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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Serie: ISTE Invoiced
- Sprache: Englisch
Archaea constitute a new branch of life alongside bacteria and eukaryotes. These microorganisms are unique in their cellular and molecular aspects. They have evolutionary links with the first eukaryotic cells and are now being used to elucidate fundamental biological questions.
Champions of extremophilicity, archaea are helping to lift the veil on the limits of life on Earth. Biology of Archaea 1 explores the discovery and evolution of the field of archaea research.
This book also looks at the evolutionary history of archaea and their integration into the tree of life, and examines this complex and extremely diverse world in terms of their ecological niches and their still largely unexplored virosphere.
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Seitenzahl: 474
Veröffentlichungsjahr: 2025
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Table of Contents
Cover
Table of Contents
Title Page
Copyright Page
Preface
Chapter 1. The Discovery of Archaea
1.1. Introduction
1.2. Prokaryotic–eukaryotic dichotomy
1.3. Two domains for prokaryotes: archaebacteria and eubacteria
1.4. The living trilogy
1.5. Archaea and high-temperature living
1.6. Non-extremophilic archaea discovered by molecular ecology: a new vision of the third domain
1.7. Conclusion
1.8. References
Chapter 2. Evolution of Archaea and Their Taxonomy
2.1. Introduction
2.2. One domain, three major branches and a few isolated “phyla”
2.3. From phyla to superphyla
2.4. Euryarchaea
2.5. A new nomenclature for the taxonomy of archaea?
2.6. Reconstructing the last common ancestor of archaea: LACA
2.7. Conclusion
2.8. References
Chapter 3. Archaea and the Tree of Life
3.1. Introduction
3.2. The progenote concept
3.3. Archaea: prokaryotes related to eukaryotes
3.4. Rooting the universal tree
3.5. The nature of LUCA
3.6. The topology of the universal tree under debate
3.7. The origin of new eukaryotic-like proteins discovered in Asgard archaea
3.8. Asgard archaea and the origin of eukaryotes
3.9. The biological issues posed by the 2D model
3.10. Viruses and the universal tree of life
3.11. Conclusion
3.12. References
Chapter 4. Archaea: Habitats and Associated Physiologies
4.1. Introduction
4.2. Archaea of extreme habitats: extremophiles
4.3. Archaea populating ordinary, non-extreme environments
4.4. Archaea resistant to cultivation efforts
4.5. Challenges and success stories
4.6. Conclusion
4.7. References
Chapter 5. Methanogenic Archaea
5.1. Diversity of methanogens and their environments
5.2. Interactions of methanogens with their environment
5.3. Bioenergetics and biochemistry of methanogenesis
5.4. Anaerobic methanotrophs and anaerobic oxidation of multi-carbon alkanes
5.5. Evolution of methanogenesis
5.6. The impact of methanogens in our modern society
5.7. References
Chapter 6. Hyperthermophilic Archaeal Viruses
6.1. Introduction
6.2. Morphological and structural diversity
6.3. Genomic features of hyperthermophilic archaeal viruses
6.4. Virus–host interactions
6.5. Conclusions
6.6. References
List of Authors
Index
End User License Agreement
List of Tables
Chapter 1
Table 1.1. Ranges of S
AB
values obtained by comparing differ...
Chapter 2
Table 2.1. Meaning of the prefixes associated with Asgard archaeal phyla...
Table 2.2. Phylum-level correspondence between the Genome Taxonomy Datab...
Chapter 4
Table 4.1. Environmental characteristics of extreme microbial habitats...
Table 4.2. Archaea breaking all records for life in extreme conditions
Table 4.3. Hypothetical metabolisms of archaeal lineages with no...
Chapter 5
Table 5.1. Estimated methane production and net emissions on land...
Table 5.2. Methanogenesis pathways and Gibbs free energies under...
Table 5.3. Methanogens in cultures from international collections...
List of Illustrations
Chapter 1
Figure 1.1. Two visions of evolution in the late 1970s
Figure 1.2. Carl Woese and the Triumph of Reductionism
Figure 1.3. Analysis of 16S rRNA by the Oligonucleotide Method. (a)...
Figure 1.4. Revealing the evolutionary link between...
Figure 1.5. The discovery of hyperthermophilic archaea and their viruses
Figure 1.6. Discovery of the first archaea with an optimal growth...
Figure 1.7. Temperature ranges for organisms in the three domains...
Chapter 2
Figure 2.1. First Universal Trees Based on 16S rRNAs
Figure 2.2. Extract from the phylogeny of 16S rRNAs on which Norman...
Figure 2.3. Simplified phylogeny from Brochier et al. (2004, 2005a,...
Figure 2.4. Simplified phylogeny according to Brochier et al. (2011)...
Figure 2.5. The two possible rootings according to the topology of...
Figure 2.6. Schematic phylogeny of the superphylum TACK. The phylu...
Figure 2.7. Consensus schematic phylogeny of the DPANN Superphylum...
Figure 2.8. Insertions common (highlighted in yellow) to the Nanoh...
Figure 2.9. Schematic phylogeny of the “superphylum”...
Figure 2.10. Schematic phylogeny of the Euryarchaea (in black) hi...
Figure 2.11. Schematic phylogeny of group I Euryarchaea. Groups...
Figure 2.12. Schematic phylogeny of Group II Euryarchaea. Groups...
Figure 2.13. Global schematic phylogeny of archaea based on the...
Figure 2.14. Trees of archaea with different roots obtained using...
Chapter 3
Figure 3.1. First universal tree based on 16S rRNA. In this tree,...
Figure 3.2. Universal schematic tree based on the concatenation of...
Figure 3.3. Universal trees of elongation factors EF1(Tu) and EF2(G)...
Figure 3.4. The Woese tree. The 16S rRNA tree from Figure 3.1, rooted...
Figure 3.5. Distribution of ribosomal proteins in the three domains....
Figure 3.6. Two evolutionary scenarios for DNA replication.
Figure 3.7. The Woese tree based on 16S rRNAs redesigned by Karl Ste...
Figure 3.8. Relationship between reverse gyrases of archaea and bact...
Figure 3.9. Scenario of independent adaptation to hyperthermophilic...
Figure 3.10. Four trees corresponding to proteins assumed to be pre....
Figure 3.11. Eukaryotic-specific proteins in the eocyte tree (2D).
Figure 3.12. The specific proteins of eukaryotes in the Woese’s...
Figure 3.13. James Lake’s hypothesis explaining the Woese tree...
Figure 3.14. The first universal tree suggesting the position of euk...
Figure 3.15. Hypothesis explaining the transformation from a 3D tree...
Figure 3.16. Correlation between protein size and phylogeny (2D or...
Figure 3.17. Two opposing topologies obtained with the same method...
Figure 3.18. Schematic phylogeny of the universal protein Kae1/TsaD...
Figure 3.19. Bayesian phylogenies obtained by concatenating the two...
Figure 3.20. Phylogenies compared: RNA polymerases with a single euk...
Figure 3.21. Schematic phylogeny of DNA topoisomerases of the IB fam...
Figure 3.22. Gene transfers coding for different ESPs (colored circl...
Figure 3.23. Schematic representation of evolutionary relationships...
Figure 3.24. Three possible scenarios of transitions between bacter...
Figure 3.25. Universal schematic phylogeny of Varidnaviria. This phy...
Chapter 4
Figure 4.1. Photographs of extreme environments harboring archaea
Figure 4.2. Photographs of extreme environments hosting microorganisms
Figure 4.3. Microphotographs of archaea living in extreme or non-extreme...
Figure 4.4. Photographs of non-extreme environments populated by arc...
Figure 4.5. Archaeal taxa of different microbiota of the human body...
Chapter 5
Figure 5.1. Phylogenetic tree of the domain Archaea
Figure 5.2. Chemical formulas of cofactors used in methanogenesis. A...
Figure 5.3. Example of the intrinsic fluorescence phenomenon in meth...
Figure 5.4. Metabolism of hydrogenotrophic methanogens. MFR, methano...
Figure 5.5. Concept of electron bifurcation illustrated by the react...
Figure 5.6. Metabolism of acetoclastic methanogens
Figure 5.7. Metabolism of methylotrophic methanogens
Figure 5.8. Metabolism of M. stadtmanae. Fd: ferredoxin; CH...
Figure 5.9. Catalytic core of MCR from Methanothermobacter marburgen...
Chapter 6
Figure 6.1. Electron micrographs of hyperthermophilic archaeal viruses....
Figure 6.2. Bipartite network approach of all dsDNA viruses. Image repr...
Figure 6.3. Lifecycles of lytic and temperate archaeal viruses. Image re...
Guide
Table of Contents
Cover Page
Title Page
Copyright
Preface
Begin Reading
Index
WILEY END USER LICENSE AGREEMENT
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SCIENCES
Biology, Field Director – Marie-Christine Maurel
Microbiology, Subject Head – Marie-Christine Maurel
Biology of Archaea 1
Discovery, Evolution and Diversity of Archaea
Coordinated by
Béatrice Clouet-d’OrvalBruno FranzettiPhilippe Oger
First published 2025 in Great Britain and the United States by ISTE Ltd and John Wiley & Sons, Inc.
Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the Copyright, Designs and Patents Act 1988, this publication may only be reproduced, stored or transmitted, in any form or by any means, with the prior permission in writing of the publishers, or in the case of reprographic reproduction in accordance with the terms and licenses issued by the CLA. Enquiries concerning reproduction outside these terms should be sent to the publishers at the undermentioned address:
ISTE Ltd27-37 St George’s RoadLondon SW19 4EUUKwww.iste.co.uk
John Wiley & Sons, Inc.111 River StreetHoboken, NJ 07030USAwww.wiley.com
© ISTE Ltd 2025The rights of Béatrice Clouet-d’Orval, Bruno Franzetti and Philippe Oger to be identified as the authors of this work have been asserted by them in accordance with the Copyright, Designs and Patents Act 1988.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s), contributor(s) or editor(s) and do not necessarily reflect the views of ISTE Group.
Library of Congress Control Number: 2024945709
British Library Cataloguing-in-Publication DataA CIP record for this book is available from the British LibraryISBN 978-1-78945-168-9
ERC code:LS8 Ecology, Evolution and Environmental BiologyLS8_10 Microbial ecology and evolution
Preface
Béatrice CLOUET-D’ORVAL1, Bruno FRANZETTI2 and Philippe OGER3
1 MCD-CBI, CNRS, Université de Toulouse, France
2 IBS, CNRS, Université Grenoble Alpes, France
3 MAP, CNRS, INSA Lyon, Villeurbanne, France
More than 40 years ago, archaea were proposed as a new domain of life alongside bacteria and eukaryotes. It is now accepted that these organisms constitute a distinct group, unique in many cellular and molecular aspects. The discovery of these universally important organisms represents one of the greatest advances in modern biology. Archaea have evolutionary links with early eukaryotic cells and are now used to elucidate fundamental biological questions. As champions of extremophilia, archaea have also shed light on the limits of life on Earth. Over the years, our understanding of archaeal microorganisms has evolved considerably. Far from being exotic forms of microbial life, archaea are found to be omnipresent in all terrestrial sites (> 20% of marine microbial biomass) and are notably present in the human microbiota. As new genomes are sequenced, it becomes evident that archaea represent a complex, extremely diverse world and also possess a largely unexplored virosphere. In soils and oceans, archaea play a key role in the planet’s major geochemical cycles. In particular, methanogens, exclusively represented by archaea, are central to issues of climate change and energy challenges. To understand their impact on the environment and human health, it is imperative to decode their unique features at a molecular level. The molecular machinery deciphered in archaea will provide key paradigms for understanding fundamental biological processes conserved across life forms. Notably, the molecular bases of genetic information processing in archaea are often very similar to their counterparts in eukaryotes (translation, transcription, replication, recombination and DNA repair), even though archaea have a cellular structure similar to bacteria. Moreover, the regulatory systems for gene expression through post-transcriptional mechanisms remain poorly understood.
Our knowledge of archaea is rapidly evolving thanks to the advent of high-throughput sequencing of entire genomes. It is time to introduce a wide audience to the advances that illuminate our understanding of biology and reveal the originality of this domain of life.
The 14 chapters, divided into two volumes, of this book review the discovery and evolution of the domain of archaea and summarize our current knowledge of cellular and molecular processes to better integrate this domain into the broader understanding of life.
November 2024
