in

Selection pressure on the rhizosphere microbiome can alter nitrogen use efficiency and seed yield in Brassica rapa

  • Hawkes, C. V., Bull, J. J. & Lau, J. A. Symbiosis and stress: how plant microbiomes affect host evolution. Philos. T. R. Soc. B. 375, 20190590 (2020).

    CAS 
    Article 

    Google Scholar 

  • Leopold, D. R. & Busby, P. E. Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function. Curr. Biol. 30, 3260–3266 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Morella, N. M. et al. Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection. Proc. Natl Acad. Sci. USA 117, 1148–1159 (2020).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Garcia, J. & Kao-Kniffin, J. Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling. Front. Plant Sci. 9, 1516 (2018).

    Article 

    Google Scholar 

  • Marschner P. Plant-Microbe Interactions in the Rhizosphere and Nutrient Cycling in Nutrient Cycling in Terrestrial Ecosystems (eds. Marschner, P. & Rengel, Z.) 159–183 (Springer, 2007).

  • Vannier, N., Agler, M. & Hacquard, S. Microbiota-mediated disease resistance in plants. PLoS Pathog. 15, e1007740 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Wei, Z. et al. Initial soil microbiome composition and functioning predetermine future plant health. Sci. Adv. 5, 6584 (2019).

    Google Scholar 

  • Bender, S. F., Wagg, C. & van der Heijden, M. G. A. An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability. Trends Ecol. Evol. 31, 440–452 (2016).

    PubMed 
    Article 

    Google Scholar 

  • Dessaux, Y., Grandclemént, C. & Faure, D. Engineering the Rhizosphere. Trends Plant Sci. 21, 266–278 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Swenson, W., Wilson, D. S. & Elias, R. Artificial ecosystem selection. Proc. Natl Acad. Sci. USA 97, 9110–9114 (2000).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Panke-Buisse, K., Poole, A., Goodrich, J., Ley, R. E. & Kao-Kniffin, J. Selection on soil microbiomes reveals reproducible impacts on plant function. ISME J. 9, 980–989 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • van den Bergh, B. et al. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol. Mol. Biol. Rev. 82, e00008–e00018 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Garcia, J. & Kao-Kniffin, J. Can dynamic network modelling be used to identify adaptive microbiomes? Funct. Ecol. 34, 2065–2074 (2020).

    Article 

    Google Scholar 

  • Faust, K. & Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10, 538–550 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Wilson, D. & Wilson, E. Evolution “for the good of the group”. Am. Sci. 96, 380–389 (2008).

    Article 

    Google Scholar 

  • de la Fuente Cantó, C. et al. An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness. Plant J. 103, 951–964 (2020).

    PubMed 
    Article 
    CAS 

    Google Scholar 

  • Sachs, J., Mueller, U., Wilcox, T. & Bull, J. The evolution of cooperation. Q. Rev. Biol. 79, 135–160 (2004).

    PubMed 
    Article 

    Google Scholar 

  • Harrington, K. & Sanchez, A. Eco-evolutionary dynamics of complex social strategies in microbial communities. Commun. Integr. Biol. 7, e28230 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Rauch, J., Kondev, J. & Sanchez, A. Cooperators trade off ecological resilience and evolutionary stability in public goods games. J. R. Soc. Interface 14, 20160967 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Sexton, D. & Schuster, M. Nutrient limitation determines the fitness of cheaters in bacterial siderophore cooperation. Nat. Commun. 8, 230 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Schmidt, J. E., Kent, A. D., Brisson, V. L. & Gaudin, A. C. M. Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling. Microbiome 7, 146 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Turner, T. et al. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere. microbiome plants ISME J. 7, 2248–2258 (2013).

    CAS 
    PubMed 

    Google Scholar 

  • Jones, D. L., Nguyen, C. & Finlay, R. D. Carbon flow in the rhizosphere: carbon trading at the soil–root interface. Plant Soil 321, 5–33 (2009).

    CAS 
    Article 

    Google Scholar 

  • George, E., Marschner, H. & Jakobsen, I. Role of Arbuscular Mycorrhizal Fungi in Uptake of Phosphorus and Nitrogen From Soil. Crit. Rev. Biotechnol. 15, 257–270 (1995).

    Article 

    Google Scholar 

  • Hodge, A. & Fitter Alastair, H. Substantial nitrogen acquisition by arbuscular mycorrhizal fungi from organic material has implications for N cycling. Proc. Natl Acad. Sci. USA 107, 13754–13759 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Lambers, H. & Teste, F. P. Interactions between arbuscular mycorrhizal and non-mycorrhizal plants: do non-mycorrhizal species at both extremes of nutrient availability play the same game. Plant Cell Environ. 36, 1911–1915 (2013).

    PubMed 

    Google Scholar 

  • Delaux, P. M. et al. Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution. PLoS Genet. 10, e1004487 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Anas, M. et al. Fate of nitrogen in agriculture and environment: agronomic, eco-physiological and molecular approaches to improve nitrogen use efficiency. Biol. Res. 53, 47 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Madhaiyan, M. et al. Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil. Int. J. Syst. Evol. Microbiol. 65, 578–586 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Song, H. et al. Environmental filtering of bacterial functional diversity along an aridity gradient. Sci. Rep. 9, 866 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Xia, L. C. et al. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. BMC Syst. Biol. 5, S15 (2011).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Kuntal, B. K., Chandrakar, P., Sadhu, S. & Mandhi, S. S. ‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets. ISME J. 13, 442–454 (2019).

    PubMed 
    Article 

    Google Scholar 

  • Layeghifard, M., Hwang, D. M. & Guttman, D. S. Disentangling Interactions in the Microbiome: A Network Perspective. Trends Microbiol. 25, 217–228 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Hu, Q. et al. Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria. NPJ Biofilms Microbiomes 6, 8 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Faust, K. et al. Cross-biome comparison of microbial association networks. Front. Microbiol. 6, 1200 (2015).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Rengel, Z. & Marschner, P. Nutrient availability and management in the rhizosphere: exploiting genotypic differences. N. Phytol. 168, 305–312 (2005).

    CAS 
    Article 

    Google Scholar 

  • Marschner, P. The Role of Rhizosphere Microorganisms in Relation to P Uptake by Plants in The Ecophysiology of Plant-Phosphorus Interactions (eds. White, P. & Hammond, J.) 165–167 (Springer, 2008).

  • Repert, D., Underwood, J., Smith, R. & Song, B. Nitrogen cycling processes and microbial community composition in bed sediments in the Yukon River at Pilot Station. J. Geophys. Res. Biogeosci. 119, 2328–2344 (2014).

    CAS 
    Article 

    Google Scholar 

  • Rolletschek, H. et al. Ectopic expression of an amino acid transporter (VfAAP1) in seeds of Vicia narbonensis and pea increases storage proteins. Plant Physiol. 137, 1236–1249 (2005).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Sanders, A. et al. AAP1 regulates import of amino acids into developing Arabidopsis embryos. Plant J. 59, 540–552 (2009).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Carter, A. M. & Tegeder, M. Increasing nitrogen fixation and seed development in soybean requires complex adjustments of nodule nitrogen metabolism and partitioning processes. Curr. Biol. 26, 2044–2051 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Meier, I. C. et al. Root exudation of mature beech forests across a nutrient availability gradient: the role of root morphology and fungal activity. N. Phytol. 226, 583–594 (2020).

    CAS 
    Article 

    Google Scholar 

  • Xu, Y., He, J., Cheng, W., Xing, X. & Li, L. Natural 15N abundance in soils and plants in relation to N cycling in a rangeland in Inner Mongolia. J. Plant Ecol. 3, 201–207 (2010).

    Article 

    Google Scholar 

  • Henneron, L. et al. Rhizosphere control of soil nitrogen cycling: a key component of plant economic strategies. N. Phytol. 228, 1269–1282 (2020).

    CAS 
    Article 

    Google Scholar 

  • Hobbie, E. A. & Högberg, P. Nitrogen isotopes link mycorrhizal fungi and plants to nitrogen dynamics. N. Phytol. 196, 367–382 (2012).

    CAS 
    Article 

    Google Scholar 

  • Zhou, S. et al. Assessing nitrification and denitrification in a paddy soil with different water dynamics and applied liquid cattle waste using the 15N isotopic technique. Sci. Total Environ. 430, 93–100 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Fuertes-Mendizábal, T. et al. 15N Natural Abundance Evidences a Better Use of N Sources by Late Nitrogen Application in Bread Wheat. Front. Plant Sci. 9, 853 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Yoneyama, T., Omata, T., Nakata, S. & Yazaki, J. Fractionation of Nitrogen Isotopes during the Uptake and Assimilation of Ammonia by Plants. Plant Cell Physiol. 32, 1211–1217 (1991).

    CAS 

    Google Scholar 

  • Vacheron, J. et al. Plant growth-promoting rhizobacteria and root system functioning. Front. Plant Sci. 4, 356 (2013).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Granada, C., Passaglia, L., de Souza, E. & Sperotto, R. Is Phosphate Solubilization the Forgotten Child of Plant Growth-Promoting Rhizobacteria? Front. Microbiol. 9, 2054 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Compant, S., Duffy, B., Nowak, J., Clément, C. & Barka, E. Use of Plant Growth-Promoting Bacteria for Biocontrol of Plant Diseases: Principles, Mechanisms of Action, and Future Prospects. Appl. Environ. Microbiol. 71, 4951 (2005).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Berges, J.A., & Mulholland, M.R. Enzymes and nitrogen cycling in Nitrogen in the marine environment (eds. Capone, D., Bronk, D., Mulholland, M., & Carpenter, E.) 1385–1444 (Elsevier 2008).

  • DeAngelis, K. M., Lindow, S. E. & Firestone, M. Bacterial quorum sensing and nitrogen cycling in rhizosphere soil. FEMS Microb. Ecol. 66, 197–207 (2008).

    CAS 
    Article 

    Google Scholar 

  • Evans, S., Martiny, J. & Allison, S. Effects of dispersal and selection on stochastic assembly in microbial communities. ISME J. 11, 176–185 (2017).

    PubMed 
    Article 

    Google Scholar 

  • Ron, R., Fragman-Sapir, O. & Kadmon, R. (2018). Dispersal increases ecological selection by increasing effective community size. Proc. Natl Acad. Sci. USA. 115, 11280–11285 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Busby, P. et al. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biol. 15, e2001793 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Sergaki, C., Lagunas, B., Lidbury, I., Gifford, M. & Schäfer, P. Challenges and Approaches in Microbiome Research: From Fundamental to Applied. Front. Plant Sci. 9, 1205 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Herlemann, D. P. et al. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Garcia, J. et al. Selection pressure on the rhizosphere microbiome alters nitrogen use efficiency and seed yield in Brassica rapa. National Center for Biotechnology Information Repository. https://www.ncbi.nlm.nih.gov/sra/PRJNA833111 (2022).

  • Ruan, Q. et al. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics 22, 2532–2538 (2006).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Pollet, T. et al. Prokaryotic community successions and interactions in marine biofilms: the key role of Flavobacteria. FEMS Microbiol. Ecol. 94, fiy083 (2018).

    Google Scholar 

  • Durno, W. E. et al. Expanding the boundaries of local similarity analysis. BMC Genomics 14, S3 (2013).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Garcia, J. et al. Selection pressure on the rhizosphere microbiome alters nitrogen use efficiency and seed yield in Brassica rapa. https://doi.org/10.5281/zenodo.6800595 (2022).


  • Source: Ecology - nature.com

    Divorce is more common in albatross couples with shy males, study finds

    A lasting — and valuable — legacy