Abstract
A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched 13CO2 atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Akiyama K, Matsuzaki K, Hayashi H . (2005). Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature 435: 824–827.
Altschul SF, Gish W, Miler W, Lipman DJ . (1990). Basic local alignment search tool. J Mol Biol 215: 403–410.
Angus JF, Gardner PA, Kirkegaard JA, Desmarchelier JM . (1994). Biofumigation: isothiocyanates released from Brassica roots inhibit growth of the take-all fungus. Plant Soil 162: 107–112.
Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM . (2006). The role of root exudates in rhizosphere interactions with plants and other organisms. Ann Rev Plant Biol 57: 233–266.
Bak S, Olsen CE, Petersen BL, Møller BL, Halkier BA . (1999). Metabolic engineering of p-hydroxybenzylglucosinolate in Arabidopsis by expression of the cyanogenic CYP79A1 from Sorghum Metaboli. Plant J 20: 663–671.
Bending GD, Lincoln SD . (2000). Inhibition of soil nitrifying bacteria communities and their activities by glucosinolate hydrolysis products. Soil Biol Biochem 32: 1261–1269.
Berge O, Lodhi A, Brandelet G, Santaella C, Roncato M, Christen R et al. (2009). Rhizobium alamii sp. nov., an exopolysaccharide producing species isolated from legume and non-legume rhizospheres. Int J Syst Evol Microbiol 59: 367–372.
Borek V, Morra MJ, McCaffrey JP . (1996). Myrosinase activity in soil extracts. Soil Sci Soc Am J 60: 1792–1797.
Brabban AD, Edwards C . (1995). The effects of glucosinolates and their hydrolysis products on microbial growth. J Appl Bacteriol 79: 171–177.
Brader G, Mikkelsen MD, Halkier BA, Palva ET . (2006). Altering glucosinolate profiles modulates diseases resistance in plants. Plant J 2006: 758–767.
Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM . (2008). Root exudates regulate soil fungal community composition and diversity. App Environ Microbiol 74: 738–744.
Brown PD, Tokuhisa JG, Reichelt M, Gershenzon J . (2003). Variation of glucosinolate accumulation among different organs and developmental stages of Arabidopsis thaliana. Phytochem 62: 471–481.
Brown PD, Morra MJ . (1997). Control of soil-borne plant pests using glucosinolate-containing plants. Adv Agron 61: 167–231.
Butler JL, Williams MA, Bottomley PJ, Myrold DD . (2003). Microbial community dynamics associated with rhizosphere carbon flow. Appl Environ Microbiol 69: 6793–6800.
Castaldini M, Turrini A, Sbrana C, Benedetti A, Marchionni M, Mocali S et al. (2005). Impact of Bt corn on rhizospheric and soil eubacterial communities and on beneficial mycorrhizal symbiosis in experimental microcosms. Appl Environ Microbiol 71: 6719–6729.
Chandra S, Choure K, Dubey RC, Maheshwari DK . (2007). Rhizosphere competent Mesorhizobium MP6 induces root hair curling, inhibits Sclerotinia sclerotiorum and enhances growth of Indian mustard (Brassica campestris). Braz. J Microbiol 38: 124–130.
Choesin DN, Boerner REJ . (1991). Allyl isothiocyanate release and the allelopathic potential of Brassica napus (Brassicaceae). Plant Physiol Biochem 78: 1083–1090.
Cohen MF, Yamasaki H, Mazzola M . (2005). Brassica napus seed meal soil amendment modifies microbial community structure, nitric oxide production and incidence of Rhizoctonia root rot. Soil Biol Biochem 37: 1215–1227.
Costa R, Gotz M, Mrotzek N, Lottmann J, Berg G, Smalla K . (2006). Effects of site and plant species on rhizosphere community structure as revealed by molecular analysis of microbial guilds. FEMS Microbiol Ecol 56: 236–249.
Dandie CE, Miller MN, Burton DL, Zebarth BJ, Trevors JT, Goyer C . (2007). Nitric oxide reductase-targeted real-time PCR quantification of denitrifier populations in soil. App Environ Microbiol 73: 4250–4258.
De Vries J, Harms K, Broer I, Kriete G, Mahn A, Düring K et al. (1999). The bacteriolytic activity in transgenic potatoes expressing a chimeric T4 lysozyme gene and the effect of T4 lysozyme on soil- and phytopathogenic bacteria. System Appl Microbiol 22: 280–286.
Dunfield KE, Germida JJ . (2003). Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus). Appl Environ Microbiol 69: 7310–7318.
Fahey JW, Zalemann AT, Talaley AT . (2001). The chemical diversity and distribution of glucosinolates and isothiocyanates among plants. Phytochem 56: 5–51.
Fierer N, Jackson JA, Vilgalys R, Jackson RB . (2005). Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays. Appl Environ Microbiol 71: 4117–4120.
Gimsing AL, Kirkegaard JA . (2006). Glucosinolate and isothiocyanate concentration in soil following incorporation of Brassica biofumigants. Soil Biol Biochem 38: 2255–2264.
Goldwasser Y, Yoneyama K, Xie X, Yoneyama K . (2008). Production of strigolactones by Arabidopsis thaliana responsible for Orobanche aegyptiaca seed germination. Plant Growth Regul 55: 21–28.
Grubb CD, Abel S . (2006). Glucosinolate metabolism and its control. TRENDS Plant Sci 11: 89–100.
Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J et al. (2008). Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2: 1221–1230.
Haichar FZ, Achouak W, Christen R, Heulin T, Marol C, Marais MF et al. (2007). Identification of cellulolytic bacteria in soil by stable isotope probing. Environ Microbiol 9: 625–634.
Halkier BA, Gershenzon J . (2006). Biology and biochemistry of glucosinolates. Ann Rev Plant Biol 57: 303–333.
Hein JW, Wolfe GV, Blee KA . (2008). Comparison of rhizosphere bacterial communities in Arabidopsis thaliana mutants for systemic acquired resistance. Microb Ecol 55: 333–343.
Hirsch AM . (2004). Plant-microbe symbioses: A continuum from commensalism to parasitism. Symbiosis 37: 345–363.
Keller M, Zengler K . (2004). Tapping into microbial diversity. Nat Rev Microbiol 2: 141–150.
Kirkegaard JA, Wong PTW, Desmarchelier JM . (1996). In vitro suppression of fungal root pathogens of cereals by Brassica tissues. Plant Path 45: 593–603.
Klein AN, Frigon D, Raskin L . (2007). Populations related to Alkanindiges, a novel genus containing obligate alkane degraders, are implicated in biological foaming in activated sludge systems. Environ Microbiol 9: 1898–1912.
Kliebenstein DJ, Rowe HC, Denby KJ . (2005). Secondary metabolites influence Arabidopsis/Botrytis interactions: variation in host production and pathogen sensitivity. Plant J 44: 25–36.
Kniskern JM, Traw MB, Bergelson J . (2007). Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana. MPMI 20: 1512–1522.
Kristensen C, Morant M, Olsen CE, Ekstrøm CT, Galbraith DW, Møller BL et al. (2005). Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. Proc Natl Acad Sci USA 102: 1779–1784.
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW et al. (2006). Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806–809.
Lottmann J, Heuer H, de Vries J, Mahn A, During K, Wackernagel W et al. (2000). Establishment of introduced antagonistic bacteria in the rhizosphere of transgenic potatoes and their effect on the bacterial community. FEMS Microbiol Ecol 33: 41–49.
Lu Y, Rosencrantz D, Liesack W, Conrad R . (2006). Structure and activity of bacterial community inhabiting rice roots and the rhizosphere. Environ Microbiol 8: 1351–1360.
Mahmood S, Paton GI, Prosser JI . (2005). Cultivation-independent in situ molecular analysis of bacteria involved in degradation of pentachlorophenol in soil. Environ Microbiol 7: 1349–1360.
Markmann K, Giczey G, Parniske M . (2008). Functional adaptation of a plant receptor-kinase paved the way for the evolution of intracellular root symbioses with bacteria. PLoS Biol 6: 497–506.
Martin-Laurent F, Barrès B, Wagschal I, Piutti S, Devers M, Soulas G et al. (2006). Impact of the maize rhizosphere on the genetic structure, the diversity and the atrazine-degrading gene composition of cultivable atrazine-degrading communities. Plant Soil 282: 99–115.
McCaig AE, Glover LA, Prosser JI . (2001). Numerical analysis of grassland bacterial community structure under different land management regimes by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl Environ Microbiol 67: 4554–4559.
Mellon FA, Bennett RN, Holst B, Williamson G . (2002). Intact glucosinolate analysis in plant extracts by Programmed Cone Voltage Electrospray LC/MS: performance and comparison with LC/MS/MS methods. Anal Biochem 306: 83–91.
Muyzer G, Waal Ecd, Uitterlinden AG . (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. App Environ Microbiol 59: 695–700.
Nicol GW, Glover LA, Prosser JI . (2003). Spatial analysis of archaeal community structure in grassland soil. Appl Environ Microbiol 69: 7420–7429.
O'Callaghan KJ, Stone PJ, Hu X, Griffiths DW, Davey MR, Cocking EC . (2000). Effects of glucosinolates and flavonoids on colonization of the roots of Brassica napus by Azorhizobium caulinodans ORS571. Appl Environ Microbiol 66: 2185–2191.
Oger PM, Mansouri H, Nesme X, Dessaux Y . (2004). Engineering root exudation of Lotus toward the production of two novel carbon compounds leads to the selection of distinct microbial populations in the rhizosphere. Microb Ecol 47: 96–103.
Paterson E, Gebbing T, Abel C, Sim A, Telfer G . (2007). Rhizodeposition shapes rhizosphere microbial community structure in organic soil. New Phytol 173: 600–610.
Petersen BL, Chen S, Hansen CH, Olsen CE, Halkier BA . (2002). Composition and content of glucosinolates in developing Arabidopsis thaliana. Planta 214: 562–571.
Pieterse CMJ, Dicke M . (2007). Plant interactions with microbes and insects: from molecular mechanisms to ecology. TRENDS Plant Sci 12: 564–569.
Pongrac P, Vogel-Mikuš K, Regvar M, Tolrà R, Poschenrieder C, Barceló J . (2008). Glucosinolate profiles change during the life cycle and mycorrhizal colonization in Cd/Zn hyperaccumulator Thlaspi praecox (Brassicaceae). J Chem Ecol 34: 1038–1044.
Radajewski S, Ineson P, Parekh NR, Murrell JC . (2000). Stable-isotope probing as a tool in microbial ecology. Nature 403: 646–649.
Rangel-Castro JI, Killham K, Ostle N, Nicol GW, Anderson IC, Scrimgeour CM et al. (2005). Stable isotope probing analysis of the influence of liming on root exudate utilization by soil microorganisms. Environ Microbiol 7: 828–838.
Ranjard L, Lejon DPH, Mougel C, Scheher L, Merdinoglu D, Chaussod R . (2003). Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ Microbiol 11: 1111–1120.
Rasche F, Hödl V, Poll C, Kandeler E, Gerzabek MH, van Elsas JD et al. (2006). Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities compared with the effects of soil, wild-type potatoes, vegetation stage and pathogen exposure. FEMS Microbiol Ecol 56: 219–235.
Roberts KJ, Anderson RC . (2001). Effect of garlic mustard [Alliaria petiolata (Beib. Cavara & Grande)] extracts on plants and arbuscular mycorrhizal (AM) fungi. Am Midl Nat 146: 146–152.
Rodgers VL, Stinson KA, Finzi AC . (2008). Ready or not, garlic mustard is moving in: Alliaria petiolata as a member of Eastern North American forests. BioSci 58: 426–436.
Rumberger A, Marschner P . (2003). 2-phenylethylisothiocyanate concentration and microbial community composition in the rhizosphere of canola. Soil Biol Biochem 35: 445–452.
Schreiner RP, Koide RT . (1993). Mustards, mustard oils and mycorrhizas. Plant Physiol 123: 107–113.
Scott JS, Knudsen GR . (1999). Soil amendment effects of rape (Brassica napus) residues on pea rhizosphere bacteria. Soil Biol Biochem 31: 1435–1441.
Smith BJ, Kirkegaard JA . (2002). In vitro inhibition of soil microorganisms by 2-phenylethylisothiocyanate. Plant Pathol 51: 585–593.
Souza-Fagundes EM, Rosa LH, Gomes NCM, Santos MH, Pimente PF . (2004). Thiocyanate degradation by pure and mixed cultures of microorganisms. Braz J Microbiol 35: 333–336.
Thioulouse J, Chessel D, Dolédec S, Olivier JM . (1997). ADE-4: a multivariate analysis and graphical display software. Stat Comput 7: 75–83.
Trinick MJ, Hadobas PA . (1995). Formation of nodular structures on the non-legumes Brassica napus, B. campestris, B juncea and Arabidopsis thaliana with Bradyrhizobium and Rhizobium isolated from Parasponia spp or legumes grown in tropical soils. Plant Soil 172: 207–219.
Trosvik P, Rudi K, Næs T, Kohler A, Chan K-S, Jakobsen KS et al. (2008). Characterizing mixed microbial population dynamics using time-series analysis. ISME J 2: 707–715.
Vainio EJ, Hantula J . (2000). Direct analysis of wood-inhabiting fungi using denaturing gradient gel electrophoresis of amplified ribosomal DNA. Mycol Res 104: 927–936.
Vierheilig H, Bennett R, Kiddle G, Kaldorf M, Ludwig-Müller J . (2000). Differences in glucosinolate patterns and arbuscular mycorrhizal status of glucosinolate-containing plant species. New Phytol 146: 343–352.
Wang Y, Hsieh YP . (2002). Uncertainties and novel prospects in the study of the soil carbon dynamics. Chemosphere 49: 791–804.
Wang ET, Rogel MA, Sui XH, Chen WX, Martínez-Romero E, van Berkum P . (2002). Mesorhizobium amorphae, a rhizobial species that nodulates Amorpha fruticosa, is native to American soils. Arch Microbiol 178: 301–305.
Wathelet J-P, Iori R, Leoni O, Rollin P, Quinsac A, Palmieri S . (2004). Guidelines for glucosinolate analysis in green tissues used for biofumigation. Agroindustria 3: 257–266.
Weir BS, Turner SJ, Silvester WB, Park D-C, Young JM . (2004). Unexpectedly diverse Mesorhizobium strains and Rhizobium leguminosarum nodulate native legume genera of New Zealand, while introduced legume weeds are nodulated by Bradyrhizobium species. Appl Environ Microbiol 70: 5980–5987.
Wertz S, Degrange V, Prosser JI, Poly F, Commeaux C, Freitag T et al. (2006). Maintenance of soil functioning following erosion of microbial diversity. Environ Microbiol 8: 2162–2169.
Whiteley AS, Manefield M, Lueders T . (2006). Unlocking the ‘microbial black box’ using RNA-based stable isotope probing technologies. Cur Op Biotechnol 17: 67–71.
Wolfe BE, Rodgers VL, Stinson KA, Pringle A . (2008). The invasive plant Alliaria petiolata (garlic mustard) inhibits ectomycorrhizal fungi in its introduced range. J Ecol 96: 777–783.
Yan X, Chen S . (2007). Regulation of plant glucosinolate metabolism. Planta 226: 1343–1352.
Yanni YG, Rizk RY, Corich V, Squatini A, Ninke K, Philip-Hollingsworth S et al. (1997). Natural endophytic association between Rhizobium leguminosarum bv. trifolii and rice roots and assessment of potential to promote rice growth. Plant Soil 194: 99–114.
Zeng RS, Mallik AU, Setliff E . (2003). Growth stimulation of ectomycorrhizal fungi by root exudates of Brassicaceae plants: role of degraded compounds of indole glucosinolates. J Chem Ecol 29: 1337–1355.
Zhu H, Riely BK, Burns NJ, Ané J-M . (2006). Tracing nonlegume orthologs of legume genes required for nodulation and arbuscular mycorrhizal symbioses. Genet 172: 2491–2499.
Acknowledgements
We thank the ‘Groupe de Recherche Appliquées en Phytotechnologies’ (IBEB/SBVME, CEA Cadarache) for plant growth and labelling. We also thank Christine Marol (GRAP, CEA Cadarache) and Jérôme Balesdent (INRA, UR1119, Unité Géochimie des Sols et des Eaux) for δ13C analyses. We are grateful to Dr Barbara Ann Halkier (Denmark) for providing transgenic CYP79A1 plant seeds and to Agnès Gastaud for her helpful assistance during plant harvesting. We thank Philippe Roumagnac and Catherine Santaella for critical reading and pertinent suggestions and Arjan de Groot for english reviewing. We thank Christophe Merlin for the A. thaliana schematic representation. This work was supported by a CEA PhD grant and by the ANR ‘ECCO’ MICROGER program.
Author information
Authors and Affiliations
Corresponding author
Additional information
Supplementary Information accompanies the paper on The ISME Journal website (http://www.nature.com/ismej)
Supplementary information
Rights and permissions
About this article
Cite this article
Bressan, M., Roncato, MA., Bellvert, F. et al. Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots. ISME J 3, 1243–1257 (2009). https://doi.org/10.1038/ismej.2009.68
Received:
Revised:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/ismej.2009.68
Keywords
This article is cited by
-
A symbiotic footprint in the plant root microbiome
Environmental Microbiome (2023)
-
Study on the soil microbial community structure of the Rhizosphere of Camellia sinensis L. in Anping Village, Kaiyang County, Guizhou Province
Annals of Microbiology (2023)
-
Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance
Environmental Microbiome (2023)
-
The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant–microbe interactions
Environmental Microbiome (2023)
-
Green manure substitution for potassium fertilizer promotes agro-ecosystem multifunctionality via triggering interactions among soil, plant and rhizosphere microbiome
Plant and Soil (2023)
