An integrated approach to the study of biosignatures in mineralizing biofilms and microbial mats [Elektronische Ressource] / vorgelegt von Christine Nora Heim

An integrated approach to the study of biosignatures
in mineralizing biofilms and microbial mats



Dissertation
Zur Erlangung des akademischen Grades
Doctor rerum naturalium
(Dr. rer. nat.)









Geowissenschaftliches Zentrum der Georg-August-Universität Göttingen
Abteilung Geobiologie









Vorgelegt von:

Diplom-Geologin
Christine Nora Heim
Göttingen 2010 D7

Gutachter:

1. Prof. Dr. Volker Thiel
2. Prof. Dr. Joachim Reitner

Tag der mündlichen Prüfung: 09.07.2010




























Acknowledgements


It’s nearly five years ago since I started this thesis, and with just a rough idea of what was expected
of me - but all in all it was a great experience and I am indebted to all my colleagues, friends and
family who helped me through this phase.
First of all, of course, great thanks to Volker Thiel and Joachim Reitner for giving me the
opportunity to join this project, and for the critical but very constructive discussions. I am grateful
to my working group, Andrea Hagemann, Cornelia Conrad, Juliane Germer, Tim Leefmann and
Martin Blumenberg for nice tea-time chats, assistance in the lab and in the Äspö tunnel. Thank you
Martin for the proofreading. Extra hours in the tunnel were brighter with Nadias Quéric’s
companionship.
I received analytical support from Klaus Simon, Jan Toporski, Erwin Schiffcyk, Bent Hansen,
Nicole Nolte, Brigitte Dietrich, Andreas Kronz, Andreas Reimer, Dorothea Hause-Reitner, Birgit
Röhring, Wolfgang Dröse, Volker Karius and Veit-Enno Hoffman. Thanks to Lothar Laake and his
colleagues from the workshop for the help with all kinds of constructions for the tunnel equipment
and further technical support from Alexander Satmatri and Michael Sosnitza.
The whole work in the Äspö tunnel wouldn’t have been possible without the support from SKB,
special thanks to Mats Ohlsson, Emmeli Johansson, Magnus Kronberg, Teresita Morales,
Carljohan Hardenby, Linda Alakangas, Irene Hultberg and Ann-Sofie Karlson. Thank you Peter
Sjövall and Jukka Lausmaa for the support during my three month stay in Borås, and thanks to
Jakob Malm for the introduction to Swedish traditions (midsommar). I had a great and productive
time with Barbara Zippel and Thomas Neu in Magdeburg.
Thomas Bode was always very helpful in all kinds of computer and software support and to remind
me to have a little break now and then. Thanks also to Sharmishtha Dattagupta and Daniel Jackson
for the recreational work distractions. Katja Milkereit, my best friend, was the special sponsor of
my thesis – thank you for all the supportive phone calls, and high energy and motivation packages.
For the everlasting support and encouragement I am especially indebted to Oliver Hach and
my family. This thesis is dedicated to my parents, Renate and Kurt Heim.


This thesis was accomplished as part of the DFG Research Group FOR 571, subproject 1
“Microbial biomineralization, biogeochemistry and biodiversity of chemolithotrophic
microorganisms in the tunnel of Äspö (Sweden).


IPreface


This doctoral thesis comprises the following papers, book entries and manuscripts:


Heim C, Lausmaa J, Sjövall P, Toporski J, Dieing T, Simon K, Hansen B, Kronz A, Reitner J,
Thiel V (2010) Ancient microbial activity recorded in fracture fillings from granitic rocks (Äspö
Hard Rock Laboratory, Sweden). Geobiology, in revision.

Heim C, Simon K, Quéric N-V, Reitner J, Thiel V (2010) Trace and rare earth element
accumulation and fractionation in microbial iron oxyhydroxides. Geochimica et Cosmochimica
Acta, in revision

Heim C (2011) Terrestrial Deep Biosphere. Encyclopedia of Geobiology, Springer, in press.

Heim C (2011) Microbial Biomineralization. Encyclopedia of Geobiology, Springer, in press.

Rodríguez-Martines M, Heim C, Quéric N-V, Reitner J (2011) Frutexites. Encyclopedia of
Geobiology, Springer, in press.

Toporski J, Dieing T, Heim C (2011) Raman microscopy (confocal). Encyclopedia of Geobiology,
Springer, in press.

Heim C, Sjövall P, Lausmaa J, Leefmann T, Thiel V (2009) Spectral characterization of eight
glycerolipids and their detection in natural samples using time-of-flight secondary ion mass
spectrometry. Rapid Communications in Mass Spectrometry, 23, 2741-2753.

Sjövall P, Thiel V, Siljeström S, Heim C, Hode T, Lausmaa J (2008) Organic geochemical
microanalysis by time-of-flight secondary ion mass spectrometry (ToF-SIMS). Geostandards and
Geoanalytical Research, 32, 267-277.

Thiel V, Heim C, Arp G, Hahmann U, Sjövall P, Lausmaa J (2007) Biomarkers at the microscopic
range: ToF-SIMS molecular imaging of Archaea-derived lipids in a microbial mat. Geobiology, 5,
413-421.


IITable of contents

Chapter 1
Introduction………………………………………………………………………………...…….1
1.1 Microbial life………………………………………………………………………………...1
1.2 Biosignatures…………………………………………………………………………...........2
1.3 Study Site – Äspö Hard Rock Laboratory Sweden....………………………………………10
1.4 Integrated analytical approach – high lateral resolution concept……………………….…..12
1.5 Introduction to the following chapters……………………………………………………...14
References ……………………………………………………………………………………...16
Chapter 2
Biomarkers at the microscopic range: ToF-SIMS molecular imaging
of Archaea-derived lipids in a microbial mat …………………………………………………. 25
2.1 Abstract ……………………………………………………………………………………..25
2.2 Introduction ………………………………………………………………………………...26
2.3 Materials and methods…………………………………………………….………………...27
2.4 Results and discussion………………………………………………………………………28
2.5 Conclusions…………………………………………………………………………………36
Acknowledgements……………………………………………………………………………..37
References………………………………………………………………………………………38
Chapter 3
Organic geochemical microanalysis by time-of-flight secondary ion mass
spectrometry (ToF-SIMS)……………………………………………………………………... 41
3.1 Abstract …………………………………………………………………………………….41
3.2 Introduction ………………………………………………………………………………...41
3.3 Capabilities and limitations of ToF-SIMS …………………………………………………42
3.4 Experimental……………………………………………………………………………..…46
3.5 Results and discussion…………………………………………………………………...…47
III3.6 Concluding remarks…………………………………………………………………….…..54
Acknowledgements……………………………………………………………………………..54
References………………………………………………………………………………………55
Chapter 4
Spectral characterization of eight glycerolipids and their detection in natural
sample using time-of-flight secondary ion mass spectrometry.……………………………….. 57
4.1 Abstract …………………………………………………………………………………….57
4.2 Introduction.………………………………………………………………………………...57
4.3 Experimental……………………………. …………………………………………………59
4.4 Results and discussion…………………………………………………………………....…61
4.5 Archaeol in a methanotrophic microbial mat…..……………………………………….…..72
4.6 Diglyceride and phosphatidylglycerol in a Gallionella-dominated microbial mat………....73
4.7 Conclusions…………………………………………………………………………………75
Acknowledgements……………………………………………………………………………..76
References………………………………………………………………………………………77
Chapter 5
Trace and rare earth element accumulation and fractionation in microbial
iron oxyhydroxides.……………………………….. …………………………………………..79
5.1 Abstract……………………………………………………………………………………..79
5.2 Introduction.………………………………………………………………………………...80
5.3 Materials and methods...……..……………………………………………………………..82
5.4 Results.………………………………………………………………………………....…...84
5.5 Discussion...…………………………………...……………………………………….…...91
5.6 Conclusions…………………………………………………………………………………95
Acknowledgements……………………………………………………………………………..95
References………………………………………………………………………………………96

IVChapter 6
Ancient microbial activity recorded in fracture fillings from granitic
rocks (Äspö Hard Rock Laboratory, Sweden)...……………………………...………………...99
6.1 Abstract……………………………………………………………………………………...99
6.2 Introduction.……………………………………………………………………………….100
6.3 Geological setting of the Äspö site...………………………………………………………101
6.4 Methods…………………..…..……………………………………………………………102
6.5 Results.…………………………………………………………………………………….103
6.6 Discussion……………………………………...……………………………………….….115
6.7 Conclusions………………………………………………………………………...……...118
Acknowledgements……………………………………………………………………………119
References……………………………………………………………………………………..119
Chapter 7
Summary and Conclusions…………………………………………………………………… 127
Appendix:
A Terrestrial Deep Biosphere………………………………………………………...….129
B Microbial Mineralization…………………………………………………………..….141
C Frutexites……………………………………………………………………………...151
D Raman Microscopy…………………………………………………………………....161

CV……………......…………………………………………………………………………….175
V Chapter 1 - Introduction
1
Introduction
1.1 Microbial life
Since the early Precambrian, microbial life sign