Persistence of dissolved organic matter explained by molecular changes during its passage through soil


Dissolved organic matter affects fundamental biogeochemical processes in the soil such as nutrient cycling and organic matter storage. The current paradigm is that processing of dissolved organic matter converges to recalcitrant molecules (those that resist degradation) of low molecular mass and high molecular diversity through biotic and abiotic processes. Here we demonstrate that the molecular composition and properties of dissolved organic matter continuously change during soil passage and propose that this reflects a continual shifting of its sources. Using ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, we studied the molecular changes of dissolved organic matter from the soil surface to 60 cm depth in 20 temperate grassland communities in soil type Eutric Fluvisol. Applying a semi-quantitative approach, we observed that plant-derived molecules were first broken down into molecules containing a large proportion of low-molecular-mass compounds. These low-molecular-mass compounds became less abundant during soil passage, whereas larger molecules, depleted in plant-related ligno-cellulosic structures, became more abundant. These findings indicate that the small plant-derived molecules were preferentially consumed by microorganisms and transformed into larger microbial-derived molecules. This suggests that dissolved organic matter is not intrinsically recalcitrant but instead persists in soil as a result of simultaneous consumption, transformation and formation.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Molecular changes in soil DOM based on FT-ICR mass spectra.
Fig. 2: Variation partitioning for potential drivers of DOM transformation.
Fig. 3: Shift of molecular DOM masses during soil passage.
Fig. 4: Proposed mechanisms for spatial and temporal evolution of DOM molecular structures during soil passage.

Data availability

The compiled dataset used in our analyses is available at and root standing biomass at The raw data are available from the corresponding author (M.L.) on request.

Code availability

The codes used for this study are available on request.


  1. 1.

    Battin, T. J. et al. The boundless carbon cycle. Nat. Geosci. 2, 598–600 (2009).

    Article  Google Scholar 

  2. 2.

    Roulet, N. & Moore, T. R. Environmental chemistry. Browning the waters. Nature 444, 283–284 (2006).

    Article  Google Scholar 

  3. 3.

    Kalbitz, K., Solinger, S., Park, J. H., Michalzik, B. & Matzner, E. Controls on the dynamics of dissolved organic matter in soils: a review. Soil Sci. 165, 277–304 (2000).

    Article  Google Scholar 

  4. 4.

    Kaiser, K. & Kalbitz, K. Cycling downwards—dissolved organic matter in soils. Soil Biol. Biochem. 52, 29–32 (2012).

    Article  Google Scholar 

  5. 5.

    Brantley, S. L., Goldhaber, M. B. & Ragnarsdottir, K. V. Crossing disciplines and scales to understand the Critical Zone. Elements 3, 307–314 (2007).

    Article  Google Scholar 

  6. 6.

    Li, L. et al. Expanding the role of reactive transport models in critical zone processes. Earth Sci. Rev. 165, 280–301 (2017).

    Article  Google Scholar 

  7. 7.

    Sanderman, J., Baldock, J. A. & Amundson, R. Dissolved organic carbon chemistry and dynamics in contrasting forest and grassland soils. Biogeochemistry 89, 181–198 (2008).

    Article  Google Scholar 

  8. 8.

    Marschner, B. et al. How relevant is recalcitrance for the stabilization of organic matter in soils? J. Plant Nutr. Soil Sc. 171, 91–110 (2008).

    Article  Google Scholar 

  9. 9.

    von Luetzow, M. et al. Stabilization of organic matter in temperate soils: mechanisms and their relevance under different soil conditions—a review. Eur. J. Soil. Sci. 57, 426–445 (2006).

    Article  Google Scholar 

  10. 10.

    Dungait, J. A. J., Hopkins, D. W., Gregory, A. S. & Whitmore, A. P. Soil organic matter turnover is governed by accessibility not recalcitrance. Glob. Change Biol. 18, 1781–1796 (2012).

    Article  Google Scholar 

  11. 11.

    Don, A., Roedenbeck, C. & Gleixner, G. Unexpected control of soil carbon turnover by soil carbon concentration. Environ. Chem. Lett. 11, 407–413 (2013).

    Article  Google Scholar 

  12. 12.

    Leinemann, T. et al. Multiple exchange processes on mineral surfaces control the transport of dissolved organic matter through soil profiles. Soil Biol. Biochem. 118, 79–90 (2018).

    Article  Google Scholar 

  13. 13.

    Marschner, B. & Kalbitz, K. Controls of bioavailability and biodegradability of dissolved organic matter in soils. Geoderma 113, 211–235 (2003).

    Article  Google Scholar 

  14. 14.

    Fontaine, S. et al. Stability of organic carbon in deep soil layers controlled by fresh carbon supply. Nature 450, 277–280 (2007).

    Article  Google Scholar 

  15. 15.

    Schmidt, M. W. I. et al. Persistence of soil organic matter as an ecosystem property. Nature 478, 49–56 (2011).

    Article  Google Scholar 

  16. 16.

    Steinbeiss, S., Temperton, V. M. & Gleixner, G. Mechanisms of short-term soil carbon storage in experimental grasslands. Soil Biol. Biochem. 40, 2634–2642 (2008).

    Article  Google Scholar 

  17. 17.

    Kaiser, K., Guggenberger, G. & Haumaier, L. Changes in dissolved lignin-derived phenols, neutral sugars, uronic acids, and amino sugars with depth in forested Haplic Arenosols and Rendzic Leptosols. Biogeochemistry 70, 135–151 (2004).

    Article  Google Scholar 

  18. 18.

    Gleixner, G., Poirier, N., Bol, R. & Balesdent, J. Molecular dynamics of organic matter in a cultivated soil. Org. Geochem. 33, 357–366 (2002).

    Article  Google Scholar 

  19. 19.

    Gleixner, G. Soil organic matter dynamics: a biological perspective derived from the use of compound-specific isotopes studies. Ecol. Res. 28, 683–695 (2013).

    Article  Google Scholar 

  20. 20.

    Klotzbücher, T., Kalbitz, K., Cerli, C., Hernes, P. J. & Kaiser, K. Gone or just out of sight? The apparent disappearance of aromatic litter components in soils. Soil 2, 325–335 (2016).

    Article  Google Scholar 

  21. 21.

    Waggoner, D. C., Chen, H., Willoughby, A. S. & Hatcher, P. G. Formation of black carbon-like and alicyclic aliphatic compounds by hydroxyl radical initiated degradation of lignin. Org. Geochem. 82, 69–76 (2015).

    Article  Google Scholar 

  22. 22.

    DiDonato, N., Chen, H., Waggoner, D. & Hatcher, P. G. Potential origin and formation for molecular components of humic acids in soils. Geochim. Cosmochim. Acta 178, 210–222 (2016).

    Article  Google Scholar 

  23. 23.

    Saidy, A. R., Smernik, R. J., Baldock, J. A., Kaiser, K. & Sanderman, J. The sorption of organic carbon onto differing clay minerals in the presence and absence of hydrous iron oxide. Geoderma 209–210, 15–21 (2013).

    Article  Google Scholar 

  24. 24.

    Keiluweit, M. et al. Mineral protection of soil carbon counteracted by root exudates. Nat. Clim. Change 5, 588–595 (2015).

    Article  Google Scholar 

  25. 25.

    Lange, M. et al. Plant diversity increases soil microbial activity and soil carbon storage. Nat. Commun. 6, 6707 (2015).

    Article  Google Scholar 

  26. 26.

    Liang, C., Schimel, J. P. & Jastrow, J. D. The importance of anabolism in microbial control over soil carbon storage. Nat. Microbiol. 2, 17105 (2017).

    Article  Google Scholar 

  27. 27.

    Miltner, A., Bombach, P., Schmidt-Bruecken, B. & Kaestner, M. SOM genesis: microbial biomass as a significant source. Biogeochemistry 111, 41–55 (2012).

    Article  Google Scholar 

  28. 28.

    Koch, B. P. & Dittmar, T. From mass to structure: an aromaticity index for high-resolution mass data of natural organic matter. Rapid Commun. Mass Spectrom. 20, 926–932 (2006); erratum 30, 250 (2016).

  29. 29.

    Hertkorn, N. et al. High-precision frequency measurements: indispensable tools at the core of the molecular-level analysis of complex systems. Anal. Bioanal. Chem. 389, 1311–1327 (2007).

    Article  Google Scholar 

  30. 30.

    Magurran A. E. Measuring Biological Diversity (Blackwell, 2004).

  31. 31.

    Seidel, M. et al. Molecular-level changes of dissolved organic matter along the Amazon river-to-ocean continuum. Mar. Chem. 177, 218–231 (2015). Part 2.

    Article  Google Scholar 

  32. 32.

    Flerus, R. et al. A molecular perspective on the ageing of marine dissolved organic matter. Biogeosciences 9, 1935–1955 (2012).

    Article  Google Scholar 

  33. 33.

    Bandowe, B. A. M. et al. Plant diversity enhances the natural attenuation of polycyclic aromatic compounds (PAHs and oxygenated PAHs) in grassland soils. Soil Biol. Biochem. 129, 60–70 (2019).

    Article  Google Scholar 

  34. 34.

    Hertkorn, N. et al. Characterization of a major refractory component of marine dissolved organic matter. Geochim. Cosmochim. Acta 70, 2990–3010 (2006).

    Article  Google Scholar 

  35. 35.

    Einsiedl, F. et al. Rapid biotic molecular transformation of fulvic acids in a karst aquifer. Geochim. Cosmochim. Acta 71, 5474–5482 (2007).

    Article  Google Scholar 

  36. 36.

    Fellman, J. B., D’Amore, D. V. & Hood, E. Fluorescence characteristics and biodegradability of dissolved organic matter in forest and wetland soils from coastal temperate watersheds in southeast Alaska. Biogeochemistry 88, 169–184 (2008).

    Article  Google Scholar 

  37. 37.

    Sanderman, J., Maddern, T. & Baldock, J. Similar composition but differential stability of mineral retained organic matter across four classes of clay minerals. Biogeochemistry 121, 409–424 (2014).

    Article  Google Scholar 

  38. 38.

    Rasmussen, C. et al. Beyond clay: towards an improved set of variables for predicting soil organic matter content. Biogeochemistry 137, 297–306 (2018).

    Article  Google Scholar 

  39. 39.

    Jap, B. & Walian, P. Structure and functional mechanism of porins. Physiol. Rev. 76, 1073–1088 (1996).

    Article  Google Scholar 

  40. 40.

    Nikaido, H. Transport across the bacterial outer membrane. J. Bioenerg. Biomembr. 25, 581–589 (1993).

    Google Scholar 

  41. 41.

    Lehmann, J. & Kleber, M. The contentious nature of soil organic matter. Nature 528, 60–68 (2015).

    Article  Google Scholar 

  42. 42.

    Osterholz, H., Niggemann, J., Giebel, H.-A., Simon, M. & Dittmar, T. Inefficient microbial production of refractory dissolved organic matter in the ocean. Nat. Commun. 6, 7422 (2015).

    Article  Google Scholar 

  43. 43.

    Amon, R. M. W. & Benner, R. Bacterial utilization of different size classes of dissolved organic matter. Limnol. Oceanogr. 41, 41–51 (1996).

    Article  Google Scholar 

  44. 44.

    Riedel, T., Zak, D., Biester, H. & Dittmar, T. Iron traps terrestrially derived dissolved organic matter at redox interfaces. Proc. Natl Acad. Sci. USA 110, 10101–10105 (2013).

    Article  Google Scholar 

  45. 45.

    Benk, S. A., Li, Y., Roth, V.-N. & Gleixner, G. Lignin dimers as potential markers for 14C-young terrestrial dissolved organic matter in the Critical Zone. Front. Earth Sci. 6, 168 (2018).

    Article  Google Scholar 

  46. 46.

    Neff, J. C. & Asner, G. P. Dissolved organic carbon in terrestrial ecosystems: synthesis and a model. Ecosystems 4, 29–48 (2001).

    Article  Google Scholar 

  47. 47.

    Roscher, C. et al. The role of biodiversity for element cycling and trophic interactions: an experimental approach in a grassland community. Basic Appl. Ecol. 5, 107–121 (2004).

    Article  Google Scholar 

  48. 48.

    Scheffer F. & Schachtschabel P. Lehrbuch der Bodenkunde (Spektrum Akademischer Verlag, 2002).

  49. 49.

    Bauriegel, A., Kühn, D., Schmidt, R., Hering, J. & Hannemann, J. Bodenübersichtskarte des Landes Brandenburg im Maßstab 1:300 000 (Kleinmachnow, Landesamt für Geowissenschaften und Rohstoffe, 2001).

  50. 50.

    Dittmar, T., Koch, B., Hertkorn, N. & Kattner, G. A simple and efficient method for the solid-phase extraction of dissolved organic matter (SPE-DOM) from seawater. Limnol. Oceanogr. Methods 6, 230–235 (2008).

    Article  Google Scholar 

  51. 51.

    Steinbeiss, S. et al. Plant diversity positively affects short-term soil carbon storage in experimental grasslands. Glob. Change Biol. 14, 2937–2949 (2008).

    Article  Google Scholar 

  52. 52.

    Ravenek, J. M. et al. Long-term study of root biomass in a biodiversity experiment reveals shifts in diversity effects over time. Oikos 123, 1528–1536 (2014).

    Article  Google Scholar 

  53. 53.

    Bligh, E. G. & Dyer, W. J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37, 911–917 (1959).

    Article  Google Scholar 

  54. 54.

    Kramer, C. & Gleixner, G. Variable use of plant- and soil-derived carbon by microorganisms in agricultural soils. Soil Biol. Biochem. 38, 3267–3278 (2006).

    Article  Google Scholar 

  55. 55.

    Mellado-Vázquez, P. G., Lange, M. & Gleixner, G. Soil microbial communities and their carbon assimilation are affected by soil properties and season but not by plants differing in their photosynthetic pathways (C3 vs. C4). Biogeochemistry 142, 175–187 (2019).

    Article  Google Scholar 

  56. 56.

    Frostegard, A. & Baath, E. The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol. Fertil. Soils 22, 59–65 (1996).

    Article  Google Scholar 

  57. 57.

    Zelles, L. Identification of single cultured micro-organisms based on their whole-community fatty acid profiles, using an extended extraction procedure. Chemosphere 39, 665–682 (1999).

    Article  Google Scholar 

  58. 58.

    Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013).

    Article  Google Scholar 

  59. 59.

    Muyzer, G., Dewaal, E. C. & Uitterlinden, A. G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695–700 (1993).

    Google Scholar 

  60. 60.

    Yu, Y., Lee, C., Kim, J. & Hwang, S. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol. Bioeng. 89, 670–679 (2005).

    Article  Google Scholar 

  61. 61.

    Ihrmark, K. et al. New primers to amplify the fungal ITS2 region—evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol. Ecol. 82, 666–677 (2012).

    Article  Google Scholar 

  62. 62.

    Gweon, H. S. et al. PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods Ecol. Evol. 6, 973–980 (2015).

    Article  Google Scholar 

  63. 63.

    Oksanen J. et al. vegan: Community ecology package. R package version 2.5-3 (2015).

  64. 64.

    Malik, A. A. et al. Linking molecular size, composition and carbon turnover of extractable soil microbial compounds. Soil Biol. Biochem. 100, 66–73 (2016).

    Article  Google Scholar 

  65. 65.

    Pohlabeln, A. M. & Dittmar, T. Novel insights into the molecular structure of non-volatile marine dissolved organic sulfur. Mar. Chem. 168, 86–94 (2015).

    Article  Google Scholar 

  66. 66.

    Koch, B. P., Dittmar, T., Witt, M. & Kattner, G. Fundamentals of molecular formula assignment to ultrahigh resolution mass data of natural organic matter. Anal. Chem. 79, 1758–1763 (2007).

    Article  Google Scholar 

  67. 67.

    Stenson, A. C., Marshall, A. G. & Cooper, W. T. Exact masses and chemical formulas of individual Suwannee River fulvic acids from ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectra. Anal. Chem. 75, 1275–1284 (2003).

    Article  Google Scholar 

  68. 68.

    R Core Team R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2016).

  69. 69.

    Bray, J. R. & Curtis, J. T. An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. 27, 326–349 (1957).

    Article  Google Scholar 

  70. 70.

    Pinheiro, J., Bates, D., DebRoy, S., Sarkar, D. & R Development Core Team. nlme: Linear and nonlinear mixed effects models. R package version 3.1-137 (2016).

  71. 71.

    Legendre, P. & Legendre, L. Numerical Ecology Vol. 20 (Elsevier, 1998).

  72. 72.

    Micallef, L. & Rodgers, P. eulerAPE: Drawing area-proportional 3-Venn diagrams using ellipses. PLOS ONE 9, e101717 (2014).

    Article  Google Scholar 

  73. 73.

    Hunt, J. F. & Ohno, T. Characterization of fresh and decomposed dissolved organic matter using excitation-emission matrix fluorescence spectroscopy and multiway analysis. J. Agric. Food Chem. 55, 2121–2128 (2007).

    Article  Google Scholar 

  74. 74.

    Merritt, K. A. & Erich, M. S. Influence of organic matter decomposition on soluble carbon and its copper-binding capacity. J. Environ. Qual. 32, 2122–2131 (2003).

    Article  Google Scholar 

  75. 75.

    Simon, C., Roth, V.-N., Dittmar, T. & Gleixner, G. Molecular signals of heterogeneous terrestrial environments identified in dissolved organic matter: a comparative analysis of orbitrap and ion cyclotron resonance mass spectrometers. Front. Earth Sci. 6, 138 (2018).

    Article  Google Scholar 

  76. 76.

    Chambers, M. C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918–920 (2012).

    Article  Google Scholar 

  77. 77.

    Strohalm, M., Kavan, D., Novak, P., Volny, M. & Havlicek, V. mMass 3: A cross-platform software environment for precise analysis of mass spectrometric data. Anal. Chem. 82, 4648–4651 (2010).

    Article  Google Scholar 

Download references


We thank U. Gerighausen for sampling and K. Klapproth for technical support with FT-ICR-MS measurements. This work was supported by the Zwillenberg-Tietz Stiftung and the Deutsche Forschungsgemeinschaft as part of the Critical Zone Observatory ‘AquaDiva’ (CRC 1076) and the Jena Experiment (FOR 1451, GL 262/14 and GL 262/19). The International Max Planck Research School for Global Biogeochemical Cycles (IMPRS-gBGC) provided the funding for the PhD scholarships of P.G.M.-V. and C.S.

Author information




V.-N.R. and G.G. conceived and designed the study. M.L., V.-N.R. and G.G. wrote the main text. V.-R.N. and T.D. measured and processed MS data, N.H. obtained the NMR data. M.L. and V.-R.N. analysed the data. V.-N.R. and S.B. performed the supplementary decomposition experiment and C.S. measured, processed and analysed the data from the supplementary sites. L.M., N.J.O. and A.W. provided root standing biomass data, P.G.M.-V. provided data on microbial biomass, and R.I.G. and T.G. provided data on microbial diversity. All authors reviewed and edited the manuscript.

Corresponding author

Correspondence to Markus Lange.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Figures 1−6 and Tables 1−4.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Roth, V., Lange, M., Simon, C. et al. Persistence of dissolved organic matter explained by molecular changes during its passage through soil. Nat. Geosci. 12, 755–761 (2019).

Download citation

Further reading


Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing