Phylogeny and Evolution of Bacteria and Mitochondria

Mauro Degli Esposti

• Publisher: CRC Press
• Year: 2018
• Print ISBN: 9781138501683
• eBook ISBN: 9781351385527
• Edition: 1
• Topic: Medicine
• Subtopic: Biochemistry in Medicine

Life on earth began with bacteria, which now colonize every corner of the planet. As the ancestors of mitochondria, bacteria are also fundamental for our cells. Most bacteria look alike, but have very different functions. Therefore, knowing the functional profile of bacteria helps understand their impact on our life. This book provides a wealth of information on the functional evolution of bacteria in a novel and coherent way. The book is aimed towards scientists as well as those who are curious about the world of bacteria and their relationships with mitochondria, the powerhouses of our cells, and us.

Contents

Dedication

Preface

1. Early Microbial Evolution from a Physiological Perspective

William F. Martin

2. Bioenergetic Function of Gram Negative Bacteria—rom Anaerobes to Aerobes

Mauro Degli Esposti

3. Gram Negative Bacteria Related to Proteobacteria

Mauro Degli Esposti

4. Proteobacteria: From Anaerobic to Aerobic Organisms

Mauro Degli Esposti

5. Gammaproteobacteria

Mauro Degli Esposti and Esperanza Martínez-Romero

6. Betaproteobacteria

Mauro Degli Esposti, Paola Bonfante, Mónica Rosenbleuth and Esperanza Martínez-Romero

7. From Alphaproteobacteria to Proto-Mitochondria

Mauro Degli Esposti, Julio Martínez and Esperanza Martínez-Romero

8. From Proto-Mitochondria to the Mitochondrial Organelles of Our Cells

Mauro Degli Esposti

Index

1

Early Microbial Evolution from a Physiological Perspective

William F. Martin

Institute for Molecular Evolution, University of Düsseldorf, Germany
Email:[email protected]

Introduction to Early Microbial Evolution

Most thinking about microbial evolution is currently couched in terms of molecular evolutionary trees, the subject matter of a discipline called phylogeny. As such, few scientists would have difficulties imagining how one might study microbial evolution and more generally the evolution of life: make trees. Life, however, is a chemical reaction. All cells rely upon a main exergonic reaction that fuels ATP synthesis to run all other life processes. The nature of that main exergonic reaction, which has driven the evolutionary process forward in uninterrupted continuity since the origin of the first cells, is a central topic of investigation in the field of physiology or, more specifically, bioenergetics. It is not immediately obvious how one might study the evolution of a chemical reaction. It is, however, obvious that in order to investigate the evolution of life’s common thread, the harnessing of exergonic chemical reactions for the purpose of conserving energy as ATP, one has to think outside the extremely narrow confines of phylogenetic trees, sequence alignments, and models that compare different trees by statistical criteria such as log likelihood values. When we consider the overall course of microbial evolution, physiology and phylogeny do not correspond well, because lateral gene transfer is very real and very prevalent among prokaryotes, and lateral gene transfer decouples physiology from phylogeny. This chapter presents a view of early microbial evolution from the author’s non-mainstream perspective. The text is based upon recently published papers about physiology, phylogeny, and evolution (Martin 2016), early CO₂ reduction (Sousa et al. 2018) and aspects concerning the advent of photosynthesis (Martin et al. 2018).

Physiology and Phylogeny

Before the days of molecular phylogenies, the standard way of viewing microbial evolution was as a process of physiological evolution (Eck and Dayhoff 1968, Decker et al. 1970, Dickerson 1980). The object of investigating physiological evolution was to order the sequence of events in which the different pathways arose that modern microbes use to harness carbon and energy. The physiological view of microbial evolution was, of course, replaced in the 1980s by a gene centered view of microbial evolution that was constructed around the ribosomal RNA tree of life, also called the universal tree or the three domain tree (Woese et al. 1990). The rRNA tree installed the order into microbial systematics that microbiologists had sought for decades (Stanier and van Niel 1962), but did not explain much about physiological evolution because physiology never mapped properly onto the rRNA tree. That was not because the branching pattern in rRNA tree missed the true branching order for microbial lineages but because microbial physiology never mapped cleanly onto any phylogenetic tree for prokaryotes, regardless of its topology, because of lateral gene transfer (LGT). Dickerson (1980) suggested that LGT could possibly even transform non-respiring lineages into respiring lineages via the transfer of many genes, something that we now know actually occurs during microbial evolution (Nelson-Sathi et al. 2012).

Is the evolutionary history of microbes a history of ribosome phylogenies, or is it a history of physiological processes? Knoll has said that Earth records its own history (Gaidos and Knoll 2012). So do genomes. Putting geological and genomic evidence into a consistent picture of microbial evolution is a challenging task, especially if energetics is to enter into the picture as well (Shock and Boyd 2015). The only connection between rocks and genes is physiology. Physiology is arguably what life is all about, because if the core ATP generating reaction of an organism comes to a halt, so does the life process and all else in the evolutionary process including population genetics, bottlenecks, drift and the like. The only microbial processes that have left an interpretable trace in the geochemical record are physiological.

Rocks preserve evidence of microbial activity in the form of carbon (Ueno et al. 2006), sulfur (Poulton et al. 2004) and nitrogen (Stüecken et al. 2015) isotopes, in addition to evidence for molecular oxygen (Fischer et al. 2016). The oldest sedimentary rocks, which are ca. 3.8 billion years of age, harbor traces for life in the form of light carbon isotopes, which is generally interpreted as evidence for biological CO₂ fixation at that time (Mojzsis et al. 1996, Ueno et al. 2002), although new findings have it that biological CO₂ fixation goes back as far as 3.95 Ga (Tashiro et al. 2017). Geologists also tell us that nitrogen fixation has been around for at least 3.2 billion years (Stüecken et al., 2015) and that molecular oxygen has been around for about 2.4 billion years (Fischer et al., 2016, Lyons et al. 2014). Rocks date the existence of microbial physiological processes, the distribution of which is rarely restricted to specific phylogenetic groups.

In the geochemical record that extends beyond roughly 1.5 billion years ago, there are only two kinds of geochemical traces that correspond to evidence for the existence of any modern prokaryotic group. One is the presence of molecular oxygen, which indicates the existence of cyanobacteria 2.4 billion years ago (Fischer et al., 2016). The other is biogenic methane in rocks 3.5 billion years of age, which provides evidence for the antiquity of archaea (Ueno et al., 2006) because methanogenesis is restricted to the archaea. The antiquity of biological methane does not, however, indicate which groups of methanogens are ancient because new phylogenetic depictions of the tree of life have methanogens basal among the archaea, with loss of methanogenesis having occurred in many independent groups (Evans et al. 2015, Williams et al. 2017), those losses corresponding to gene acquisitions from bacteria and changes in physiology in some cases (Nelson Sathi et al. 2012, 2015). LGT thus decouples phylogeny from physiology in the methanogens, too, which now appear to be the most ancient archaea, but no longer appear as a monophyletic group (Fig. 1).

Most physiological traits that are preserved as isotopic evidence in ancient rocks, whether CO₂ reduction (Fuchs 2011, Berg et al. 2010), N₂ reduction (Zehr et al. 2001), or sulfur reduction (Rabus et al. 2015), are present in many different prokaryotic groups, both among the archaea and among the bacteria. There can also be little doubt that those physiological traits, regardless of whether they were present in the last universal common ance...

Table of contents

• Cover
• Halftitle
• Title Page
• Copyright Page
• Dedication
• Preface
• Table of Contents