Carbon isotope fractionation during the anaerobic degradation of acetate [Elektronische Ressource] / vorgelegt von Dennis Gövert

Goevert

Sujets

• Biologie

Informations

• Publié par: philipps-universitat_marburg
• Publié le: 01 janvier 2008
• Nombre de lectures: 13
• Langue: English

Extrait

Carbon isotope fractionation during the anaerobic
degradation of acetate











Dissertation


zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.)

dem Fachbereich Biologie der Philipps-Universität Marburg

vorgelegt von












Dennis Gövert
aus Essen








Marburg/Lahn 2008

Die Untersuchungen zur folgenden Arbeit wurden von Mai 2005 bis Februar 2008 am Max-
Planck-Institut für terrestrische Mikrobiologie in Marburg unter Anleitung von Prof. Dr. Ralf
Conrad durchgeführt.






























Vom Fachbereich Biologie der Philipps-Universität Marburg als Dissertation angenommen
am:

Erstgutachter: Prof. Dr. Ralf Conrad
Zweitgutachter: Prof. Dr. Wolfgang Buckel

Tag der Disputation:
2

Die in dieser Dissertation beschriebenen Ergebnisse sind in den folgenden Artikeln zur
Veröffentlichung eingereicht bzw. vorgesehen:


1. Goevert, D. and R. Conrad (2008) Carbon isotope fractionation during acetoclastic
methanogenesis by Methanosarcina barkeri and Methanosarcina acetivorans
(in preparation)

2. Goevert, D. and R. Conrad (2008) Carbon isotope fractionation by sulfate-reducing
bacteria using different pathways for the oxidation of acetate (submitted to
Environmental Science & Technology on 31st January 2008)

3. Goevert, D. and R. Conrad (2008) Stable carbon isotope fractionation by
acetotrophic sulfur reducers (in preparation)

4. Goevert, D. and R. Conrad (2008) Effects of the competition for acetate between
methanogens and sulfate reducers on carbon isotope fractionation (in preparation)

3

This work is dedicated to two beloved people, who passed away during my PhD,


my mother Birgitt Gövert

and

my former colleague John Morton who called himself just a ‘dirty microbiologist’.

4 Contents


Contents

ABBREVIATIONS ............................................................................................ 7
ZUSAMMENFASSUNG ................................................................................... 8
SUMMARY ....................................................................................................... 9
I. INTRODUCTION ......................................................................................... 10
I.1 Anaerobic degradation of organic matter ......................................................................10
I.2 Utilization of acetate among methanogens, sulfate reducers, and sulfur reducers........11
I.3 Principles of stable carbon isotope fractionation ...........................................................13
I.4 Objectives of this study.................................................................................................15
II. MATERIALS AND METHODS................................................................... 16
II.1 Sterilization practices...................................................................................................16
II.2 Chemicals and gases...................................................................................................16
II.3 Cultures .......................................................................................................................16
II.4 Growth conditions ........................................................................................................16
II.4.1 Growth of sulfate-reducing bacteria ......................................................................20
II.4.2 Growth of methanogenic archaea.........................................................................21
II.4.3 Growth of sulfur-reducing bacteria........................................................................21
II.5 Incubation of rice field soil............................................................................................22
II.6 Chemical analyses.......................................................................................................23
II.6.1 Quantitative chromatographic analyses................................................................23
II.6.1.1 Analysis of CH and CO ...............................................................................23 4 2
II.6.1.2 Analysis of acetate ........................................................................................23
II.6.1.3 Analysis of sulfate .........................................................................................23
II.6.2 Determination of stable carbon isotope ratios.......................................................24
II.6.2.1 CH and CO .................................................................................................24 4 2
II.6.2.2 Acetate..........................................................................................................25
II.6.2.3 Methyl group of acetate (off-line pyrolysis and GC-C–IRMS) ........................26
II.6.2.4 Biomass (EA-IRMS) ......................................................................................26
II.6.3 Determination of sulfide........................................................................................27
II.6.4 Determif pH and optical density ...............................................................27
II.6.5 Radiotracer experiments.......................................................................................27
II.6.6 Calculations..........................................................................................................28
II.6.6.1 Moles of gases ..............................................................................................28
II.6.6.2 Moles of inorganic carbon .............................................................................28
5 Contents


II.6.6.3 Isotope fractionation ......................................................................................28
II.6.6.4 Carbon isotope signature of total inorganic carbon........................................29
II.7 Molecular analyses ......................................................................................................30
II.7.1 DNA extraction .....................................................................................................30
II.7.2 DNA amplification by PCR....................................................................................30
II.7.3 T-RFLP analysis ...................................................................................................32
III. RESULTS .................................................................................................. 33
III.1 Carbon isotope fractionation during acetoclastic methanogenesis by Methanosarcina
barkeri and Methanosarcina acetivorans......................................................................33
III.2 Carbon isotope fractionation by sulfate-reducing bacteria using different pathways for
the oxidation of acetate ................................................................................................47
III.3 Stable carbon isotope fractionation by acetotrophic sulfur reducers ...........................58
III.4 Effects of the competition for acetate between methanogens and sulfate reducers on
carbon isotope fractionation .........................................................................................64
IV. GENERAL DISCUSSION ......................................................................... 78
IV.1 Acetoclastic methanogenesis .....................................................................................78
IV.2 Dissimilatory sulfate reduction....................................................................................80
IV.3 Acetotrophic reduction of sulfur ..................................................................................82
IV.4 Conclusions and outlook ............................................................................................84
VI. LITERATURE............................................................................................ 87
VII. APPENDIX ............................................................................................... 93
Index of figures ..................................................................................................................93
Index of tables ...................................................................................................................94
Curriculum Vitae ................................................................................................................95
Contribution to national and international conferences ......................................................96
Acknowledgments..............................................................................................................97
Erklärung ...........................................................................................................................98
6 Abbreviations