Molecular characterization of methanotrophic and chemoautotrophic communities at cold seeps [Elektronische Ressource] / vorgelegt von Tina Lösekann

Tina Masson

Sujets

• Biologie

Informations

• Publié par: universitat_bremen
• Publié le: 01 janvier 2006
• Nombre de lectures: 18
• Langue: Deutsch
• Poids de l'ouvrage: 8 Mo

Extrait

Molecular Characterization of
Methanotrophic and Chemoautotrophic
Communities at Cold Seeps




Dissertation
zur Erlangung des Grades eines
Doktors der Naturwissenschaften
- Dr. rer. nat. -




dem Fachbereich Biologie/Chemie der
Universität Bremen
vorgelegt von




Tina Lösekann




Bremen
März 2006 Die Untersuchungen zur vorliegenden Doktorarbeit wurden in der Zeit von September 2002
bis März 2006 am Max-Planck-Institut für Marine Mikrobiologie in Bremen durchgeführt.





















1. Gutachterin: Prof. Dr. A. Boetius
2. Gutachter: Prof. Dr. R. Amann


Weitere Prüfer:
Prof. Dr. U. Fischer
Dr. K. Knittel



Tag des Promotionskolloquiums: 30. März 2006 Table of Contents
Summary ................................................................................................................................... 1
Zusammenfassung..................................................................................................................... 2

Part I: Combined Presentation of Results
A Introduction.............................................................................................................. 5
1 Reducing Habitats in the Ocean............................................................................. 6
1.1 Oxygen Minimum Zones............................................................................. 7
1.2 Large Organic Falls..................................................................................... 7
1.3 Hydrothermal Vents 8
1.4 Cold Seeps................................................................................................... 8
2 Key Biogeochemical Processes in Reducing Habitats .......................................... 10
2.1 Methanogenesis........................................................................................... 10
2.2 Anaerobic Oxidation of Methane................................................................. 11
2.3 Sulfate Reduction......................................................................................... 14
2.4 Oxidation of Sulfide 14
2.5 Aerobic Oxidation of Methane .................................................................... 16
2.6 Oxidation of Other Reduced Elements ........................................................ 18
3 Key Players in Reducing Habitats ......................................................................... 18
3.1 Anaerobic Methane-Oxidizing Archaea...................................................... 18
3.2 Sulfate-Reducing Bacteria........................................................................... 21
3.3 Sulfide-Oxidizing .......................................................................... 22
3.4 Aerobic Methane-Oxidizing Bacteria.......................................................... 23
3.5 Symbiont-Bearing Marine Invertebrates 24
4 Cultivation-Independent Methods for the Identification of Microorganisms........ 27
4.1 The Full Cycle rRNA Approach.................................................................. 27
4.2 Lipid Biomarkers......................................................................................... 28
4.3 Metagenomics.............................................................................................. 28
5 Thesis Outline........................................................................................................ 29
B Results and Discussion............................................................................................. 31
1 Haakon Mosby Mud Volcano (Barents Sea) ......................................................... 31
1.1 Methanotrophic Communities in Surface Sediments .................................. 31
1.2 Microbial Communities in Subsurface Sediments....................................... 35
1.3 unities in Mats of Sulfur-Oxidizing Bacteria ................... 36
1.4 Symbioses between Bacteria and Siboglinid Tubeworms ........................... 38
1.5 Diversity of mcrA Genes.............................................................................. 39
2 Cascadia Margin (Hydrate Ridge, coast off Oregon) ............................................ 41
2.1 Detection and Quantification of ANME-2 Subgroups in
Surface Sediments........................................................................................ 42
2.2 Detection of ANME-3 in Surface Sediments............................................... 43
2.3 Methanotrophic Communities in Shallow Subsurface Sediments and
Gas Hydrates................................................................................................ 43
3 Final Discussion..................................................................................................... 44
3.1 Key Microbial Players and Their Distribution.............................................
3.2 Difference between Surface and Subsurface Communities......................... 47
3.3 Interspecies Associations............................................................................. 48
3.4 Environmental Selection of ANME Groups................................................ 49
3.5 Outlook........................................................................................................ 53
C References ................................................................................................................. 55
Part II: Publications
A List of Publications................................................................................................... 65
B Publications............................................................................................................... 69
1 Fluid Flow Controls Distribution of Methanotrophic Microorganisms
at Submarine Cold Seeps....................................................................................... 69
2 Novel Clusters of Aerobic and Anaerobic Methane Oxidizers at
an Arctic Cold Seep (Haakon Mosby Mud Volcano, Barents Sea)....................... 87
3 Endosymbioses between Bacteria and Deep-Sea Siboglinid Tubeworms
from an Arctic Cold Seep (Haakon Mosby Mud Volcano, Barents Sea).............. 117
4 Microbial Diversity and Community Composition in Gas Hydrates and
Hydrate-Bearing Sediments of the Cascadia Margin (Hydrate Ridge) ................. 145
5 Diversity and Distribution of Methanotrophic Archaea at
Cold Seeps............................................................................................................. 177


Part III: Appendix
A List of Clones ............................................................................................................ 191

Acknowledgement..................................................................................................................... 197 Summary

Summary
Cold seeps are complex ecosystems based on chemosynthesis. Sulfide and methane are
available in high concentrations and support a variety of highly adapted microorganisms and
symbiont-bearing invertebrates. The anaerobic oxidation of methane (AOM) is a key
biogeochemical process at cold seeps and is assumed to be mediated by a consortium of
anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria.
In this thesis I used 16S rRNA-based molecular methods to identify and quantify
methanotrophic and chemoautotrophic, sulfur-oxidizing communities at two cold seeps and
collaborated with scientists from other disciplines to correlate the molecular results with
biogeochemical, geological, and physical data sets. Two types of cold seeps were studied, the
Arctic Haakon Mosby Mud Volcano (HMMV; 1250 m water depth) and the Hydrate Ridge at
the Cascadia Margin (700 m water depth) off the coast of Oregon.
The actively methane-seeping HMMV hosts novel clades of aerobic and anaerobic
methanotrophs. The distribution of the methanotrophic guilds is controlled by fluid flow and
bioirrigation activities of marine invertebrates. The center of the volcano is characterized by
high upward fluid flow. High numbers of novel aerobic methanotrophs were detected in the
upper millimeters of the sediment. These dominated the microbial community in surface
sediments of HMMV. At sites with decreased upward fluid flow, a new group of ANME
archaea (ANME-3) was identified, dominating the zone of AOM in 1-4 cm sediment depth. In
this zone, the microbial biomass was almost entirely comprised by ANME-3 archaea which
form consortia with sulfate-reducing bacteria of the Desulfobulbus branch. In bioirrigated
sediments populated by siboglinid tubeworms, sulfate is transported deeper into the sediment
and here the AOM consortia were found at the base of the tubeworm roots.
The symbioses between bacteria and the tubeworms at HMMV were characterized. Two
species of tubeworms coexist at the same site and represent the dominant megafauna at
HMMV. The symbionts of Sclerolinum contortum were identified as chemoautotrophic sulfur