Developing a Molecular Picture of Soil Organic Matter–Mineral Interactions by Quantifying Organo–Mineral Binding
Abstract
Long residence times of soil organic matter have been attributed to reactive mineral surface sites that sorb organic species and cause inaccessibility due to isolation and chemical stabilization at the organic-mineral interface. Instrumentation for probing this interface is limited. As a result, much of the micron- and molecular-scale knowledge about organic-mineral interactions remains largely qualitative. We report the use of force spectroscopy to directly measure the binding between organic ligands with known chemical functionalities to soil minerals in aqueous environments. By systematically studying the role of organic functional group chemistry with model minerals, we demonstrate that the chemistry of both the organic ligand and mineral contribute to values of binding free energy and that changes in pH and ionic strength produce significant differences in binding energies. These direct measurements of molecular binding provide mechanistic insights into organo-mineral interactions, which could potentially inform land-carbon models that explicitly include mineral-bound C pools.
- Authors:
-
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Univ. of Washington, Seattle, WA (United States). Dept. of Materials Science and Engineering
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1406734
- Alternate Identifier(s):
- OSTI ID: 1398203
- Report Number(s):
- PNNL-SA-121086; PNNL-SA-124131
Journal ID: ISSN 2041-1723; 49124
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 58 GEOSCIENCES; Environmental Molecular Sciences Laboratory; soil organic matter; dynamic force microscopy; mineral; interface; Carbon cycle; Geochemistry
Citation Formats
Newcomb, Christina J., Qafoku, Nikolla P., Grate, Jay W., Bailey, Vanessa L., and De Yoreo, James J. Developing a Molecular Picture of Soil Organic Matter–Mineral Interactions by Quantifying Organo–Mineral Binding. United States: N. p., 2017.
Web. doi:10.1038/s41467-017-00407-9.
Newcomb, Christina J., Qafoku, Nikolla P., Grate, Jay W., Bailey, Vanessa L., & De Yoreo, James J. Developing a Molecular Picture of Soil Organic Matter–Mineral Interactions by Quantifying Organo–Mineral Binding. United States. https://doi.org/10.1038/s41467-017-00407-9
Newcomb, Christina J., Qafoku, Nikolla P., Grate, Jay W., Bailey, Vanessa L., and De Yoreo, James J. Wed .
"Developing a Molecular Picture of Soil Organic Matter–Mineral Interactions by Quantifying Organo–Mineral Binding". United States. https://doi.org/10.1038/s41467-017-00407-9. https://www.osti.gov/servlets/purl/1406734.
@article{osti_1406734,
title = {Developing a Molecular Picture of Soil Organic Matter–Mineral Interactions by Quantifying Organo–Mineral Binding},
author = {Newcomb, Christina J. and Qafoku, Nikolla P. and Grate, Jay W. and Bailey, Vanessa L. and De Yoreo, James J.},
abstractNote = {Long residence times of soil organic matter have been attributed to reactive mineral surface sites that sorb organic species and cause inaccessibility due to isolation and chemical stabilization at the organic-mineral interface. Instrumentation for probing this interface is limited. As a result, much of the micron- and molecular-scale knowledge about organic-mineral interactions remains largely qualitative. We report the use of force spectroscopy to directly measure the binding between organic ligands with known chemical functionalities to soil minerals in aqueous environments. By systematically studying the role of organic functional group chemistry with model minerals, we demonstrate that the chemistry of both the organic ligand and mineral contribute to values of binding free energy and that changes in pH and ionic strength produce significant differences in binding energies. These direct measurements of molecular binding provide mechanistic insights into organo-mineral interactions, which could potentially inform land-carbon models that explicitly include mineral-bound C pools.},
doi = {10.1038/s41467-017-00407-9},
journal = {Nature Communications},
number = 1,
volume = 8,
place = {United States},
year = {Wed Aug 30 00:00:00 EDT 2017},
month = {Wed Aug 30 00:00:00 EDT 2017}
}
Web of Science
Works referenced in this record:
From The Cover: Adhesion at calcium oxalate crystal surfaces and the effect of urinary constituents
journal, December 2004
- Sheng, X.; Jung, T.; Wesson, J. A.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 2
Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several tropical forests
journal, January 2016
- Zhu, Q.; Riley, W. J.; Tang, J.
- Biogeosciences, Vol. 13, Issue 1
Influence of Structural Features on Sorption of NOM-Analogue Organic Acids to Goethite
journal, October 1998
- Evanko, Cynthia R.; Dzombak, David A.
- Environmental Science & Technology, Vol. 32, Issue 19
Multi-elemental scanning transmission X-ray microscopy–near edge X-ray absorption fine structure spectroscopy assessment of organo–mineral associations in soils from reduced environments
journal, January 2015
- Chen, Chunmei; Sparks, Donald L.
- Environmental Chemistry, Vol. 12, Issue 1
Effect of dehydration on dicarboxylic acid coordination at goethite/water interface
journal, April 2008
- Kang, Seunghun; Amarasiriwardena, Dula; Xing, Baoshan
- Colloids and Surfaces A: Physicochemical and Engineering Aspects, Vol. 318, Issue 1-3
Reconciling disparate views of template-directed nucleation through measurement of calcite nucleation kinetics and binding energies
journal, January 2014
- Hamm, L. M.; Giuffre, A. J.; Han, N.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 4
Understanding the incremental value of novel diagnostic tests for tuberculosis
journal, December 2015
- Arinaminpathy, Nimalan; Dowdy, David
- Nature, Vol. 528, Issue 7580
Benzenecarboxylate surface complexation at the goethite (α-FeOOH)/water interface: II. Linking IR spectroscopic observations to mechanistic surface complexation models for phthalate, trimellitate, and pyromellitate
journal, October 2000
- Boily, Jean-François; Persson, Per; Sjöberg, Staffan
- Geochimica et Cosmochimica Acta, Vol. 64, Issue 20
Calorimetry and soil
journal, June 2007
- Barros, N.; Salgado, J.; Feijóo, S.
- Thermochimica Acta, Vol. 458, Issue 1-2
Adsorption of oxalate and malonate at the water-goethite interface: Molecular surface speciation from IR spectroscopy
journal, February 2005
- Persson, Per; Axe, Kristina
- Geochimica et Cosmochimica Acta, Vol. 69, Issue 3
Nanoscale chemical analysis by tip-enhanced Raman spectroscopy
journal, February 2000
- Stöckle, Raoul M.; Suh, Yung Doug; Deckert, Volker
- Chemical Physics Letters, Vol. 318, Issue 1-3, p. 131-136
Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several tropical forests
journal, January 2015
- Zhu, Q.; Riley, W. J.; Tang, J.
- Biogeosciences Discussions, Vol. 12, Issue 5
Influence of mineral characteristics on the retention of low molecular weight organic compounds: A batch sorption–desorption and ATR-FTIR study
journal, October 2014
- Yeasmin, Sabina; Singh, Balwant; Kookana, Rai S.
- Journal of Colloid and Interface Science, Vol. 432
Preferential adsorption of extracellular polymeric substances from bacteria on clay minerals and iron oxide
journal, March 2011
- Cao, Yuanyuan; Wei, Xing; Cai, Peng
- Colloids and Surfaces B: Biointerfaces, Vol. 83, Issue 1
Energetic basis for the molecular-scale organization of bone
journal, December 2014
- Tao, Jinhui; Battle, Keith C.; Pan, Haihua
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 2
Dynamic force spectroscopy of parallel individual Mucin1-antibody bonds
journal, November 2005
- Sulchek, T. A.; Friddle, R. W.; Langry, K.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 46
Coating of AFM probes with aquatic humic and non-humic NOM to study their adhesion properties
journal, June 2013
- Aubry, Cyril; Gutierrez, Leonardo; Croue, Jean Philippe
- Water Research, Vol. 47, Issue 9
Submicron structures provide preferential spots for carbon and nitrogen sequestration in soils
journal, January 2014
- Vogel, Cordula; Mueller, Carsten W.; Höschen, Carmen
- Nature Communications, Vol. 5, Issue 1
Multiband Variability Analysis of 3C 454.3 and Implications for the Center Structure
journal, January 2015
- Li, H. Z.; Chen, L. E.; Yi, T. F.
- Publications of the Astronomical Society of the Pacific, Vol. 127, Issue 947
Persistence of soil organic matter as an ecosystem property
journal, October 2011
- Schmidt, Michael W. I.; Torn, Margaret S.; Abiven, Samuel
- Nature, Vol. 478, Issue 7367
Soil carbon storage controlled by interactions between geochemistry and climate
journal, August 2015
- Doetterl, Sebastian; Stevens, Antoine; Six, Johan
- Nature Geoscience, Vol. 8, Issue 10
Force Titrations and Ionization State Sensitive Imaging of Functional Groups in Aqueous Solutions by Chemical Force Microscopy
journal, February 1997
- Vezenov, Dmitri V.; Noy, Aleksandr; Rozsnyai, Lawrence F.
- Journal of the American Chemical Society, Vol. 119, Issue 8
Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains
journal, April 2017
- Bailey, V. L.; Smith, A. P.; Tfaily, M.
- Soil Biology and Biochemistry, Vol. 107
Adsorption of Glyphosate on Goethite (α-FeOOH): Surface Complexation Modeling Combining Spectroscopic and Adsorption Data
journal, April 2008
- Jonsson, Caroline M.; Persson, Per; Sjöberg, Staffan
- Environmental Science & Technology, Vol. 42, Issue 7
Extent of coverage of mineral surfaces by organic matter in marine sediments
journal, January 1999
- Mayer, L. M.
- Geochimica et Cosmochimica Acta, Vol. 63, Issue 2
Comparison of calibration methods for atomic-force microscopy cantilevers
journal, December 2002
- Burnham, N. A.; Chen, X.; Hodges, C. S.
- Nanotechnology, Vol. 14, Issue 1
Bonding Mechanisms of Salicylic Acid Adsorbed onto Illite Clay: An ATR−FTIR and Molecular Orbital Study
journal, March 1997
- Kubicki, James D.; Itoh, Mika J.; Schroeter, Lynette M.
- Environmental Science & Technology, Vol. 31, Issue 4
Molecular Fractionation of Dissolved Organic Matter with Metal Salts
journal, March 2012
- Riedel, Thomas; Biester, Harald; Dittmar, Thorsten
- Environmental Science & Technology, Vol. 46, Issue 8
A Surface Structural Approach to Ion Adsorption: The Charge Distribution (CD) Model
journal, May 1996
- Hiemstra, T.; Van Riemsdijk, W. H.
- Journal of Colloid and Interface Science, Vol. 179, Issue 2
Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling
journal, February 2014
- Wang, Gangsheng; Mayes, Melanie A.; Gu, Lianhong
- PLoS ONE, Vol. 9, Issue 2
On the protonation of oxo- and hydroxo-groups of the goethite (α-FeOOH) surface: A FTIR spectroscopic investigation of surface O–H stretching vibrations
journal, July 2008
- Boily, Jean-François; Felmy, Andrew R.
- Geochimica et Cosmochimica Acta, Vol. 72, Issue 14
Interpreting the widespread nonlinear force spectra of intermolecular bonds
journal, August 2012
- Friddle, R. W.; Noy, A.; De Yoreo, J. J.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 34
Retention of dissolved organic matter by phyllosilicate and soil clay fractions in relation to mineral properties
journal, March 2004
- Kahle, Maren; Kleber, Markus; Jahn, Reinhold
- Organic Geochemistry, Vol. 35, Issue 3
Soil carbon in a beer can
journal, August 2015
- Davidson, Eric A.
- Nature Geoscience, Vol. 8, Issue 10
Ultrabroadband infrared nanospectroscopic imaging
journal, May 2014
- Bechtel, H. A.; Muller, E. A.; Olmon, R. L.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 20
Probing Surface Charge Potentials of Clay Basal Planes and Edges by Direct Force Measurements
journal, November 2008
- Zhao, Hongying; Bhattacharjee, Subir; Chow, Ross
- Langmuir, Vol. 24, Issue 22
Weaker soil carbon–climate feedbacks resulting from microbial and abiotic interactions
journal, November 2014
- Tang, Jinyun; Riley, William J.
- Nature Climate Change, Vol. 5, Issue 1
Microbe-driven turnover offsets mineral-mediated storage of soil carbon under elevated CO2
journal, November 2014
- Sulman, Benjamin N.; Phillips, Richard P.; Oishi, A. Christopher
- Nature Climate Change, Vol. 4, Issue 12
Higher Molecular Mass Organic Matter Molecules Compete with Orthophosphate for Adsorption to Iron (Oxy)hydroxide
journal, July 2016
- Chassé, Alexander W.; Ohno, Tsutomu
- Environmental Science & Technology, Vol. 50, Issue 14
Mineral–Organic Associations: Formation, Properties, and Relevance in Soil Environments
book, December 2014
- Kleber, Markus; Eusterhues, Karin; Keiluweit, Marco
The Adsorption of 2-Ketogluconate by Goethite
journal, July 2010
- Journey, J. S.; Anderson, R. M.; Essington, M. E.
- Soil Science Society of America Journal, Vol. 74, Issue 4
Adsorption of monocarboxylates at the water/goethite interface: The importance of hydrogen bonding
journal, December 2007
- Norén, Katarina; Persson, Per
- Geochimica et Cosmochimica Acta, Vol. 71, Issue 23
A conceptual model of organo-mineral interactions in soils: self-assembly of organic molecular fragments into zonal structures on mineral surfaces
journal, June 2007
- Kleber, M.; Sollins, P.; Sutton, R.
- Biogeochemistry, Vol. 85, Issue 1
Chemical Force Spectroscopy Evidence Supporting the Layer-by-Layer Model of Organic Matter Binding to Iron (oxy)Hydroxide Mineral Surfaces
journal, August 2015
- Chassé, Alexander W.; Ohno, Tsutomu; Higgins, Steven R.
- Environmental Science & Technology, Vol. 49, Issue 16
Interaction between humic acid and montmorillonite in the presence of calcium ions I. Interfacial and aqueous phase equilibria: Adsorption and complexation
journal, August 2007
- Majzik, Andrea; Tombácz, Etelka
- Organic Geochemistry, Vol. 38, Issue 8
Single-Molecule Determination of the Face-Specific Adsorption of Amelogenin’s C-Terminus on Hydroxyapatite
journal, June 2011
- Friddle, Raymond W.; Battle, Keith; Trubetskoy, Vasily
- Angewandte Chemie International Edition, Vol. 50, Issue 33
Nanomorphology of montmorillonite particles: Estimation of the clay edge sorption site density by low-pressure gas adsorption and AFM observations
journal, November 2003
- Tournassat, Christophe; Neaman, Alexander; Villiéras, Frédéric
- American Mineralogist, Vol. 88, Issue 11-12
Glycine at the Pyrite−Water Interface: The Role of Surface Defects
journal, October 2006
- Nair, Nisanth N.; Schreiner, Eduard; Marx, Dominik
- Journal of the American Chemical Society, Vol. 128, Issue 42
Theory of rapid force spectroscopy
journal, July 2014
- Bullerjahn, Jakob T.; Sturm, Sebastian; Kroy, Klaus
- Nature Communications, Vol. 5, Issue 1
Surface complexes of acetate on edge surfaces of 2:1 type phyllosilicate: Insights from density functional theory calculation
journal, December 2008
- Liu, Xiandong; Lu, Xiancai; Wang, Rucheng
- Geochimica et Cosmochimica Acta, Vol. 72, Issue 24
Adsorption and desorption of natural organic matter on iron oxide: mechanisms and models
journal, January 1994
- Gu, Baohua.; Schmitt, Juergen.; Chen, Zhihong.
- Environmental Science & Technology, Vol. 28, Issue 1
Stabilization of organic matter in temperate soils: mechanisms and their relevance under different soil conditions - a review
journal, August 2006
- Lutzow, M. v.; Kogel-Knabner, I.; Ekschmitt, K.
- European Journal of Soil Science, Vol. 57, Issue 4
Interaction of Hydrophobic Organic Compounds with Mineral-Bound Humic Substances
journal, July 1994
- Murphy, Ellyn M.; Zachara, John M.; Smith, Steven C.
- Environmental Science & Technology, Vol. 28, Issue 7
Persistence of soil organic matter as an ecosystem property
text, January 2011
- Schmidt, M. W. I.; Torn, M. S.; Abiven, S.
- Nature Publishing Group
Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling
text, January 2013
- Wang, Gangsheng; Mayes, Melanie A.; Gu, Lianhong
- arXiv
Works referencing / citing this record:
Controlling protein assembly on inorganic crystals through designed protein interfaces
journal, July 2019
- Pyles, Harley; Zhang, Shuai; De Yoreo, James J.
- Nature, Vol. 571, Issue 7764
Minimal biomass deposition in banded iron formations inferred from organic matter and clay relationships
journal, November 2019
- Dodd, Matthew S.; Papineau, Dominic; Pirajno, Franco
- Nature Communications, Vol. 10, Issue 1
A farm-scale investigation of the organic matter composition and soil chemistry of Andisols as influenced by land use and management
journal, July 2018
- Kov, Ritha; Camps-Arbestain, Marta; Calvelo Pereira, Roberto
- Biogeochemistry, Vol. 140, Issue 1
Accessing crystal–crystal interaction forces with oriented nanocrystal atomic force microscopy probes
journal, September 2018
- Zhang, Xin; He, Yang; Liu, Jia
- Nature Protocols, Vol. 13, Issue 9
Exploring the role of ectomycorrhizal fungi in soil carbon dynamics
journal, February 2019
- Zak, Donald R.; Pellitier, Peter T.; Argiroff, WilliamA.
- New Phytologist, Vol. 223, Issue 1
Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates
journal, November 2018
- Arachchige, Pavithra S. Pitumpe; Hettiarachchi, Ganga M.; Rice, Charles W.
- Scientific Reports, Vol. 8, Issue 1
Using chromate to investigate the impact of mineral–organic contact time on the surface reactivity of goethite
journal, January 2018
- Hales-Messenger, Stacey; Swindle, Andrew
- Environmental Science: Processes & Impacts, Vol. 20, Issue 10
Soil carbon losses due to higher pH offset vegetation gains due to calcium enrichment in an acid mitigation experiment
journal, August 2018
- Marinos, Richard E.; Bernhardt, Emily S.
- Ecology, Vol. 99, Issue 10
Effects of altered dry season length and plant inputs on soluble soil carbon
journal, August 2018
- Homyak, Peter M.; Blankinship, Joseph C.; Slessarev, Eric W.
- Ecology, Vol. 99, Issue 10
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
journal, January 2010
- Chaudhury, S.; Lyskov, S.; Gray, J. J.
- Bioinformatics, Vol. 26, Issue 5, p. 689-691
One-Pot Transformation of Technical Lignins into Humic-Like Plant Stimulants through Fenton-Based Advanced Oxidation: Accelerating Natural Fungus-Driven Humification
journal, July 2018
- Jeong, Hae Jin; Cha, Joon-Yung; Choi, Jung Hoon
- ACS Omega, Vol. 3, Issue 7
Minimal biomass deposition in banded iron formations inferred from organic matter and clay relationships
journal, November 2019
- Dodd, Matthew S.; Papineau, Dominic; Pirajno, Franco
- Nature Communications, Vol. 10, Issue 1
Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates
journal, November 2018
- Arachchige, Pavithra S. Pitumpe; Hettiarachchi, Ganga M.; Rice, Charles W.
- Scientific Reports, Vol. 8, Issue 1