skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates

Abstract

Direct evidence-based approaches are vital to evaluating newly proposed theories on the persistence of soil organic carbon and establishing the contributions of abiotic and biotic controls. Our primary goal was to directly identify the mechanisms of organic carbon stabilization in native-state, free soil microaggregates without disrupting the aggregate microstructure using scanning transmission x-ray microscopy coupled with near edge x-ray absorption fine structure spectroscopy (STXM-NEXAFS). The influence of soil management practices on microaggregate associated-carbon was also assessed. Free, stable soil microaggregates were collected from a tropical agro-ecosystem in Cruz Alta, Brazil. The long-term experimental plots (>25 years) comparing two tillage systems: no-till and till with a complex crop rotation. Based on simultaneously collected multi-elemental associations and speciation, STXM-NEXAFS successfully provided submicron level information on organo-mineral associations. Simple organic carbon sources were found preserved within microaggregates; some still possessing original morphology, suggesting that their stabilization was not entirely governed by the substrate chemistry. Bulk analysis showed higher and younger organic carbon in microaggregates from no-till systems than tilled systems. These results provide direct submicron level evidence that the surrounding environment is involved in stabilizing organic carbon, thus favoring newly proposed concepts on the persistence of soil organic carbon.

Authors:
 [1]; ORCiD logo [1];  [1]; ORCiD logo [2];  [3];  [2];  [2]; ORCiD logo [4];  [1];  [5];  [6]
  1. Kansas State Univ., Manhattan, KS (United States). Dept. of Agronomy
  2. Canadian Light Sources, Inc., Saskatoon, SK (Canada)
  3. Kansas Dept. of Health and Environment, Topeka, KS (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)
  5. Federal Univ. of Santa Maria, Santa Maria, Rio Grande do Sul (Brazil)
  6. Univ. of Cruz Alta, Rio Grande do Sul (Brazil). CCGL Tec
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1542344
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
58 GEOSCIENCES; 54 ENVIRONMENTAL SCIENCES

Citation Formats

Arachchige, Pavithra S. Pitumpe, Hettiarachchi, Ganga M., Rice, Charles W., Dynes, James J., Maurmann, Leila, Wang, Jian, Karunakaran, Chithra, Kilcoyne, A. L. David, Attanayake, Chammi P., Amado, Telmo J. C., and Fiorin, Jackson E. Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates. United States: N. p., 2018. Web. doi:10.1038/s41598-018-34981-9.
Arachchige, Pavithra S. Pitumpe, Hettiarachchi, Ganga M., Rice, Charles W., Dynes, James J., Maurmann, Leila, Wang, Jian, Karunakaran, Chithra, Kilcoyne, A. L. David, Attanayake, Chammi P., Amado, Telmo J. C., & Fiorin, Jackson E. Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates. United States. doi:10.1038/s41598-018-34981-9.
Arachchige, Pavithra S. Pitumpe, Hettiarachchi, Ganga M., Rice, Charles W., Dynes, James J., Maurmann, Leila, Wang, Jian, Karunakaran, Chithra, Kilcoyne, A. L. David, Attanayake, Chammi P., Amado, Telmo J. C., and Fiorin, Jackson E. Wed . "Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates". United States. doi:10.1038/s41598-018-34981-9. https://www.osti.gov/servlets/purl/1542344.
@article{osti_1542344,
title = {Sub-micron level investigation reveals the inaccessibility of stabilized carbon in soil microaggregates},
author = {Arachchige, Pavithra S. Pitumpe and Hettiarachchi, Ganga M. and Rice, Charles W. and Dynes, James J. and Maurmann, Leila and Wang, Jian and Karunakaran, Chithra and Kilcoyne, A. L. David and Attanayake, Chammi P. and Amado, Telmo J. C. and Fiorin, Jackson E.},
abstractNote = {Direct evidence-based approaches are vital to evaluating newly proposed theories on the persistence of soil organic carbon and establishing the contributions of abiotic and biotic controls. Our primary goal was to directly identify the mechanisms of organic carbon stabilization in native-state, free soil microaggregates without disrupting the aggregate microstructure using scanning transmission x-ray microscopy coupled with near edge x-ray absorption fine structure spectroscopy (STXM-NEXAFS). The influence of soil management practices on microaggregate associated-carbon was also assessed. Free, stable soil microaggregates were collected from a tropical agro-ecosystem in Cruz Alta, Brazil. The long-term experimental plots (>25 years) comparing two tillage systems: no-till and till with a complex crop rotation. Based on simultaneously collected multi-elemental associations and speciation, STXM-NEXAFS successfully provided submicron level information on organo-mineral associations. Simple organic carbon sources were found preserved within microaggregates; some still possessing original morphology, suggesting that their stabilization was not entirely governed by the substrate chemistry. Bulk analysis showed higher and younger organic carbon in microaggregates from no-till systems than tilled systems. These results provide direct submicron level evidence that the surrounding environment is involved in stabilizing organic carbon, thus favoring newly proposed concepts on the persistence of soil organic carbon.},
doi = {10.1038/s41598-018-34981-9},
journal = {Scientific Reports},
number = 1,
volume = 8,
place = {United States},
year = {2018},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

Fractionation of Organic Matter Due to Reaction with Ferrihydrite: Coprecipitation versus Adsorption
journal, January 2011

  • Eusterhues, Karin; Rennert, Thilo; Knicker, Heike
  • Environmental Science & Technology, Vol. 45, Issue 2
  • DOI: 10.1021/es1023898

Soil carbon sequestration to mitigate climate change
journal, November 2004


Mineralogical impact on organic nitrogen across a long-term soil chronosequence (0.3–4100kyr)
journal, April 2010

  • Mikutta, Robert; Kaiser, Klaus; Dörr, Nicole
  • Geochimica et Cosmochimica Acta, Vol. 74, Issue 7
  • DOI: 10.1016/j.gca.2010.01.006

ATHENA , ARTEMIS , HEPHAESTUS : data analysis for X-ray absorption spectroscopy using IFEFFIT
journal, June 2005


Nanoscale Biogeocomplexity of the Organomineral Assemblage in Soil
journal, January 2006

  • Kinyangi, James; Solomon, Dawit; Liang, Biqing
  • Soil Science Society of America Journal, Vol. 70, Issue 5
  • DOI: 10.2136/sssaj2005.0351

Nitrogen K -edge XANES – an overview of reference compounds used to identify `unknown' organic nitrogen in environmental samples
journal, October 2007

  • Leinweber, Peter; Kruse, Jens; Walley, Fran L.
  • Journal of Synchrotron Radiation, Vol. 14, Issue 6
  • DOI: 10.1107/S0909049507042513

Green Rust Formation during Fe(II) Oxidation by the Nitrate-Reducing Acidovorax sp. Strain BoFeN1
journal, January 2012

  • Pantke, Claudia; Obst, Martin; Benzerara, Karim
  • Environmental Science & Technology, Vol. 46, Issue 3
  • DOI: 10.1021/es2016457

Mechanisms of Carbon Sequestration in Soil Aggregates
journal, November 2004


Interferometer-controlled scanning transmission X-ray microscopes at the Advanced Light Source
journal, February 2003

  • Kilcoyne, A. L. D.; Tyliszczak, T.; Steele, W. F.
  • Journal of Synchrotron Radiation, Vol. 10, Issue 2
  • DOI: 10.1107/S0909049502017739

Sorption of naphthalene and phenanthrene by soil humic acids
journal, February 2001


Innershell Absorption Spectroscopy of Amino Acids
journal, April 2002

  • Kaznacheyev, K.; Osanna, A.; Jacobsen, C.
  • The Journal of Physical Chemistry A, Vol. 106, Issue 13
  • DOI: 10.1021/jp013385w

Mineral protection of soil carbon counteracted by root exudates
journal, March 2015

  • Keiluweit, Marco; Bougoure, Jeremy J.; Nico, Peter S.
  • Nature Climate Change, Vol. 5, Issue 6
  • DOI: 10.1038/nclimate2580

Protection of organic carbon in soil microaggregates via restructuring of aggregate porosity and filling of pores with accumulating organic matter
journal, October 2008

  • McCarthy, John F.; Ilavsky, Jan; Jastrow, Julie D.
  • Geochimica et Cosmochimica Acta, Vol. 72, Issue 19
  • DOI: 10.1016/j.gca.2008.06.015

Protection of soil organic C and N in temperate and tropical soils: effect of native and agroecosystems
journal, November 2008

  • Fabrizzi, Karina P.; Rice, Charles W.; Amado, Telmo J. C.
  • Biogeochemistry, Vol. 92, Issue 1-2
  • DOI: 10.1007/s10533-008-9261-0

Soil organic matter, biota and aggregation in temperate and tropical soils - Effects of no-tillage
journal, November 2002

  • Six, Johan; Feller, Christian; Denef, Karolien
  • Agronomie, Vol. 22, Issue 7-8
  • DOI: 10.1051/agro:2002043

What is recalcitrant soil organic matter?
journal, January 2010

  • Kleber, Markus
  • Environmental Chemistry, Vol. 7, Issue 4
  • DOI: 10.1071/EN10006

Humic Substances in Soils:  Are They Really Chemically Distinct?
journal, August 2006

  • Kelleher, Brian. P.; Simpson, Andre. J.
  • Environmental Science & Technology, Vol. 40, Issue 15
  • DOI: 10.1021/es0608085

Chemical characteristics of fulvic acids from Arctic surface waters: Microbial contributions and photochemical transformations: CHARACTERISTICS OF ARCTIC FULVIC ACIDS
journal, December 2007

  • Cory, Rose M.; McKnight, Diane M.; Chin, Yu-Ping
  • Journal of Geophysical Research: Biogeosciences, Vol. 112, Issue G4
  • DOI: 10.1029/2006JG000343

Quantitative mapping of chlorhexidine in natural river biofilms
journal, October 2006


Speciation and Quantitative Mapping of Metal Species in Microbial Biofilms Using Scanning Transmission X-ray Microscopy
journal, March 2006

  • Dynes, James J.; Tyliszczak, Tolek; Araki, Tohru
  • Environmental Science & Technology, Vol. 40, Issue 5
  • DOI: 10.1021/es0513638

Relationship of soil organic matter dynamics to physical protection and tillage
journal, February 2000


Soft X-ray Spectromicroscopy Study of Mineral-Organic Matter Associations in Pasture Soil Clay Fractions
journal, May 2014

  • Chen, Chunmei; Dynes, James J.; Wang, Jian
  • Environmental Science & Technology, Vol. 48, Issue 12
  • DOI: 10.1021/es405485a

Stability of coprecipitated natural humic acid and ferrous iron under oxidative conditions
journal, April 2015

  • Colombo, Claudio; Palumbo, Giuseppe; Sellitto, Vincenzo Michele
  • Journal of Geochemical Exploration, Vol. 151
  • DOI: 10.1016/j.gexplo.2015.01.003

Validating the Scalability of Soft X-ray Spectromicroscopy for Quantitative Soil Ecology and Biogeochemistry Research
journal, January 2015

  • Dynes, James J.; Regier, Tom Z.; Snape, Ian
  • Environmental Science & Technology, Vol. 49, Issue 2
  • DOI: 10.1021/es505271p

Biodegradation of forest floor organic matter bound to minerals via different binding mechanisms
journal, May 2007

  • Mikutta, Robert; Mikutta, Christian; Kalbitz, Karsten
  • Geochimica et Cosmochimica Acta, Vol. 71, Issue 10
  • DOI: 10.1016/j.gca.2007.03.002

Developing a molecular picture of soil organic matter–mineral interactions by quantifying organo–mineral binding
journal, August 2017


Carbon stock and its compartments in a subtropical oxisol under long-term tillage and crop rotation systems
journal, June 2011

  • Campos, Ben-Hur Costa de; Amado, Telmo Jorge Carneiro; Bayer, Cimélio
  • Revista Brasileira de Ciência do Solo, Vol. 35, Issue 3
  • DOI: 10.1590/S0100-06832011000300016

Effect of organic matter applications on 13 C-NMR spectra of humic acids of soil
journal, June 2008


Nanoscale evidence of contrasted processes for root-derived organic matter stabilization by mineral interactions depending on soil depth
journal, June 2015


Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls
journal, November 2016

  • Kallenbach, Cynthia M.; Frey, Serita D.; Grandy, A. Stuart
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13630

Precipitation of amorphous CaCO3 (aragonite-like) by cyanobacteria: A STXM study of the influence of EPS on the nucleation process
journal, July 2009


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
  • DOI: 10.1038/nature10386

Sorptive stabilization of organic matter by microporous goethite: sorption into small pores vs. surface complexation
journal, February 2007


Mineral Availability as a Key Regulator of Soil Carbon Storage
journal, April 2017

  • Yu, Guanghui; Xiao, Jian; Hu, Shuijin
  • Environmental Science & Technology, Vol. 51, Issue 9
  • DOI: 10.1021/acs.est.7b00305

Characterization and structural modelling of humic substances in field soil displaying significant differences from previously proposed structures
journal, August 2008


Nitrogen-rich microbial products provide new organo-mineral associations for the stabilization of soil organic matter
journal, December 2017

  • Kopittke, Peter M.; Hernandez-Soriano, Maria C.; Dalal, Ram C.
  • Global Change Biology, Vol. 24, Issue 4
  • DOI: 10.1111/gcb.14009

Crop rotational diversity enhances belowground communities and functions in an agroecosystem
journal, May 2015

  • Tiemann, L. K.; Grandy, A. S.; Atkinson, E. E.
  • Ecology Letters, Vol. 18, Issue 8
  • DOI: 10.1111/ele.12453

Soft X-ray spectroscopy from image sequences with sub-100 nm spatial resolution
journal, February 2000


Cluster analysis of soft X-ray spectromicroscopy data
journal, July 2004


Soil macroaggregate turnover and microaggregate formation: a mechanism for C sequestration under no-tillage agriculture
journal, December 2000


Biodegradation of ferrihydrite-associated organic matter
journal, January 2014


Spatial complexity of soil organic matter forms at nanometre scales
journal, March 2008

  • Lehmann, Johannes; Solomon, Dawit; Kinyangi, James
  • Nature Geoscience, Vol. 1, Issue 4
  • DOI: 10.1038/ngeo155

Review on iron availability in soil: interaction of Fe minerals, plants, and microbes
journal, November 2013

  • Colombo, Claudio; Palumbo, Giuseppe; He, Ji-Zheng
  • Journal of Soils and Sediments, Vol. 14, Issue 3
  • DOI: 10.1007/s11368-013-0814-z

Alteration of Biochar Carbon Chemistry during Soil Incubations: SR-FTIR and NEXAFS Investigation
journal, January 2014

  • Mukome, Fungai N. D.; Kilcoyne, Arthur L. D.; Parikh, Sanjai J.
  • Soil Science Society of America Journal, Vol. 78, Issue 5
  • DOI: 10.2136/sssaj2014.05.0206

Organic carbon distribution, speciation, and elemental correlations within soil microaggregates: Applications of STXM and NEXAFS spectroscopy
journal, November 2007

  • Wan, Jiamin; Tyliszczak, Tolek; Tokunaga, Tetsu K.
  • Geochimica et Cosmochimica Acta, Vol. 71, Issue 22
  • DOI: 10.1016/j.gca.2007.07.030

Effects of mineral and monocarboxylic acids on the molecular association of dissolved humic substances
journal, December 1999


Soil aggregate formation and the accrual of particulate and mineral-associated organic matter
journal, April 1996


Chemical composition of the organic matter in forest soils: The humus layer
journal, January 1988

  • Kögel-Knabner, Ingrid; Zech, Wolfgang; Hatcher, Patrick G.
  • Zeitschrift für Pflanzenernährung und Bodenkunde, Vol. 151, Issue 5
  • DOI: 10.1002/jpln.19881510512

The distribution of anoxic volume in a fractal model of soil
journal, March 1999


Soft X-ray spectromicroscopy of nickel sorption in a natural river biofilm
journal, September 2009


Nanoscale detection of organic signatures in carbonate microbialites
journal, June 2006

  • Benzerara, K.; Menguy, N.; Lopez-Garcia, P.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 25
  • DOI: 10.1073/pnas.0603255103

Biogeochemistry of mineral–organic associations across a long-term mineralogical soil gradient (0.3–4100kyr), Hawaiian Islands
journal, April 2009

  • Mikutta, Robert; Schaumann, Gabriele E.; Gildemeister, Daniela
  • Geochimica et Cosmochimica Acta, Vol. 73, Issue 7
  • DOI: 10.1016/j.gca.2008.12.028

Organic matter and water-stable aggregates in soils
journal, June 1982


Impact of Tillage and Crop Rotation on Aggregate-Associated Carbon in Two Oxisols
journal, January 2005

  • Zotarelli, L.; Alves, B. J. R.; Urquiaga, S.
  • Soil Science Society of America Journal, Vol. 69, Issue 2
  • DOI: 10.2136/sssaj2005.0482

Soft X-ray spectromicroscopy beamline at the CLS: Commissioning results
journal, November 2007

  • Kaznatcheev, K. V.; Karunakaran, Ch.; Lanke, U. D.
  • Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 582, Issue 1
  • DOI: 10.1016/j.nima.2007.08.083

Sorption of dissolved organic nitrogen by acid subsoil horizons and individual mineral phases
journal, September 2000


Aluminium X-ray absorption Near Edge Structure in model compounds and Earth's surface minerals
journal, January 1998

  • Ildefonse, P.; Cabaret, D.; Sainctavit, P.
  • Physics and Chemistry of Minerals, Vol. 25, Issue 2
  • DOI: 10.1007/s002690050093

Stabilization of Natural Organic Matter by Short-Range-Order Iron Hydroxides
journal, November 2016

  • Chen, Kai-Yue; Chen, Tsan-Yao; Chan, Ya-Ting
  • Environmental Science & Technology, Vol. 50, Issue 23
  • DOI: 10.1021/acs.est.6b02793

How relevant is recalcitrance for the stabilization of organic matter in soils?
journal, February 2008

  • Marschner, Bernd; Brodowski, Sonja; Dreves, Alexander
  • Journal of Plant Nutrition and Soil Science, Vol. 171, Issue 1
  • DOI: 10.1002/jpln.200700049

Microaggregates in soils
journal, August 2017

  • Totsche, Kai Uwe; Amelung, Wulf; Gerzabek, Martin H.
  • Journal of Plant Nutrition and Soil Science, Vol. 181, Issue 1
  • DOI: 10.1002/jpln.201600451

A history of research on the link between (micro)aggregates, soil biota, and soil organic matter dynamics
journal, September 2004


How does organic matter constrain the nature, size and availability of Fe nanoparticles for biological reduction?
journal, July 2011

  • Pédrot, Mathieu; Boudec, Ange Le; Davranche, Mélanie
  • Journal of Colloid and Interface Science, Vol. 359, Issue 1
  • DOI: 10.1016/j.jcis.2011.03.067

Identification of Distinct Functional Microstructural Domains Controlling C Storage in Soil
journal, October 2017

  • Steffens, Markus; Rogge, Derek M.; Mueller, Carsten W.
  • Environmental Science & Technology, Vol. 51, Issue 21
  • DOI: 10.1021/acs.est.7b03715

Soil Organic Matter Functional Group Composition in Relation to Organic Carbon, Nitrogen, and Phosphorus Fractions in Organically Managed Tomato Fields
journal, January 2015

  • Margenot, Andrew J.; Calderón, Francisco J.; Bowles, Timothy M.
  • Soil Science Society of America Journal, Vol. 79, Issue 3
  • DOI: 10.2136/sssaj2015.02.0070

Some concepts of soil organic carbon characteristics and mineral interaction from a review of literature
journal, March 2016


Transformation mechanism of amorphous calcium carbonate into calcite in the sea urchin larval spicule
journal, November 2008

  • Politi, Y.; Metzler, R. A.; Abrecht, M.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 45
  • DOI: 10.1073/pnas.0806604105

Overview of the Symposium Proceedings, “Meaningful Pools in Determining Soil Carbon and Nitrogen Dynamics”
journal, January 2006

  • Olk, Daniel C.; Gregorich, Edward G.
  • Soil Science Society of America Journal, Vol. 70, Issue 3
  • DOI: 10.2136/sssaj2005.0111

Stabilization of organic matter in temperate soils: mechanisms and their relevance under different soil conditions - a review
journal, August 2006


Aged black carbon identified in marine dissolved organic carbon: AGED BLACK CARBON IN MARINE DOC
journal, August 2010

  • Ziolkowski, L. A.; Druffel, E. R. M.
  • Geophysical Research Letters, Vol. 37, Issue 16
  • DOI: 10.1029/2010GL043963

Introduction of Soft X-Ray Spectromicroscopy as an Advanced Technique for Plant Biopolymers Research
journal, March 2015


Molecular C dynamics downstream: The biochemical decomposition sequence and its impact on soil organic matter structure and function
journal, October 2008


Scanning Transmission X-Ray, Laser Scanning, and Transmission Electron Microscopy Mapping of the Exopolymeric Matrix of Microbial Biofilms
journal, September 2003