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

Lynn Abramson, Sue Wirick, Cindy Lee*, Chris Jacobsen, Jay A. Brandes

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

31 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)1369-1380
Number of pages12
JournalDeep-Sea Research Part II: Topical Studies in Oceanography
Issue number18
StatePublished - Aug 15 2009


  • Degradation
  • Diatom frustules
  • Minerals
  • Organic matter
  • Preservation

ASJC Scopus subject areas

  • Oceanography


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