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Methods for Root Exudate Collection and Analysis

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The Plant Microbiome

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2232))

Abstract

Plant root exudation has long been recognized as a vital communication system between plants and microbial communities populating the rhizosphere. Due to the high complexity of the collection process and analysis, a variety of techniques have been developed to mimic natural exudation conditions. In addition, significant progress improving existing techniques and developing new methodologies of root exudate collection and analysis have been made. However, optimal standard methods that compare closely with environmental soil conditions are not yet available. In this review, we provide an overview of all those topics and provide suggestions for improvement.

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References

  1. Koo BJ, Adriano DC, Bolan NS et al (2005) Root exudates and microorganisms. In: Hillel D (ed) Encyclopedia of soils in the environment. Elsevier, Oxford, pp 421–428

    Chapter  Google Scholar 

  2. LA Inderjit W (2003) Root exudates: an overview. In: de Kroon H, Visser EJW (eds) Root ecology. Springer, Berlin, pp 235–255

    Chapter  Google Scholar 

  3. Walker TS, Bais HP, Halligan KM et al (2003) Metabolic profiling of root exudates of Arabidopsis Thaliana. J Agric Food Chem 51(9):2548–2554. https://doi.org/10.1021/jf021166h

    Article  CAS  PubMed  Google Scholar 

  4. Chaparro JM, Badri DV, Bakker MG et al (2013) Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions. PLoS One 8(2):e55731. https://doi.org/10.1371/journal.pone.0055731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Canarini A, Kaiser C, Merchant A et al (2019) Root exudation of primary metabolites: mechanisms and their roles in plant responses to environmental stimuli. Front Plant Sci 10:157. https://doi.org/10.3389/fpls.2019.00157

    Article  PubMed  PubMed Central  Google Scholar 

  6. Baetz U, Martinoia E (2014) Root exudates: the hidden part of plant defense. Trends Plant Sci 19(2):90–98. https://doi.org/10.1016/j.tplants.2013.11.006

    Article  CAS  PubMed  Google Scholar 

  7. Gargallo-Garriga A, Preece C, Sardans J et al (2018) Root exudate metabolomes change under drought and show limited capacity for recovery. Sci Rep 8(1):12696. https://doi.org/10.1038/s41598-018-30150-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Vranova V, Rejsek K, Skene KR et al (2013) Methods of collection of plant root exudates in relation to plant metabolism and purpose: a review. J Plant Nutr Soil Sci 176(2):175–199. https://doi.org/10.1002/jpln.201000360

    Article  CAS  Google Scholar 

  9. Badri DV, Vivanco JM (2009) Regulation and function of root exudates. Plant Cell Environ 32(6):666–681. https://doi.org/10.1111/j.1365-3040.2009.01926.x

    Article  CAS  PubMed  Google Scholar 

  10. Strehmel N, Mönchgesang S, Herklotz S et al (2016) Piriformospora indica stimulates root metabolism of Arabidopsis thaliana. Int J Mol Sci 17(7):1091. https://doi.org/10.3390/ijms17071091

    Article  CAS  PubMed Central  Google Scholar 

  11. Contreras-Cornejo HA, Macías-Rodríguez L, Alfaro-Cuevas R et al (2014) Trichoderma spp. improve growth of Arabidopsis seedlings under salt stress through enhanced root development, osmolite production, and Na+ elimination through root exudates. Mol Plant Microbe Interact 27(6):503–514. https://doi.org/10.1094/mpmi-09-13-0265-r

    Article  CAS  PubMed  Google Scholar 

  12. Larsen PB, Degenhardt J, Tai C-Y et al (1998) Aluminum-resistant Arabidopsis mutants that exhibit altered patterns of aluminum accumulation and organic acid release from roots. Plant Physiol 117(1):9–17. https://doi.org/10.1104/pp.117.1.9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zhang R, Vivanco JM, Shen Q (2017) The unseen rhizosphere root–soil–microbe interactions for crop production. Curr Opin Microbiol 37:8–14. https://doi.org/10.1016/j.mib.2017.03.008

    Article  PubMed  Google Scholar 

  14. Silva-Filho MC, Vivanco JM (2017) Guest editorial: plants and their surrounding microorganisms: a dynamic world of interactions. Curr Opin Microbiol 37:v–vi. https://doi.org/10.1016/j.mib.2017.09.016

    Article  PubMed  Google Scholar 

  15. Walker TS, Bais HP, Grotewold E et al (2003) Root exudation and rhizosphere biology. Plant Physiol 132(1):44–51. https://doi.org/10.1104/pp.102.019661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Grayston SJ, Vaughan D, Jones D (1997) Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability. Appl Soil Ecol 5(1):29–56. https://doi.org/10.1016/S0929-1393(96)00126-6

    Article  Google Scholar 

  17. Marschener H (1998) Role of root growth, arbuscular mycorrhiza, and root exudates for the efficiency in nutrient acquisition. Field Crop Res 56(1–2):203–207. https://doi.org/10.1016/S0378-4290(97)00131-7

    Article  Google Scholar 

  18. Hinsinger P (2001) Bioavailability of soil inorganic P in the rhizosphere as affected by root-induced chemical changes: a review. Plant Soil 237(2):173–195. https://doi.org/10.1023/a:1013351617532

    Article  CAS  Google Scholar 

  19. Coskun D, Britto DT, Shi W et al (2017) How plant root exudates shape the nitrogen cycle. Trends Plant Sci 22(8):661–673. https://doi.org/10.1016/j.tplants.2017.05.004

    Article  CAS  PubMed  Google Scholar 

  20. Chutia R, Abel S, Ziegler J (2019) Iron and phosphate deficiency regulators concertedly control coumarin profiles in Arabidopsis thaliana roots during iron, phosphate, and combined deficiencies. Front Plant Sci 10:113. https://doi.org/10.3389/fpls.2019.00113

    Article  PubMed  PubMed Central  Google Scholar 

  21. Dakora FD, Phillips DA (2002) Root exudates as mediators of mineral acquisition in low-nutrient environments. In: Adu-Gyamfi JJ (ed) Food security in nutrient-stressed environments: exploiting plants’ genetic capabilities. Springer, Dordrecht, pp 201–213

    Chapter  Google Scholar 

  22. Bais HP, Weir TL, Perry LG et al (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57(1):233–266. https://doi.org/10.1146/annurev.arplant.57.032905.105159

    Article  CAS  PubMed  Google Scholar 

  23. Guyonnet J, Guillemet M, Dubost A et al (2018) Plant nutrient resource use strategies shape active rhizosphere microbiota through root exudation. Front Plant Sci 9:1662. https://doi.org/10.3389/fpls.2018.01662

    Article  PubMed  PubMed Central  Google Scholar 

  24. Bates GH (1937) A device for the observation of root growth in the soil. Nature 139(3527):966–967. https://doi.org/10.1038/139966b0

    Article  Google Scholar 

  25. Jacoby RP, Martyn A, Kopriva S (2018) Exometabolomic profiling of bacterial strains as cultivated using arabidopsis root extract as the sole carbon source. Mol Plant Microbe Interact 31(8):803–813. https://doi.org/10.1094/MPMI-10-17-0253-R

    Article  PubMed  Google Scholar 

  26. Meier IC, Finzi AC, Phillips RP (2017) Root exudates increase N availability by stimulating microbial turnover of fast-cycling N pools. Soil Biol Biochem 106:119–128. https://doi.org/10.1016/j.soilbio.2016.12.004

    Article  CAS  Google Scholar 

  27. Yuan Y, Zhao W, Zhang Z et al (2018) Impacts of oxalic acid and glucose additions on N transformation in microcosms via artificial roots. Soil Biol Biochem 121:16–23. https://doi.org/10.1016/j.soilbio.2018.03.002

    Article  CAS  Google Scholar 

  28. Pausch J, Kuzyakov Y (2018) Carbon input by roots into the soil: quantification of rhizodeposition from root to ecosystem scale. Glob Chang Biol 24(1):1–12. https://doi.org/10.1111/gcb.13850

    Article  PubMed  Google Scholar 

  29. Weng J, Wang Y, Li J et al (2013) Enhanced root colonization and biocontrol activity of Bacillus amyloliquefaciens SQR9 by abrB gene disruption. Appl Microbiol Biotechnol 97(19):8823–8830. https://doi.org/10.1007/s00253-012-4572-4

    Article  CAS  PubMed  Google Scholar 

  30. Neal AL, Ahmad S, Gordon-Weeks R et al (2012) Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere. PLoS One 7(4):e35498. https://doi.org/10.1371/journal.pone.0035498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Yoneyama K, Xie X, Kim HI et al (2012) How do nitrogen and phosphorus deficiencies affect strigolactone production and exudation? Planta 235(6):1197–1207. https://doi.org/10.1007/s00425-011-1568-8

    Article  CAS  PubMed  Google Scholar 

  32. Broeckling CD, Broz AK, Bergelson J et al (2008) Root exudates regulate soil fungal community composition and diversity. Appl Environ Microbiol 74(3):738–744. https://doi.org/10.1128/aem.02188-07

    Article  CAS  PubMed  Google Scholar 

  33. Yuan J, Zhang N, Huang Q et al (2015) Organic acids from root exudates of banana help root colonization of PGPR strain Bacillus amyloliquefaciens NJN-6. Sci Rep 5:13438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Giles CD, Richardson AE, Cade-Menun BJ et al (2018) Phosphorus acquisition by citrate- and phytase-exuding Nicotiana tabacum plant mixtures depends on soil phosphorus availability and root intermingling. Physiol Plant 163(3):356–371. https://doi.org/10.1111/ppl.12718

    Article  CAS  Google Scholar 

  35. Curl EA, Truelove B (1986) Root exudates. In: The rhizosphere. Springer, Berlin, pp 55–92

    Chapter  Google Scholar 

  36. Harmsen G, Jager G (1962) Determination of the quantity of carbon and nitrogen in the rhizosphere of young plants. Soil organisms. In: Proceedings of the colloquium on soil fauna, soil microflora and their relationships, Osterbeek, The Netherlands, pp 245–251

    Google Scholar 

  37. Badri DV, Chaparro JM, Zhang R et al (2013) Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chem 288(7):4502–4512. https://doi.org/10.1074/jbc.M112.433300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Wang JY, Haider I, Jamil M et al (2019) The apocarotenoid metabolite zaxinone regulates growth and strigolactone biosynthesis in rice. Nat Commun 10(1):810

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Jin Y, Zhu H, Luo S et al (2019) Role of maize root exudates in promotion of colonization of Bacillus Velezensis strain s3-1 in rhizosphere soil and root tissue. Curr Microbiol 76(7):855–862

    Article  CAS  PubMed  Google Scholar 

  40. Ray S, Mishra S, Bisen K et al (2018) Modulation in phenolic root exudate profile of Abelmoschus esculentus expressing activation of defense pathway. Microbiol Res 207:100–107. https://doi.org/10.1016/j.micres.2017.11.011

    Article  CAS  PubMed  Google Scholar 

  41. Nguyen QT, Kozai T (2001) Growth of in vitro banana (Musa SPP.) shoots under photomixotrophic and photoautotrophic conditions. In Vitro Cell Dev Biol Plant 37(6):824. https://doi.org/10.1007/s11627-001-0137-4

    Article  Google Scholar 

  42. Oburger E, Jones DL (2018) Sampling root exudates – Mission impossible? Rhizosphere 6:116–133. https://doi.org/10.1016/j.rhisph.2018.06.004

    Article  Google Scholar 

  43. Pinton R, Varanini Z, Nannipieri P (2007) The rhizosphere: biochemistry and organic substances at the soil-plant interface. CRC Press, Boca Raton

    Book  Google Scholar 

  44. Miller SB, Heuberger AL, Broeckling CD et al (2019) Non-targeted metabolomics reveals sorghum rhizosphere-associated exudates are influenced by the belowground interaction of substrate and sorghum genotype. In J Mol Sci 20(2):431. https://doi.org/10.3390/ijms20020431

    Article  CAS  Google Scholar 

  45. Zhu S, Vivanco JM, Manter DK (2016) Nitrogen fertilizer rate affects root exudation, the rhizosphere microbiome and nitrogen-use-efficiency of maize. Appl Soil Ecol 107:324–333. https://doi.org/10.1016/j.apsoil.2016.07.009

    Article  Google Scholar 

  46. Haase S, Neumann G, Kania A et al (2007) Elevation of atmospheric CO2 and N-nutritional status modify nodulation, nodule-carbon supply, and root exudation of Phaseolus vulgaris L. Soil Biol Biochem 39(9):2208–2221. https://doi.org/10.1016/j.soilbio.2007.03.014

    Article  CAS  Google Scholar 

  47. Neumann G (2006) Root exudates and organic composition of plant roots. In: Luster J, Finlay R (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmensdorf

    Google Scholar 

  48. Sasse J, Martinoia E, Northen T (2018) Feed your friends: do plant exudates shape the root microbiome? Trends Plant Sci 23(1):25–41. https://doi.org/10.1016/j.tplants.2017.09.003

    Article  CAS  PubMed  Google Scholar 

  49. Phillips RP, Erlitz Y, Bier R et al (2008) New approach for capturing soluble root exudates in forest soils. Funct Ecol 22(6):990–999. https://doi.org/10.1111/j.1365-2435.2008.01495.x

    Article  Google Scholar 

  50. Gao J, Sasse J, Lewald KM et al (2018) Ecosystem fabrication (EcoFAB) protocols for the construction of laboratory ecosystems designed to study plant-microbe interactions. J Vis Exp 134:57170. https://doi.org/10.3791/57170

    Article  CAS  Google Scholar 

  51. Simon L, Haichar FEZ (2019) Determination of root exudate concentration in the rhizosphere using 13C labeling. Bio Protoc 9(9):e3228. https://doi.org/10.21769/BioProtoc.3228

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Schwab W (2003) Metabolome diversity: too few genes, too many metabolites? Phytochemistry 62(6):837–849. https://doi.org/10.1016/S0031-9422(02)00723-9

    Article  CAS  PubMed  Google Scholar 

  53. Zhang A, Sun H, Wang P et al (2012) Modern analytical techniques in metabolomics analysis. Analyst 137(2):293–300. https://doi.org/10.1039/C1AN15605E

    Article  CAS  PubMed  Google Scholar 

  54. Fuhrer T, Zamboni N (2015) High-throughput discovery metabolomics. Curr Opin Biotechnol 31:73–78. https://doi.org/10.1016/j.copbio.2014.08.006

    Article  CAS  PubMed  Google Scholar 

  55. Parkinson D (1955) Liberation of amino-acids by oat seedlings. Nature 176(4470):35–36. https://doi.org/10.1038/176035a0

    Article  CAS  Google Scholar 

  56. Lowry OH, Rosebrough NJ, Farr AL et al (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193(1):265

    CAS  PubMed  Google Scholar 

  57. Schlub RL (1978) Effects of soybean seed coat cracks on seed exudation and seedling quality in soil infested with pythium ultimum. Phytopathology 68(8):1186. https://doi.org/10.1094/Phyto-68-1186

    Article  Google Scholar 

  58. Katznelson H, Rouatt JW, Payne TMB (1955) The liberation of amino acids and reducing compounds by plant roots. Plant Soil 7(1):35–48. https://doi.org/10.1007/BF01343545

    Article  CAS  Google Scholar 

  59. Rovira A (1956) Plant root excretions in relation to the rhizosphere effect. Plant Soil 7(2):178–194. https://doi.org/10.1007/BF01343726

    Article  Google Scholar 

  60. Rovira AD, Harris JR (1961) Plant root excretions in relation to the rhizosphere effect. Plant Soil 14(3):199–214. https://doi.org/10.1007/BF01343852

    Article  CAS  Google Scholar 

  61. Stotzky G, Goos RD, Timonin MI (1962) Microbial changes occurring in soil as a result of storage. Plant Soil 16(1):1–18. https://doi.org/10.1007/BF01378154

    Article  Google Scholar 

  62. Linderman R, Gilbert R (1975) Influence of volatiles of plant origin on soil-borne plant pathogens. In: Bruehl GW (ed) Biology and control of soil borne plant pathogens international symposium. The American Phytopathological Society, St. Paul, MN

    Google Scholar 

  63. Dundek P, Holík L, Rohlík T et al (2011) Methods of plant root exudates analysis: a review. Acta Univ Agric Silvic Mendel Brun 59(3):241–246. https://doi.org/10.11118/actaun201159030241

    Article  Google Scholar 

  64. Van Dam NM, Bouwmeester HJ (2016) Metabolomics in the rhizosphere: tapping into belowground chemical communication. Trends Plant Sci 21(3):256–265. https://doi.org/10.1016/j.tplants.2016.01.008

    Article  CAS  PubMed  Google Scholar 

  65. Dunn WB, Erban A, Weber RJM et al (2013) Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics 9(1):44–66. https://doi.org/10.1007/s11306-012-0434-4

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Center for Rhizosphere Biology and Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA

    Hugo A. Pantigoso, Yanhui He, Michael J. DiLegge & Jorge M. Vivanco

  2. Xi’an Key Laboratory of Textile Chemical Engineering Auxiliaries, School of Environmental and Chemical Engineering, Xi’an Polytechnic University, Xi’an, China

    Yanhui He

Authors
  1. Hugo A. Pantigoso
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  2. Yanhui He
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  3. Michael J. DiLegge
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  4. Jorge M. Vivanco
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Corresponding author

Correspondence to Jorge M. Vivanco .

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Editors and Affiliations

  1. Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia

    Lilia C. Carvalhais

  2. School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia

    Paul G. Dennis

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Pantigoso, H.A., He, Y., DiLegge, M.J., Vivanco, J.M. (2021). Methods for Root Exudate Collection and Analysis. In: Carvalhais, L.C., Dennis, P.G. (eds) The Plant Microbiome. Methods in Molecular Biology, vol 2232. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1040-4_22

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  • DOI: https://doi.org/10.1007/978-1-0716-1040-4_22

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