Biology and Fertility of Soils

, Volume 52, Issue 5, pp 615–627 | Cite as

Microbial utilization of rice root exudates: 13C labeling and PLFA composition

  • Hongzhao Yuan
  • Zhenke Zhu
  • Shoulong Liu
  • Tida Ge
  • Hongzhen Jing
  • Baozhen Li
  • Qiong Liu
  • Tin Mar Lynn
  • Jinshui Wu
  • Yakov Kuzyakov
Original Paper


The soluble components of rhizodeposition—root exudates—are the most important sources of readily available carbon (C) for rhizosphere microorganisms. The first steps of exudate utilization by microorganisms define all further flows of root C in the soil, including recycling and stabilization. Nevertheless, most studies have traced root exudates C much later after its initial uptake by microorganisms. To understand microbial uptake and utilization of rice root exudates, we traced 13C incorporated into microbial groups by 13C profiles of phospholipid fatty acids (PLFAs) within a short time (6 h) after 13CO2 pulse labeling. Labeling was conducted five times during three growth stages: active root growth (within the 21 days after transplanting), rapid shoot growth (37 and 45 days), and rapid reproduction (53 and 63 days). 13C was quickly assimilated throughout the rhizosphere microorganism, and the incorporation rate increased with rice maturity. Despite low redox conditions in paddy soil, fungi outcompeted bacteria in utilizing the root exudates. At all growth stages, fungal PLFAs (18:2 w6, 9c/18:0) showed the highest 13C levels, whereas actinomycete PLFAs (16:0 10-methyl) showed the lowest 13C incorporation. Principal component analysis revealed that the rhizosphere microbial community differed among rice growth stages, whereas the whole microbial community remained stable. In conclusion, the rapid incorporation of carbon from root exudates into microorganisms in paddy soils depends on the growth stage of the rice plant and is the first step of C utilization in rice rhizosphere, further defining C utilization and stabilization.


Rice (Oryza sativa L.) Rhizodeposition 13CO2 labeling Microbial utilization Phospholipid fatty acids (PLFAs) Paddy soils 



This study was financially supported by the National Natural Science Foundation of China (41430860; 41301275), NSFC Research Fund for International Young Scientists (41450110432), Royal Society Newton Advanced Fellowship (NA150182), China-ASEAN Talented Young Scientists Program (Myanmar—14-003), international cooperation and regional science and technology of Hunan Province (2015WK3044), and the Recruitment Program of High-end Foreign Experts of the State Administration of Foreign Experts Affairs awarded to Y. K. (GDW20144300204).


  1. Abraham WR (2014) Applications and impacts of stable isotope probing for analysis of microbial interactions. Appl Microbiol Biotechnol 98:4817–4828CrossRefPubMedGoogle Scholar
  2. Allen SE (1989) Chemical analysis of ecological material. Blackwell, Oxford, p 386Google Scholar
  3. Amaya-Carpio L, Davies FT, Fox T, He C (2009) Arbuscular mycorrhizal fungi and organic fertilizer influence photosynthesis, root phosphatase activity, nutrition, and growth of Ipomoea carnea ssp. fistulosa. Photosynthetica 47:1–10CrossRefGoogle Scholar
  4. Barnard RL, Salmon Y, Kodama N, Sörgel K, Holst J, Rennenberg H, Gessler A, Buchmann N (2007) Evaporative enrichment and time lags between δ18O of leaf water and organic pools in a pine stand. Plant Cell Environ 30:539–550CrossRefPubMedGoogle Scholar
  5. Benesch M, Glaser B, Dippold M, Zech W (2015) Soil microbial C and N turnover under Cupressus lusitanica and natural forests in southern Ethiopia assessed by decomposition of 13C- and 15N-labelled litter under field conditions. Plant Soil 388:133–146CrossRefGoogle Scholar
  6. Brundrett MC (2002) Coevolution of roots and mycorrhizas of land plants. New Phytol 154:275–304CrossRefGoogle Scholar
  7. Butler JL, Williams MA, Bottomley PJ, Myrold DD (2002) Microbial community dynamics associated with rhizosphere carbon flow. Appl Environ Microbiol 69:6793–6800CrossRefGoogle Scholar
  8. Butler JL, Bottomley PJ, Griffith SM, Myrold DD (2004) Distribution and turnover of recently fixed photosynthate in ryegrass rhizospheres. Soil Biol Biochem 36:371–382CrossRefGoogle Scholar
  9. Chen H, Mothapo NV, Shi W (2015) Soil moisture and pH control relative contributions of fungi and bacteria to N2O production. Microb Ecol 69:180–191CrossRefPubMedGoogle Scholar
  10. Colwell JD (1963) The estimation of phosphorus fertilizer requirements of wheat in Southern New South Wales by soil analysis. Anim Reprod Sci 3:190–197Google Scholar
  11. Darrah PR (1991) Measuring the diffusion coefficient of rhizosphere exudates in soil I. The diffusion of non-sorbing compounds. J Soil Sci 42:413–420CrossRefGoogle Scholar
  12. De Boer W, Folman LB, Summerbell RC, Boddy L (2005) Living in a fungal world: impact of fungi on soil bacterial niche development. FEMS Microbiol Rev 29:795–811CrossRefPubMedGoogle Scholar
  13. De Ridder-Duine AS, Kowalchuk GA, Klein Gunnewiek PJA, Smant W, van Veen JA, de Boer W (2005) Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition. Soil Biol Biochem 37:349–357CrossRefGoogle Scholar
  14. Delmont TO, Francioli D, Jacquesson S, Laoudi S, Nesme MJ, Ceccherini MT, Nannipieri P, Simonet P, Vogel TM (2014) Microbial community development and unseen diversity recovery in inoculated sterile soil. Biol Fertil Soils 50:1069–1076CrossRefGoogle Scholar
  15. Doran G, Eberbach P, Helliwell S (2006) The impact of rice plant roots on the reducing conditions in flooded rice soils. Chemosphere 63:1892–1902CrossRefPubMedGoogle Scholar
  16. Dungait JAJ, Kemmitt SJ, Michallon L, Guo S, Wen Q, Brookes PC, Evershed RP (2011) Variable responses of the soil microbial biomass to trace concentrations of 13C-labelled glucose, using 13C-PLFA analysis. Eur J Soil Sci 62:117–126CrossRefGoogle Scholar
  17. Fadrus H, Malý J (1975) Rapid extraction-photometric determination of traces of iron (II) and iron (III) in water with 1,10-phenanthroline. Anal Chim Acta 77:315–316CrossRefGoogle Scholar
  18. FAO (2011) Rice Market Monitor. April 2011. Vol XIV issue no. 2. P2.
  19. Fischer H, Ingwersen J, Kuzyakov Y (2010) Microbial uptake of low-molecular-weight organic substances out-competes sorption in soil. Eur J Soil Sci 61:504–513CrossRefGoogle Scholar
  20. Frostegård A, Bååth E, Tunlid A (1993) Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis. Soil Biol Biochem 25:723–730CrossRefGoogle Scholar
  21. Gale WJ, Cambardella CA, Bailey TB (2000) Root-derived carbon and the formation and stabilization of aggregates. Soil Sci Soc Am J 64:201–207CrossRefGoogle Scholar
  22. Ganzert L, Lipski A, Hubberten H, Wagner D (2011) The impact of different soil parameters on the community structure of dominant bacteria from nine different soils located on Livingston Island, South Shetland Archipelago, Antarctica. FEMS Microbiol Ecol 76:476–491CrossRefPubMedGoogle Scholar
  23. Garbeva PV, Van Elsas JD, van Veen JA (2008) Rhizosphere microbial community and its response to plant species and soil history. Plant Soil 302:19–32CrossRefGoogle Scholar
  24. Gavrichkova O, Kuzyakov Y (2012) Direct phloem transport and pressure concentration waves in linking shoot and rhizosphere activity. Plant Soil 351:23–30CrossRefGoogle Scholar
  25. Gavrichkova O, Proietti S, Moscatello S, Portarena S, Battistelli A, Matteucci G, Brugnoli E (2011) Short-term natural δ13C variations in pools and fluxes in a beech forest: the transfer of isotopic signal from recent photosynthates to soil respired CO. Biogeosciences 8:2403–2437CrossRefGoogle Scholar
  26. Ge TD, Yuan HZ, Zhu HH, Wu XH, Nie SA, Liu C, Tong CL, Wu J, Brookes P (2012) Biological carbon assimilation and dynamics in a flooded rice–soil system. Soil Biol Biochem 48:39–46CrossRefGoogle Scholar
  27. Ge T, Liu C, Yuan H, Zhao Z, Wu X, Zhu Z, Brookes P, Wu J (2015) Tracking the photosynthesized carbon input into soil organic carbon pools in a rice soil fertilized with nitrogen. Plant Soil 392:17–25CrossRefGoogle Scholar
  28. Göttlicher GS, Steinmann K, Betson N, Högberg P (2006) The dependence of soil microbial activity on recent photosynthate from trees. Plant Soil 287:85–94CrossRefGoogle Scholar
  29. Grayston SJ, Griffith GS, Mawdsley JL, Campbell CD, Bardgett RD (2001) Accounting for variability in soil microbial communities of temperate upland grassland ecosystems. Soil Biol Biochem 33:533–551CrossRefGoogle Scholar
  30. Gregory PJ (2006) Roots, rhizosphere and soil: the route to a better understanding of soil science? Eur J Soil Sci 57:2–12CrossRefGoogle Scholar
  31. Gunina A, Kuzyakov Y (2015) Sugars in soil and sweets for microorganisms: review of origin, content, composition and fate. Soil Biol Biochem 90:87–100CrossRefGoogle Scholar
  32. Hafner S, Wiesenberg GLB, Stolnikova E, Merz K, Kuzyakov Y (2014) Spatial distribution and turnover of root-derived carbon in alfalfa rhizosphere depending on top- and subsoil properties and mycorrhization. Plant Soil 380:101–115CrossRefGoogle Scholar
  33. Hannula SE, Boschker HTS, Boer WD, Veen JAV (2012) 13C-pulse-labeling assessment of the community structure of active fungi in the rhizosphere of a genetically starch-modified potato (Solanum tuberosum) cultivar and its parental isoline. New Phytol 194:784–799CrossRefPubMedGoogle Scholar
  34. He Y, Siemens J, Amelung W, Goldbach H, Wassmann R, Alberto MCR, Lücke A, Lehndorff E (2015) Carbon release from rice roots under paddy rice and maize–paddy rice cropping. Agric Ecosyst Environ 210:15–24CrossRefGoogle Scholar
  35. Hill GT, Mitkowski NA, Aldrich-Wolfe L, Emele LR, Jurkonie DD, Ficke A, Maldonado-Ramireza S, Lyncha ST, Nelsona EB (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15:25–36CrossRefGoogle Scholar
  36. Högberg P, Read DJ (2006) Towards a more plant physiological perspective on soil ecology. Trends Ecol Evol 21:548–554CrossRefPubMedGoogle Scholar
  37. Högberg P, Högberg MN, Göttlicher SG, Betson NR, Keel SG, Metcalfe DB, Campbell C, Schindlbacher A, Hurry V, Lundmark T, Linder S, Näsholm T (2008) High temporal resolution tracing of photosynthate carbon from the tree canopy to forest soil microorganisms. New Phytol 177:220–228PubMedGoogle Scholar
  38. Keeney DR, Nelson DW (1982) Nitrogen inorganic forms. In: Page AL, Miller RH, Keeney DR (eds) Methods of soil analysis. Agronomy monograph 9 part 2, 2nd edn. American Society of Agronomy, Madison, pp 643–698Google Scholar
  39. Knudsen D, Peterson GA, Pratt PF (1982) Lithium, sodium, and potassium. In: Page AL, Miller RH, Keeny DR (Eds) Methods of soil analysis. Part 2. Chemical and Microbiological Properties, 2nd ed. Agronomy No. 9. American Society of Agronomy, Madison, WI, pp 225–246Google Scholar
  40. Kögel-Knabner I, Amelung W, Cao Z, Fiedler S, Frenzel P, Jahn R, Kalbitz K, Kölbl A, Schloter M (2010) Biogeochemistry of paddy soils. Geoderma 157:1–14CrossRefGoogle Scholar
  41. Kuzyakov Y, Cheng W (2001) Photosynthesis controls of rhizosphere respiration and organic matter decomposition. Soil Biol Biochem 33:1915–1925CrossRefGoogle Scholar
  42. Kuzyakov Y, Domanski G (2000) Carbon input by plants into the soil. Review. J Plant Nutr Soil Sci 163:421–431CrossRefGoogle Scholar
  43. Kuzyakov Y, Domanski G (2002) Model for rhizodeposition and CO2 efflux from planted soil and its validation by 14C pulse labeling of ryegrass. Plant Soil 239:87–102CrossRefGoogle Scholar
  44. Kuzyakov Y, Gavrichkova O (2010) Review: time lag between photosynthesis and carbon dioxide efflux from soil: a review of mechanisms and controls. Glob Chang Biol 16:3386–3406CrossRefGoogle Scholar
  45. Kuzyakov Y, Larionova AA (2005) Root and rhizomicrobial respiration: a review of approaches to estimate respiration by autotrophic and heterotrophic organisms in soil. J Plant Nutr Soil Sci 168:503–520CrossRefGoogle Scholar
  46. Kuzyakov Y, Leinweber P, Sapronov D, Eckhardt K (2003) Qualitative assessment of rhizodeposits in non-sterile soil by analytical pyrolysis. J Plant Nutr Soil Sci 166:719–723CrossRefGoogle Scholar
  47. Lal R (2004) Offsetting China’s CO2 emissions by soil carbon sequestration. Clim Chang 65:263–275CrossRefGoogle Scholar
  48. Lu Y, Watanabe A, Kimura M (2002a) Input and distribution of photosynthesized carbon in a flooded rice soil. Glob Biogeochem Cycles 16:32-1–32-8CrossRefGoogle Scholar
  49. Lu Y, Watanabe A, Kimura M (2002b) Contribution of plant-derived carbon to soil microbial biomass dynamics in a paddy rice microcosm. Biol Fertil Soils 36:136–142CrossRefGoogle Scholar
  50. Lu Y, Abraham W, Conrad R (2007) Spatial variation of active microbiota in the rice rhizosphere revealed by in situ stable isotope probing of phospholipid fatty acids. Environ Microbiol 9:474–481CrossRefPubMedGoogle Scholar
  51. Meng F, Dungait JAJ, Zhang X, He M, Guo Y, Wu W (2013) Investigation of photosynthate-C allocation 27 days after 13C-pulse labeling of Zea mays. at different growth stages. Plant Soil 1–2:755–764CrossRefGoogle Scholar
  52. Moran-Zuloaga D, Dippold MA, Glaser B, Kuzyakov Y (2015) Organic nitrogen uptake by plants: reevaluation by position-specific labeling of amino acids. Biogeochemistry 125:1–16CrossRefGoogle Scholar
  53. Nawaz MF, Bourrie G, Gul S, Trolard F, Ahmad I, Tanvir MA, Mouret J (2012) Impacts of rice plant roots on the variation in electro-physico-chemical properties of soil waters. Pak J Bot 44:1891–1896Google Scholar
  54. Nguyen C (2003) Rhizodeposition of organic C by plant: mechanisms and controls. Agronomie 23:375–396CrossRefGoogle Scholar
  55. Nikolausz M, Kappelmeyer U, Székely A, Rusznyák A, Márialigeti K, Kästner (2008) Diurnal redox fluctuation and microbial activity in the rhizosphere of wetland plants. Eur J Soil Biol 44:324–333CrossRefGoogle Scholar
  56. Nobel PS (2005) Physicochemical and environmental plant physiology, 3rd edn. Elsevier Academic Press, New YorkGoogle Scholar
  57. Olsen SR, Somers LE (1982) Phosphorus. In: Page AL, Miller RH, Keene DR (eds) Methods of soil analysis, vol 2. Soil Science Society of America, Madison, pp 403–448Google Scholar
  58. Olsson PA, Thingstrup I, Jakobsen I, Bååth E (1999) Estimation of the biomass of arbuscular mycorrhizal fungi in a linseed field. Soil Biol Biochem 31:1879–1887CrossRefGoogle Scholar
  59. Palacios OA, Bashan Y, De-Bashan LE (2014) Proven and potential involvement of vitamins in interactions of plants with plant growth-promoting bacteria—an overview. Biol Fertil Soils 50:415–432CrossRefGoogle Scholar
  60. Paterson E, Gebbing T, Abel C, Sim A, Telfer G (2007) Rhizodeposition shapes rhizosphere microbial community structure in organic soil. New Phytol 173:600–610CrossRefPubMedGoogle Scholar
  61. Paterson E, Midwoo AJ, Millard P (2009) Through the eye of the needle: a review of isotope approaches to quantify microbial processes mediating soil carbon balance. New Phytol 184:19–33CrossRefPubMedGoogle Scholar
  62. Pausch J, Tian J, Riederer M, Kuzyakov Y (2013) Estimation of rhizodeposition at field scale: upscaling of a 14C labeling study. Plant Soil 364:273–285CrossRefGoogle Scholar
  63. Philippot L, Raaijmakers J, Lemanceau P, Putten VDWH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11:789–799CrossRefPubMedGoogle Scholar
  64. Pii Y, Mimmo T, Tomasi N, Terzano R, Cesco S, Crecchio C (2015) Microbial interactions in the rhizosphere: beneficial influences of plant growth-promoting rhizobacteria on nutrient acquisition process. A review. Biol Fertil Soils 51:403–415CrossRefGoogle Scholar
  65. Priha O, Grayston SJ, Hiukka R, Pennanen T, Smolander A (2001) Microbial community structure and characteristics of the organic matter in soils under Pinus sylvestris, Picea abies and Betula pendula at two forest sites. Biol Fertil Soils 33:17–24CrossRefGoogle Scholar
  66. Qin H, Wang H, James Strong P, Li Y, Xu Q, Wu Q (2014) Rapid soil fungal community response to intensive management in a bamboo forest developed from rice paddies. Soil Biol Biochem 68:177–184CrossRefGoogle Scholar
  67. Ragnarsdottir KV, Hawkins DP (2006) Bioavailable copper and manganese in soils from Iceland and their relationship with scrapie occurrence in sheep. J Geochem Explor 88:228–234CrossRefGoogle Scholar
  68. Ramanathan K, Krishnamoorthy K (1973) Nutrient uptake by paddy during the main three stages of growth. Plant Soil 39:29–33CrossRefGoogle Scholar
  69. Rhoades JD (1982) Cation exchangeable capacity. In: Page AL, Miller RH, Keene DR (eds) Methods of soil analysis: part 2—chemical and microbiological properties, 2nd edn. American Society of Agronomy, Inc. and Soil Science Society of America, Inc, Madison, pp 149–165Google Scholar
  70. Roth PJ, Lehndorff E, Hahn A, Frenzel P, Amelung W (2013) Cycling of rice rhizodeposits through peptide-bound amino acid enantiomers in soils under 50 and 2000 years of paddy management. Soil Biol Biochem 65:227–235CrossRefGoogle Scholar
  71. Shade A, Hogan CS, Klimowicz AK, Linske M, McManus PS, Handelsman J (2012) Culturing captures members of the soil rare biosphere. Environ Microbiol 14:2247–2252CrossRefPubMedPubMedCentralGoogle Scholar
  72. Sollins P, Homann P, Caldwell BA (1996) Stabilization and destabilization of soil organic matter: mechanisms and controls. Geoderma 74:65–105CrossRefGoogle Scholar
  73. Thompson MV, Holbrook MN (2003) Scaling phloem transport: water potential equilibrium and osmoregulatory flow. Plant Cell Environ 26:1561–1577CrossRefGoogle Scholar
  74. Thornton B, Zhang Z, Mayes RW, Hogberg MN, Midwood AJ (2011) Can gas chromatography combustion isotope ratio mass spectrometry be used to quantify organic compound abundance? Rapid Commun Mass Sp 25:2433–2438CrossRefGoogle Scholar
  75. Tian J, Dippold M, Pausch J, Blagodatskaya E, Fan M, Li X, Kuzyakov Y (2013) Microbial response to rhizodeposition depending on water regimes in paddy soils. Soil Biol Biochem 65:195–203CrossRefGoogle Scholar
  76. Tunlid A, White DC (1992) Biochemical analysis of biomass community structure, nutritional status and metabolic activity of microbial communities in soil. Soil Biol Biochem 7:229–262Google Scholar
  77. Wang J, Chapmanc SJ, Yao H (2016) Incorporation of 13C-labelled rice rhizodeposition into soil microbial communities under different fertilizer applications. Appl Soil Ecol 101:11–19CrossRefGoogle Scholar
  78. Webster G, Watt LC, Rinna J, Fry JC, Evershed RP, Parkes RJ, Weightman AJ (2006) A comparison of stable-isotope probing of DNA and phospholipid fatty acids to study prokaryotic functional diversity in sulfate-reducing marine sediment enrichment slurries. Environ Microbiol 8:1575–1589CrossRefPubMedGoogle Scholar
  79. Werth M, Kuzyakov Y (2010) 13C fractionation at the root–microorganisms–soil interface: a review and outlook for partitioning studies. Soil Biol Biochem 42:1372–1384CrossRefGoogle Scholar
  80. White DC, Davis WM, Nickels JS, King JD, Bobbie RJ (1979) Determination of the sedimentary microbial biomass by extractible lipid phosphate. Oecologia 40:51–62CrossRefGoogle Scholar
  81. Wiesenberg GLB, Gocke M, Kuzyakov Y (2010) Fast incorporation of root-derived lipids and fatty acids into soil–evidence from a short term multiple 14CO2 pulse labelling experiment. Org Geochem 41:1049–1055CrossRefGoogle Scholar
  82. Wu J, Joergensen RG, Pommerening B, Chaussod R, Brookes PC (1990) Measurement of soil microbial biomass C by fumigation-extraction—an automated procedure. Soil Biol Biochem 22:1167–1169CrossRefGoogle Scholar
  83. Wu Y, Ding N, Wang G, Xu J, Wu J, Brookes PC (2009) Effects of different soil weights, storage times and extraction methods on soil phospholipid fatty acid analyses. Geoderma 150:171–178CrossRefGoogle Scholar
  84. Yao H, Chapman SJ, Thornton B, Paterson E (2015) 13C-PLFA: a key to open the soil microbial black box? Plant Soil 392:3–15CrossRefGoogle Scholar
  85. Yevdokimov I, Ruser R, Buegger F, Marx M, Munch JC (2006) Microbial immobilisation of 13 C rhizodeposits in rhizosphere and root-free soil under continuous 13C-labelling of oats. Soil Biol Biochem 38:1202–1211CrossRefGoogle Scholar
  86. Zelles L, Bai QY, Beck T, Beese F (1992) Signature fatty acids in phospholipids and lipopolysaccharides as indicators of microbial biomass and community structure in agricultural soils. Soil Biol Biochem 24:317–323CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Hongzhao Yuan
    • 1
  • Zhenke Zhu
    • 1
  • Shoulong Liu
    • 1
  • Tida Ge
    • 1
  • Hongzhen Jing
    • 1
  • Baozhen Li
    • 1
  • Qiong Liu
    • 1
  • Tin Mar Lynn
    • 1
    • 2
  • Jinshui Wu
    • 1
  • Yakov Kuzyakov
    • 1
    • 3
  1. 1.Changsha Research Station for Agricultural and Environmental Monitoring and Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
  2. 2.Department of BiotechnologyMandalay Technological UniversityPatheingyiMyanmar
  3. 3.Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil ScienceUniversity of GöttingenGöttingenGermany

Personalised recommendations