Differences in the relationship between metabolomic and ionomic traits of Quercus variabilis growing at contrasting geologic-phosphorus sites in subtropics

  • Huawei Ji
  • Vladimir Ossipov
  • Baoming Du
  • Jiahao Wen
  • Chunjiang LiuEmail author
Regular Article



Subtropical ecosystems are generally characterized by phosphorus (P)-deficient soils; however, extreme P-rich soils develop on phosphate rocks. We aimed to integrate metabolomic and ionomic analyses to survey how in situ trees adaptively respond to such contrasting P soils.


Gas (GC-MS) or liquid (LC-MS) chromatography-mass spectrometry and inductively coupled plasma-optical emission spectrometer (ICP-OES) were used to analyze leaf metabolome and ionome of Quercus variabilis, which grew at two geologic P-rich and P-deficient sites in subtropical China.


Two Q. variabilis populations were significantly discriminated in terms of metabolome and ionome, with major contributions from 25 identified metabolites (e.g. sugars and P-containing compounds) and P and four other chemical elements. And of these 25 metabolites, orthophosphate was predominant in influencing the variation in the metabolomes of Q. variabilis between the two P-type sites. Moreover, orthophosphate was correlated with leaf P (r = 0.85, p < 0.001), while leaf P was significantly influenced only by soil resident P at the P-rich site. Furthermore, the metabolic pathway analysis indicated four critical metabolic pathways: galactose metabolism, amino sugar and nucleotide sugar metabolism, glyoxylate and dicarboxylate metabolism, fructose and mannose metabolism.


These findings suggested that there were distinct ionome-metabolome interactions in Q. variabilis populations, between P-rich and P-deficient sites, which contributed to novel insights into how plants interactively adapt to P-limiting soils.


Ionome Metabolome Phosphate rocks Soil nutrient variation Adaptation Quercus variabilis 



This study was funded by the National Natural Science Foundation of China (No. 31670626, No. 31270640, and No. 31070532) and the National Key R&D Program of China (2017YFC0505501). We thank the Instrumental Analysis Center of Shanghai Jiao Tong University for the support on chemical analysis.

Data accessibility

All data are included in the manuscript and the supplementary files, and all metabolites identified by GC-TOF-MS and UHPLC-QTOF-MS are included in the excel file named “ESM 2”.

Authors’ contributions

C. Liu designed the study, H. Ji, B. Du and J. Wen collected field samples and data, H. Ji performed the experiments, and H. Ji, V. Ossipov and C. Liu analyzed the data and wrote the manuscript.

Compliance with ethical standards

Competing interests

The authors declare no competing interests.

Supplementary material

11104_2019_4020_MOESM1_ESM.pdf (1.3 mb)
ESM 1 (PDF 1336 kb)
11104_2019_4020_MOESM2_ESM.xlsx (19 kb)
ESM 2 (XLSX 19 kb)


  1. Amtmann A, Armengaud P (2009) Effects of N, P, K and S on metabolism: new knowledge gained from multi-level analysis. Curr Opin Plant Biol 12:275–283CrossRefGoogle Scholar
  2. Ashraf M, Foolad MR (2007) Roles of glycine betaine and proline in improving plant abiotic stress resistance. Environ Exp Bot 59:206–216CrossRefGoogle Scholar
  3. Attiwill PM, Adams MA (1993) Nutrient cycling in forests. New Phytol 124:561–582CrossRefGoogle Scholar
  4. Balemi T, Negisho K (2012) Management of soil phosphorus and plant adaptation mechanisms to phosphorus stress for sustainable crop production: a review. J Soil Sci Plant Nutr 12:547–562CrossRefGoogle Scholar
  5. Brosché M, Vinocur B, Alatalo ER, Lamminmäki A, Teichmann T, Ottow EA, Djilianov D, Afif D, Bogeat-Triboulot M-B, Altman A (2005) Gene expression and metabolite profiling of Populus euphratica growing in the Negev desert. Genome Biol 6:R101CrossRefGoogle Scholar
  6. Carillo P, Mastrolonardo G, Nacca F, Parisi D, Verlotta A, Fuggi A (2008) Nitrogen metabolism in durum wheat under salinity: accumulation of proline and glycine betaine. Funct Plant Biol 35:412–426CrossRefGoogle Scholar
  7. Cernusak LA, Winter K, Turner BL (2010) Leaf nitrogen to phosphorus ratios of tropical trees: experimental assessment of physiological and environmental controls. New Phytol 185:770–779CrossRefGoogle Scholar
  8. Chen D, Zhang X, Kang H, Sun X, Yin S, Du H, Yamanaka N, Gapare W, Wu HX, Liu C (2012) Phylogeography of Quercus variabilis based on chloroplast DNA sequence in East Asia: multiple glacial refugia and mainland-migrated island populations. PLoS One 7:e47268CrossRefGoogle Scholar
  9. Cleveland CC, Townsend AR, Taylor P, Alvarez-Clare S, Bustamante M, Chuyong G, Dobrowski SZ, Grierson P, Harms KE, Houlton BZ (2011) Relationships among net primary productivity, nutrients and climate in tropical rain forest: a pan-tropical analysis. Ecol Lett 14:939–947CrossRefGoogle Scholar
  10. Crews TE, Kitayama K, Fownes JH, Riley RH, Herbert DA, Mueller-Dombois D, Vitousek PM (1995) Changes in soil phosphorus fractions and ecosystem dynamics across a long chronosequence in Hawaii. Ecology 76:1407–1424CrossRefGoogle Scholar
  11. Cronan CS, Grigal DF (1995) Use of calcium/aluminum ratios as indicators of stress in forest ecosystems. J Environ Qual 24:209–226CrossRefGoogle Scholar
  12. Davey MP, Burrell MM, Woodward FI, Quick WP (2008) Population-specific metabolic phenotypes of Arabidopsis lyrata ssp. petraea. New Phytol 177:380–388Google Scholar
  13. De Vos RCH, Moco S, Lommen A, Keurentjes JJB, Bino RJ, Hall RD (2007) Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat Protoc 2:778–791CrossRefGoogle Scholar
  14. Di Martino C, Delfine S, Pizzuto R, Loreto F, Fuggi A (2003) Free amino acids and glycine betaine in leaf osmoregulation of spinach responding to increasing salt stress. New Phytol 158:455–463CrossRefGoogle Scholar
  15. Elser JJ, Fagan WF, Kerkhoff AJ, Swenson NG, Enquist BJ (2010) Biological stoichiometry of plant production: metabolism, scaling and ecological response to global change. New Phytol 186:593–608CrossRefGoogle Scholar
  16. FAO I (1998) World reference base for soil resources. World soil resources reportsGoogle Scholar
  17. Fester T, Merbach I, Schulz E, Härtig C (2014) Metabolic response of Medicago sativa to severe nutrient imbalances and disturbances under field conditions. J Plant Nutr Soil Sci 177:245–259CrossRefGoogle Scholar
  18. Fonville JM, Richards SE, Barton RH, Boulange CL, Ebbels TMD, Nicholson JK, Holmes E, Dumas M-E (2010) The evolution of partial least squares models and related chemometric approaches in metabonomics and metabolic phenotyping. J Chemom 24:636–649CrossRefGoogle Scholar
  19. Gan H, Jiao Y, Jia J, Wang X, Li H, Shi W, Peng C, Polle A, Luo Z (2015) Phosphorus and nitrogen physiology of two contrasting poplar genotypes when exposed to phosphorus and/or nitrogen starvation. Tree Physiol 36:22–38CrossRefGoogle Scholar
  20. Grattan SR, Grieve CM (1985) Betaine status in wheat in relation to nitrogen stress and to transient salinity stress. Plant Soil 85:3–9CrossRefGoogle Scholar
  21. Guo R, Shi L, Yang C, Yan C, Zhong X, Liu Q, Xia X, Li H (2016) Comparison of ionomic and metabolites response under alkali stress in old and young leaves of cotton (Gossypium hirsutum L.) seedlings. Front. Plant Sci 7:1785Google Scholar
  22. Güsewell S (2004) N: P ratios in terrestrial plants: variation and functional significance. New Phytol 164:243–266CrossRefGoogle Scholar
  23. Han W, Fang J, Guo D, Zhang Y (2005) Leaf nitrogen and phosphorus stoichiometry across 753 terrestrial plant species in China. New Phytol 168:377–385CrossRefGoogle Scholar
  24. Hänsch R, Mendel RR (2009) Physiological functions of mineral micronutrients (cu, Zn, Mn, Fe, Ni, Mo, B, cl). Curr Opin Plant Biol 12:259–266CrossRefGoogle Scholar
  25. Hernández G, Ramírez M, Valdés-López O, Tesfaye M, Graham MA, Czechowski T, Schlereth A, Wandrey M, Erban A, Cheung F (2007) Phosphorus stress in common bean: root transcript and metabolic responses. Plant Physiol 144:752–767CrossRefGoogle Scholar
  26. Huang CY, Roessner U, Eickmeier I, Genc Y, Callahan DL, Shirley N, Langridge P, Bacic A (2008) Metabolite profiling reveals distinct changes in carbon and nitrogen metabolism in phosphate-deficient barley plants (Hordeum vulgare L.). Plant Cell Physiol 49:691–703CrossRefGoogle Scholar
  27. Irakli L, Elser JJ (2011) The origins of the Redfield nitrogen-to-phosphorus ratio are in a homoeostatic protein-to-rRNA ratio. Ecol Lett 14:244–250CrossRefGoogle Scholar
  28. Ji H, Du B, Liu C (2017) Elemental stoichiometry and compositions of weevil larvae and two acorn hosts under natural phosphorus variation. Sci Rep 7:45810CrossRefGoogle Scholar
  29. Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation. Ecol Lett 7:1225–1241CrossRefGoogle Scholar
  30. Kimmins JP (2004) Forest ecology. Benjamin-Cummings Publishing Company, Menlo Park, CaliforniaGoogle Scholar
  31. Kind T, Wohlgemuth G, Lee DY, Lu Y, Palazoglu M, Shahbaz S, Fiehn O (2009) FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem 81:10038–10048CrossRefGoogle Scholar
  32. Koerselman W, Meuleman AFM (1996) The vegetation N:P ratio: a new tool to detect the nature of nutrient limitation. J Appl Ecol 33:1441–1450CrossRefGoogle Scholar
  33. Lisec J, Schauer N, Kopka J, Willmitzer L, Fernie AR (2006) Gas chromatography mass spectrometry–based metabolite profiling in plants. Nat Protoc 1:387–396CrossRefGoogle Scholar
  34. Lundstedt T, Seifert E, Abramo L, Thelin B, Nyström Å, Pettersen J, Bergman R (1998) Experimental design and optimization. Chemom Intell Lab Syst 42:3–40CrossRefGoogle Scholar
  35. Matzek V, Vitousek PM (2009) N: P stoichiometry and protein: RNA ratios in vascular plants: an evaluation of the growth-rate hypothesis. Ecol Lett 12:765–771CrossRefGoogle Scholar
  36. Monreal JA, Jimenez ET, Remesal E, Morillo-Velarde R, García-Mauriño S, Echevarría C (2007) Proline content of sugar beet storage roots: response to water deficit and nitrogen fertilization at field conditions. Environ Exp Bot 60:257–267CrossRefGoogle Scholar
  37. Morcuende R, Bari R, Gibon Y, Zheng W, Pant BD, BLÄSING O, Usadel B, Czechowski T, Udvardi MK, Stitt M (2007) Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. Plant Cell Environ 30:85–112CrossRefGoogle Scholar
  38. Mulholland MM, Otte ML (2000) Effects of varying sulphate and nitrogen supply on DMSP and glycine betaine levels in Spartina anglica. J Sea Res 43:199–207CrossRefGoogle Scholar
  39. Mulholland MM, Otte ML (2002) The effects of nitrogen supply and salinity on DMSP, glycine betaine and proline concentrations in leaves of Spartina anglica. Aquat Bot 72:193–200CrossRefGoogle Scholar
  40. Nanamori M, Shinano T, Wasaki J, Yamamura T, Rao IM, Osaki M (2004) Low phosphorus tolerance mechanisms: phosphorus recycling and photosynthate partitioning in the tropical forage grass, Brachiaria hybrid cultivar Mulato compared with rice. Plant Cell Physiol 45:460–469CrossRefGoogle Scholar
  41. Plaxton WC, Carswell MC (1999) Metabolic aspects of the phosphate starvation response in plants. In: Lerner HR (ed) Plant responses to environmental stresses: from phytohormones to genome reorganization. Marcel Dekker, Inc., New York, pp 349–372Google Scholar
  42. Plaxton WC, Tran HT (2011) Metabolic adaptations of phosphate-starved plants. Plant Physiol 156:1006–1015CrossRefGoogle Scholar
  43. Raghothama KG (1999) Phosphate acquisition. Annu Rev Plant Biol 50:665–693CrossRefGoogle Scholar
  44. Reich PB, Oleksyn J (2004) Global patterns of plant leaf N and P in relation to temperature and latitude. Proc Natl Acad Sci U S A 101:11001–11006CrossRefGoogle Scholar
  45. Ribeiro DM, Silva Júnior DD, Cardoso FB, Martins AO, Silva WA, Nascimento VL, Araújo WL (2016) Growth inhibition by selenium is associated with changes in primary metabolism and nutrient levels in Arabidopsis thaliana. Plant Cell Environ 39:2235–2246CrossRefGoogle Scholar
  46. Rivas-Ubach A, Sardans J, Pérez-Trujillo M, Estiarte M, Peñuelas J (2012) Strong relationship between elemental stoichiometry and metabolome in plants. Proc Natl Acad Sci U S A 109:4181–4186CrossRefGoogle Scholar
  47. Sanchez DH, Pieckenstain FL, Escaray F, Erban A, Kraemer U, Udvardi MK, Kopka J (2011) Comparative ionomics and metabolomics in extremophile and glycophytic Lotus species under salt stress challenge the metabolic pre-adaptation hypothesis. Plant Cell Environ 34:605–617CrossRefGoogle Scholar
  48. Sánchez-Calderón L, Chacon-López A, Pérez-Torres CA, Herrera-Estrella L (2010) Phosphorus: plant strategies to cope with its scarcity. In: Hell R, Mendel RR (eds) Cell biology of metals and nutrients. Springer, Berlin, Heidelberg, pp 173–198CrossRefGoogle Scholar
  49. Sardans J, Peñuelas J, Rivas-Ubach A (2011a) Ecological metabolomics: overview of current developments and future challenges. Chemoecology 21:191–225CrossRefGoogle Scholar
  50. Sardans J, Rivas-Ubach A, Peñuelas J (2011b) Factors affecting nutrient concentration and stoichiometry of forest trees in Catalonia (NE Spain). For Ecol Manage 262:2024–2034CrossRefGoogle Scholar
  51. Savolainen O, Pyhäjärvi T, Knürr T (2007) Gene flow and local adaptation in trees. Annu Rev Ecol Evol Syst 38:595–619CrossRefGoogle Scholar
  52. Sawai Y, Yamaguchi Y, Miyama D, Yoshitomi H (2001) Cycling treatment of anaerobic and aerobic incubation increases the content of γ-aminobutyric acid in tea shoots. Amino Acids 20:331–334CrossRefGoogle Scholar
  53. Schachtman DP, Reid RJ, Ayling SM (1998) Phosphorus uptake by plants: from soil to cell. Plant Physiol 116:447–453CrossRefGoogle Scholar
  54. Serraj R, Shelp BJ, Sinclair TR (1998) Accumulation of γ-aminobutyric acid in nodulated soybean in response to drought stress. Physiol Plant 102:79–86CrossRefGoogle Scholar
  55. Shaver GR, Chapin FSI, Billings WD (1979) Ecotypic differentiation in Carex aquatilis on ice-wedge polygons in the Alaskan coastal tundra. J Ecol 67:1025–1045CrossRefGoogle Scholar
  56. Shen J, Yuan L, Zhang J, Li H, Bai Z, Chen X, Zhang W, Zhang F (2011) Phosphorus dynamics: from soil to plant. Plant Physiol 156:997–1005CrossRefGoogle Scholar
  57. Shi C, Han R, Wu P, Fang M, Lai H, Shentu L (2011) Geochemistry and provenance of source rock for matoushan formation rocks (late cretaceous) in the Mouding area, Central Yunnan. Acta Sedimentol Sin 29:303–311Google Scholar
  58. Silberbush M, Waisel Y, Kafkafi U (1981) The role of soil phosphorus in differentiation of edaphic ecotypes in Aegilops peregrina. Oecologia 49:419–424CrossRefGoogle Scholar
  59. Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G (2006) XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem 78:779–787CrossRefGoogle Scholar
  60. Snaydon RW, Bradshaw AD (1962) Differences between natural populations of Trifolium repens L. in response to mineral nutrients. J Exp Bot 13:422–434CrossRefGoogle Scholar
  61. Soetan KO, Olaiya CO, Oyewole OE (2010) The importance of mineral elements for humans, domestic animals and plants: a review. Afr J Food Sci 4:200–222Google Scholar
  62. Sterner RW, Elser JJ (2002) Ecological stoichiometry: the biology of elements from molecules to the biosphere. Princeton University Press, Princeton, NJGoogle Scholar
  63. Sun X, Kang H, Du H, Hu H, Zhou J, Hou J, Zhou X, Liu C (2012) Stoichiometric traits of oriental oak (Quercus variabilis) acorns and their variations in relation to environmental variables across temperate to subtropical China. Ecol Res 27:765–773CrossRefGoogle Scholar
  64. Tao Y (2005) A proximate mathematical model of the content of main chemical constituents in an industrial phosphorus ore. Yunnan Geol 24:151–166Google Scholar
  65. Tawaraya K, Horie R, Shinano T, Wagatsuma T, Saito K, Oikawa A (2014) Metabolite profiling of soybean root exudates under phosphorus deficiency. Soil Sci Plant Nutr 60:679–694CrossRefGoogle Scholar
  66. Tiessen H (2008) Phosphorus in the global environment. In: White PJ, Hammond JP (eds) The ecophysiology of plant-phosphorus interactions. Springer, Dordrecht, pp 1–7Google Scholar
  67. Tillberg JE, Rowley JR (1989) Physiological and structural effects of phosphorus starvation on the unicellular green alga Scenedesmus. Physiol Plant 75:315–324CrossRefGoogle Scholar
  68. Tissue DT, Lewis JD, Niinemets Ü (2010) Photosynthetic responses of cottonwood seedlings grown in glacial through future atmospheric [CO2] vary with phosphorus supply. Tree Physiol 30:1361–1372CrossRefGoogle Scholar
  69. Uhde-Stone C, Zinn KE, Ramirez-Yáñez M, Li A, Vance CP, Allan DL (2003) Nylon filter arrays reveal differential gene expression in proteoid roots of white lupin in response to phosphorus deficiency. Plant Physiol 131:1064–1079CrossRefGoogle Scholar
  70. Vance CP, Uhde-Stone C, Allan DL (2003) Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource. New Phytol 157:423–447CrossRefGoogle Scholar
  71. Vitousek P (1982) Nutrient cycling and nutrient use efficiency. Am Nat 119:553–572CrossRefGoogle Scholar
  72. Vitousek PM, Porder S, Houlton BZ, Chadwick OA (2010) Terrestrial phosphorus limitation: mechanisms, implications, and nitrogen-phosphorus interactions. Ecol Appl 20:5–15CrossRefGoogle Scholar
  73. Walker TW, Syers JK (1976) The fate of phosphorus during pedogenesis. Geoderma 15:1–19CrossRefGoogle Scholar
  74. Warren CR (2011) How does P affect photosynthesis and metabolite profiles of Eucalyptus globulus? Tree Physiol 31:727–739CrossRefGoogle Scholar
  75. Westheimer FH (1987) Why nature chose phosphates. Science 235:1173–1178CrossRefGoogle Scholar
  76. Wright IJ, Reich PB, Westoby M, Ackerly DD, Baruch Z, Bongers F, Cavender-Bares J, Chapin T, Cornelissen JH, Diemer M (2004) The worldwide leaf economics spectrum. Nature 428:821–827CrossRefGoogle Scholar
  77. Wu Z, Zhu Y, Jiang H (1987) The vegetation of Yunnan. Science, BeijingGoogle Scholar
  78. Wu D, Shen Q, Cai S, Chen Z, Dai F, Zhang G (2013) Ionomic responses and correlations between elements and metabolites under salt stress in wild and cultivated barley. Plant Cell Physiol 54:1976–1988CrossRefGoogle Scholar
  79. Xia J, Wishart DS (2010) MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res 38:W71–W77CrossRefGoogle Scholar
  80. Xia J, Sinelnikov IV, Han B, Wishart DS (2015) MetaboAnalyst 3.0—making metabolomics more meaningful. Nucleic Acids Res 43:W251–W257CrossRefGoogle Scholar
  81. Xiao G, Li T, Zhang X, Yu H, Huang H, Gupta DK (2009) Uptake and accumulation of phosphorus by dominant plant species growing in a phosphorus mining area. J Hazard Mater 171:542–550CrossRefGoogle Scholar
  82. Yan X, Lynch JP, Beebe SE (1995) Genetic variation for phosphorus efficiency of common bean in contrasting soil types: I. Vegetative response. Crop Sci 35:1086–1093CrossRefGoogle Scholar
  83. Yan K, Fu D, He F, Duan C (2011) Leaf nutrient stoichiometry of plants in the phosphorus-enriched soils of the Lake Dianchi watershed, southwestern China. Chin J Plant Ecol 35:353–361CrossRefGoogle Scholar
  84. Yan K, Ranjitkar S, Zhai D, Li Y, Xu J, Li B, Lu Y (2017) Current re-vegetation patterns and restoration issues in degraded geological phosphorus-rich mountain areas: a synthetic analysis of Central Yunnan, SW China. Plant Diversity 39:140–148CrossRefGoogle Scholar
  85. Yu Q, Wu H, He N, Lü X, Wang Z, Elser JJ, Wu J, Han X (2012) Testing the growth rate hypothesis in vascular plants with above-and below-ground biomass. PLoS One 7:e32162CrossRefGoogle Scholar
  86. Zhou X, Sun X, Du B, Yin S, Liu C (2015) Multielement stoichiometry in Quercus variabilis under natural phosphorus variation in subtropical China. Sci Rep 5:7839CrossRefGoogle Scholar
  87. Zhu F, Lu X, Liu L, Mo J (2015) Phosphate addition enhanced soil inorganic nutrients to a large extent in three tropical forests. Sci Rep 5:7923CrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.School of Agriculture and Biology and Research Centre for Low-Carbon AgricultureShanghai Jiao Tong UniversityShanghaiChina
  2. 2.Shanghai Urban Forest Research StationState Forestry AdministrationBeijingChina
  3. 3.Natural Chemistry Research Group, Department of ChemistryUniversity of TurkuTurkuFinland
  4. 4.Laboratory of MetabolomicsAll-Russian Institute of Medicinal and Aromatic PlantsMoscowRussia
  5. 5.Key Laboratory of Urban AgricultureMinistry of AgricultureBeijingChina

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