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Microbial community characterization and carbon turnover in methane-rich marine environments [Elektronische Ressource] : case studies in the Gulf of Mexico and the Black Sea / vorgelegt von Florence Schubotz

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Microbial community characterization and carbon turnover in methane-rich marine environments - case studies in the Gulf of Mexico and the Black SeaDissertationzur Erlangung des Doktorgradesder Naturwissenschaften- Dr. rer. nat. -Am Fachbereich Geowissenschaftender Universität Bremenvorgelegt vonFlorence SchubotzBremenOktober 2009 1. Gutachter: Prof. Dr. Kai-Uwe Hinrichs2. . Stuart G. WakehamDate of defense: October 26, 2009 Science is a way of studying the world around us, not a set of facts.(Tori Hoehler)TABLE OF CONTENTSAbstract Thesis abstract .......................................................................................... I Zusammenfassung .................................................................................... IIIList of Abbreviations ....................................................................................................... VList of Figures .................................................................................................................. IXList of Tables ..................................................................................................................... XIIChapter I Introduction and Methods ......................................................................... 1 I.1. General Introduction .................. 2 I.2. Objectives of this Thesis ................................................................... 13 I.3. Methods ................................................

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Microbial community characterization and carbon
turnover in methane-rich marine environments - case
studies in the Gulf of Mexico and the Black Sea
Dissertation
zur Erlangung des Doktorgrades
der Naturwissenschaften
- Dr. rer. nat. -
Am Fachbereich Geowissenschaften
der Universität Bremen
vorgelegt von
Florence Schubotz
Bremen
Oktober 2009
1. Gutachter: Prof. Dr. Kai-Uwe Hinrichs
2. . Stuart G. Wakeham
Date of defense: October 26, 2009
Science is a way of studying the world around us, not a set of facts.
(Tori Hoehler)TABLE OF CONTENTS
Abstract Thesis abstract .......................................................................................... I
Zusammenfassung .................................................................................... III
List of Abbreviations ....................................................................................................... V
List of Figures .................................................................................................................. IX
List of Tables ..................................................................................................................... XII
Chapter I Introduction and Methods ......................................................................... 1
I.1. General Introduction .................. 2
I.2. Objectives of this Thesis ................................................................... 13
I.3. Methods ............................................................................................. 15
I.4. Contribution to Publications.............................................................. 31
I.5. References ................................. 32
Chapter II Detection of microbial biomass by intact polar membrane lipid analysis
in the water column and surface sediments of the Black Sea ................. 51
II.1 Summary .......................................................................................... 52
II.2 Introduction ...................................................................................... 52
II.3. Results and Discussion .................................................................... 53
II.4. Experimental Procedures ................................................................. 66
II.5. Acknowledgements .................. 68
II.6. References ................................ 68
II.S1. Supporting Information .......... 72
II.S2. Supporting Information - References ............................................ 74
Chapter III Chemosynthetic life at the Chapopote asphalt volcano - insights
from stable carbon isotopes and intact polar membrane lipid analyses ... 77
III.1. Abstract .......................................................................................... 78
III.2. Introduction .................................................................................... 78
III.3. Material and Methods ..................................................................... 80
III.4. Results and Discussion .................................................................. 84
III.5. Summary and Conclusions ........................................................... 104
III.6. Acknowledgements ...................................................................... 105
III.7. References ............................... 105
Chapter IV Sulfate-reduction, methanotrophy, and methanogenesis at the
Chapopoteasphaltvolcanodecipher edbyheadgroup-specificstable
carbon isotopic analysis of intact polar membrane lipids ..................... 113
IV.1. Abstract ......................................................................................... 114
IV.2. Introduction .................................................................................. 114
IV.3. Material and Methods ................................................................... 115
IV.4. Results .......................................................................................... 124
IV.5. Discussion .................................................................................... 124
IV.6. Summary and Conclusions ...... 131
IV.7. Acknowledgements ................. 132
IV.8. References .................................................................................... 132Chapter V. Determining total petroleum hydrocarbon degradation and
weathering by comprehensive GC×GC at an asphalt seep
in the southern Gulf of Mexico ............................................................. 141
V.1. Abstract .......................................................................................... 142
V.2. Introduction .............................. 142
V.3. Experimental ............................. 143
V.4. Results and Discussion .................................................................. 146
V.5. Acknowledgements ....................................................................... 154
V.6. References ..................................................................................... 155
V.S1. Supplementary Material ......... 158
V.S2. References .............................. 162
Chapter VIb. Methaneandsulfidefluxesinperma nentanoxia:in-situ studies at the
Dvurechenskii mud volcano (Sorokin Trough, Black Sea) ................... 165
Chapter VIc. Bacterial symbionts of Bathymodiolus mussels and Escarpia
tubeworms from an asphaltic deep-sea environment in the
southern Gulf of Mexico ....................................................................... 169
Chapter VII. Concluding Remarks and Outlook ........................................................ 173
Summary and Conclusions .............. 174
Outlook ................................................................................................. 178
References ............................................................................................ 179
Acknowledgements ......................................................................................................... 183
Appendix ......................................................................................................................... 187
Published Manuscript I: Rock weathering creates oases of life in a
High Arctic Desert ................................................................................ 189
Published Manuscript II: Methane-producing microbial community
in a coal bed of the Illinois Basin .......................................................... 193
Curriculum Vitae ................................................................................. 196
Thesis Declaration .......................................................................................................... 199Thesis abstract
THESIS ABSTRACT
This thesis investigated patterns in the distribution of intact polar membrane lipids (IPLs) in
the marine environment. IPL analysis is a relatively new tool in microbial ecology to study (i)
live microbial biomass and (ii) the dominating microbial players. This technique was applied
for the first time to study the oxic and anoxic water column of the Black Sea and observed a
stratification of IPLs according to geochemical zonat ion. Export of IPLs to the sediment was
found to be selective and the distribution of IPLs in the upper 2 cm of the sediments reflects
de novo production of IPLs by indigenous microbes, putative ly identified as sulfate-reducing
bacteria and benthic archaea. The distribution of archaeal IPLs in the anoxic water body did
not indicate the abundant presence of methanotrophic archaea, which were presumed in earlier
studies due to high estimated methane oxidation rates. The presence of betaine lipids and
glycosidic sphingolipids in the anoxic water column could be linked to unknown anaerobic
bacteria and is a novel finding as these lipids are primarily known to be produced by eukaryotes.
Investigations of microbial communities associated to the Chapopote asphalt seep in the
southern Gulf of Mexico revealed the presence of a diverse array of IPLs from both Bacteria and
Archaea. IPL concentrations in the sediments were correlated with the abundant presence of oil
and methane, indicating that the petroleum hydrocarbons are a major stimulant for microbial
activity. Bacterial IPL concentrations decreased with decreasing sulfate concentrations over
depth, whereas archaeal IPLs increased simultaneously and comprised up to 80% of total IPLs
at ca. 15 cm sediment depth. Bacterial lipids mainly included phospholipids with the polar head
groups phosphatidylethanolamine (PE), phosphatidyl-(N)-methylethanolamine (PME), and
phosphatidylglycerol (PG). The assignment of these IPLs to sulfate-reducing bacteria (SRB)
was confirmed by the presence of SRB-characteristi c fatty acids. Polar head group-specific
isotope analysis of the SRB core lipids revealed that the majority of the SRB population is
autotrophic and involved in the anaerobic oxidation of methane. However, a large amount
of SRB are heterotrophic hydrocarbon-degrading bacteria. The oil-degrading bacteria mainly
contained PME as head group. Archaeal IPLs indicated the presence of ANME-1 archaea
comprised of diglycosidic glyceroldibiphytanylglyceroltetraethers (2Gly-GDGT) accompanied
by ANME-2 archaea suggested by phosphate-based hydroxyarchaeols. Polar head group-
specific stable carbon isotope analysis of the archaeal IPLs confirmed the association of those
lipids to methanotrophic archaea and could also show that phosphate-based archaeols and
GDGTs with mixed glycosidic and phosphate-based head groups were mainly derived from
methanogenic archaea. In subsurface sediments of the oil-influenced Chapopote asphalt seep
abundant archaeal IPLs were detected close to a sulfate-methane transition zone. Here, bacterial
lipids were only a minor part of the total IPLs and were dominated by diether lipids with PE
headgroups. Phosphate-based hydroxyarchaeols and diglycosidic GDGTs could be assigned
to both methanogenic and methanotrophic sources. Methane is thus a major intermediate in
microbial metabolism at the Chapopote asphalt volcano.
Investigations of biological and physical weathering of the deposited asphalts showed
IThesis abstract
that the asphalts are an important substrate for the microbial community. The removal of
n-alkanes, branched alkanes, isoprenoids and low molecular weight polyaromatic hydrocarbon
compounds could be primarily assigned to biodegradation. Biomarkers such as steranes and
hopanes were most recalcitrant and were still observed in highly weathered brittle asphalts.
Comparison of fresh and weathered asphalts allowed to estimate total petroleum hydrocarbon
losses into the environment. Assessment of the potential of total hydrocarbon emission from
the Chapopote asphalt seep amounts to up to 1,540 ± 770 tons. However, there is indication
that a lar ge fraction of these hydrocarbons are alread y efficiently recycled by the indigenous
microorganisms associated to the asphalts.
II