Carbon X-ray Absorption Near-edge Structure Research Articles

The use of soft X-ray spectromicroscopy to investigate the distribution and composition of organic matter in a diatom frustule and a biomimetic analog

Diatoms play a significant role in the global carbon cycle through their role in biogenic silica production and the transport of organic matter to the seafloor. Recent work has shown that silicified diatom frustules contain a significant amount of organic matter, and that the proportion of diatom-bound organic matter increases with depth in the water column and sediments. Here, we investigate the association between organic matter and the mineral phase. We used a combination of scanning transmission X-ray microscopy (STXM) and carbon X-ray absorption near-edge structure (XANES) spectroscopy to characterize the distribution and composition of organic matter in frustules of the diatom Cylindrotheca closterium and a biomimetic silica gel. To our knowledge, this study represents the first successful attempt to simultaneously image and obtain chemical information about the organic matter within a diatom frustule using X-ray spectromicroscopy near the carbon edge. Organic carbon, most likely protein, was distributed throughout the frustules and was not removed by harsh chemical treatment. The physical structure of the frustules appeared to be related to the chemical composition of this organic matter, with aromatic or unsaturated carbon being concentrated in the most intricately patterned regions of the frustule. A similar physical and chemical structure was observed in a biomimetic silica gel precipitated spontaneously with polylysine. These results are consistent with the theory that organic constituents of diatom frustules direct silica precipitation and become incorporated within the silica matrix as it forms. The relationship between organic matter composition and silica morphology, the failure of harsh chemical treatments to remove this organic matter, and the spontaneous nature of the co-precipitation of silica and organic matter indicate some chemical interaction between the siliceous and organic components of diatom frustules. Frustule-bound organic matter should therefore be protected from decomposition in the water column or diagenetic alteration in sediments unless the frustule dissolves.

Chemical composition of the graphitic black carbon fraction in riverine and marine sediments at sub-micron scales using carbon X-ray spectromicroscopy

The chemical composition of the graphitic black carbon (GBC) fraction of marine organic matter was explored in several marine and freshwater sedimentary environments along the west coast of North America and the Pacific Ocean. Analysis by carbon X-ray absorption near-edge structure spectroscopy and scanning transmission X-ray microscopy shows the GBC fraction of Stillaguamish River surface sediments to be dominated by more highly ordered and impure forms of graphite, together forming about 80% of the GBC, with a smaller percent of an aliphatic carbon component. Eel River Margin surface sediments had very little highly ordered graphite, and were instead dominated by amorphous carbon and to a lesser extent, impure graphite. However, the GBC of surface sediments from the Washington State Slope and the Mexico Margin was composed almost solely of amorphous carbon. Pre-anthropogenic, highly oxidized deep-sea sediments from the open Equatorial Pacific Ocean contained over half their GBC in different forms of graphite as well as highly aliphatic carbon, low aromatic/highly acidic aliphatic carbon, low aromatic/highly aliphatic carbon, and amorphous forms of carbon. Our results clearly show the impact of graphite and amorphous C phases in the BC fraction in modern riverine sediments and nearby marine shelf deposits. The pre-anthropogenic Equatorial Pacific GBC fraction is remarkable in the existence of highly ordered graphite.

Examining marine particulate organic matter at sub-micron scales using scanning transmission X-ray microscopy and carbon X-ray absorption near edge structure spectroscopy

Marine sinking particulate organic matter (POM) represents the link between surface primary production and burial of organic matter in marine sediments. As such, the nature of this material has been the subject of numerous studies attempting to characterize its composition. The results of these studies have shown that a significant proportion of POM is not recognizable as known compounds, and that the proportion of uncharacterized material increases with age/depth/diagenesis. However, few studies have examined the spatial heterogeneity of this material. This study uses a new tool, scanning transmission X-ray microscopy (STXM), together with carbon X-ray absorption near edge structure (C-XANES), to examine POM collected from sediment traps deployed at one location in the Arabian Sea as part of the JGOFS program. The results indicate that POM is composed primarily of four distinct phases: protein, an aliphatic rich phase, a carboxylic-acid-rich phase, and a phase with complex unsaturated and quinone character. This last phase may be a condensation product between carbohydrates and proteins, or from degraded plant pigments. Many particles consisted of a single chemical phase; however, in particles with mixed compositions, individual domains retained distinctive chemical signatures at the instrument's resolution limit (50 nm). All major chemical phases were observed in sediment trap particles from 531 to 3369 m depth, supporting the hypothesis that non-selective degradation dominates particle remineralization, and that overall particle compositions are determined by near surface processes. Only one particle, out of more than 60 examined, exhibited soot-like composition. The lack of a significant black carbon/soot component may be attributable to sampling during the winter monsoon period.

The Origin of Organic Matter in the Solar System: Evidence from the Interplanetary Dust Particles

Interplanetary dust particles (IDPs), ∼ 10μm particles from comets and asteroids, have been collected by NASA from the Earth's stratosphere. We compared carbon X-ray Absorption Near-Edge Structure (XANES) and Fourier Transform Infra-Red (FTIR) spectra of anhydrous and hydrated interplanetary dust particles and found that anhydrous and hydrated IDPs have similar types and abundances of organic carbon. This is different from results on meteorites, which show that hydrated carbonaceous meteorites contain abundant organic matter, while anhydrous carbonaceous meteorites contain less carbon mostly in elemental form. But all anhydrous carbonaceous meteorites are depleted in moderately volatile and volatile elements in a pattern that suggested they experienced temperatures in excess of 1200°C, a temperature sufficient to destroy any organic matter they originally contained, while many anhydrous IDPs show no evidence of severe heating. These IDP results indicate that the bulk of the pre-biotic organic matter in extraterrestrial materials formed before aqueous processing, possibly by irradiation of C-bearing ices or by a Fisher-Tropsch type process operating in the gas phase of the nebula or in the interstellar medium.

The origin of organic matter in the solar system: evidence from the interplanetary dust particles

The detailed examination of meteorites and interplanetary dust particles provides an opportunity to infer the origin of the organic matter found in primitive Solar System materials. If this organic matter were produced by aqueous alteration of elemental (graphitic or amorphous) carbon on an asteroid, then we would expect to see the organic matter occurring preferentially in interplanetary materials that exhibit evidence of aqueous activity, such as the presence of hydrated silicates. On the other hand, if the organic matter were produced either during the nebula phase of Solar System evolution or in the interstellar medium, we might expect this organic matter to be incorporated into the dust as it formed. In that case pre-biotic organic matter would be present in both the anhydrous and the hydrated interplanetary materials. We have performed carbon X-ray absorption near-edge structure spectroscopy and infrared spectroscopy on primitive anhydrous and hydrated interplanetary dust particles (IDPs) collected by NASA from the Earth's stratosphere. We find that organic matter is present in similar types and abundances in both the anhydrous and the hydrated IDPs, and, in the anhydrous IDPs some of this organic matter is the “glue” that holds grains together. These measurements provide the first direct, experimental evidence from the comparison of extraterrestrial samples that the bulk of the pre-biotic organic matter occurs in similar types and abundances in both hydrated and anhydrous samples. This indicates that the bulk of the pre-biotic organic matter in the Solar System did not form by aqueous processing, but, instead, had already formed at the time that primitive, anhydrous dust was being assembled. Thus, the bulk of the pre-biotic organic matter in the Solar System was formed by non-aqueous processing, occurring in either the Solar nebula or in an interstellar environment. Aqueous processing on asteroids may have altered this pre-existing organic matter, but such processing did not affect in any substantial way the C=O content of the organic matter, the aliphatic C-H abundance, or the mean aliphatic chain length.