Spatial Arrangement of Organic Compounds on a Model Mineral Surface: Implications for Soil Organic Matter Stabilization

2013 ◽  
Vol 48 (1) ◽  
pp. 79-84 ◽  
Author(s):  
Loukas Petridis ◽  
Haile Ambaye ◽  
Sindhu Jagadamma ◽  
S. Michael Kilbey ◽  
Bradley S. Lokitz ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Organic Compounds ◽  
Spatial Arrangement ◽  
Mineral Surface ◽  
Organic Matter Stabilization

scholarly journals Integrating plant litter quality, soil organic matter stabilization, and the carbon saturation concept

2015 ◽  
Vol 21 (9) ◽  
pp. 3200-3209 ◽  
Author(s):  
Michael J. Castellano ◽  
Kevin E. Mueller ◽  
Daniel C. Olk ◽  
John E. Sawyer ◽  
Johan Six
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Litter Quality ◽  
Plant Litter ◽  
Carbon Saturation ◽  
Organic Matter Stabilization

A molecular dynamic study of Soil Organic Matter stabilization mechanisms

2021 ◽  
Author(s):  
Edgar Galicia-Andrés ◽  
Yerko Escalona ◽  
Peter Grančič ◽  
Chris Oostenbrink ◽  
Daniel Tunega ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Humic Substances ◽  
Clay Mineralogy ◽  
Metal Cations ◽  
Dense Matter ◽  
Chemical Degradation ◽  
Molecular Graphics ◽  
Organic Matter Stabilization ◽  
Reactive Surfaces

<p>It is well known that some fractions of soil organic matter (SOM) can resist to physical and (bio)chemical degradation which can be attributed to factors ranging from molecular properties to the preference for digesting other molecular species by microorganisms. Some mechanisms, by which organic matter is protected, are often referred to as: physical stabilization through microaggregation, chemical stabilization by formation of SOM-mineral aggregates, and biochemical stabilization through the formation of recalcitrant SOM.</p><p>Protection mechanisms are responsible for the accumulation process of organic carbon, reducing the exposure of organic matter and making it less vulnerable to microbial, enzymatic or chemical attacks. In these mechanisms, water molecular bridges and metal cation bridges play a key role. Cation bridges serve as aggregation sites on humic substances, forming dense matter, in comparison to systems where bridges are missing. This effect is enhanced in systems with cations at higher oxidation states.</p><p>By using the modeler tool developed in our group (Vienna Soil–Organic–Matter Modeler, VSOMM2) (Escalona et al., 2021), we generated aggregate models of humic substances at atomistic scale reflecting the diversity in composition, size and conformations of the constituting molecules. Further, we built models of organo-clay aggregates using kaolinite and montmorillonite as typical soil minerals. This allowed a systematic study to understand the effect of the surrounding environment at microscopic scale, not fully accessible experimentally.</p><p>Molecular simulations of the adsorption process of SOM aggregates on the reactive surfaces of led to two observations: 1) the humic substances aggregates were able to interact with the reactive surfaces mainly via hydrogen bonds forming stable organic matter-clay complexes and 2) the aggregates subsequently lost rigidity and stability after metal cations removing, consequently leading to a gradual loss of humic substance molecules, evidencing the role of metal cations in the protection mechanism of soil organic matter aggregates and possibly explaining its recalcitrance (Galicia-Andrés et al., 2021).</p><p>References</p><ul><li>Escalona, Y., Petrov, D., & Oostenbrink, C. (2021). Vienna soil organic matter modeler 2 (VSOMM2). Journal of Molecular Graphics and Modelling, 103, 107817. https://doi.org/10.1016/j.jmgm.2020.107817</li> <li>Galicia-Andrés, E., Grančič, P., Gerzabek, M. H., Oostenbrink, C., & Tunega, D. (2021). Modeling of interactions in natural and synthetic organoclays. In I. C. Sainz Diaz (Ed.), Computational modeling in clay mineralogy.</li> </ul>

Soil organic matter in soils of the Russian Arctic: insights from 13C-NMR spectroscopy

2020 ◽  
Author(s):  
Ivan Alekseev ◽  
Evgeny Abakumov
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Organic Carbon ◽  
Humic Acids ◽  
13C Nmr ◽  
Cold Climate ◽  
Molecular Organization ◽  
Cold Temperatures ◽  
Organic Matter Stabilization ◽  
Global Carbon

<p>Polar soils play a key role in global carbon circulation and stabilization as they contain maximum stocks of soil organic matter (SOM) within the whole pedosphere. Cold climate and active layer dynamics result in the stabilization of essential amounts of organic matter in soils, biosediments, and grounds of the polar biome. Chemical composition of soil organic carbon (SOC) determines its decomposability and may affect soil organic matter stabilization (SOM) rate (Beyer, 1995). This is quite important for understanding variability in SOC pools and stabilization rate in context of changes in plant cover or climate (Rossi et al. 2016). <sup>13</sup>C nuclear magnetic resonance spectroscopy, which provides detailed information on diversity of structural composition of humic acids and SOM, may also be used to study the SOM dynamics under decomposition and humification proceses (Kogel-Knabner, 1997; Zech et al., 1997). This study aims to characterize molecular organization of the humic acids, isolated from various permafrost-affected soils of Yamal region and to assess the potential vulnerability of soils organic matter in context of possible mineralization processes. Organic carbon stocks for studied area were 7.85 ± 2.24 kg m-2 (for 0-10 cm layer), 14.97 ± 5.53 kg m-2 (for 0-30 cm), 23.99 ± 8.00 kg m-2 (for 0-100 cm). Results of solid-state 13C-NMR spectrometry showed low amounts of aromatic components in studied soils. All studied humic powders are characterized by predominance of aliphatic structures, and also carbohydrates, polysaccharides, ethers and amino acids. High content of aliphatic fragments in studied humic acids shows their similarity fulvic acids. Low level of aromaticity reflects the accumulation in soil of lowly decomposed organic matter due to cold temperatures. Our results provide further evidence of high vulnerability and sensitivity of permafrost-affected soils organic matter to Arctic warming. Consequently, these soils may play a crucial role in global carbon balance under effects of climate warming.</p>

Spatial organization of soil microaggregates

2020 ◽  
Author(s):  
Eva Lehndorff ◽  
Nele Meyer ◽  
Andrey Radionov ◽  
Lutz Plümmer ◽  
Peter Rottmann ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Spatial Organization ◽  
Inorganic Compounds ◽  
Spatial Relationship ◽  
Clay Content ◽  
Spatial Arrangement ◽  
C Sequestration ◽  
Spatial Correlations ◽  
Soil Minerals

<p>The physical arrangement of soil compounds in microaggregates is important in many ways, e.g. by controlling soil stability and C sequestration. However, little is known about the spatial arrangement of organic and inorganic compounds in soil microaggregates, due to the lack of in-situ analyses in undisturbed material. Here we hypothesize that microaggregates are spatially organized, resulting in deterministic, predictable spatial patterns of different organic matter and mineral phases and that this organization depends on the abundance of specific phases such as on clay mineral content. We separated the water stable, occluded large and small microaggregate fractions from Ap horizons of a sequence of sandy to loamy Luvisols (19 to 35% clay, Scheyern, Germany) and subjected in total 60 individual aggregates to elemental mapping by electron probe micro analysis (EPMA), which recorded C, N, P, Al, Fe, Ca, K, Cl, and Si contents at µm scale resolution. Spatial arrangements of soil organic matter and soil minerals were extracted using cluster analyses. We found a pronounced heterogeneity in aggregate structure and composition, which was not reproducible and largely independent from clay content in soil. However, neighborhood analyses revealed close spatial correlations between organic matter debris (C:N app. 100:10) and microbial organic matter (C:N app. 10:1) indicating a spatial relationship between source and consumer. There was no systematic relationship between soil minerals and organic matter, suggesting that well-established macroscale correlations between contents of pedogenic oxides and clay minerals with soil organic matter storage do not apply to soil microaggregates.</p>

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