Molecular Basis of Symbiosis

316 Pages·2006·2.641 MB·English

by  Bernhard Schink (auth.), Professor Dr. Jörg Overmann (eds.)

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Volume 41
Molecular Basis of Symbiosis
J. Overmann (Ed.)
Jörg Overmann (Ed.)
Molecular Basis of Symbiosis
With 60 Figures, 5 in Color, and 10 Tables
Professor Dr. JÖRG OVERMANN
Section of Microbiology
Department of Biology
Maria-Ward-Str. 1a
80638 Munich
Germany
ISSN 0079-6484
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ISBN-13 978-3-540-28210-5
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Preface
Symbiotic associations involving prokaryotes are known from many different
phylogenetic lineages and occur ubiquitously. The significance of these asso-
ciations is well established for insects, where 15–20% (i.e., up to 190,000) of
the species depend on symbioses with bacteria (Buchner 1965). As another
example, up to 85% of all prokaryotes in the termite hindgut occur in ecto- or
endosymbiotic associations with flagellates (Berchtold et al. 1999). In some
aquatic environments, essentially all cells of Green Sulfur Bacteria occur in
the symbiotic state (Glaeser and Overmann 2003). Finally, whereas a total of
200 bacterial species are considered human pathogens (Lengeler et al. 1999),
the number of autochthonous (commensal and symbiotic) bacterial species as-
sociated just with the human intestinal tract is more than three times higher
(Suau et al. 1999). Obviously, symbiosis represents a typical way of prokary-
otic life.
In comparison to the approximately 6,000 validly described and mostly
well-studied species of prokaryotes, much less is known about symbiotic asso-
ciations. This is largely due to technical limitations. Maintaining and espe-
cially growing symbiotic associations in the laboratory is inherently difficult.
Since the advent of the era of molecular ecology, however, 16S rRNA-based
culture-independent techniques continue to reveal novel phylotypes of symbi-
otic prokaryotes. A comprehensive search of the Genbank database yielded
937 entries of 16S rRNA gene sequences for symbiotic Bacteria or Archaea
(Overmann and Schubert 2002). Yet, this latter number represents only a few
percent of the total number of 16S rRNA gene sequences in the database and
hence most likely is not representative for the entire diversity of symbiotic
prokaryotes.
Where estimated, the age of symbiotic associations ranges from 250
(Baumann et al. 1998) to 20 million years (Dubilier et al. 1995). During these
long time periods, co-evolution of the partner organisms occurred (Bandi et al.
1996; Baumann et al. 1998; Sauer et al. 2000), leading to specific mechanisms
of organismic interactions, and resulting in novel physiological capabilities of
the association as compared to those of the individual partners. Well-known
examples include the colonization of nutrient-poor soils by legumes associated
with N -fixing rhizobia, or the colonization of Arctic and Antarctic extreme
2
habitats by lichens. Mechanisms of symbiotic interaction may have already
evolved in association with former, different partner organisms, as has been
proposed for opportunistic human pathogens which appear to have developed
their virulence factors in interactions with non-mammalian eukaryotes (Hogan
and Kolter 2002).
The exchange of specific signals, the reciprocal regulation, and the physio-
logical interactions developed in symbiotic associations have always attracted
VI Preface
the interest of researchers. In the past, the complex nature of these interactions
and the lack of suitable laboratory models often impeded the understanding of
these fundamental processes. However, symbiosis research has recently en-
tered an exciting era because molecular biology now provides us with a wealth
of suitable and sophisticated novel techniques. These tools are particularly
useful for studying associations in which the partners cannot be separated
from each other or cannot be grown in the laboratory.
Recent advances in molecular symbiosis research permit a first comparison
across different symbiotic and also pathogenic systems. Indeed, common mo-
lecular principles of organismic interaction begin to emerge. With reference to
the symbiotic systems covered in this book, the recent discovery of RTX
toxin-like components in two very different symbiotic associations, namely
phototrophic consortia (Chap. 2) and the association of Riftia pachyptila with
chemoautotrophic bacteria (Cavanaugh 2004; Chap. 10) was unexpected and
suggests that this module is employed in phylogenetically very distant sys-
tems. Future research will reveal whether these modules evolved from the
same ancestor and thus are homologous, or whether they developed independ-
ently by convergent evolution.
It is the goal of this book to contribute towards a broader perspective of the
diversity of symbiotic systems. The identification of unifying themes among
different systems will stimulate research in this fascinating topic even further.
To this end, a set of 14 different model systems have been chosen. They com-
prise some well-known symbioses for which a considerable amount of infor-
mation has already been gathered over the past few years. Nevertheless, im-
portant novel aspects of symbiotic interactions have recently emerged. Other
experimental systems have only recently become amenable to experimental
manipulation, but already provided exciting insights into the molecular
mechanisms of symbiosis.
It is the belief of the editor as well as the authors, that a better understand-
ing of the molecular mechanisms of symbioses ultimately will also lead to
novel strategies for the exploitation of such systems for biotechnological
purposes, and potentially also help to improve strategies for the treatment of
(human) pathogens.
References
Bandi C, Siron M, Damiani G, Magrassi L, Nalepa CA, Laudani U, Sacchi L (1996)
The establishment of intracellular symbiosis in an ancestor of cockroaches and ter-
mites. Proc R Soc Lond B 259:293–299
Baumann P, Baumann L, Clark MA, Thao ML (1998) Buchnera aphidicola: the endo-
symbiont of aphids. ASM News 64:203–209
Berchtold M, Chatzinotas A, Schönhuber W, Brune A, Amann R, Hahn D, König H
(1999) Differential enumeration and in situ localization of micro-organisms in the
Preface VII
hindgut of the lower termite Mastotermes darwiniensis by hybridization with
rRNA-targeted probes. Arch Microbiol 172:407–416
Buchner P (1965) Endosymbiosis of animals with plant microorganisms. Interscience,
New York
Cavanaugh CM (2004) Evolution of chemoautotrophic symbionts: emerging patterns
and implications for cospeciation. 10th international symposium on microbial ecol-
ogy, Cancun, Mexico
Dubilier N, Giere O, Distel DL, Cavanaugh CM (1995) Characterization of chemo-
autotrophic bacterial symbionts in a gutless marine worm (Oligochaeta, Annelida)
by phylogenetic 16S rRNA sequence analysis and in situ hybridization. Appl Envi-
ron Microbiol 61:2346–2350
Glaeser J, Overmann J (2003) Characterization and in situ carbon metabolism of pho-
totrophic consortia. Appl Environ Microbiol 69:3739–3750
Hogan D, Kolter R (2002) Pseudomonas-Candida interactions: an ecological role for
virulence factors. Science 296:2229–2232
Lengeler JW, Drews G, Schlegel HG (1999) Biology of the prokaryotes. Thieme,
Stuttgart, 955 pp
Overmann J, Schubert K (2002) Phototrophic consortia: model systems for symbiotic
interrelations between prokaryotes. Arch Microbiol 177:201–208
Sauer C, Stackebrandt E, Gadau J, Hölldobler B, Gross R (2000) Systematic relation-
ships and cospeciation of bacterial endosymbionts and their carpenter ant host spe-
cies: proposal of the new taxon Candidatus Blochmannia gen. nov. Int J Syst Evol
Microbiol 50:1877–1886
Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, Collins MD, Dore J (1999)
Direct analysis of genes encoding 16S rRNA from complex communities
reveals many novel molecular species within the human gut. Appl Environ
Microbiol 65:4799–4807
Contents
Syntrophic Associations in Methanogenic Degradation …………………1
B. Schink
1 Introduction...................................................................................................1
2 Types of Cooperation among Anaerobic Microorganisms...........................2
3 Energetical Aspects.......................................................................................5
4 Concept of Syntrophic Energy Metabolism..................................................6
5 Energy Metabolism in Syntrophically Fermenting Bacteria.........................7
5.1 Butyrate Oxidation...............................................................................7
5.2 Syntrophic Propionate Oxidation.........................................................8
5.3 Syntrophic Ethanol Oxidation..............................................................9
5.4 Fermentation of Acetone......................................................................9
5.5 Syntrophic Oxidation of Hexoses......................................................10
5.6 Anaerobic Oxidation of Methane.......................................................11
6 Types of Interspecies Metabolite Transfer..................................................13
7 Outlook.......................................................................................................14
References.......................................................................................................15
Symbiosis between Non-Related Bacteria in Phototrophic Consortia......21
J. Overmann
1 Introduction.................................................................................................21
2 Types of Phototrophic Consortia................................................................23
3 Identification of the Bacteria which Constitute Phototrophic Consortia.....24
3.1 The Epibiont.......................................................................................24
3.2 The Central Bacterium.......................................................................27
4 Modes and Specificity of Interaction between the Bacterial Partners.........29
5 Selective Advantage of the Interaction.......................................................31
6 “Symbiosis Genes” of the Epibiont.............................................................33
7 Outlook.......................................................................................................33
References.......................................................................................................34
Prokaryotic Symbionts of Termite Gut Flagellates: Phylogenetic and
Metabolic Implications of a Tripartite Symbiosis......................................39
A. Brune, U. Stingl
1 Introduction.................................................................................................39
2 The Termite Gut Microecosystem..............................................................40
2.1 Lignocellulose Degradation...............................................................40
2.2 The Gut Microenvironment...............................................................40
2.3 Prokaryotic Diversity.........................................................................41
3 Hindgut Protozoa........................................................................................42
3.1 Phylogeny..........................................................................................43
3.2 Physiology and Function....................................................................43
X Contents
4 Symbiotic Associations with Prokaryotes...................................................45
4.1 Prokaryotic Epibionts.........................................................................45
4.1.1 Methanogens.............................................................................48
4.1.2 Spirochaetes..............................................................................48
4.1.3 Bacteroidales............................................................................49
4.2 Prokaryotic Endosymbionts...............................................................50
4.2.1 Methanogens.............................................................................50
4.2.2 The ‘Endomicrobia’..................................................................50
4.2.3 Endonuclear Bacteria................................................................52
5 Functional and Metabolic Implications.......................................................52
5.1 Hydrogen Metabolism........................................................................52
5.2 Other Possible Functions...................................................................53
6 Conclusions.................................................................................................54
References.......................................................................................................55
Towards an Understanding of the Killer Trait: Caedibacter
Endocytobionts in Paramecium....................................................................61
J. Kusch, H.-D. Görtz
1 Introduction.................................................................................................61
2 Evolutionary Ecology of the Caedibacter Symbiosis and R Body
Production...................................................................................................63
3 Host Specificity of Caedibacter..................................................................67
4 Molecular Evolution of R body Production................................................69
5 Conclusions.................................................................................................72
References.......................................................................................................72
Bacterial Ectosymbionts which Confer Motility:
Mixotricha paradoxa from the Intestine of the Australian
Termite Mastotermes darwiniensis................................................................77
Helmut König, Li Li, Marika Wenzel, Jürgen Fröhlich
1 Introduction.....................................................................................................77
2 The Intestinal Microbiota of Mastotermes darwiniensis...............................78
3 Symbiotic Interactions between Spirochetes and Flagellates........................81
4 Morphology of Mixotricha paradoxa............................................................82
5 Phylogenetic Position of Mixotricha paradoxa.............................................84
6 Glycolytic Activities of Mastotermes darwiniensis and its Flagellates........84
7 Identification of the Ectosymbiotic Spirochetes of Mixotricha paradoxa....87
8 Identification of the Ectosymbiotic Rod-Shaped Bacterium of
Mixotricha paradoxa...............................................................................88
9 Assignment of 16S rDNA Sequences to the Corresponding
Ectosymbiotic Bacterial Morphotypes....................................................88
10 Conclusions.............................................................................................91
References.......................................................................................................91
Contents XI
Extrusive Bacterial Ectosymbiosis of Ciliates.............................................97
G. Rosati
1 Introduction.................................................................................................97
2 The Ciliate Host..........................................................................................98
3 The Epixenososomal Band..........................................................................99
4 Epixenosomes...........................................................................................100
4.1 Nature and Phylogenetic affiliation.................................................100
4.2 Morphological Characteristics.........................................................102
4.3 The Dome-Shaped Zone and Inclusion Body..................................104
4.4 The Extrusive Apparatus..................................................................104
4.5 The Basket Tubules..........................................................................106
5 Can Euplotidium and Epixenosomes Survive on their Own?...................107
6 The Ejection Mechanism and its Significance..........................................108
7 Why Does Euplotidium Maintain its Epixenosomes?...............................109
8 Concluding Remarks and Future Perspectives..........................................110
References.....................................................................................................112
Hydrogenosomes and Symbiosis................................................................117
J.H.P. Hackstein, N. Yarlett
1 Introduction...............................................................................................117
2 Hydrogenosomes and Mitochondrial Remnant Organelles
Evolved Repeatedly..................................................................................118
3 Hydrogenosomes: Organelles that Can Use Protons
as Electron Acceptors................................................................................122
3.1 Hydrogenosomes of Trichomonas vaginalis....................................122
3.2 Hydrogenosomes of Anaerobic Ciliates: at Least One Appears
to be a Mitochondrion that Produces Hydrogen...............................126
3.3 Hydrogenosomes of Anaerobic Chytrids: an Alternative Way to
Adapt to Anaerobic Environments...................................................128
4 A Common Ancestor that Produced Hydrogen........................................131
5 Symbiotic Associations that Depend on Intracellularly
Generated Hydrogen.................................................................................132
6 Conclusions...............................................................................................135
References.....................................................................................................135
Molecular Interactions between Rhizobium and Legumes.......................143
P. Skorpil, W.J. Broughton
1 Introduction...............................................................................................143
2 Nod-Factors...............................................................................................144
3 Nod-Factor Perception..............................................................................146
4 Surface Polysaccharides............................................................................149
5 Secreted Proteins.......................................................................................152
6 Conclusions...............................................................................................153
References.....................................................................................................154