Bacteria-Mineral Colloid Interactions in Biofilms: An Ultrastructural and Microanalytical Approach

  • Heinrich LünsdorfEmail author
Part of the Springer Protocols Handbooks book series (SPH)


Simple reproducible experimental set-ups are described to study initial growth and interactions of bacteria with clay colloids and soil nanoparticles or with dissolved metal ions as primordial biofilms. These bacteria-nanoparticle constructs, exemplified by so-called clay hutches, are accessible to ultrastructural and microanalytical electron microscopical analysis. By this, the spatial arrangements and in part the physiological state of the involved autochthonous bacteria can be studied, leading to an estimate of the mineral-organic nutritional sphere the bacteria need for growth. It further leads to an entry to additional chemical, microbial and macromolecular traits of experimental follow-ups to analyse the mineral-organic chemistry, to isolate pollutant-adapted bacteria and to get information on the complex community structure of this kind of biofilms.


Electron energy loss spectroscopy (EELS) ‘In situ/in vitro’ biofilms 


  1. 1.
    Heim D (1990) Tone und Tonminerale – Grundlagen der Sedimentologie und Mineralogie. Ferdinand Enke, StuttgartGoogle Scholar
  2. 2.
    Hepper EN, Buschiazzo DE, Hevia GG, Urioste A, Antón L (2006) Clay mineralogy, cation exchange capacity and specific surface area of loess soils with different volcanic ash contents. Geoderma 135:216–223CrossRefGoogle Scholar
  3. 3.
    Schwertmann (1984) Tonminerale. In: Scheffer, Schachtschabel, Lehrbuch der Bodenkunde. Enke, Stuffgart, pp 23–28Google Scholar
  4. 4.
    Lagaly G (1993) Praktische Verwendung und Einsatzmöglichkeiten von Tonen. In: Jasmund K, Lagaly G (eds) Tonminerale und Tone. Steinkopff, Darmstadt, pp 358–427CrossRefGoogle Scholar
  5. 5.
    Nogales B, Moore ERB, Abraham WR, Timmis KN (1999) Identification of the metabolically- active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil. Environ Microbiol 1:199–212CrossRefPubMedGoogle Scholar
  6. 6.
    Nogales B, Moore ERB, Llobet-Brossa E, Rossello-Mora R, Amann R, Timmis KN (2001) Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 67:1874–1884CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Harkness MR, McDermott JB, Abramowicz DA, Salvo JJ, Flanagan WP, Stepens ML, Mondello FJ, May RJ, Lobos JH, Carroll KM, Brennan MJ, Bracco AA, Fish KM, Warner GL, Wilson PR, Dietrich DK, Lin DT, Morgan CB, Gately WL (1993) In situ stimulation of aerobic PCB biodegradation in Hudson river sediments. Science 259:503–507CrossRefPubMedGoogle Scholar
  8. 8.
    Lünsdorf H, Erb RW, Abraham WR, Timmis KN (2000) ‘Clay hutches’: a novel interaction between bacteria and clay minerals. Environ Microbiol 2:161–168CrossRefPubMedGoogle Scholar
  9. 9.
    Perfil’ev BV, Gabe DR (1969) Capillary methods of investigating micro-organisms. Oliver and Boyd, Edinburgh, Great BritainGoogle Scholar
  10. 10.
    Marcedo A, Kuhlicke U, Neu T, Timmis KN, Abraham WR (2005) Three stages of a biofilm community developing at the liquid-liquid interface between polychlorinated biphenyls and water. Appl Environ Microbiol 71:7301–7309CrossRefGoogle Scholar
  11. 11.
    Valentin K, John U, Medlin L (2005) Nucleic acid isolation from environmental aqueous samples. Methods Enzymol 395:15–37CrossRefPubMedGoogle Scholar
  12. 12.
    MacGregory BJ, Amann R (2006) Single-stranded conformational polymorphism for separation of mixed rRNAS (rRNA-SSCP), a new method for profiling microbial communities. Syst Appl Microbiol 29:661–670CrossRefGoogle Scholar
  13. 13.
    Smalla K, Oros-Sichler M, Milling A, Heuer H, Baumgarte S, Becker R, Neuber G, Kropf S, Ulrich A, Tebbe CC (2007) Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results? J Microbiol Methods 69:470–479CrossRefPubMedGoogle Scholar
  14. 14.
    Lünsdorf H, Strömpl C, Osborn AM, Bennasar A, Moore ERB, Abraham WR, Timmis KN (2001) Approach to analyze interactions of microorganisms, hydrophobic substrates, and soil colloids leading to formation of composite biofilms, and to study initial events in microbiogeological processes. Methods Enzymol 336:317–331CrossRefPubMedGoogle Scholar
  15. 15.
    Glauert AM (1975) Fixation, dehydration and embedding of biological specimens. Volume 3, part 1 in the Glauert series. Elsevier, AmsterdamGoogle Scholar
  16. 16.
    Glauert AM (1991) Epoxy resins: an update on their selection and use. Microsc Anal 25:15–20Google Scholar
  17. 17.
    Spurr AR (1969) A low viscosity epoxy resin embedding medium for electron microscopy. J Ultrastruct Res 26:31–43CrossRefPubMedGoogle Scholar
  18. 18.
    Reynolds ES (1963) The use of lead citrate at high pH as an electron-opaque stain in electron microscopy. J Cell Biol 17:208–212CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Lünsdorf H, Kristen I, Barth E (2006) Colloidal hydrous thorium dioxide colloids – a useful tool for staining negatively charged surface matrices of bacteria for use in energy-filtered transmission electron microscopy. BMC Microbiol 6:59CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Kapp N, Studer D, Gehr P, Geiser M (2010) Electron energy-loss spectroscopy as a tool for elemental analysis in biological specimens. Methods Mol Biol 369:431–447CrossRefGoogle Scholar
  21. 21.
    Egerton RF (1996) Electron energy-loss spectroscopy in the electron microscope. Plenum Press, New York/LondonCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Helmholtz Center for Infection Research, Central facility for microscopyBraunschweigGermany

Personalised recommendations