Skip to main content

Advertisement

SpringerLink
Log in

Transcriptomic and metabolic responses of mycorrhizal roots to nitrogen patches under field conditions

  • Regular Article
  • Published:
Plant and Soil Aims and scope Submit manuscript

Abstract

Background

Arbuscular mycorrhizal (AM) fungi contribute to plant nutrient uptake in systems managed with reduced fertilizer and pesticide inputs such as organic agriculture by extending the effective size of the rhizosphere and delivering minerals to the root. Connecting the molecular study of the AM symbiosis with agriculturally- and ecologically-relevant field environments remains a challenge and is a largely unexplored research topic.

Methods

This study utilized a cross-disciplinary approach to examine the transcriptional, metabolic, and physiological responses of tomato (Solanum lycopersicum) AM roots to a localized patch of nitrogen (N). A wild-type mycorrhizal tomato and a closely-related non-mycorrhizal mutant were grown at an organic farm in soil that contained an active AM extraradical hyphal network and soil microbe community.

Results

The majority of genes regulated by upon enrichment of nitrogen were similarly expressed in mycorrhizal and non-mycorrhizal roots, suggesting that the primary response to an enriched N patch is mediated by mycorrhiza-independent root processes. However where inorganic N concentrations in the soil were low, differential regulation of key tomato N transport and assimilation genes indicate a transcriptome shift towards mycorrhiza-mediated N uptake over direct root supplied N. Furthermore, two novel mycorrhizal-specific tomato ammonium transporters were also found to be regulated under low N conditions. A conceptual model is presented integrating the transcriptome response to low N and highlighting the mycorrhizal-specific ammonium transporters.

Conclusions

These results enhance our understanding of the role of the AM symbiosis in sensing and response to an enriched N patch, and demonstrate that transcriptome analyses of complex plant-microbe-soil interactions provide a global snapshot of biological processes relevant to soil processes in organic agriculture.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Abbreviations

AM:

arbuscular mycorrhiza

N:

nitrogen

P:

phosphate

Pi:

inorganic phosphate

Zn:

zinc

S:

sulfur

Cu:

copper

PT:

phosphate transporter

NH +4 :

ammonium

NO −3 :

nitrate

AMT:

ammonium transporter

NRT:

nitrate transporter

PSR:

phosphate starvation response

References

  • Allen JW, Shachar-Hill Y (2009) Sulfur transfer through an arbuscular mycorrhiza. Plant Physiol 149:549–560

    Article  PubMed  CAS  Google Scholar 

  • Aono T, Maldonado-Mendoza IE, Dewbre GR, Harrison MJ, Saito M (2004) Expression of alkaline phosphatase genes in arbuscular mycorrhizas. New Phytol 162:525–534

    Article  CAS  Google Scholar 

  • Asghari HR, Chittleborough DJ, Smith FA, Smith SE (2005) Influence of arbuscular mycorrhizal (AM) symbiosis on phosphorus leaching through soil cores. Plant and Soil 275:181–193

    Article  CAS  Google Scholar 

  • Banerjee R, Evande R, Kabil Ã, Ojha S, Taoka S (2003) Reaction mechanism and regulation of cystathionine β-synthase. Biochimica et Biophysica Acta— Proteins and Proteomics 1647:30–35

    Article  CAS  Google Scholar 

  • Barker SJ, Stummer B, Gao L, Dispain I, O’Connor PJ, Smith SE (1998) A mutant in Lycopersicon esculentum Mill. with highly reduced VA mycorrhizal colonization: Isolation and preliminary characterisation. Plant J 15:791–797

    Article  CAS  Google Scholar 

  • Bevan M, Bancroft I, Bent E, Love K, Goodman H, Dean C, Bergkamp R, Dirkse W, Van Staveren M, Stiekema W, Drost L, Ridley P, Hudson SA, Patel K, Murphy G, Piffanelli P, Wedler H, Wedler E, Wambutt R, Weitzenegger T, Pohl TM, Terryn N, Gielen J, Villarroel R, De Clerck R, Van Montagu M, Lecharny A, Auborg S, Gy I, Kreis M, Lao N, Kavanagh T, Hempel S, Kotter P, Entian KD, Rieger M, Schaeffer M, Funk B, Mueller-Auer S, Silvey M, James R, Montfort A, Pons A, Puigdomenech P, Douka A, Voukelatou E, Milioni D, Hatzopoulos P, Piravandi E, Obermaier B, Hilbert H, Düsterhöft A, Moores T, Jones JDG, Eneva T, Palme K, Benes V, Rechman S, Ansorge W, Cooke R, Berger C, Delseny M, Voet M, Volckaert G, Mewes HW, Klosterman S, Schueller C, Chalwatzis N (1998) Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391:485–488

    Article  PubMed  CAS  Google Scholar 

  • Blee KA, Anderson AJ (1998) Regulation of arbuscule formation by carbon in the plant. Plant J 16:523–530

    Article  Google Scholar 

  • Blilou I, Ocampo JA, García-Garrido JM (1999) Resistance of pea roots to endomycorrhizal fungus or Rhizobium correlates with enhanced levels of endogenous salicylic acid. J Exp Bot 50:1663–1668

    Article  CAS  Google Scholar 

  • Blilou I, Ocampo JA, García-Garrido JM (2000) Induction of LTP (lipid transfer protein) and Pal (phenylalanine ammonia-lyase) gene expression in rice roots colonized by the arbuscular mycorrhizal fungus Glomus mosseae. J Exp Bot 51:1969–1977

    Article  PubMed  CAS  Google Scholar 

  • Bloom AJ, Meyerhoff PA, Taylor AR, Rost TL (2002) Root development and absorption of ammonium and nitrate from the rhizosphere. J Plant Growth Regul 21:416–431

    Article  CAS  Google Scholar 

  • Bruce A, Smith SE, Tester M (1994) The development of mycorrhizal infection in cucumber: effects of P supply on root growth, formation of entry points and growth of infection units. New Phytol 127:507–514

    Article  Google Scholar 

  • Bucher M (2007) Functional biology of plant phosphate uptake at root and mycorrhiza interfaces. New Phytol 173:11–26

    Article  PubMed  CAS  Google Scholar 

  • Burger M, Jackson LE (2005) Plant and microbial nitrogen use and turnover: rapid conversion of nitrate to ammonium in soil with roots. Plant and Soil 266:289–301

    Article  Google Scholar 

  • Burger M, Jackson LE, Lundquist EJ, Louie DT, Miller RL, Rolston DE, Scow KM (2005) Microbial responses and nitrous oxide emissions during wetting and drying of organically and conventionally managed soil under tomatoes. Biol Fertil Soils 42:109–118

    Article  CAS  Google Scholar 

  • Cavagnaro TR, Jackson LE, Six J, Ferris H, Goyal S, Asami D, Scow KM (2006) Arbuscular mycorrhizas, microbial communities, nutrient availability, and soil aggregates in organic tomato production. Plant and Soil 282:209–225

    Article  CAS  Google Scholar 

  • Cavagnaro TR, Langley AJ, Jackson LE, Smukler SM, Koch GW (2008) Growth, nutrition, and soil respiration of a mycorrhiza-defective tomato mutant and its mycorrhizal wild-type progenitor. Funct Plant Biol 35:228–235

    Article  CAS  Google Scholar 

  • Conyers MK, Moody PW (2009) A conceptual framework for improving the P efficiency of organic farming without inputs of soluble P fertiliser. Crop and Pasture Science 60:100–104

    Article  CAS  Google Scholar 

  • Cruz C, Egsgaard H, Trujillo C, Ambus P, Requena N, Martins-Loução MA, Jakobsen I (2007) Enzymatic evidence for the key role of arginine in nitrogen translocation by arbuscular mycorrhizal fungi. Plant Physiol 144:782–792

    Article  PubMed  CAS  Google Scholar 

  • Fitter AH, Helgason T, Hodge A (2011) Nutritional exchanges in the arbuscular mycorrhizal symbiosis: implications for sustainable agriculture. Fungal Biology Reviews 25:68–72

    Article  Google Scholar 

  • Foster JC (1995) Soil nitrogen. In: Alef K, Nannipieri P (eds) Methods in applied soil microbiology and biochemistry. Academic, San Diego, pp 79–87

    Google Scholar 

  • García Garrido JM, León Morcillo RJ, Martín Rodríguez JA, Ocampo Bote JA (2010) Variations in the mycorrhization characteristics in roots of wild-type and ABA-deficient tomato are accompanied by specific transcriptomic alterations. Mol Plant Microbe Interact 23:651–664

    Article  Google Scholar 

  • Gomez S K, Javot H, Deewatthanawong P, Torres-Jerez I, Tang Y, Blancaflor E B, Udvardi MK and Harrison MJ (2009) Medicago truncatula and Glomus intraradices gene expression in cortical cells harboring arbuscules in the arbuscular mycorrhizal symbiosis. BMC Plant Biology 9:10

    Google Scholar 

  • Govindarajulu M, Pfeffer PE, Jin H, Abubaker J, Douds DD, Allen JW, Bücking H, Lammers PJ, Shachar-Hill Y (2005) Nitrogen transfer in the arbuscular mycorrhizal symbiosis. Nature 435:819–823

    Article  PubMed  CAS  Google Scholar 

  • Granato TC, Raper CD Jr (1989) Proliferation of maize (Zea mays L.) roots in response to localized supply of nitrate. J Exp Bot 40:263–275

    Article  PubMed  CAS  Google Scholar 

  • Guether M, Balestrini R, Hannah M, He J, Udvardi MK, Bonfante P (2009a) Genome-wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in Lotus japonicus. New Phytol 182:200–212

    Article  PubMed  CAS  Google Scholar 

  • Guether M, Neuhäuser B, Balestrini R, Dynowski M, Ludewig U, Bonfante P (2009b) A mycorrhizal-specific ammonium transporter from lotus japonicus acquires nitrogen released by Arbuscular Mycorrhizal Fungi. Plant Physiol 150:73–83

    Article  PubMed  CAS  Google Scholar 

  • Guo T, Zhang J, Christie P, Li X (2006) Effects of arbuscular mycorrhizal fungi and ammonium: nitrate ratios on growth and pungency of onion seedlings. J Plant Nutr 29:1047–1059

    Article  CAS  Google Scholar 

  • Gutjahr C, Banba M, Croset V, An K, Miyao A, An G, Hirochika H, Imaizumi-Anraku H, Paszkowski U (2008) Arbuscular mycorrhiza-specific signaling in rice transcends the common symbiosis signaling pathway. Plant Cell 20:2989–3005

    Article  PubMed  CAS  Google Scholar 

  • Hause B, Mrosk C, Isayenkov S, Strack D (2007) Jasmonates in arbuscular mycorrhizal interactions. Phytochemistry 68:101–110

    Article  PubMed  CAS  Google Scholar 

  • Hildebrandt U, Schmelzer E, Bothe H (2002) Expression of nitrate transporter genes in tomato colonized by an arbuscular mycorrhizal fungus. Physiol Plant 115:125–136

    Article  PubMed  CAS  Google Scholar 

  • Hodge A (2004) The plastic plant: Root responses to heterogeneous supplies of nutrients. New Phytol 162:9–24

    Article  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Hohnjec N, Vieweg MF, Pühler A, Becker A, Küster H (2005) Overlaps in the transcriptional profiles of Medicago truncatula roots inoculated with two different Glomus fungi provide insights into the genetic program activated during arbuscular mycorrhiza. Plant Physiol 137:1283–1301

    Article  PubMed  CAS  Google Scholar 

  • Jackson LE, Miller D, Smith SE (2002) Arbuscular mycorrhizal colonization and growth of wild and cultivated lettuce in response to nitrogen and phosphorus. Sci Hortic 94:205–218

    Article  Google Scholar 

  • Javot H, Pumplin N, Harrison MJ (2007) Phosphate in the arbuscular mycorrhizal symbiosis: transport properties and regulatory roles. Plant Cell Environ 30:310–322

    Article  PubMed  CAS  Google Scholar 

  • Jiang C, Gao X, Liao L, Harberd NP, Fu X (2007) Phosphate starvation root architecture and anthocyanin accumulation responses are modulated by the gibberellin-DELLA signaling pathway in Arabidopsis. Plant Physiol 145:1460–1470

    Article  PubMed  CAS  Google Scholar 

  • Jin H, Pfeffer PE, Douds DD, Piotrowski E, Lammers PJ, Shachar-Hill Y (2005) The uptake, metabolism, transport and transfer of nitrogen in an arbuscular mycorrhizal symbiosis. New Phytol 168:687–696

    Article  PubMed  CAS  Google Scholar 

  • Kobae Y, Tamura Y, Takai S, Banba M, Hata S (2010) Localized expression of arbuscular mycorrhiza-inducible ammonium transporters in soybean. Plant Cell Physiol 51:1411–1415

    Article  PubMed  CAS  Google Scholar 

  • Lammers PJ, Jun J, Abubaker J, Arreola R, Gopalan A, Bago B, Hernandez-Sebastia C, Allen JW, Douds DD, Pfeffer PE, Shachar-Hill Y (2001) The glyoxylate cycle in an arbuscular mycorrhizal fungus. Carbon flux and gene expression. Plant Physiology 127:1287–1298

    Article  PubMed  CAS  Google Scholar 

  • Leigh J, Hodge A, Fitter AH (2009) Arbuscular mycorrhizal fungi can transfer substantial amounts of nitrogen to their host plant from organic material. New Phytol 181:199–207

    Article  PubMed  CAS  Google Scholar 

  • Linn DM, Doran JW (1984) Effect of water-filled pore space on carbon dioxide and nitrous oxide production in tilled and nontilled soils. Soil Science Society of America Journal 48:1267–1272

    Article  CAS  Google Scholar 

  • Liu A, Hamel C, Hamilton RI, Ma BL, Smith DL (2000) Acquisition of Cu, Zn, Mn and Fe by mycorrhizal maize (Zea mays L.) grown in soil at different P and micronutrient levels. Mycorrhiza 9:331–336

    Article  CAS  Google Scholar 

  • Liu J, Blaylock LA, Endre G, Cho J, Town CD, VandenBosch KA, Harrison MJ (2003) Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis. Plant Cell 15:2106–2123

    Article  PubMed  CAS  Google Scholar 

  • Lopes MS, Araus JL (2008) Comparative genomic and physiological analysis of nutrient response to NH4+, NH4+:NO3- and NO3- in barley seedlings. Physiol Plant 134:134–150

    Article  PubMed  CAS  Google Scholar 

  • López-Ráez JA, Verhage A, Fernández I, García JM, Azcón-Aguilar C, Flors V, Pozo MJ (2010) Hormonal and transcriptional profiles highlight common and differential host responses to arbuscular mycorrhizal fungi and the regulation of the oxylipin pathway. J Exp Bot 61:2589–2601

    Article  PubMed  Google Scholar 

  • Mader P, Fliebbach A, Dubois D, Gunst L, Fried P, Niggli U (2002) Soil fertility and biodiversity in organic farming. Science 296:1694–1697

    Article  PubMed  CAS  Google Scholar 

  • McGonigle TP, Miller MH, Evans DG, Fairchild GL, Swan JA (1990) A new method which gives an objective measure of colonization of roots by vesicular-arbuscular mycorrhizal fungi. New Phytol 115:495–501

    Article  Google Scholar 

  • Mendoza RE, Pagani EA (1997) Influence of phosphorus nutrition on mycorrhizal growth response and morphology of mycorrhizee in Lotus tenuis. J Plant Nutr 20:625–639

    Article  CAS  Google Scholar 

  • Meyer G, Keliher PN (1992) An overview of analysis by inductively coupled plasma-atomic emission spectrometry. VCH Publishers Inc, New York NY, pp 473–516

    Google Scholar 

  • Miller RM, Reinhardt DR, Jastrow JD (1995) External hyphal production of vesicular-arbuscular mycorrhizal fungi in pasture and tallgrass prairie communities. Oecologia 103:17–23

    Article  Google Scholar 

  • Miranda KM, Espey MG, Wink DA (2001) A rapid, simple spectrophotometric method for simultaneous detection of nitrate and nitrite. Nitric Oxide—Biology and Chemistry 5:62–71

    Article  CAS  Google Scholar 

  • Nagy R, Drissner D, Amrhein N, Jakobsen I, Bucher M (2009) Mycorrhizal phosphate uptake pathway in tomato is phosphorus-repressible and transcriptionally regulated. New Phytol 181:950–959

    Article  PubMed  CAS  Google Scholar 

  • Olsson PA, Burleigh SH, Van Aarle IM (2005) The influence of external nitrogen on carbon allocation to Glomus intraradices in monoxenic arbuscular mycorrhiza. New Phytol 168:677–686

    Article  PubMed  CAS  Google Scholar 

  • Raun WR, Johnson GV (1999) Improving nitrogen use efficiency for cereal production. Agron J 91:357–363

    Article  Google Scholar 

  • Remans T, Nacry P, Pervent M, Filleur S, Diatloff E, Mounier E, Tillard P, Forde BG, Gojon A (2006) The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches. Proc Natl Acad Sci USA 103:19206–19211

    Article  PubMed  CAS  Google Scholar 

  • Rillig MC, Mummey DL (2006) Mycorrhizas and soil structure. New Phytol 171:41–53

    Article  PubMed  CAS  Google Scholar 

  • Ruzicka DR, Barrios-Masias FH, Hausmann NT, Jackson LE, Schachtman DP (2010) Tomato root transcriptome response to a nitrogen-enriched soil patch. BMC Plant Biology 10:75

    Google Scholar 

  • Sah RN, Miller RO (1992) Spontaneous reaction for acid dissolution of biological tissues in closed vessels. Anal Chem 64:230–233

    Article  PubMed  CAS  Google Scholar 

  • Shaul-Keinan O, Gadkar V, Ginzberg I, Grunzweig JM, Chet I, Elad Y, Wininger S, Belausov E, Eshed Y, Ben-Tal Y, Kapulnik Y (2002) Hormone concentrations in tobacco roots change during arbuscular mycorrhizal colonization with Glomus intraradices. New Phytol 154:501–507

    Article  CAS  Google Scholar 

  • Smith SE, Read DJ (2008) Mycorrhizal Symbiosis. Academic, New York

    Google Scholar 

  • Smukler SM, Sanchez-Moreno S, Fonte SJ, Ferris H, Klonsky K, O’Geen AT, Scow KM, Steenwerth KL, Jackson LE (2010) Biodiversity and multiple ecosystem functions in an organic farmscape. Agric Ecosyst Environ 139:80–97

    Article  Google Scholar 

  • Takacs T, Voros I, Biro I (2007) Changes in infectivity and effectiveness of Glomus mosseae in relation to soil nitrogen nutrition. Symbiosis 44:101–107

    CAS  Google Scholar 

  • Tanaka Y, Yano K (2005) Nitrogen delivery to maize via mycorrhizal hyphae depends on the form of N supplied. Plant Cell Environ 28:1247–1254

    Article  CAS  Google Scholar 

  • Tian C, Kasiborski B, Koul R, Lammers PJ, Bucking H, Shachar-Hill Y (2010) Regulation of the nitrogen transfer pathway in the arbuscular mycorrhizal symbiosis: Gene characterization and the coordination of expression with nitrogen flux. Plant Physiol 153:1175–1187

    Article  PubMed  CAS  Google Scholar 

  • Verhoeven KJF, Simonsen KL, McIntyre LM (2005) Implementing false discovery rate control: increasing your power. Oikos 108:643–647

    Article  Google Scholar 

  • Vlot CA, Dempsey DA, Klessig DF (2009) Salicylic acid, a multifaceted hormone to combat disease. Ann Rev Phytopath pp 177–206.

  • Von Wirén N, Lauter FR, Ninnemann O, Gillissen B, Walch-Liu P, Engels C, Jost W, Frommer WB (2000) Differential regulation of three functional ammonium transporter genes by nitrogen in root hairs and by light in leaves of tomato. Plant J 21:167–175

    Article  Google Scholar 

Download references

Acknowledgements

This research was supported by the National Science Foundation Environmental Genomics grant number 0723775 to DPS and LEJ. We thank Julie Chou, Kimberly Jacobs, Joel Kramer, Julien Linares, Walter Lopez, Annie Young-Matthews and other members of the Jackson lab for their assistance with field work and sample processing, the University of Missouri DNA Core Facility for microarray processing, the Danforth Center Proteomics and Mass Spectrometry Facility for plant hormone analysis, and Lauren McIntyre for consultation regarding microarray analysis.

Author information

Authors and Affiliations

  1. Donald Danforth Plant Science Center, 975 N Warson Rd., St. Louis, MO, 63132, USA

    Daniel R. Ruzicka & Daniel P. Schachtman

  2. Department of Land, Air, and Water Resources, University of California, 1 Shields Avenue, Davis, CA, 95616, USA

    Natasha T. Hausmann, Felipe H. Barrios-Masias & Louise E. Jackson

Authors
  1. Daniel R. Ruzicka
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Natasha T. Hausmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Felipe H. Barrios-Masias
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Louise E. Jackson
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Daniel P. Schachtman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Daniel P. Schachtman.

Additional information

Responsible Editor: Peter Christie.

Daniel R. Ruzicka and Natasha T. Hausmann contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resource 1

Detailed materials and methods description of acidic plant hormone analysis by LC-MS/MS. (DOC 44 kb)

Online Resource 2

Complete data table of Affymetrix microarray analysis across all samples, treatments, and genotypes. Columns include Affymetrix probeset ID and log base 2 (signal intensity) values for each sample. (XLS 7082 kb)

Online Resource 3

Primer sequences for qPCR (DOC 31.5 kb)

Online Resource 4

Selected tomato genes with significantly different expression between the mycorrhizal wild-type (76R MYC+) and non-mycorrhizal mutant (rmc) identified by Affymetrix microarray analysis. Columns include Affymetrix probset ID, fold change, FDR adjusted p-value, and annotation information. (XLS 90 kb)

Online Resource 5

Tomato genes that differ significantly by ammonium treatment (water, 6.5 μg 15NH4-N, or 65 μg 15NH +4 -N per gram of soil) identified by Affymetrix microarray analysis. Columns include Affymetrix probset ID, fold change, FDR adjusted p-value, and annotation information. (XLS 204 kb)

Online Resource 6

Tomato genes similarly regulated by the nitrogen patch treatments between field and greenhouse (Ruzicka et al. 2010) studies using field soil. (DOC 74 kb)

Online Resource 7

Physiological analysis of field-grown tomato plants (DOC 24.5 kb)

Online Resource 8

Nutrient analysis of plants grown for production biomass (DOC 36 kb)

Online Resource 9

Phylogenetic analysis of plant ammonium transporters including known Lotus japonicus and Medicago truncatula mycorrhizal-specific AMTs and new tomato mycorrhizal specific AMT4 and AMT5 reported here. (DOC 30 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ruzicka, D.R., Hausmann, N.T., Barrios-Masias, F.H. et al. Transcriptomic and metabolic responses of mycorrhizal roots to nitrogen patches under field conditions. Plant Soil 350, 145–162 (2012). https://doi.org/10.1007/s11104-011-0890-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11104-011-0890-z

Keywords

Search

Navigation