Microbial communities performing anaerobic oxidation of methane [Elektronische Ressource] : diversity of lipid signatures and habitats / vorgelegt von Pamela E. Rossel Cartes

Microbial communities performing
anaerobic oxidation of methane:
diversity of lipid signatures and habitats



Dissertation
zur Erlangung des Doktorgrades
der Naturwissenschaften
- Dr. rer. Nat. -


Am Fachbereich Geowissenschaften
der Universität Bremen


vorgelegt von


Pamela E. Rossel Cartes


Bremen
Februar 2009






















1. Gutachter: Prof. Dr. Kai-Uwe Hinrichs, University of Bremen, Germany
2. Gutachter: Prof. Dr. Antje Boetius, Max Planck Institute for Marine Microbiology,
Bremen, Germany
















No viniste de lejos, ni siquiera has llegado. Estabas desde siempre, como un lenguaje
escrito en el fondo de mí…
Para Xavi con mucho amor







TABLE OF CONTENTS

Abstract Thesis abstract……………………………………………………..I
Kurzfassung……………………………………………………...III

Acknowledgements………………………………………………………………………V

List of Figures……………………………………………………….............................VII

List of Tables………………………………………………………................................IX

List of Abbreviations………………………………………………………....................X

Chapter I: Introduction…………………………………………………….................1
General introduction………………………………………………………2
I.1. Properties and importance of methane………………………………..2
I.2. Production and consumption of methane……………………………..4
I.3. Microbial communities performing AOM…………………..............11
I.4. Distribution/Habitats of AOM communities………………………...13
I.5. Lipid signatures of communities performing AOM…………………18
I.6. Intact polar membrane lipids (IPLs)…..……………………………..21
I.7. Methods……………………………………………………………...28
I.8. Hypothesis and objectives…………………………………………...29
I.9. Contribution to publications…………………………………………30
I.10. References………………………………………………………….33

Chapter II: Intact polar lipids of anaerobic methanotrophic archaea and……………45
associated bacteria
II.1. Printed manuscript…………………………………………………..46
II.2. Supplementary online material……………………………………...61


Chapter III: Factors controlling the distribution of anaerobic………………………...63
methanotrophic communities in marine environments:
evidence from intact polar membrane lipids
III.1. Manuscript…………………………………………………………64
III.2. Supplementary material………..…………………...…………….106

Chapter IV: Experimental approach to evaluate stability and reactivity…………….111
of intact polar membrane lipids of archaea and bacteria in
marine sediments

Chapter V: Diversity of intact polar membrane lipids in marine…………………...125
seep environments

Chapter VI: Concluding remarks and perspectives………………………………….149
VI.1. Conclusions……………………………………………………….150
VI.2. Future perspectives……………………………………………….155
VI.3. Presentations and other activities…………………………………159

Thesis abstract
________________________________________________________________________
THESIS ABSTRACT

The main aim of this thesis was to study different microbial communities
involved in the process of anaerobic oxidation of methane (AOM) using lipid analysis.
During this work a variety of globally distributed methane-bearing systems characterized
by different environmental factors and anaerobic methanotrophic consortia were analyzed
for intact polar lipid (IPL) and apolar lipid composition. Moreover, an experiment was
designed in order to evaluate the stability of archaeal and bacterial IPLs in marine
sediments.
The three phylogenetically distinct clusters of Euryarchaeota called ANME-1, -2
and -3, which have been observed in association with sulfate-reducing bacteria of the
Desulfosarcina/Desulfococcus group (‘‘ANME-1/DSS and -2/DSS aggregates”) or
Desulfobulbus spp (‘‘ANME-3/DBB aggregates”) could be clearly distinguished by IPL
composition but not by apolar lipids. ANME-1/DSS was characterized by
glyceroldialkylglyceroltetraethers (GDGTs) with glycosidic, phospho, as well as mixed
of both , whereas diagnostic IPLs of ANME-2/DSS were archaeols with both glycosidic
and phospho headgroups. Distinctly, ANME-3/DBB contained neither glycosidic-
archaeols nor GDGT-based IPLs, but the phospho-archaeol composition was very similar
to ANME-2/DSS. The main and distinguishing feature of ANME-3/DBB was the high
contribution of the bacterial IPLs phosphatidyl-(N)-methylethanolamine (PME) and
phosphatidyl-(N,N)-dimethylethanolamine (PDME). Other bacterial IPLs that were
mainly found in ANME-2/DSS-dominated carbonate mats were IPLs with non-phospho
headgroups such as ornithine lipids, surfactins and betaine lipids, the latter with odd fatty
acid chains. In contrast, IPLs with phospho headgroups were generally more abundant in
sediment environments. The high contribution of glycosidic archaeal IPLs and the
presence of bacterial IPLs with non-phospho headgroups in carbonate mats can be
explained by adsorption of phosphate onto calcium carbonate.
In addition to the general differences in IPL composition of each of three AOM-
community types, the IPL distribution was also associated with several environmental
factors, allowing the characterization of their different habitats. ANME-1/DSS dominates
IThesis abstract
________________________________________________________________________
habitats with high temperature and low oxygen content in bottom waters. For ANME-
2/DSS systems, it was possible to differentiate between carbonate reef habitats and
sediment settings, with the former characterized by low temperature, high oxygen content
in bottom waters and high methane and sulfate concentrations, whereas the latter was
associated with higher sulfate reduction rates. ANME-3/DBB presented similar
environmental characteristics to ANME-2/DSS.
Furthermore, degradation of archaeal and bacterial IPLs was evaluated in marine
sediments, showing a loss of 80% for the archaeal and ~50% for the bacterial IPL at 5°C
after 465 days of incubation under sterile conditions. However, in non-sterile conditions
at 5°C, an increase in concentration of both IPLs at the end of the experiment was
observed. Therefore, biotic degradation of IPLs could not be proved because the pools of
produced and degraded IPLs in the non-sterile conditions were indistinguishable.
The results obtained during this thesis support the distinction of microbial
communities performing AOM based on IPL diversity and address the role of
environmental factors in the distribution of three major AOM-community types. This
work contributes substantially to the understanding of the distribution of AOM systems
on a global scale.


IIKurzfassung
________________________________________________________________________
KURZFASSUNG

Der Schwerpunkt dieser Doktorarbeit liegt auf der Untersuchung von
unterschiedlichen Mikrobengemeinschaften, die an der anaeroben Oxidation von Methan
(AOM) beteiligt sind mit Hilfe von Lipidanalysen. Die Zusammensetzung von apolaren
und intakten polaren Lipiden (IPLs) wurde an einer breitgefächerten Auswahl von
methangeladenen Systemen analysiert, die durch verschiedene Umweltfaktoren und
anaerobische methanotrophische Konsortien charakterisiert sind. Außerdem wurde ein
Experiment konzipiert, um die Stabilität von bakteriellen und von Archaeen stammenden
IPLs in marinen Sedimenten zu untersuchen.
Die drei phylogenetisch unterschiedlichen Cluster von Euryarchaeen namens
ANME-1, -2 und -3, die oft zusammen mit sulfatreduzierenden Bakterien der Gruppe
Desulfosarcina/Desulfococcus (‘‘ANME-1/DSS und -2/DSS Aggregate”) oder
Desulfobulbus spp (‘‘ANME-3/DBB Aggregate”) beobachtet worden sind, konnten
eindeutig anhand der Zusammensetzung ihrer IPLs unterschieden werden, aber nicht
durch ihre apolaren Lipide. Charakteristisch für ANME-1/DSS sind
Glyceroldialkylglyceroltetraether (GDGT) mit sowohl glykosidischen, phospho und
gemischten Kopfgruppen, wohingegen diagnostische IPLs für ANME-2/DSS Archaeole
mit sowohl glycosidischen als auch phospho Kopfgruppen waren. Im Gegensatz dazu
zeigten ANME-3/DBB weder glykosidische Archaeole noch GDGT-basierte IPLs, aber
dafür eine zu ANME-2/DSS sehr ähnliche Zusammensetzung der Phosphoarchaeole. Der
größte Unterschied von ANME-3/DBB waren die bakteriellen IPLs phosphatidyl-(N)-
methylethanolamine (PME) und phosphatidyl-(N,N)-dimethylethanolamine (PDME).
Andere bakterielle IPLs, die hauptsächlich in ANME-2/DSS dominierten Karbonatmatten
gefunden wurden waren IPLs ohne phosphatbasierende Kopfgruppe wie Ornithinlipide,
Surfactin und Betainlipide, letztere mit ungeraden Fettsäureketten. Im Gegensatz dazu
hatten Lipide mit phosphatbasierenden Kopfgruppen einen höheren Anteil in
sedimentären Umgebungen. Der hohe Anteil von glykosidischen Archaeenlipiden und
bakteriellen IPLs ohne phosphatbasierende Kopfgruppen in Karbonatmatten kann