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Soil Carbon pp 163-172 | Cite as

Carbon Storage and DNA Adsorption in Allophanic Soils and Paleosols

  • Yu-Tuan Huang
  • David J. Lowe
  • G. Jock Churchman
  • Louis A. Schipper
  • Nicolas J. Rawlence
  • Alan Cooper
Chapter
Part of the Progress in Soil Science book series (PROSOIL)

Abstract

Andisols and andic paleosols dominated by the nanocrystalline mineral allophane sequester large amounts of carbon (C), attributable mainly to its chemical bonding with charged hydroxyl groups on the surface of allophane together with its physical protection in nanopores within and between allophane nanoaggregates. C near-edge X-ray absorption fine structure (NEXAFS) spectra for a New Zealand Andisol (Tirau series) showed that the organic matter (OM) mainly comprises quinonic, aromatic, aliphatic, and carboxylic C. In different buried horizons from several other Andisols, C contents varied but the C species were similar, attributable to pedogenic processes operating during developmental upbuilding, downward leaching, or both. The presence of OM in natural allophanic soils weakened the adsorption of DNA on clay; an adsorption isotherm experiment involving humic acid (HA) showed that HA-free synthetic allophane adsorbed seven times more DNA than HA-rich synthetic allophane. Phosphorus X-ray absorption near-edge structure (XANES) spectra for salmon-sperm DNA and DNA-clay complexes indicated that DNA was bound to the allophane clay through the phosphate group, but it is not clear if DNA was chemically bound to the surface of the allophane or to OM, or both. We plan more experiments to investigate interactions among DNA, allophane (natural and synthetic), and OM. Because DNA shows a high affinity to allophane, we are studying the potential to reconstruct late Quaternary palaeoenvironments by attempting to extract and characterise ancient DNA from allophanic paleosols.

Keywords

Andisols Allophane Carbon sequestration C NEXAFS P XANES Ancient DNA 

Notes

Acknowledgements

This research was supported by the Marsden Fund (10-UOW-056) through the Royal Society of New Zealand. We thank NSRRC, Taiwan, and especially Dr. Tsan-Yao Chen for technical instruction and support, Ling-Yun Jang for P XANES spectra for salmon-sperm DNA, Prof Shin-Ichiro Wada (Kyushu University) for advice on allophane synthesis, Dr. Emma Summers, Janine Ryburn, and Lynne Parker (Waikato University) for help with experiments, and Prof Kevin McSweeney (University of Wisconsin—Madison) for reviewing the paper.

References

  1. Bakker L, Lowe DJ, Jongmans AG (1996) A micromorphological study of pedogenic processes in an evolutionary soil sequence formed on Late Quaternary rhyolitic tephra deposits, North Island, New Zealand. Quat Int 34–36:249–261CrossRefGoogle Scholar
  2. Basile-Doelsch I, Amundson R, Stone WEE, Masiello CA, Bottero JY, Colin F, Borschneck D, Meunier JD (2005) Mineralogical control of organic carbon dynamics in a volcanic ash soil on La Réunion. Eur J Soil Sci 56:689–703Google Scholar
  3. Batjes NH (1996) Total carbon and nitrogen in the soils of the world. Eur J Soil Sci 47:151–163CrossRefGoogle Scholar
  4. Blanco-Canqui H, Lal R (2004) Mechanisms of carbon sequestration in soil aggregates. Crit Rev Plant Sci 23:481–504CrossRefGoogle Scholar
  5. Buurman P, Peterse F, Almendros MG (2007) Soil organic matter chemistry in allophanic soils: a pyrolysis-GC/MS study of a Costa Rican Andosol catena. Eur J Soil Sci 58:1330–1347CrossRefGoogle Scholar
  6. Cai P, Huang Q-Y, Zhang X-W (2006a) Interactions of DNA with clay minerals and soil colloidal particles and protection against degradation by DNase. Environ Sci Technol 40:2971–2976CrossRefGoogle Scholar
  7. Cai P, Huang Q, Jiang D, Rong X, Liang W (2006b) Microcalorimetric studies on the adsorption of DNA by soil colloidal particles. Colloids Surf B: Biointerfaces 49:49–54CrossRefGoogle Scholar
  8. Calabi-Floody M, Bendall JS, Jara AA, Welland ME, Theng BKG, Rumpel C, Mora ML (2011) Nanoclays from an Andisol: extraction, properties and carbon stabilization. Geoderma 161:159–167CrossRefGoogle Scholar
  9. Chevallier T, Woignier T, Toucet J, Blanchart E (2010) Organic carbon stabilization in the fractal pore structure of Andosols. Geoderma 159:182–188CrossRefGoogle Scholar
  10. Churchman GJ, Lowe DJ (2012) Alteration, formation, and occurrence of minerals in soils. In: Huang PM, Li Y, Sumner ME (eds) Handbook of soil sciences, vol 1, 2nd edn, Properties and processes. CRC Press, Boca Raton, pp 20.1–20.72Google Scholar
  11. Dahlgren RA, Saigusa M, Ugolini FC (2004) The nature, properties and management of volcanic soils. Adv Agron 82:113–182CrossRefGoogle Scholar
  12. Elliott ET (1986) Aggregate structure and carbon, nitrogen, and phosphorus in native and cultivated soils. Soil Sci Soc Am J 50:627–633CrossRefGoogle Scholar
  13. Greaves MP, Wilson MJ (1970) The degradation of nucleic acids and montmorillonite-nucleic-acid complexes by soil microorganisms. Soil Biol Biochem 2:257–268CrossRefGoogle Scholar
  14. Harsh J (2012) Poorly crystalline aluminosilicate clay minerals. In: Huang PM, Li Y, Sumner ME (eds) Handbook of soil sciences, vol 1, 2nd edn, Properties and processes. CRC Press, Boca Raton, pp 23.1–23.13Google Scholar
  15. Kizewski F, Liu Y-T, Morris A, Hesterberg D (2011) Spectroscopic approaches for phosphorus speciation in soils and other environmental systems. J Environ Qual 40:751–766CrossRefGoogle Scholar
  16. Kleber M, Mikutta R, Torn MS, Jahn R (2005) Poorly crystalline mineral phases protect organic matter in acid subsoil horizons. Eur J Soil Sci 56:717–725Google Scholar
  17. Lehmann J (2005) Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy for mapping nano-scale distribution of organic carbon forms in soil: application to black carbon particles. Glob Biogeochem Cycles 19:GB1013Google Scholar
  18. Lehmann J, Solomon D (2010) Organic carbon chemistry in soils observed by synchrotron-based spectroscopy. In: Singh B, Gräfe M (eds) Synchrotron-based techniques in soils and sediments. Elsevier, Amsterdam, pp 289–312CrossRefGoogle Scholar
  19. Lehmann J, Kinyangi J, Solomon D (2007) Organic matter stabilization in soil microaggregates: implications from spatial heterogeneity of organic carbon contents and carbon forms. Biogeochemistry 85:45–57CrossRefGoogle Scholar
  20. Lowe DJ, Lanigan KM, Palmer DJ (2012) Where geology meets pedology: Late Quaternary tephras, loess, and paleosols in the Mamaku Plateau and Lake Rerewhakaaitu areas. Geosci Soc N Z Misc Publ 134B:2.1–2.45Google Scholar
  21. McCarthy J, Ilavsky J, Jastrow J, Mayer L, Perfect E, Zhuang J (2008) Protection of organic carbon in soil microaggregates via restructuring of aggregate porosity and filling of pores with accumulating organic matter. Geochim Cosmochim Acta 72:4725–4744CrossRefGoogle Scholar
  22. McDaniel PA, Lowe DJ, Arnalds O, Ping C-L (2012) Andisols. In: Huang PM, Li Y, Sumner ME (eds) Handbook of soil sciences, vol 1, 2nd edn, Properties and processes. CRC Press, Boca Raton, pp 33.29–33.48Google Scholar
  23. Ohashi F, Wada S-I, Suzuki M, Maeda M, Tomura S (2002) Synthetic allophane from high concentration solutions: nanoengineering of the porous solid. Clay Miner 37:451–456CrossRefGoogle Scholar
  24. Paget E, Simonet P (1994) On the track of natural transformation in soil. FEMS Microbiol Ecol 15:109–118CrossRefGoogle Scholar
  25. Parfitt RL (2009) Allophane and imogolite: role in soil biogeochemical processes. Clay Miner 44:135–155CrossRefGoogle Scholar
  26. Parfitt RL, Fraser AR, Farmer VC (1977) Adsorption on hydrous oxides. III. Fulvic acid and humic acid on goethite, gibbsite and imogolite. J Soil Sci 28:289–296CrossRefGoogle Scholar
  27. Saeki K, Sakai M, Wada S-I (2010) DNA adsorption on synthetic and natural allophanes. Appl Clay Sci 50:493–497CrossRefGoogle Scholar
  28. Saeki K, Ihyo Y, Sakai M, Kunito T (2011) Strong adsorption of DNA molecules on humic acids. Environ Chem Lett 9:505–509CrossRefGoogle Scholar
  29. Schmidt MWI, Torn MS, Abiven S, Dittmar T, Guggenberger G, Janssens I, Kleber M, Kögel-Knabner I, Lehmann J, Manning DAC, Nannipieri P, Rasse DP, Weiner S, Trumboe S (2011) Persistence of soil organic matter as ecosystem property. Nature 478:49–56CrossRefGoogle Scholar
  30. Strong DT, Wever HD, Merckx R, Recous S (2004) Spatial location of carbon decomposition in the soil pore system. Eur J Soil Sci 55:739–750CrossRefGoogle Scholar
  31. Sutton SR, Caffee MW, Dove MT (2006) Synchrotron radiation, neutron, and mass spectrometry techniques at user facilities. Elements 2:15–21CrossRefGoogle Scholar
  32. Wan J, Tyliszczak T, Tokunaga T (2007) Organic carbon distribution, speciation, and elemental correlations within soil microaggregates: applications of STXM and NEXAFS spectroscopy. Geochim Cosmochim Acta 71:5439–5449CrossRefGoogle Scholar
  33. Yuan G, Theng BKG (2012) Clay-organic interactions in soil environments. In: Huang PM, Li Y, Sumner ME (eds) Handbook of soil sciences, vol 2, 2nd edn, Resource management and environmental impacts. CRC Press, Boca Raton, pp 2.1–2.20Google Scholar

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Yu-Tuan Huang
    • 1
  • David J. Lowe
    • 1
  • G. Jock Churchman
    • 2
  • Louis A. Schipper
    • 1
  • Nicolas J. Rawlence
    • 3
  • Alan Cooper
    • 4
  1. 1.Department of Earth and Ocean SciencesUniversity of WaikatoHamiltonNew Zealand
  2. 2.School of Agriculture, Food and Wine, and School of Earth and Environmental SciencesUniversity of AdelaideAdelaideAustralia
  3. 3.Allan Wilson Centre for Molecular Ecology and Evolution, Department of ZoologyUniversity of OtagoDunedinNew Zealand
  4. 4.Australian Centre for Ancient DNA, School of Earth and Environmental ScienceUniversity of AdelaideAdelaideAustralia

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