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Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history

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  • 1.

    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.

    PubMed  PubMed Central  Google Scholar 

  • 2.

    Philippot L, Raaijmakers JM, Lemanceau P, Van Der Putten WH. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol. 2013;11:789–99.

    CAS  PubMed  Google Scholar 

  • 3.

    Hartmann A, Schmid M, van Tuinen D, Berg G. Plant-driven selection of microbes. Plant Soil. 2009;321:235–57.

    CAS  Google Scholar 

  • 4.

    PAHM Bakker, Berendsen RL, Doornbos RF, PCA Wintermans, CMJ. Pieterse. The rhizosphere revisited: root microbiomics. Front Plant Sci. 2013;4:165.

    Google Scholar 

  • 5.

    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.

    CAS  PubMed  Google Scholar 

  • 6.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 7.

    Zgadzaj R, Garrido-Oter R, Jensen DB, Koprivova A, Schulze-Lefert P, Radutoiu S. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proc Natl Acad Sci. 2016;113:E7996–E8005.

    CAS  PubMed  Google Scholar 

  • 8.

    Haney CH, Samuel BS, Bush J, Ausubel FM. Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat Plants. 2015;1:15051.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 9.

    Pérez-Jaramillo JE, Carrión VJ, Bosse M, Ferrão LFV, De Hollander M, Garcia AAF, et al. Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME J. 2017;11:2244–57.

    PubMed  PubMed Central  Google Scholar 

  • 10.

    Castrillo G, PJPL Teixeira, Paredes SH, Law TF, De Lorenzo L, Feltcher ME, et al. Root microbiota drive direct integration of phosphate stress and immunity. Nature. 2017;543:513–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 11.

    Huang AC, Jiang T, Liu YX, Bai YC, Reed J, Qu B, et al. A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science. 2019;364:eaau6389.

    CAS  PubMed  Google Scholar 

  • 12.

    Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science. 2015;349:860–4.

    CAS  PubMed  Google Scholar 

  • 13.

    Kardol P, De Deyn GB, Laliberté E, Mariotte P, Hawkes CV. Biotic plant-soil feedbacks across temporal scales. J Ecol. 2013;101:309–15.

    Google Scholar 

  • 14.

    Pigliucci M. Ecology and evolutionary biology of Arabidopsis. Arabidopsis Book. 2002;1:e0003.

    PubMed  PubMed Central  Google Scholar 

  • 15.

    Warembourg FR. The’ rhizosphere effect’: a plant strategy for plants to exploit and colonize nutrient-limited habitats. Bocconea. 1997;7:187–94.

    Google Scholar 

  • 16.

    Deyn GBD. Plant life history and above–belowground interactions: missing links. Oikos. 2017;126:497–507.

    Google Scholar 

  • 17.

    Hakes AS, Cronin JT. Successional changes in plant resistance and tolerance to herbivory. Ecology. 2012;93:1059–70.

    PubMed  Google Scholar 

  • 18.

    Morriën E, Hannula SE, Snoek LB, Helmsing NR, Zweers H, De Hollander M, et al. Soil networks become more connected and take up more carbon as nature restoration progresses. Nat Commun. 2017;8:14349.

    PubMed  PubMed Central  Google Scholar 

  • 19.

    Scheres B, Van Der Putten WH. The plant perceptron connects environment to development. Nature. 2017;543:337–45.

    CAS  PubMed  Google Scholar 

  • 20.

    Van der Putten WH, Mortimer SR, Hedlund K, Van Dijk C, Brown VK, Lepä J, et al. Plant species diversity as a driver of early succession in abandoned fields: a multi-site approach. Oecologia. 2000;124:91–99.

    PubMed  Google Scholar 

  • 21.

    Bezemer TM, Van der Putten WH. Diversity and stability in plant communities. Nature. 2007;446:E6–7. discussion E7-8

    CAS  PubMed  Google Scholar 

  • 22.

    Schneijderberg M, Schmitz L, Cheng X, Polman S, Franken C, Geurts R, et al. A genetically and functionally diverse group of non-diazotrophic Bradyrhizobium spp. colonizes the root endophytic compartment of Arabidopsis thaliana. BMC Plant Biol. 2018;18:61.

    PubMed  PubMed Central  Google Scholar 

  • 23.

    Vieira S, Sikorski J, Dietz S, Herz K, Schrumpf M, Bruelheide H, et al. Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands. ISME J. 2019;14:463–75.

    PubMed  PubMed Central  Google Scholar 

  • 24.

    Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T. Roots shaping their microbiome: global hotspots for microbial activity. Annu Rev Phytopathol. 2015;53:403–24.

    CAS  PubMed  Google Scholar 

  • 25.

    Hacquard S. Disentangling the factors shaping microbiota composition across the plant holobiont. N. Phytol. 2016;209:454–7.

    Google Scholar 

  • 26.

    Lorite MJ, Estrella MJ, Escaray FJ, Sannazzaro A, Videira E Castro IM, et al. The Rhizobia-Lotus symbioses: deeply specific and widely diverse. Front Microbiol. 2018;9:2055. Frontiers Media S.A., 9

  • 27.

    Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009;26:139–40.

    PubMed  PubMed Central  Google Scholar 

  • 28.

    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. 2018;28:E1157 LP–E1165.

    Google Scholar 

  • 29.

    Cosme M, Fernández I, Van der Heijden MGA, Pieterse CMJ. Non-Mycorrhizal Plants: The Exceptions that Prove the Rule. Trends Plant Sci. 2018;23:577–87. Elsevier Ltd.

    CAS  PubMed  Google Scholar 

  • 30.

    Demars BG, Boerner REJ. Vesicular arbuscular mycorrhizal development in the Brassicaceae in relation to plant life span. Flora. 1996;191:179–89.

    Google Scholar 

  • 31.

    Dawson W, Hör J, Egert M, van Kleunen M, Peste M. A small number of low-abundance bacteria dominate plant species-specific responses during rhizosphere colonization. Front Microbiol. 2017;8:975.

    PubMed  PubMed Central  Google Scholar 

  • 32.

    Bergelson J, Mittelstrass J, Horton MW. Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome. Sci Rep. 2019;9:24.

    PubMed  PubMed Central  Google Scholar 

  • 33.

    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.

    PubMed  PubMed Central  Google Scholar 

  • 34.

    Van Der Wal A, De Boer W, Lubbers IM, Van Veen JA. Concentration and vertical distribution of total soil phosphorus in relation to time of abandonment of arable fields. Nutr Cycl Agroecosystems. 2007;79:73–79.

    Google Scholar 

  • 35.

    Veiga RSL, Faccio A, Genre A, Pieterse CMJ, Bonfante P, van der Heijden MGA. Arbuscular mycorrhizal fungi reduce growth and infect roots of the non-host plant Arabidopsis thaliana. Plant Cell Environ. 2013;36:1926–37.

    PubMed  Google Scholar 

  • 36.

    Jones DL, Nguyen C, Finlay RD. Carbon flow in the rhizosphere: carbon trading at the soil-root interface. Plant Soil. 2009;321:5–33.

    CAS  Google Scholar 

  • 37.

    Hirsch PR, Miller AJ, Dennis PG. Do root exudates exert more influence on rhizosphere bacterial community structure than other rhizodeposits? Mol Micro Ecol Rhizosph. 2013;1:229–42.

    Google Scholar 

  • 38.

    Micallef SA, Shiaris MP, Colón-Carmona A. Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. J Exp Bot. 2009;60:1729–42.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 39.

    PAHM Bakker, Berendsen RL, Doornbos RF, PCA Wintermans, CMJ Pieterse. The rhizosphere revisited: Root microbiomics. Front Plant Sci. 2013;4:165. Frontiers Research Foundation

    Google Scholar 

  • 40.

    Yuan J, Zhao J, Wen T, Zhao M, Li R, Goossens P, et al. Root exudates drive the soil-borne legacy of aboveground pathogen infection. Microbiome. 2018;6:156.

    PubMed  PubMed Central  Google Scholar 

  • 41.

    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.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 42.

    Badri DV, Quintana N, El Kassis EG, Kim HK, Choi YH, Sugiyama A, et al. An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota. Plant Physiol. 2009;151:2006–17.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 43.

    Stringlis IA, Yu K, Feussner K, De Jonge R, Van Bentum S, Van Verk MC, et al. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc Natl Acad Sci USA. 2018;115:E5213–E5222.

    CAS  PubMed  Google Scholar 

  • 44.

    MJEEE Voges, Bai Y, Schulze-Lefert P, Sattely ES. Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome. Proc Natl Acad Sci USA. 2019;116:12558–65.

    Google Scholar 

  • 45.

    Sergaki C, Lagunas B, Lidbury I, Gifford ML, Schäfer P. Challenges and approaches in microbiome research: from fundamental to applied. Front Plant Sci. 2018;9:1205. Frontiers Media S.A.

    PubMed  PubMed Central  Google Scholar 

  • 46.

    Sessitsch A, Pfaffenbichler N, Mitter B. Microbiome applications from lab to field: facing complexity. Trends Plant Sci. 2019;24:194–8. Elsevier Ltd

    CAS  PubMed  Google Scholar 

  • 47.

    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.

    CAS  PubMed  Google Scholar 

  • 48.

    Yeoh YK, Dennis PG, Paungfoo-Lonhienne C, Weber L, Brackin R, Ragan MA, et al. Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nat Commun. 2017;8:215.

    PubMed  PubMed Central  Google Scholar 

  • 49.

    Wilschut RA, van der Putten WH, Garbeva P, Harkes P, Konings W, Kulkarni P, et al. Root traits and belowground herbivores relate to plant–soil feedback variation among congeners. Nat Commun. 2019;10:1–9.

    CAS  Google Scholar 

  • 50.

    Fukami T, Bezemer TM, Mortimer SR, Van Der Putten WH. Species divergence and trait convergence in experimental plant community assembly. Ecol Lett. 2005;8:1283–90.

    Google Scholar 

  • 51.

    Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinforma. 2012;13:31.

    CAS  Google Scholar 

  • 52.

    Zhang Y, Sun Y, Cole JR. A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data. PLoS Comput Biol. 2014;10:e1003737.

    PubMed  PubMed Central  Google Scholar 

  • 53.

    Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.

    CAS  PubMed  Google Scholar 

  • 54.

    Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.

    PubMed  PubMed Central  Google Scholar 

  • 55.

    Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 56.

    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 57.

    McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 58.

    Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633–D642.

    CAS  PubMed  Google Scholar 

  • 59.

    Koster J, Rahmann S. Snakemake-a scalable bioinformatics workflow engine. Bioinformatics. 2012;28:2520–2.

    PubMed  Google Scholar 

  • 60.

    Bushnell B, Rood J, Singer E. BBMerge – Accurate paired shotgun read merging via overlap. PLoS One. 2017;12:e0185056.

    PubMed  PubMed Central  Google Scholar 

  • 61.

    Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10.

    Google Scholar 

  • 62.

    Gweon HS, Oliver A, Taylor J, Booth T, Gibbs M, Read DS, et al. PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods Ecol Evol. 2015;6:973–80.

    PubMed  PubMed Central  Google Scholar 

  • 63.

    Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol. 2013;4:n/a–n/a.

    Google Scholar 

  • 64.

    Nilsson RH, Larsson K-H, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D, et al. The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 2019;47:D259–D264.

    CAS  PubMed  Google Scholar 

  • 65.

    Paulson JN, Colin Stine O, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013;10:1200–2.

    CAS  PubMed  PubMed Central  Google Scholar 


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