Soil Organic Matter Dynamics and Structure

Chapter
Part of the Sustainable Agriculture Reviews book series (SARV, volume 12)

Abstract

Soil ecosystem functions have significantly deteriorated due to agricultural intensification with dramatic consequences on carbon loss, loss of soil biodiversity, erosion, compaction as well as unsustainable use of water and mineral resources. Sustainable agricultural practices are necessary if we are to face the challenge of food security while preserving the integrity of soil and aquatic ecosystems. Conservation agriculture, which is comprised of zero or minimum tillage, carbon amendments and crop rotations, holds great promise in delivering higher yields, using water and soil resources in a sustainable manner and increasing soil biodiversity. This article presents a synthesis of current knowledge on soil ecosystem processes and modeling with a focus on carbon and nitrogen dynamics and their link to soil structure, and proposes a conceptual framework for model parameterization capable of predicting critical soil functions and potential shifts.

We reviewed the dynamics of carbon, nitrogen and soil structure with an emphasis in elucidating predominant state variables and the interaction with plants and food web dynamics. Existing models that simulate the dynamics of organic matter and structure in soils at various scales were evaluated for their ability to simulate the functions of soil ecosystem. Current modeling approaches treat carbon, nitrogen and soil structure for the most part separately without incorporating feedback mechanisms. The synergistic and antagonistic processes between bacteria and plants and fungi and plants are partially understood and more importantly the community lacks the knowledge to predict if and when these processes fail and any related potential ecosystem shift. A conceptual modeling framework is proposed, developed along the following three axes: incorporate emerging ecosystem state variables, account for the ecology of life in soils, and model processes from first principles. A synthesis of the carbon and nitrogen cycles is suggested in which the dynamics of the two cycles are interlinked. State variables in soil ecosystem models that link carbon and nitrogen dynamics with soil structure and the biological community are recommended. Plant feedback mechanisms with the physical, biochemical and biotic soil components and the symbiotic relationship between bacteria, fungi, and plants should be modeled using principles from the ecological succession theory that would relate the taxonomic structure with function and nutrient fluxes. A conceptual model of soil structure and soil stability is suggested that links the soil organic matter sub-model to an aggregation sub-model and a dynamic soil structure sub-model. The development of new generation soil ecosystem models is a necessary step to better quantify soil functions, assess possible soil tipping points, and develop methods to restore soil functions.

Keywords

Soil carbon Soil nitrogen Soil structure Model Feedback mechanisms 

Abbreviations

POM

Particulate Organic Matter

SOM

Soil Organic Matter

Notes

Acknowledgements

Funding for this work was provided by the EU FP7-ENV-2009 Project SoilTrEC “Soil Transformations in European Catchments” (Grant #244118). This work was conducted at the Institute for Environment and Sustainability of the Joint Research Centre (JRC) of the European Commission. Professor Nikolaidis is grateful for the Technical University of Crete financial support of his sabbatical leave at the JRC.

References

  1. Abiven S, Menasseri S, Angers DA, Leterme P (2007) Dynamics of aggregate stability and biological binding agents during decomposition of organic materials. EurJ Soil Sci 58:239–247CrossRefGoogle Scholar
  2. Abiven S, Menasseri S, Angers DA, Leterme P (2008) A model to predict soil aggregate stability dynamics following organic residue incorporation under field conditions. Soil Sci Soc Am J 72:119–125CrossRefGoogle Scholar
  3. Abiven S, Menasseri S, Chenu C (2009) The effects of organic input over time on soil aggregate stability – a literature analysis. Soil Biol Biochem 41:1–12CrossRefGoogle Scholar
  4. Alaoui A, Lipiec J, Gerke HH (2011) A review of the changes in the soil pore system due to soil deformation: a hydrodynamic perspective. Soil Till Res 115–116:1–15CrossRefGoogle Scholar
  5. Alcamo J, van Vuuren D, Ringler C, Cramer W, Masui T, Alder J, Schulze K (2006) Changes in nature’s balance sheet: model-based estimates of future worldwide ecosystem services. Ecol Soc 10:1551–1601Google Scholar
  6. Allen CD, Macalady AK, Chenchouni H, Bachelet D, McDowell N, Vennetier M, Kitzberger T, Rigling A, Breshears DD, Hogg EH, Gonzalez P, Fensham R, Zhang Z, Castro J, Demidova N, Lim J-H, Allard G, Running SW, Semerci A, Cobb N (2010) A global overview of drought and heat-induced tree mortality reveals emerging changes risks for forests. For Ecol Manage 259:660–684CrossRefGoogle Scholar
  7. Aune JB (2012) Conventional, organic and conservation agriculture: production and environmental impact. In: Lichtfouse E (ed) Agroecology and strategies for climate change, vol 8, Sustainable agriculture reviews. Springer Science  +  Business Media B.V., Dordrecht, pp 149–165. doi: 10.1007/978-90-007-1905-7_7 CrossRefGoogle Scholar
  8. Baker B, Zambryski P, Staskawicz B, Dinesh-Kumar SP (1997) Signaling in plant-microbe interactions. Science 276:726–733PubMedCrossRefGoogle Scholar
  9. Barot S, Blouin M, Fontaine S, Jouquet P, Lata J-C, mathieu J (2007) A tale of four stories: soil ecology, theory, evolution and the publication system. PLoS One 11:1248CrossRefGoogle Scholar
  10. Barto EK, Alt F, Oelmann Y, Wilcke W, Rillig MC (2010) Contributions of biotic and abiotic factors to soil aggregation across a land use gradient. Soil Biol Biochem 42:2316–2324CrossRefGoogle Scholar
  11. Batlle-Aguilar J, Brovelli A, Porporato A, Barry DA (2011) Modelling soil carbon and nitrogen cycles during land use change: a review. Agron Sustain Dev 31(2):251–274.Google Scholar
  12. Biggs R, Carpenter SR, Brock WA (2009) Turning back from the brink: detecting and impeding regime shift in time to avert it. Proc Natl Acad Sci 106:826–831PubMedCrossRefGoogle Scholar
  13. Blagodatskaya E, Kuzyakov Y (2008) Mechanisms of real and apparent priming effects and their dependence on soil microbial biomass and community structure: critical review. Biol Fertil Soils 45:115–131CrossRefGoogle Scholar
  14. Bonfante P, Genre A (2010) Mechanisms underlying beneficial plant-fungus interactions in mycorrhizal symbiosis. Nat Commun 1(48):1–11CrossRefGoogle Scholar
  15. Bronick CJ, Lal R (2005) Soil structure and management: a review. Geoderma 124:3–22CrossRefGoogle Scholar
  16. Butler CD, Oluoch-Kosura W (2006) Linking future ecosystem services and future human well-being, ecology and society, 11, 30 www.ecologyandsociety.org/vol11/iss1/art30/
  17. Camilli A, Bassler BL (2006) Bacterial small-molecule signaling pathways. Science 311:1113–1116PubMedCrossRefGoogle Scholar
  18. Carpenter SR, Bennett EM, Peterson GD (2006) Scenarios for ecosystem services: an overview, ecology and society, 11, 29 www.ecologyandsociety.org/vol11/iss1/art29/
  19. Chen Y, Zhang X, He H, Xie H, Yan Y, Zhu P, Ren J, Wang L (2010) Carbon and nitrogen pools in different aggregates of a Chinese Mollisol as influenced by long-term fertilization. J Soil Sediment 10:1018–1026CrossRefGoogle Scholar
  20. Cheng Z, McConkey J, Glick BR (2010) Proteomic studies of plant-bacterial interactions. Soil Biol Biochem 42:1673–1684CrossRefGoogle Scholar
  21. Clark JS, Tillman D (2008) Loss of plant species after chronic low-level nitrogen deposition to prairie grasslands. Nature 451:712–715PubMedCrossRefGoogle Scholar
  22. Clark JS, Carpenter SR, Barber M, Collins S, Dobson A, Foley JA, Lodge DM, Pascual M, Pielke R Jr, Pizer W, Pringle C, Reid WV, Rose KA, Sala O, Schlesinger WH, Wall DH, Wear D (2001) Ecological forecasts: an emerging imperative. Science 293:657–660PubMedCrossRefGoogle Scholar
  23. Coleman K, Jenkinson DS (1999) RothC-26.3 – a model for the turnover of carbon in soil – model description and users guide. IACR, RothamstedGoogle Scholar
  24. Compant S, Clement C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo- and endosphere of plants: the role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 42:669–678CrossRefGoogle Scholar
  25. Courty PE, Buee M, Diedhiou AG, Frey-Klett P, Le Tacon F, Rineau F, Turpault MP, Uroz S, Garbaye J (2010) The role of ectomycorrhizal communities in forest ecosystem processes: new perspectives and emerging concepts. Soil Biol Biochem 42:679–698CrossRefGoogle Scholar
  26. Cowling RM, Egoh B, Knight AT, O’Farrell PJ, Reyers B, Rouget M, Roux DJ, Welz A, Wilhelm-Rechman A (2008) An operational model for mainstreaming ecosystem services for implementation. Proc Natl Acad Sci 105:9483–9488PubMedCrossRefGoogle Scholar
  27. Crawford JW, Harris JA, Ritz K, Young IM (2005) Towards an evolutionary ecology of life in soil. Trends Ecol Evol 20:81–87PubMedCrossRefGoogle Scholar
  28. Dawson JJC, Smith P (2007) Carbon losses from soil and its consequences for land-use management. Sci Total Environ 382:165–190PubMedCrossRefGoogle Scholar
  29. De Gryze S, Six J, Brits C, Merckx R (2005) A quantification of short-term macroaggregate dynamics: influences of wheat residue input and texture. Soil Biol Biochem 37:55–66CrossRefGoogle Scholar
  30. De Gryze S, Six J, Merckx R (2006) Quantifying water-stable soil aggregate turnover and its implication for soil organic matter dynamics in a model study. Eur J Soil Sci 57:693–707CrossRefGoogle Scholar
  31. Debele B, Srinivasan R, Parlange J-Y (2008) Hourly analyses of hydrological and water quality simulations using the ESWAT model. Water Resour Manag 23:303–324CrossRefGoogle Scholar
  32. Ehrenfeld JG, Ravit B, Elgersma K (2005) Feedback in the plant-soil system. Ann Rev Environ Resour 30:75–115CrossRefGoogle Scholar
  33. Falloon PD, Smith P (2000) Modelling refractory soil organic matter. Biol Fertil Soils 30:388–398CrossRefGoogle Scholar
  34. Fierer N, Grandy AS, Six J, Paul EA (2009) Searching for unifying principles in soil ecology. Soil Biol Biochem 41:2249–2256CrossRefGoogle Scholar
  35. Finke PA, Hutson JL (2008) Modelling soil genesis in calcareous loess. Geoderma 145:462–479CrossRefGoogle Scholar
  36. Gardenas AI, Agren GI, Bird JA, Clarholm M, Hallin S, Ineson P, Katterer T, Knicker H, Nilsson SI, Nasholm T, Ogle S, Paustian K, Persson T, Stendahl J (2011) Knowledge gaps in soil carbon and nitrogen interactions – from molecular to global scale. Soil Biol Biochem 43:702–717CrossRefGoogle Scholar
  37. Geisseler D, Horwath WR, Joergensen RG, Ludwig B (2010) Pathways of nitrogen utilization by microorganisms – a review. Soil Biol Biochem 42:2058–2067CrossRefGoogle Scholar
  38. Gillis JD, Price GW (2011) Comparison of a novel model to three conventional models describing carbon mineralization from soil amended with organic residues. Geoderma 160:304–310CrossRefGoogle Scholar
  39. Heller M (2009) Climate change: impact on agriculture and costs of adaptation. International Food Policy Research Institute (IFPRI). http://www.ifpri.org/publication/climate-change-impact-agriculture-and-costs-adaptation. Accessed 13 Feb 2012
  40. Ingwersen J, Poll C, Streck T, Kandeler E (2008) Micro-scalemodelling of carbon turnover driven by microbial succession at a biogeochemical interface. Soil Biol Biochem 40:864–878CrossRefGoogle Scholar
  41. Jamtgard S, Nasholm T, Huss-Danell K (2010) Nitrogen compounds in soil solutions of agricultural land. Soil Biol Biochem 42:2325–2330CrossRefGoogle Scholar
  42. Jastrow JD, Amonette JE, Bailey VL (2007) Mechanisms controlling soil carbon turnover and their potential application for enhancing carbon sequestration. Clim Change 80:5–23CrossRefGoogle Scholar
  43. Kleber M, Sollins P, Sutton R (2007) A conceptual model of organo-mineral interactions in soils: self-assembly of organic molecular fragments into zonal structures on mineral surfaces. Biogeochemistry 85:9–24CrossRefGoogle Scholar
  44. Knicker H (2011) Soil organic N – an under-rated player for C sequestration in soils? Soil Biol Biochem 43:1118–1129CrossRefGoogle Scholar
  45. Kuka K, Franko U, Ruhlmann J (2007) Modelling the impact of pore space distribution on carbon turnover. Ecol Model 208:295–306CrossRefGoogle Scholar
  46. Kutilek M (2011) Soils and climate change. Soil Till Res 117:1–7CrossRefGoogle Scholar
  47. Kuzyakov Y (2010) Priming effects: interactions between living and dead organic matter. Soil Biol Biochem 42:1363–1371CrossRefGoogle Scholar
  48. Lorenz K, Lal R, Preston CM, Nierop KGJ (2007) Strengthening the soil organic pool by increasing contributions from recalcitrant aliphatic bio(macro)molecules. Geoderma 142:1–10CrossRefGoogle Scholar
  49. Malamoud K, McBratney AB, Minasny B, field DJ (2009) Modelling how carbon affects soil structure. Geoderma 149:19–26CrossRefGoogle Scholar
  50. Manzoni S, Porporato A (2009) Soil carbon and nitrogen mineralization: theory and models across scales. Soil Biol Biochem 41:1355–1379CrossRefGoogle Scholar
  51. McGuire KL, Treseder KK (2010) Microbial communities and their relevance for ecosystem models: decomposition as a case study. Soil Biol Biochem 42:529–535CrossRefGoogle Scholar
  52. Minasny B, McBratney AB, Salvador-Blanes S (2008) Quantitative models for pedogenesis – a review. Geoderma 144:140–157CrossRefGoogle Scholar
  53. Nannipieri P, Eldor P (2009) The chemical and functional characterization of soil N and its biotic component. Soil Biol Biochem 41:2357–2369CrossRefGoogle Scholar
  54. Nelson GC, Bennett E, Berhe AA, Cassman K, DeFries R, Dietz T, Dobermann A, Dobson A, Janetos A, Levy M, Marco D, Nakicenovic N, O’Neill B, Norgaard R, Petschel-Held G, Ojima D, Pingali P, Watson R, Zurek M (2006) Anthropogenic drivers of ecosystem change: an overview, ecology and society, 11, 29 www.ecologyandsociety.org/vol11/iss2/art29/
  55. Nikolaidis NP (2011) Human impacts on soil: tipping points and knowledge gaps. Appl Geochem 26:230–233CrossRefGoogle Scholar
  56. Olson KR, Lang JM, Ebelhar SA (2005) Soil organic carbon changes after 12 years of no-tillage and tillage of grantsburg soils in southern Illinois. Soil Till Res 81:217–225CrossRefGoogle Scholar
  57. Paul K, Polglase P, Coops N, O’Connel T, Grove T, Mendham D, Carlyle C, May B, Smethurst P, Baillie C (2002) Modelling change in soil carbon following afforestation or reforestation, CSIRO forestry and forest products, national carbon accounting system technical report no 29. Australian Greenhouse Office, Canberra, ACT, p 108Google Scholar
  58. Plante AF, Feng Y, McGill WB (2002) A modeling approach to quantifying soil macroaggregate dynamics. Can J Soil Sci 82:181–190CrossRefGoogle Scholar
  59. Post J, Krysanova V, Suckow F, Mirschel W, Rogasik J, Merbach I (2007) Integrated eco-hydrological modeling of soil organic matter dynamics for the assessment of environmental change impacts in meso- and macro-scale river basins. Ecol Model 206:93–109CrossRefGoogle Scholar
  60. Ramirez KS, Craine JM, Fierer N (2010) Nitrogen fertilization inhibits soil microbial respiration regardsless of the form of nitrogen applied. Soil Biol Biochem 42:2336–2338CrossRefGoogle Scholar
  61. Rillig MC, Caldwell BA, Wosten HAB, Sollins P (2007) Role of proteins in soil carbon and nitrogen storage: controls on persistence. Biogeochemistry 85:25–44CrossRefGoogle Scholar
  62. Rockstrom J, Steffen W, Noone K, Persson E, Chapin FS, Lambin EF, Lenton TM, Scheffer M, Folke C, Schellnhuber HJ, Nykvist B, de Wit CA, Hughes T, van der Leeuw S, Rodhe H, Sorlin S, Snyder PK, Costanza R, Svedin U, Falkenmark M, Karlberg L, Corell RW, Fabry VJ, Hansen J, Walker B, Liverman D, Richardson K, Crutzen P, Foley JA (2009) A safe operating space for humanity. Nature 461:472–475PubMedCrossRefGoogle Scholar
  63. Rovira P, Rovira R (2010) Fitting litter decomposition datasets to mathematical curves: towards a generalised exponential approach. Geoderma 155:329–343CrossRefGoogle Scholar
  64. Saha S (2010) Soil functions and diversity in organic and conventional farming. In: Lichtfouse E (ed) Sociology, organic farming, climate change and soil science, vol 3, Sustainable agriculture reviews. Springer, Dordrecht, pp 275–301. doi: 10.1007/978-90-481-3333-8_10 CrossRefGoogle Scholar
  65. Sapkota TB (2012) Conservation tillage impact on soil aggregation, organic matter turnover and biodiversity. In: Lichtfouse E (ed) Organic fertilization, soil quality and human health, vol 9, Sustainable agriculture reviews. Springer, Dordrecht, pp 141–160. doi: 10.1007/978-94-007-4113-3_6 CrossRefGoogle Scholar
  66. Schimel JP, Bennett J (2004) Nitrogen mineralization: challenges of a changing paradigm. Ecology 85:591–602CrossRefGoogle Scholar
  67. Schmidt SK, Costello EK, Nemergut DR, Cleveland CC, Reed SC, Weintraub MN, Meyer AF, Martin AM (2007) Biogeochemical consequences of rapid microbial turnover and seasonal succession in soil. Ecology 88:1379–1385PubMedCrossRefGoogle Scholar
  68. Schroter D, Cramer W, Leemans R, Prentice IC, Araujo MB, Arnell NW, Bondeau A, Bugmann H, Carter TR, Gracia CA, de la Vega-Leinert AC, Erhard M, Ewert F, Glendining M, House JI, Kankaanpaa S, Klein RJT, Lavorel S, Lindner M, Metzger MJ, Meyer J, Mitchell TD, Reginster I, Rounsevell M, Sabate S, Sitch S, Smith B, Smith J, Smith P, Sykes MT, Thonicke K, Thuiller W, Tuck G, Zaehle S, Zierl B (2005) Ecosystem service supply and vulnerability to global change in Europe. Science 310:1333–1337PubMedCrossRefGoogle Scholar
  69. Schulten HR, Schnitzer M (1998) The chemistry of soil organic nitrogen: a review. Biol Fertil Soils 26:1–15CrossRefGoogle Scholar
  70. Science (2004) Soils-the final frontier. Sci Spec Issue 304:1549–1700CrossRefGoogle Scholar
  71. Shibu ME, Leffelaar PA, Van Keulen H, Aggarwal PK (2006) Quantitative description of soil organic matter dynamics – a review of approaches with reference to rice-based cropping systems. Geoderma 137:1–18CrossRefGoogle Scholar
  72. Sinsabaugh RL (2010) Phenol oxidase, peroxidase and organic matter dynamics of soil. Soil Biol Biochem 42:391–404CrossRefGoogle Scholar
  73. Six J, Bossuyt H, Degryze S, Denef K (2004) A history of research on the link between (micro) aggregates, soil biota, and soil organic matter dynamics. Soil Till Res 79:7–31CrossRefGoogle Scholar
  74. Stagnari F, Ramazzotti S, Pisante M (2009) Conservation agriculture: a different approach for crop production through sustainable soil and water management: a Review. In: Lichtfouse E (ed) Organic farming, pest control and remediatione, vol 1, Sustainable agriculture reviews. Springer, Dordrecht, pp 55–83CrossRefGoogle Scholar
  75. Steffen W (2009) Interdisciplinary research for managing ecosystem services. Proc Natl Acad Sci 106:1301–1302PubMedCrossRefGoogle Scholar
  76. Stevens CJ, Dise NB, Mountford JO, Gowing DJ (2004) Impact of nitrogen deposition on the species richness of grasslands. Science 303:1876–1879PubMedCrossRefGoogle Scholar
  77. Stevenson JF (1994) Humus chemistry: genesis, composition, reactions, 2nd edn. Wiley, New YorkGoogle Scholar
  78. Sutton R, Sposito G (2005) Molecular structure in soil humic substances: the new view. Environ Sci Technol 39:90099015CrossRefGoogle Scholar
  79. Szanser M, Ilieva-Makulec K, Kajak A, Gorska E, Kusinska A, Kisiel M, Olejniczak I, Russel S, Sieminiak D, Wojewoda D (2011) Impact of litter species diversity on decomposition processes and communities of soil organisms. Soil Biol Biochem 43:9–19CrossRefGoogle Scholar
  80. Tallis HM, Kareiva P (2006) Shaping global environmental decisions using socio-ecological models. Trends Ecol Evol 21:562–568PubMedCrossRefGoogle Scholar
  81. Thevenot M, Dignac M, Rumpel C (2010) Fate of lignins in soils: a review. Soil Biol Biochem 42:1200–1211CrossRefGoogle Scholar
  82. Tilman D (2010) Understanding the present and projecting the future of global food demand. AAAS Annual Meeting. AAAS, San DiegoGoogle Scholar
  83. UN FAO (2011) Food agriculture and cities: challenges of food and nutrition security, agriculture and ecosystem management in an urbanizing world –food for the cities multi-disciplinary initiative. www.fao.org/fcit. Accessed 13 Feb 2012
  84. Wardle DA (2002) Communities and ecosystems: linking the aboveground and belowground components. Princeton University Press, Monographs in Population Dynamics, p 400Google Scholar
  85. Wu T (2011) Can ectomycorrhizal fungi circumvent the nitrogen mineralization for plant nutrition in temperate forest ecosystems? Soil Biol Biochem 43:1109–1117CrossRefGoogle Scholar
  86. Wu G-L, Li W, Shi Z-H, Shangguan Z-P (2011) Aboveground dominant functional group predicts belowground properties in an alpine grassland community of western China. J Soil Sediment 11:1011–1019CrossRefGoogle Scholar
  87. Zhang L, Xu Z (2008) Assessing bacterial diversity in soil. J Soil Sediment 8:379–388CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Department of Environmental EngineeringTechnical University of CreteChaniaGreece
  2. 2.Institute for Environment and Sustainability, Joint Research CentreEuropean CommissionISPRAItaly

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