical computing . R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Reich, P.B., Walters, M.B. & Ellsworth, D.S. (1997). From tropics to tundra: Global convergence in plant functioning. Proc. Natl. Acad. Sci. , 94, 13730–13734.
Runquist, R.D.B., Gorton, A.J., Yoder, J.B., Deacon, N.J., Grossman, J.J., Kothari, S., et al. (2020). Context dependence of local adaptation to abiotic and biotic environments: A quantitative and qualitative synthesis. Am. Nat. , 195, 412–431.
Santhanam, R., Luu, V.T., Weinhold, A., Goldberg, J., Oh, Y. & Baldwin, I.T. (2015). Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping. Proc. Natl. Acad. Sci. , 112, E5013–E5120.
Singer, E., Bonnette, J., Woyke, T. & Juenger, T.E. (2019). Conservation of endophyte bacterial community structure across two panicum grass species. Front. Microbiol ., 10.
Sukumar, P., Legué, V., Vayssières, A., Martin, F., Tuskan, G.A. & Kalluri, U.C. (2013). Involvement of auxin pathways in modulating root architecture during beneficial plant – microorganism interactions.Plant, Cell and Envir., 36, 909–919.
Trivedi, P., Leach, J.E., Tringe, S.G., Sa, T. & Singh, B.K.  (2020). Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol ., 18, 607–621.
Vij, S. & Tyagi, A.K. (2007). Emerging trends in the functional genomics of the abiotic stress response in crop plants. Plant Biotechnol. J., 5, 361–380.
Vorholt, J.A., Vogel, C. & Carlstro, C.I. (2017). Establishing causality: opportunities of synthetic communities for plant microbiome research. Cell Host and Microbe , 22, 142–155.
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 wildArabidopsis relative. Ecology Letters 17, 717–726.
Wagner, M.R., Lundberg, D.S., 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. Nat. Commun., 7, 1–15.
Weng, X., Haque, T., Lovell, J.T., Schwartz, S.L., Razzaque, S. & Juenger, T.E. (2019). Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C 4 grass. Plant Cell and Envir., 42, 2165–2182.
Winer, B.J. (1971). Statistical Principles in Experimental Design . 2nd ed. New York, USA, McGraw-Hill.