in

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat

  • 1.

    Nesbitt, M. & Samuel, D. Wheat domestication: Archaeobotanical evidence. Science 279, 1431–1431 (1998).

    ADS  Google Scholar 

  • 2.

    Hammer, K. Das Domestikationssyndrom. Kult. 32, 11–34 (1984).

    Google Scholar 

  • 3.

    Peleg, Z., Fahima, T., Korol, A. B., Abbo, S. & Saranga, Y. Genetic analysis of wheat domestication and evolution under domestication. J. Exp. Bot. 62, 5051–5061 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 4.

    Simons, K. J. et al. Molecular characterization of the major wheat domestication gene Q. Genetics 172, 547 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 5.

    Simonetti, M. C. et al. Quantitative trait loci influencing free-threshing habit in tetraploid wheats. Genet. Resour. Crop Evol. 46, 267–271 (1999).

    Google Scholar 

  • 6.

    Tzarfati, R. et al. Threshing efficiency as an incentive for rapid domestication of emmer wheat. Ann. Bot. 112, 829–837 (2013).

    PubMed  PubMed Central  Google Scholar 

  • 7.

    Matsuoka, Y. Evolution of polyploid triticum wheats under cultivation: The role of domestication, natural hybridization and allopolyploid speciation in their diversification. Plant Cell Physiol. 52, 750–764 (2011).

    CAS  PubMed  Google Scholar 

  • 8.

    Araus, J. L., Bort, J., Steduto, P., Villegas, D. & Royo, C. Breeding cereals for Mediterranean conditions: Ecophysiological clues for biotechnology application. Ann. Appl. Biol. 142, 129–141 (2003).

    Google Scholar 

  • 9.

    Gioia, T. et al. Impact of domestication on the phenotypic architecture of durum wheat under contrasting nitrogen fertilization. J. Exp. Bot. 66, 5519–5530 (2015).

    CAS  PubMed  Google Scholar 

  • 10.

    Thuillet, A.-C., Bataillon, T., Poirier, S., Santoni, S. & David, J. L. Estimation of long-term effective population sizes through the history of durum wheat using microsatellite data. Genetics 169, 1589 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 11.

    Haudry, A. et al. Grinding up wheat: A massive loss of nucleotide diversity since domestication. Mol. Biol. Evol. 24, 1506–1517 (2007).

    CAS  PubMed  Google Scholar 

  • 12.

    Pérez-Jaramillo, J. E., Mendes, R. & Raaijmakers, J. M. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol. Biol. 90, 635–644 (2016).

    PubMed  Google Scholar 

  • 13.

    Philippot, L., Raaijmakers, J. M., Lemanceau, P. & van der Putten, W. H. Going back to the roots: The microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 11, 789 (2013).

    CAS  PubMed  Google Scholar 

  • 14.

    Pozo, M. J. & Azcón-Aguilar, C. Unraveling mycorrhiza-induced resistance. Curr. Opin. Plant Biol. 10, 393–398 (2007).

    CAS  PubMed  Google Scholar 

  • 15.

    Cook, R. J. et al. Molecular mechanisms of defense by rhizobacteria against root disease. Proc. Natl. Acad. Sci. 92, 4197 (1995).

    ADS  CAS  PubMed  Google Scholar 

  • 16.

    Lundberg, D. S. et al. Defining the core Arabidopsis thaliana root microbiome. Nature 488, 86 (2012).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • 17.

    Peiffer, J. A. et al. Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc. Natl. Acad. Sci. 110, 6548 (2013).

    ADS  CAS  PubMed  Google Scholar 

  • 18.

    İnceoğlu, Ö, Salles, J. F., van Overbeek, L. & van Elsas, J. D. Effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields. Appl. Environ. Microbiol. 76, 3675 (2010).

    PubMed  PubMed Central  Google Scholar 

  • 19.

    Bulgarelli, D. et al. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488, 91 (2012).

    ADS  CAS  PubMed  Google Scholar 

  • 20.

    Hardoim, P. R. et al. Rice root-associated bacteria: Insights into community structures across 10 cultivars. FEMS Microbiol. Ecol. 77, 154–164 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 21.

    Pérez-Jaramillo, J. E. et al. Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME J. 11, 2244 (2017).

    PubMed  PubMed Central  Google Scholar 

  • 22.

    Bulgarelli, D. et al. Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe 17, 392–403 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 23.

    Leff, J. W., Lynch, R. C., Kane, N. C. & Fierer, N. Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus. New Phytol. 214, 412–423 (2017).

    CAS  PubMed  Google Scholar 

  • 24.

    Roucou, A. et al. Shifts in plant functional strategies over the course of wheat domestication. J. Appl. Ecol. 55, 25–37 (2018).

    CAS  Google Scholar 

  • 25.

    Röder, M. S. et al. A microsatellite map of wheat. Genetics 149, 2007 (1998).

    PubMed  PubMed Central  Google Scholar 

  • 26.

    Berry, D., Ben Mahfoudh, K., Wagner, M. & Loy, A. Barcoded Primers used in multiplex amplicon pyrosequencing bias amplification. Appl. Environ. Microbiol. 77, 7846 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 27.

    Takahashi, S., Tomita, J., Nishioka, K., Hisada, T. & Nishijima, M. Development of a prokaryotic universal primer for simultaneous analysis of bacteria and archaea using next-generation sequencing. PLoS ONE 9, e105592 (2014).

    ADS  PubMed  PubMed Central  Google Scholar 

  • 28.

    Muyzer, G., de Waal, E. C. & Uitterlinden, A. G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 29.

    White, T. J., Bruns, T., Lee, S. & Taylor, J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols (eds Innis, M. A. et al.) 315–322 (Academic Press, Cambridge, 1990).

    Google Scholar 

  • 30.

    Tourna, M., Freitag, T. E., Nicol, G. W. & Prosser, J. I. Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ. Microbiol. 10, 1357–1364 (2008).

    CAS  PubMed  Google Scholar 

  • 31.

    Leininger, S. et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442, 806–809 (2006).

    ADS  CAS  PubMed  Google Scholar 

  • 32.

    Henry, S. et al. Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR. J. Microbiol. Methods 59, 327–335 (2004).

    CAS  PubMed  Google Scholar 

  • 33.

    Henry, S., Bru, D., Stres, B., Hallet, S. & Philippot, L. Quantitative detection of the nosZ Gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Appl. Environ. Microbiol. 72, 5181 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 34.

    Jones, C. M., Graf, D. R., Bru, D., Philippot, L. & Hallin, S. The unaccounted yet abundant nitrous oxide-reducing microbial community: A potential nitrous oxide sink. ISME J. 7, 417 (2012).

    PubMed  PubMed Central  Google Scholar 

  • 35.

    Bru, D. et al. Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME J. 5, 532 (2010).

    PubMed  PubMed Central  Google Scholar 

  • 36.

    Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: A fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30, 614–620 (2013).

    PubMed  PubMed Central  Google Scholar 

  • 37.

    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 38.

    Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: A versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).

    PubMed  PubMed Central  Google Scholar 

  • 39.

    Caporaso, J. G. et al. PyNAST: A flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266–267 (2009).

    PubMed  PubMed Central  Google Scholar 

  • 40.

    Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—Approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    ADS  PubMed  PubMed Central  Google Scholar 

  • 41.

    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).

    CAS  PubMed  Google Scholar 

  • 42.

    McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610 (2011).

    PubMed  PubMed Central  Google Scholar 

  • 43.

    Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    CAS  PubMed  Google Scholar 

  • 44.

    Nilsson, R. H. et al. The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 47, D259–D264 (2019).

    CAS  PubMed  Google Scholar 

  • 45.

    Rohart, F., Gautier, B., Singh, A. & Cao, K.-A.L. mixOmics: An R package for ‘omics feature selection and multiple data integration. PLoS Comput. Biol. 13, e1005752 (2017).

    PubMed  PubMed Central  Google Scholar 

  • 46.

    A. Singh, et al., DIABLO—An integrative, multi-omics, multivariate method for multi-group classification. bioRxiv, 067611 (2016).

  • 47.

    Fierer, N., Bradford, M. A. & Jackson, R. B. Toward an ecological classification of soil bacteria. Ecology 88, 1354–1364 (2007).

    PubMed  Google Scholar 

  • 48.

    Anderson, P. K. et al. Emerging infectious diseases of plants: Pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19, 535–544 (2004).

    PubMed  Google Scholar 

  • 49.

    Dreaden, T. J. et al. Development of multilocus PCR assays for Raffaelea lauricola, causal agent of laurel wilt disease. Plant Dis. 98, 379–383 (2013).

    Google Scholar 

  • 50.

    Takahashi, Y., Matsushita, N. & Hogetsu, T. Spatial distribution of Raffaelea quercivora in xylem of naturally infested and inoculated oak trees. Phytopathology 100, 747–755 (2010).

    PubMed  Google Scholar 

  • 51.

    Gramaje, D., Armengol, J. & Ridgway, H. J. Genetic and virulence diversity, and mating type distribution of Togninia minima causing grapevine trunk diseases in Spain. Eur. J. Plant Pathol. 135, 727–743 (2013).

    Google Scholar 

  • 52.

    Corradi, N. & Bonfante, P. The arbuscular mycorrhizal symbiosis: Origin and evolution of a beneficial plant infection. PLoS Pathog. 8, e1002600 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 53.

    Maherali, H. & Klironomos, J. N. Influence of phylogeny on fungal community assembly and ecosystem functioning. Science 316, 1746–1748 (2007).

    ADS  CAS  PubMed  Google Scholar 

  • 54.

    Gosling, P., Proctor, M., Jones, J. & Bending, G. D. Distribution and diversity of Paraglomus spp. in tilled agricultural soils. Mycorrhiza 24, 1–11 (2014).

    PubMed  Google Scholar 

  • 55.

    B. D. Emmett, N. D. Youngblut, D. H. Buckley, L. E. Drinkwater, plant phylogeny and life history shape rhizosphere bacterial microbiome of summer annuals in an agricultural field. Front. Microbiol. 8, 2414 (2017).

  • 56.

    Hernández, M., Dumont, M. G., Yuan, Q. & Conrad, R. Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon. Appl. Environ. Microbiol. 81, 2244–2253 (2015).

    PubMed  PubMed Central  Google Scholar 

  • 57.

    DeBruyn, J. M., Nixon, L. T., Fawaz, M. N., Johnson, A. M. & Radosevich, M. Global biogeography and quantitative seasonal dynamics of gemmatimonadetes in soil. Appl. Environ. Microbiol. 77, 6295 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 58.

    Oldroyd, G. E. D. Speak, friend, and enter: Signalling systems that promote beneficial symbiotic associations in plants. Nat. Rev. Microbiol. 11, 252 (2013).

    CAS  PubMed  Google Scholar 

  • 59.

    Sikes, B. A. When do arbuscular mycorrhizal fungi protect plant roots from pathogens?. Plant Signal. Behav. 5, 763–765 (2010).

    PubMed  PubMed Central  Google Scholar 


  • Source: Ecology - nature.com

    Publisher Correction: Impacts of hydrothermal plume processes on oceanic metal cycles and transport

    Covid-19 shutdown led to increased solar power output