Molecular ecology of the NOR5-OM60 group of gammaproteobacteria [Elektronische Ressource] / vorgelegt von Yan Shi

Syan

Description

Molecular Ecology of the NOR5/OM60 Group of Gammaproteobacteria Dissertation zur Erlangung des akademischen Grades Doktors der Naturwissenschaften (Dr. rer. nat.) Dem Fachbereich Biologie/Chemie der Universität Bremen vorgelegt von YAN Shi Bremen Februar 2009 Die vorliegende Arbeit wurde in der Zeit von April 2006 bis Februar 2009 am Max-Planck-Institut für marine Mikrobiologie in Bremen angefertigt. 1. Gutachter: Prof. Dr. Rudolf Amann 2. Gutachter: Ulrich Fischer Tag des Promotionskolloquiums: 26. März 2009 ?U,Table of Contents Summary............................................................................................................................ 1 Zusammenfassung............................................................. 2 .................................................................................................................................... 3 List of Abbreviations ........................................................................................................ 4 1 Introduction.................................................................................................................5 1.1 Marine bacteria that utilize light............................................................................ 5 1.2 The NOR5/OM60 group............................ 6 1.2.1 Phylogeny of Bacteria ...........................

Sujets

• Biologie

Informations

• Publié par: universitat_bremen
• Publié le: 01 janvier 2009
• Nombre de lectures: 15
• Langue: Deutsch
• Poids de l'ouvrage: 4 Mo

Extrait

Molecular Ecology of the NOR5/OM60 Group
of Gammaproteobacteria






Dissertation zur Erlangung des akademischen Grades

Doktors der Naturwissenschaften

(Dr. rer. nat.)



Dem Fachbereich Biologie/Chemie der

Universität Bremen vorgelegt von





YAN Shi



Bremen
Februar 2009 Die vorliegende Arbeit wurde in der Zeit von April 2006 bis Februar 2009 am Max-
Planck-Institut für marine Mikrobiologie in Bremen angefertigt.





















1. Gutachter: Prof. Dr. Rudolf Amann
2. Gutachter: Ulrich Fischer



Tag des Promotionskolloquiums: 26. März 2009

Table of Contents

Summary............................................................................................................................ 1
Zusammenfassung............................................................. 2
.................................................................................................................................... 3
List of Abbreviations ........................................................................................................ 4

1 Introduction.................................................................................................................5
1.1 Marine bacteria that utilize light............................................................................ 5
1.2 The NOR5/OM60 group............................ 6
1.2.1 Phylogeny of Bacteria ............................................................................................ 6
1.2.2 History, phylogeny and abundance of the NOR5/OM60 clade .............................. 7
1.2.3 Strain KT71........................................................................................................... 10
1.2.4 Members of NOR5/OM60 group are AAnPs ....................................................... 11
1.3 Sampling stations ................................................................... 11
1.3.1 Yangtze River estuary........................................................................... 11
1.3.2 Namibian upwelling region................................................................................... 12
1.3.3 Vision cruise......................................... 13
1.3.4 German Bight........................................................................................ 14
1.3.5 North Sea sediment............................................................... 14
1.3.6 Other sampling stations...................................................................... 15
1.4 Methodological aspects.......................................... 15
1.4.1 The 16S rRNA approach....................................................................... 16
1.4.2 Genomics and metagenomics............................................................................... 17
1.4.3 Culturing............................................................................................................... 17
1.5 Aims of this study................................................................................................... 17

2 Results and Discussion.............................................................................................. 18
2.1 Phylogeny................................................................................................................ 18
2.2 Biogeography.......................................................................................................... 20
2.2.1 Worldwide existence............................................. 20
?U,2.2.2 Design and optimization of new probes sets......................................................... 24
2.2.3 Quantification of NOR5/OM60 in the environment............................................. 26
2.3 North Sea strains of NOR5/OM60........................................................................ 28
2.3.1 Isolation sources and growth features................................... 28
2.3.2 Pigments................................................................................................................ 30
2.3.3 General genomic features..................................................................................... 30
2.3.4 pufM genes............................................................................................................ 31
2.4 Genomics................................................................................................................. 31
2.4.1 General comparison of the genomes..................................................................... 31
2.4.2 Functional genes................................................................................... 34
2.5 Evolution and functions of NOR5/OM60 group in the ocean............................ 39

3 Outlook....................................................................................................................... 41
3.1 Phylogeny and biogeography................................................... 41
3.2 Comparative genomics............................................................................................. 41
3.3 Gene searching in metagenomic libraries................................................................ 42
3.4 Combining detection of FISH and functions ........................................................... 42
3.5 Physiological tests for the model strains of NOR5/OM60 ...................... 42
4 References.................................................................................................................. 44

List of Publications and Manuscripts ........................................................................... 49
Unit 1 Biogeography and phylogeny of the NOR5/OM60 clade of
Gammaproteobacteria................................................................................................ 51
Unit 2 Potential novel photoautotrophy in the NOR5/OM60 clade of
Gammaproteobacteria discovered by genome comparison .................................... 83
Unit 3 Characterization of the NOR5/OM60 strains from the North Sea............... 113

Acknowledgement......................................................................................................... 122


Summary
In this thesis, a newly discovered gammaproteobacterial group – the
NOR5/OM60 clade, which includes the novel aerobic anoxygenic phototrophs (AAnPs),
was studied in the aspects of phylogeny, biogeography and physiology using both
molecular and culturing methods.
By means of 16S rRNA phylogenetic analysis, NOR5/OM60 group was defined
as a monophyletic clade inside the class Gammaproteobacteria. More than 500 16S
rRNA sequences of this clade were retrieved from public databases. Further studies
classified the sequences into 13 subclades. My studies on the biogeography of
NOR5/OM60 clade showed a cosmopolitan distribution. They were found in all oceans
and at the coasts of all the continents. NOR5/OM60 seems to be most abundant in marine
coastal water and sediment. However, they have also been encountered in surface water
of open ocean, deep-sea sediment, freshwater, saline lakes and soil.
The abundance of members of the NOR5/OM60 clade in various marine sites was
determined by fluorescence in situ hybridization (FISH) with a newly designed and
optimized probe set. In the ocean, the common relative abundance ranges from <1% in
the open ocean to about 10% in the North Sea coastal water. The existence in coastal
sediment and freshwater was also proved by FISH.
More than 30 strains of the NOR5/OM60 clades had been isolated as pure
cultures in several studies. Of these, the genomes of five strains (KT71, RAp1red, Ivo14,
HTCC2080 and HTCC2148) were fully sequenced. In this thesis, these five genomes
were compared to each other and to a closely related strain, HTCC2143 from the BD1-7
group. The photosynthesis (PS) superoperon, the key genes of 3-hydroxypropionate cycle
for carbon fixation, and the sox operon for sulfur compound oxidation were found in four
strains: KT71, RAp1red, Ivo14 and HTCC2080. Genomic comparison indicated that, like
KT71, many NOR5/OM60 members may also be AAnPs and potentially be able to use
light as energy source.
1
Zusammenfassung
In dieser Arbeit wurde eine kürzlich entdeckte Gruppe, die NOR5/OM60-Gruppe
der Gammaproteobacteria, einige von dessen Mitglieder den aeroben anoxygenen und
phototrophen Bakterien (AAnP) gehöhren, in Phylogenie, Biogeographie und Physiologie
anhand molekularer und kultivierungsbasierender Methoden untersucht.
Anhand der phylogenetischen Analyse der 16S rRNA Sequenzen wurde die
NOR5/OM60-Gruppe als eine Monophylie in der Klasse Gammaproteobacteria begrenzt.
Mehr als 500 16S rRNA Sequenzen aus dieser Gruppe wurden in öffentlichen Daten-
banken gefunden. Weitere Studien klassifizierten die Sequenzen in 13 Untergruppen.
Biogeographische Untersuchungen zeigten eine weltweite Verteilung der NOR5/OM60-
Gruppe, welche in allen Ozeanen und an Küsten aller Kontinenten vorkommt. Diese
Organismen scheinen am häufigsten in marinen Kü