Organic matter sequestered in potential energy fields predicted by 3-D clay microstructure model

Bennett, Richard H.; Hulbert, Matthew H.; Curry, Kenneth J.; Curry, Ann; Douglas, Jessica R.

doi:10.1016/j.margeo.2012.04.009

Cited by 17 publications

(10 citation statements)

References 36 publications

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“…Peptides identified in smaller than expected molecular weight ranges could be due to partial hydrolysis [50]. Covalent modifications [13,51,52], hydrophobic interactions [12,13] and sequestration in potential energy fields [53] have been proposed as mechanisms for enhanced protein preservation, which could influence the gel migration of proteins to be in larger than expected molecular weight sections. The denaturing conditions of the SDS-PAGE gels used in this study indicate that charge alteration could also play a role in protein mobility.…”

Section: Resultsmentioning

confidence: 99%

Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments

et al. 2014

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Abstract:Proteins are the largest defined molecular component of marine organic nitrogen, and hydrolysable amino acids, the building blocks of proteins, are important components of particulate nitrogen in marine sediments. In oceanic systems, the largest contributors are phytoplankton proteins, which have been tracked from newly produced bloom material through the water column to surface sediments in the Bering Sea, but it is not known if proteins buried deeper in sediment systems can be identified with confidence. Electrophoretic gel protein extraction methods followed by proteomic mass spectrometry and database searching were used as the methodology to identify buried phytoplankton proteins in sediments from the 8-10 cm section of a Bering Sea sediment core. More peptides and proteins were identified using an SDS-PAGE tube gel than a standard 1D flat gel or digesting the sediment directly with trypsin. The majority of proteins identified correlated to the marine diatom, Thalassiosira pseudonana, rather than bacterial protein sequences, indicating an algal source not only dominates the input, but also the preserved protein fraction. Abundant RuBisCO and fucoxanthin chlorophyll a/c binding proteins were identified, supporting algal sources of these proteins and reinforcing the proposed mechanisms that might protect proteins for long time periods. Some preserved peptides were identified in OPEN ACCESSChromatography 2014, 1 177 unexpected gel molecular weight ranges, indicating that some structural changes or charge alteration influenced the mobility of these products during electrophoresis isolation. Identifying buried photosystem proteins suggests that algal particulate matter is a significant fraction of the preserved organic carbon and nitrogen pools in marine sediments.

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Section: Resultsmentioning

confidence: 99%

Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments

et al. 2014

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“…In these calculations, we assume there is no change of total sample volume when organic matter is hydrated and that the salinity of the water of hydration is the same salinity as that of the free pore water. The organic matter will occupy pore space and is often observed, via Transmissions Electron Microscope (TEM) images, attached to clay particles (Avnimelech and Menzel, 1984;Avnimelech et al, 1982;Baerwald et al, 1991;Bennett et al, 1991Bennett et al, , 1996Bennett et al, , 2012Curry et al, 2009). Just as seawater may be considered to be composed of dry salt and fresh water, the hydrated OM may be considered to be composed of OMd and bound seawater of The total grams of the dry OMd in the subsample determined above (Example B, salt free) is 1.7568 g with density (γomd) of 1.45 gcc -1 .…”

Section: B Water and Salt Discussionmentioning

confidence: 99%

“…As observed in Figures 3 and 4(a), OMh can attach to each type of clay fabric signature and occupy pore space in the clay fabric structure. OMh bonds to clay fabric signatures in edgeto-face contact, on the flat faces, the edges and in the offset face-to-face contacts of clay particles with varying degrees of bonding strength (Bennett et al, 1999a and b;Curry et al, 2009;Bennett et al, 2012). The charged or polar organic matter is bound to the charged clay mineral particles by physico-chemical interaction in seawater.…”

Section: Organic Matter Phasementioning

confidence: 99%

Impact of organic matter on the physical and dynamic properties of marine mud

Bennett¹,

Hulbert²,

Meredith³

2017

The Journal of the Acoustical Society of America

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The mass physical and dynamic properties of marine mud deposits are a function of the interaction among a maximum of four sediment Phases as follows: (1) clay mineral solids that often include silt and sand size particles of different mineralogy, (2) semisolid hydrated organic matter, (3) free pore water, and (4) free gas when present. Historically, the total water was removed by oven drying which includes the seawater of hydration of the organic matter (OM); thus, the total water content was considered free pore water in several research disciplines. The semisolid hydrated OM resists transport through the mud pore space and the water that is bound to the OM is not free pore water. Calculations of marine mud mass-physical properties without consideration and correction for the presence of hydrated organic matter can introduce significant error in the amount of free water content of the pore space in the mud and the quantitative differences in both porosity and void ratio. Simulations reveal absolute relative differences due to the presence of hydrated OM that can reach meaningful values even when the %TOC values are below ~3%. Relevance is determined by comparing the differences due to the hydrated OM Phase with the differences in the fluid saturation Phase at 100% and at 90%.Understanding the presence and characteristics of hydrated OM is expected to engage important future research in several sciences and in geotechnical engineering of terrestrial and marine mud deposits.

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“…Gold coating is 20 nm. Pore size was measured on SEM images using the Imageproplus software (Bennett et al, 2012;Dong and Harris, 2013). Maximum length was measured for isolated pores.…”

Section: Scanning Electron Microscopy and Pore Analysismentioning

confidence: 99%

Characteristics of silty laminae in Zhangjiatan Shale of southeastern Ordos Basin, China: Implications for shale gas formation

et al. 2015

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Shale oil and gas have been discovered in the lacustrine organicrich Zhangjiatan Shale of the Upper Triassic Yanchang Formation, Ordos Basin, China. Core observations indicate abundant silty laminae in the producing shales. This study documents the stratigraphic distribution of silty laminae and their relationship with interlaminated clay laminae. The type, structure, and characteristics of pores and mineral composition of silty laminae were observed and analyzed through thin section and scanning electron microscopy, X-ray diffraction, low-pressure CO 2 and N 2 adsorption, mercury porosimetry, and helium pycnometry. Results from silty laminae are compared with those of clayey laminae. The frequency and thickness of silty laminae vary over a wide range. The thickness ranges from 0.2 to 4 mm and is 1.5 mm on average; the frequency ranges from 4 to 32 laminae/m and is 23 laminae/m on average. The thickness percentage of silty laminae in the measured segments ranges from 6% to 17%. Silty laminae consist of quartz, feldspar, mixed-layer montmorillonite, and chlorite. In comparison to clayey laminae, non-clay detrital grains are larger, quartz and feldspar are more common, and clay minerals are less abundant. Pores in silty laminae are primary interparticle, dissolutional, intercrystalline, and microfracture types. Mesopores (2-50 nm in diameter) and macropores (50 nm-1 μm) are common, whereas, micropores ð<2 nmÞ are rare; the distribution of pore diameters is multimodal. However, microscopic pores with a diameter commonly smaller than 100 nm are common in

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Organic matter sequestered in potential energy fields predicted by 3-D clay microstructure model

Cited by 17 publications

References 36 publications

Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments

Electrophoretic Extraction and Proteomic Characterization of Proteins Buried in Marine Sediments

Impact of organic matter on the physical and dynamic properties of marine mud

Characteristics of silty laminae in Zhangjiatan Shale of southeastern Ordos Basin, China: Implications for shale gas formation

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