Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett. 2014;17:717–26.
Google Scholar
de Vries FT, Griffiths RI, Knight CG, Nicolitch O, Williams A. Harnessing rhizosphere microbiomes for drought-resilient crop production. Science. 2020;368:270–4.
Google Scholar
Compant S, Clément C, Sessitsch A. Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem. 2010;42:669–78.
Google Scholar
Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol. 2020;18:607–21.
Google Scholar
Berendsen RL, Vismans G, Yu K, Song Y, de Jonge R, Burgman WP, et al. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J. 2018;12:1496–507.
Google Scholar
Nelson EB. Microbial dynamics and interactions in the spermosphere. Annu Rev Phytopathol. 2004;42:271–309.
Google Scholar
Nelson EB. The seed microbiome: origins, interactions, and impacts. Plant Soil Springe Int Publ. 2018;422:7–34.
Google Scholar
Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, et al. Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci USA. 2015;112:E911–20.
Google Scholar
Fitzpatrick CR, Salas-González I, Conway JM, Finkel OM, Gilbert S, Russ D, et al. The plant microbiome: from ecology to reductionism and beyond. Annu Rev Microbiol. 2020;74:81–100.
Google Scholar
Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F, et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature. 2012;488:91–95.
Google Scholar
Naylor D, DeGraaf S, Purdom E, Coleman-Derr D. Drought and host selection influence bacterial community dynamics in the grass root microbiome. ISME J. 2017;11:2691–704.
Google Scholar
Chaparro JM, Badri DV, Vivanco JM. Rhizosphere microbiome assemblage is affected by plant development. ISME J. 2014;8:790–803.
Google Scholar
Fitzpatrick CR, Copeland J, Wang PW, Guttman DS, Kotanen PM, Johnson MTJ. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc Natl Acad Sci USA. 2018;115:E1157–65.
Google Scholar
Grady KL, Sorensen JW, Stopnisek N, Guittar J, Shade A. Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nat Commun. 2019;10:4135.
Google Scholar
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. 2012;488:86–90.
Google Scholar
Schlaeppi K, Dombrowski N, Oter RG, Ver Loren Van Themaat E, Schulze-Lefert P. Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci USA. 2014;111:585–92.
Google Scholar
Bulgarelli D, Garrido-Oter R, Münch PC, Weiman A, Dröge J, Pan Y, et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe. 2015;17:392–403.
Google Scholar
Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci USA. 2013;110:6548–53.
Google Scholar
Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol. 2013;64:807–38.
Google Scholar
Coleman-Derr D, Desgarennes D, Fonseca-Garcia C, Gross S, Clingenpeel S, Woyke T, et al. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. N Phytol. 2016;209:798–811.
Google Scholar
de Souza RSC, Okura VK, Armanhi JSL, Jorrín B, Lozano N, da Silva MJ, et al. Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome. Sci Rep. 2016;6:28774.
Google Scholar
Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, et al. Genomic features of bacterial adaptation to plants. Nat Genet. 2017;50:138–50.
Google Scholar
Vannier N, Mony C, Bittebiere A-K, Michon-Coudouel S, Biget M, Vandenkoornhuyse P. A microorganisms’ journey between plant generations. Microbiome. 2018;6:79.
Google Scholar
Tobias TB, Farrer EC, Rosales A, Sinsabaugh RL, Suding KN, Porras-Alfaro A. Seed-associated fungi in the alpine tundra: both mutualists and pathogens could impact plant recruitment. Fungal Ecol. 2017;30:10–18.
Google Scholar
Truyens S, Weyens N, Cuypers A, Vangronsveld J. Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environ Microbiol Rep. 2015;7:40–50.
Google Scholar
Shade A, Jacques M-A, Barret M. Ecological patterns of seed microbiome diversity, transmission, and assembly. Curr Opin Microbiol. 2017;37:15–22.
Google Scholar
Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, et al. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev. 2015;79:293–320.
Google Scholar
Normander BO, Prosser JI. Bacterial origin and community composition in the barley phytosphere as a function of habitat and presowing conditions. Appl Environ Microbiol. 2000;66:4372–7.
Google Scholar
Green SJ, Inbar E, Michel FC, Hadar Y, Minz D. Succession of bacterial communities during early plant development: transition from seed to root and effect of compost amendment. Appl Environ Microbiol. 2006;72:3975–83.
Google Scholar
Ofek M, Hadar Y, Minz D. Colonization of cucumber seeds by bacteria during germination. Environ Microbiol. 2011;13:2794–807.
Google Scholar
OECD-FAO. Agricultural Outlook 2020–2029.
Fierer N. Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017;15:579–90.
Google Scholar
Rath KM, Fierer N, Daniel, Murphy V, Rousk J. Linking bacterial community composition to soil salinity along environmental gradients. ISME J. 2018;13:836–46.
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA. 2011;108:4516–22.
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Google Scholar
Oliverio A, Holland-Moritz H. dada2 tutorial with MiSeq dataset for Fierer Lab. 2019.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–596.
Google Scholar
Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics. 2005;21:456–63.
Google Scholar
Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007;23:127–8.
Google Scholar
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing; 2020.
Wickham H. ggplot2: elegant graphics for data analysis. Springer-Verlag: New York; 2016.
Becker RA, Wilks AR, Minka TP, Deckmyn A. maps: draw geographical maps. 2018.
Jari Oksanen F, Blanchet G, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: community ecology package. R. 2019. p. R package version 2.5-6.
Rochefort A, Simonin M, Marais C, Guillerm-Erckelboudt A-Y, Barret M, Sarniguet A. Asymmetric outcome of community coalescence of seed and soil microbiota during early seedling growth. bioRxiv. 2020.11.19.390344.
Minich JJ, Sanders JG, Amir A, Humphrey G, Gilbert JA, Knight R. Quantifying and understanding well-to-well contamination in microbiome research. mSystems. 2019;4:e00186–19.
Google Scholar
Cribari-Neto F, Zeileis A. Beta regression in R. J Stat Software; Vol 1, Issue 2. 2010.
Douma JC, Weedon JT. Analysing continuous proportions in ecology and evolution: a practical introduction to beta and Dirichlet regression. Methods. Ecol Evol. 2019;10:1412–30.
Kuhn M. caret: classification and regression training. 2020.
Wright MN, Ziegler A. Ranger: a fast implementation of random forests for high dimensional data in C++ and R. J Stat Softw. 2017;77:1–17.
Google Scholar
Thiergart T, Durán P, Ellis T, Vannier N, Garrido-Oter R, Kemen E, et al. Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nat Ecol Evol. 2019;4:122–31.
Google Scholar
Simonin M, Dasilva C, Terzi V, Ngonkeu ELM, Diouf D, Aboubacry K. et al. Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European Soils. FEMS Microbiol Ecol. 2016;96:fiaa067
Google Scholar
Robinson RJ, Fraaije BA, Clark IM, Jackson RW, Hirsch PR, Mauchline TH. Wheat seed embryo excision enables the creation of axenic seedlings and Koch’s postulates testing of putative bacterial endophytes. Sci Rep. 2016;6:25581.
Google Scholar
Walterson AM, Stavrinides J. Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiol Rev. 2015;39:968–84.
Google Scholar
Hardoim PR, Hardoim CCP, van Overbeek LS, van Elsas JD. Dynamics of seed-borne rice endophytes on early plant growth stages. PLoS One. 2012;7:e30438.
Google Scholar
Liu F, Hewezi T, Lebeis SL, Pantalone V, Grewal PS, Staton ME. Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly. BMC Microbiol. 2019;19:201.
Google Scholar
Nelson EB, Simoneau P, Barret M. Editorial special issue: the soil, the seed, the microbes and the plant. Plant Soil. 2018;422:1–5.
Google Scholar
Shmida A, Wilson MV. Biological determinants of species diversity. J Biogeogr. 1985;12:1–20.
Google Scholar
Hannula SE, Kielak AM, Steinauer K, Huberty M, Jongen R, De Long JR, et al. Time after time: temporal variation in the effects of grass and forb species on soil bacterial and fungal communities. MBio. 2019;10:e02635–19.
Google Scholar
Jack ALH, Nelson EB. A seed-recruited microbiome protects developing seedlings from disease by altering homing responses of Pythium aphanidermatum zoospores. Plant Soil. 2018;422:209–22.
Google Scholar
Verma SK, Kharwar RN, White JF. The role of seed-vectored endophytes in seedling development and establishment. Symbiosis. 2019;78:107–13.
Google Scholar
Carlström CI, Field CM, Bortfeld-Miller M, Müller B, Sunagawa S, Vorholt JA. Synthetic microbiota reveal priority effects and keystone strains in the Arabidopsis phyllosphere. Nat Ecol Evol. 2019;3:1445–54.
Google Scholar
Busby PE, Soman C, Wagner MR, Friesen ML, Kremer J, Bennett A, et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 2017;15:e2001793.
Google Scholar
Finkel OM, Castrillo G, Herrera Paredes S, Salas González I, Dangl JL. Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol. 2017;38:155–63.
Google Scholar
Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, et al. Core microbiomes for sustainable agroecosystems. Nat Plants. 2018;4:247–57.
Google Scholar
Maignien L, DeForce EA, Chafee ME, Murat Eren A, Simmons SL. Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities. MBio. 2014;5:e00682–13.
Google Scholar
Wei Z, Gu Y, Friman V-P, Kowalchuk GA, Xu Y, Shen Q, et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci Adv. 2019;5:eaaw0759.
Google Scholar
Durán P, Thiergart T, Garrido-Oter R, Agler M, Kemen E, Schulze-Lefert P, et al. Microbial interkingdom interactions in roots promote arabidopsis survival. Cell. 2018;175:973–83.
Google Scholar
Hamonts K, Trivedi P, Garg A, Janitz C, Grinyer J, Holford P, et al. Field study reveals core plant microbiota and relative importance of their drivers. Environ Microbiol. 2018;20:124–40.
Google Scholar
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