Characterization of mineral surfaces using FIB and TEM: A case study of naturally weathered alkali feldspars

Lee, Martin; Brown, David J.; Smith, C. L.; Hodson, Mark E.; Mackenzie, Mhairi; Hellmann, Roland

doi:10.2138/am.2007.2453

Cited by 75 publications

(51 citation statements)

References 43 publications

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“…The biotite flake was first sputter coated with gold (~100 nm). This was for both charge reduction during SEM analysis and as a protective layer to stop irradiation damage from the focused ion beam during initial deposition of the ion-beam deposited platinum protection layer (for a description of this damage process, see Lee (2007)). …”

Section: Fib Sample Preparationmentioning

confidence: 99%

Investigating the role of microbes in mineral weathering: Nanometre-scale characterisation of the cell–mineral interface using FIB and TEM

Ward

Kapitulčinová

Brown

et al. 2013

Micron

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Focused ion beam (FIB) sample preparation in combination with subsequent transmission electron microscopy (TEM) analysis are powerful tools for nanometre-scale examination of the cell-mineral interface in bio-geological samples. In this study, we used FIB-TEM to investigate the interaction between a cyanobacterium (Hassallia byssoidea) and a common sheet silicate mineral (biotite) following a laboratory-based bioweathering, incubation experiment. We discuss the FIB preparation of cross-sections of the cell mineral interface for TEM investigation. We also establish an electron fluence threshold in biotite for the transition from scanning (S)TEM electron beam induced contamination build up on the surface of biotite thin sections to mass loss, or hole-drilling within the sections. Working below this threshold fluence nanometre-scale structural and elemental information has been obtained from biotite directly underneath cyanobacterial cells incubated on the biotite for three months. No physical alteration of the biotite was detected by TEM imaging and diffraction with little or no elemental alteration detected by STEM energy dispersive X-ray (EDX) elemental line scanning nor by energy filtered TEM (EF-TEM) jump ratio elemental mapping. As such we present evidence that the cyanobacterial strain of Hassallia byssoidea did not cause any measurable alteration of biotite, within the resolution limits of the analysis techniques used, after three months of incubation on its surface.

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Section: Fib Sample Preparationmentioning

confidence: 99%

Investigating the role of microbes in mineral weathering: Nanometre-scale characterisation of the cell–mineral interface using FIB and TEM

Ward

Kapitulčinová

Brown

et al. 2013

Micron

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“…Sample damage is a concern for FIB prepared foils (Benzerara et al, 2005;Obst et al, 2005;Lee et al, 2007). For minerals such as calcite, the potential depth of side-wall sample damage was modeled by Obst et al to be approximately 20-30 nm.…”

Section: Diffraction Of Electrons and X-rays At Nano-and Micrometer Smentioning

confidence: 99%

Biogenic iron oxyhydroxide formation at mid-ocean ridge hydrothermal vents: Juan de Fuca Ridge

Toner

Santelli

Marcus

et al. 2009

Geochimica et Cosmochimica Acta

150

158

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Here we examine Fe speciation within Fe-encrusted biofilms formed during 2-month seafloor incubations of sulfide mineral assemblages at the Main Endeavor Segment of the Juan de Fuca Ridge. The biofilms were distributed heterogeneously across the surface of the incubated sulfide and composed primarily of particles with a twisted stalk morphology resembling those produced by some aerobic Fe-oxidizing microorganisms. Our objectives were to determine the form of biofilm-associated Fe, and identify the sulfide minerals associated with microbial growth. We used micro-focused synchrotron-radiation X-ray fluorescence mapping (lXRF), X-ray absorption spectroscopy (lTXAFS), and X-ray diffraction (lXRD) in conjunction with focused ion beam (FIB) sectioning, and high resolution transmission electron microscopy (HRTEM). The chemical and mineralogical composition of an Fe-encrusted biofilm was queried at different spatial scales, and the spatial relationship between primary sulfide and secondary oxyhydroxide minerals was resolved. The Fe-encrusted biofilms formed preferentially at pyrrhotite-rich (Fe 1Àx S, 0 6 x 6 0.2) regions of the incubated chimney sulfide. At the nanometer spatial scale, particles within the biofilm exhibiting lattice fringing and diffraction patterns consistent with 2-line ferrihydrite were identified infrequently. At the micron spatial scale, Fe lEXAFS spectroscopy and lXRD measurements indicate that the dominant form of biofilm Fe is a short-range ordered Fe oxyhydroxide characterized by pervasive edge-sharing Fe-O 6 octahedral linkages. Double corner-sharing Fe-O 6 linkages, which are common to Fe oxyhydroxide mineral structures of 2-line ferrihydrite, 6-line ferrihydrite, and goethite, were not detected in the biogenic iron oxyhydroxide (BIO). The suspended development of the BIO mineral structure is consistent with Fe(III) hydrolysis and polymerization in the presence of high concentrations of Fe-complexing ligands. We hypothesize that microbiologically produced Fe-complexing ligands may play critical roles in both the delivery of Fe(II) to oxidases, and the limited Fe(III) oxyhydroxide crystallinity observed within the biofilm. Our research provides insight into the structure and formation of naturally occurring, microbiologically produced Fe oxyhydroxide minerals in the deep-sea. We describe the initiation of microbial seafloor weathering, and the morphological and mineralogical signals that result from that process. Our observations provide a starting point from which progressively older and more extensively weathered seafloor sulfide minerals may be examined, with the ultimate goal of improved interpretation of ancient microbial processes and associated biological signatures.

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“…As the foils had to be tilted typically by a couple of degrees for effective imaging (i.e. so that the electron beam is nearly parallel to a prominent zone axis), the outermost 42.5 nm of the feldspar grain may be obscured by the material above and below, thus imposing ã 2.5 nm limit on the minimum thicknesses of amorphous layers that could be confidently identified (Lee et al, 2007).…”

Section: Sem Fib and Temmentioning

confidence: 99%

Weathering microenvironments on feldspar surfaces: implications for understanding fluid-mineral reactions in soils

Lee¹,

Brown²,

Hodson³

et al. 2008

Mineral. mag.

Self Cite

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The mechanisms by which coatings develop on weathered grain surfaces, and their potential impact on rates of fluid-mineral interaction, have been investigated by examining feldspars from a 1.1 ky old soil in the Glen Feshie chronosequence, Scottish highlands. Using the focused ion beam technique, electron-transparent foils for characterization by transmission electron microscopy were cut from selected parts of grain surfaces. Some parts were bare whereas others had accumulations, a few micrometres thick, of weathering products, often mixed with mineral and microbial debris. Feldspar exposed at bare grain surfaces is crystalline throughout and so there is no evidence for the presence of the amorphous 'leached layers' that typically form in acid-dissolution experiments and have been described from some natural weathering contexts. The weathering products comprise sub-mm thick crystallites of an Fe-K aluminosilicate, probably smectite, that have grown within an amorphous and probably organic-rich matrix. There is also evidence for crystallization of clays having been mediated by fungal hyphae. Coatings formed within Glen Feshie soils after~1.1 ky are insufficiently continuous or impermeable to slow rates of fluid-feldspar reactions, but provide valuable insights into the complex weathering microenvironments on debris and microbe-covered mineral surfaces.

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Characterization of mineral surfaces using FIB and TEM: A case study of naturally weathered alkali feldspars

Abstract: International audienc

Cited by 75 publications

References 43 publications

Investigating the role of microbes in mineral weathering: Nanometre-scale characterisation of the cell–mineral interface using FIB and TEM

Investigating the role of microbes in mineral weathering: Nanometre-scale characterisation of the cell–mineral interface using FIB and TEM

Biogenic iron oxyhydroxide formation at mid-ocean ridge hydrothermal vents: Juan de Fuca Ridge

Weathering microenvironments on feldspar surfaces: implications for understanding fluid-mineral reactions in soils

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