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

Michael B. Ward; Dana Kapitulčinová; Andrew P. Brown; Peter J. Heard; David Cherns; Charles S. Cockell; Keith R. Hallam; K. Vala Ragnarsdóttir

doi:10.1016/j.micron.2012.12.006

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

Michael B. Ward, Dana Kapitulčinová, Andrew P. Brown, Peter J. Heard, David Cherns, Charles S. Cockell, Keith R. Hallam, K. Vala Ragnarsdóttir

Faculty of Earth Sciences

University of Iceland

Research output: Contribution to journal › Article › peer-review

Abstract

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 (at 200. keV) 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 3 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 or by energy filtered TEM (EF-TEM) jump ratio elemental mapping. As such we present evidence that the cyanobacterial strain of H. byssoidea did not cause any measurable alteration of biotite, within the resolution limits of the analysis techniques used, after 3 months of incubation on its surface.

Original language	English
Pages (from-to)	10-17
Number of pages	8
Journal	Micron
Volume	47
DOIs	https://doi.org/10.1016/j.micron.2012.12.006
Publication status	Published - Apr 2013

Bibliographical note

Funding Information: This study was supported by the Marie Curie Early Stage Training Programme (MEST-CT-2005-020828) MISSION of the European Commission. The FIB and TEM work at the LENNF (University of Leeds) was funded by the Engineering and Physical Sciences Research Council, UK ( EP/F056311/1 ). We acknowledge the LENNF team for the performed analyses and general advice on FIB and TEM methods. We are thankful to Tomáš Hauer, University of South Bohemia, for provision of the cyanobacterial strain. We thank Steeve Bonneville, Université Libre de Bruxelles, for advice on the STEM/EDX data normalisation procedure ( Fig. 5 ). Discussions with members of the Weathering Science Consortium – Universities of Bristol, Sheffield and Leeds; Natural Environment Research Council, UK (NE/C521001/1) and the MISSION team members were highly valuable for this study.

Other keywords

Biotite
Cell-mineral interface
Cyanobacteria
FIB
TEM
Weathering

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10.1016/j.micron.2012.12.006

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@article{c0df3d8bb8af4d9f9f2a7ee99cc8b40d,

title = "Investigating the role of microbes in mineral weathering: Nanometre-scale characterisation of the cell-mineral interface using FIB and TEM",

abstract = "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 (at 200. keV) 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 3 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 or by energy filtered TEM (EF-TEM) jump ratio elemental mapping. As such we present evidence that the cyanobacterial strain of H. byssoidea did not cause any measurable alteration of biotite, within the resolution limits of the analysis techniques used, after 3 months of incubation on its surface.",

keywords = "Biotite, Cell-mineral interface, Cyanobacteria, FIB, TEM, Weathering",

author = "Ward, \{Michael B.\} and Dana Kapitul{\v c}inov{\'a} and Brown, \{Andrew P.\} and Heard, \{Peter J.\} and David Cherns and Cockell, \{Charles S.\} and Hallam, \{Keith R.\} and Ragnarsd{\'o}ttir, \{K. Vala\}",

note = "Funding Information: This study was supported by the Marie Curie Early Stage Training Programme (MEST-CT-2005-020828) MISSION of the European Commission. The FIB and TEM work at the LENNF (University of Leeds) was funded by the Engineering and Physical Sciences Research Council, UK ( EP/F056311/1 ). We acknowledge the LENNF team for the performed analyses and general advice on FIB and TEM methods. We are thankful to Tom{\'a}{\v s} Hauer, University of South Bohemia, for provision of the cyanobacterial strain. We thank Steeve Bonneville, Universit{\'e} Libre de Bruxelles, for advice on the STEM/EDX data normalisation procedure ( Fig. 5 ). Discussions with members of the Weathering Science Consortium – Universities of Bristol, Sheffield and Leeds; Natural Environment Research Council, UK (NE/C521001/1) and the MISSION team members were highly valuable for this study.",

year = "2013",

month = apr,

doi = "10.1016/j.micron.2012.12.006",

language = "English",

volume = "47",

pages = "10--17",

journal = "Micron",

issn = "0968-4328",

publisher = "Elsevier Ltd.",

}

TY - JOUR

T1 - Investigating the role of microbes in mineral weathering

T2 - Nanometre-scale characterisation of the cell-mineral interface using FIB and TEM

AU - Ward, Michael B.

AU - Kapitulčinová, Dana

AU - Brown, Andrew P.

AU - Heard, Peter J.

AU - Cherns, David

AU - Cockell, Charles S.

AU - Hallam, Keith R.

AU - Ragnarsdóttir, K. Vala

N1 - Funding Information: This study was supported by the Marie Curie Early Stage Training Programme (MEST-CT-2005-020828) MISSION of the European Commission. The FIB and TEM work at the LENNF (University of Leeds) was funded by the Engineering and Physical Sciences Research Council, UK ( EP/F056311/1 ). We acknowledge the LENNF team for the performed analyses and general advice on FIB and TEM methods. We are thankful to Tomáš Hauer, University of South Bohemia, for provision of the cyanobacterial strain. We thank Steeve Bonneville, Université Libre de Bruxelles, for advice on the STEM/EDX data normalisation procedure ( Fig. 5 ). Discussions with members of the Weathering Science Consortium – Universities of Bristol, Sheffield and Leeds; Natural Environment Research Council, UK (NE/C521001/1) and the MISSION team members were highly valuable for this study.

PY - 2013/4

Y1 - 2013/4

N2 - 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 (at 200. keV) 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 3 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 or by energy filtered TEM (EF-TEM) jump ratio elemental mapping. As such we present evidence that the cyanobacterial strain of H. byssoidea did not cause any measurable alteration of biotite, within the resolution limits of the analysis techniques used, after 3 months of incubation on its surface.

AB - 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 (at 200. keV) 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 3 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 or by energy filtered TEM (EF-TEM) jump ratio elemental mapping. As such we present evidence that the cyanobacterial strain of H. byssoidea did not cause any measurable alteration of biotite, within the resolution limits of the analysis techniques used, after 3 months of incubation on its surface.

KW - Biotite

KW - Cell-mineral interface

KW - Cyanobacteria

KW - FIB

KW - TEM

KW - Weathering

UR - https://www.scopus.com/pages/publications/84875100875

U2 - 10.1016/j.micron.2012.12.006

DO - 10.1016/j.micron.2012.12.006

M3 - Article

SN - 0968-4328

VL - 47

SP - 10

EP - 17

JO - Micron

JF - Micron

ER -

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

Abstract

Bibliographical note

Other keywords

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