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Microbes and Evolution: The World That Darwin Never Saw

Editors: Roberto Kolter1, Stanley Maloy2
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Affiliations: 1: Harvard Medical School, Boston, MA 02115; 2: San Diego State University, San Diego, CA 92182-1010;
Content Type: Trade
Publication Year: 2012

Category: General Interest; Microbial Genetics and Molecular Biology

Inspired by a 2009 colloquium on microbial evolution convened at the Galapagos Islands, celebrates Charles Darwin and his landmark book . Through this collection of 40 first-person essays written by microbiologists with a passion for evolutionary biology, you'll come to understand how their thinking and career paths in science were influenced by Darwin's seminal work.

The essays in explore how the evidence of microbial evolution deeply and personally affected each scientist. Prepare to be suprised and delighted with their views on the importance of evolutionary principles in the study of a variety of aspects of life science, from taxonomy, speciation, adaptation, social structure, and symbiosis to antibiotic resistance, genetics, and genomics.

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Small Things Considered

02 June 2013

Maybe it’s the lava fields in the Galapagos, maybe it's the giant tortoises, but something caused a bunch of microbiological luminaries to come out of their shells and write a bit about what they think and feel regarding evolution. A meeting held in those islands in 2009—being Darwin’s 200th birthday—brought together some 40 people instructed to discuss microbes and evolution. Out of this came an extraordinary thin volume, an anthology of lively essays that largely succeeded in laying bare the personal reflections of the participants. And they wrote in plain English. This is quite an unusual book in the history of scientific writing. Although many people have written notable personal accounts of how they relate to their science, rarely has there been such a successful convergent effort.

The book encompasses a large variety of topics related to the subject at hand. Relatively few chapters actually focus on evolution directly, but this probably reflects the relative newness and paucity of laboratory studies in evolutionary microbiology. In some cases, the connection seems to be a bit of a stretch, based perhaps on the Dobzanskyian dictum. By stating that Nothing in biology makes sense except in the light of evolution, Dobzansky forced all biologists to pay at least lip service to connections between their work and the Big E. This is not always an easy thing to do, and in some cases, the efforts in the book can be called intrepid. But even in the seemingly less-related chapters, the nexus is not perfunctory and Darwin’s presence is keenly felt. And the ideas are consistently presented in a readable, ever stimulating fashion. In the end, about half of the participants had something to say about Darwin; the other half, what Darwin would have said about them.

To give you the flavor of what's inside this book, here are a few bons mots, chosen almost at random.

Whether viewed from the bow of the Beagle or through the lens of the microscope, all life is bound by the same evolutionary rules. P. 41

Please don't tell my mother, but for years I’ve wanted to be Charles Darwin. P. 263

...we can expect natural environments to contain a lumpy continuum of microbial genotypes and phenotypes. P. 273

So most of the evolution on this planet is actually being carried out by entities Darwin never imagined and at a scale he never could have considered. P. 69

I found this a most satisfying book, laced with charm and sharp insights. Buy it, treasure it, and keep it for your grandchildren. It will wear well. And, at the price, this is a bargain you may never see again.

Small Things Considered

Reviewer: Elio

Review Date: July 2012

Microbe Magazine

30 May 2013

The idea for this book emerged from an American Academy of Microbiology Colloquium in 2007 in the Galapagos, and was intended by the editors to celebrate the 200th anniversary of the publication of Darwin’s Origin of the Species and the Descent of Man. The editors have assembled 40 provocative chapters by some of the leading evolutionary microbiologists who resent their personal perspectives of their work. The microbiological sweep of the book is irresistible, including evolution of diversity, speciation, phylogeny, shape, the origin of mutation, social behavior, adaptation, antibiosis, photosynthesis, ants, geomicrobiology, sex, and roller derby. But there is an underlying theme to the book that unites the topical diversity and reflects Dobzhansky’s aphorism that “Nothing in biology makes sense except in the light of evolution.” It is almost as if the book were really titled If Darwin Were Alive Today, What Would He Be Thinking About?

As I read each of the essays in preparation for this review, my strategy was to describe only a small handful of the essays as exemplars. Alas, after reading the fırst 15, I had selected all of them. So I have instead relied on my own biases and interests to select the exemplars, but I assure you that every one of the 40 essays in this remarkable book merits your attention.

Imagine a system for studying an animal microbe symbiosis where the host doesn’t bite, goes through a developmental cycle that can be duplicated in the lab, whose microbe is a luminescent bacterium, confıned as a pure culture in a defıned space and able to be easily cultivated. And oh, by the way, lives in the warm waters of Hawaii. Ned Ruby and Margaret McFall-Ngai have characterized such a system and de- scribe it in their essay “Deciphering the Language of Diplomacy: Give and Take in the Study of the Squid-Vibrio Symbiosis.”

For those for whom the 16S RNA-based Tree of Life and the phylogenetic approach to understanding the relationships among microbes are dogma, the following quote from Ford Doolitle’s essay “Postphylogenetics” will give pause. “. . . it seems likely that neither the Tree of Life . . . nor the phylotype-based environmental microbiology will survive the 21st century with all its paradigms intact.” But more optimistically “. . . there is beyond a doubt a Tree of Life connecting all organisms (Howard Ochman, “Sexual Diffıculties”).

Forest Rowher (“Phage: An Important Evolutionary Force Darwin Never Knew”) discusses an aspect of evolu- tionary change that Darwin never had a clue about, namely the immense genomic potential of the collective viral genome. Given the approximately 1031 bacteriophage particles on planet Earth and their role in horizontal gene transfer, phage-driven microbial evolution represents a major driving force in evolution.

For students wondering if there are still new worlds to discover, Sallie Chisholm‘s essay “Unveiling Prochlorococcus: the Life and Times of the World’s Smallest Photosynthetic Cell” is reassuring. This smallest inhabitantof the world’s oceans was recognized a mere 25 years ago. It is ubiquitous in the ocean—shallow, deep, east, west, tropical, or cold. It has adapted to all these environments over millions of years but has only recently been discovered.

John Roth (“How Bacteria Revealed Darwin’s Mistake”) is concerned with the pesky question of the origins of mu- tations. Did the classic Luria-Delbruck experiment answer the question? And did the later Cairns experiment raise the issue anew? Roth points out that Darwin’s idea of stress-induced mutation was wrong, that the Luria-Del-bruck experiment was incomplete, and that Cairns’ experiment was flawed. He emphasizes the powerful and often overlooked role of common small effect mutations on evolution.

For those who may fınd themselves seduced by the Circe of irreducible complexity, the essays of Andres Moyas (“Minimal Genomes and Reducible Compexity”) which discusses the minimal genome and motility apparatus of the aphid symbiont Buchnera, plus the discussion of flagellar assembly by Blair and Hughes (“Irreducible Complexity? Not!”) will provide a persuasive antidote.

We have all read that conventional sampling techniques provide us with only a tiny glimpse of the true spectrum of microbial diversity. Mitch Sogin (“Trying to Make Sense of the Microbial Census”) discusses this challenge and suggests that based on statistical analyses and new approaches “. . . theory predicts that diversity in the microbial world might be too great to fully measure.”

It is also fun to watch the transition made by Jessica Green, aka “Thumper” Green, a microbial biogeographer and a blocker in the Flat Track Furies, a Roller Derby team, as she moves from the spatial dynamics of her teammate Lady Lump’s mouthguard flora to bio-geography.

Philippe Sansonetti (“On the Origin of Bacterial Pathogenic Species by Means of Natural Selection: A Tale of Coevolution”) discusses the conversion to virulence resulting from the rapid acquisition, via horizontal transfer of genome sequences, often followed by massive genome reduction. Equally interesting are the genetic “black holes” that either are responsible for genome reduction or may result in decreases in virulence.

In some of the essays, e.g. Tom Schmidt’s “Bacteria Battling for Survival” and Dianne Newman’s “In Pursuit of Billion-Year-Old Rosetta Stones,” we are privileged to learn the answer to ”And just how did you get to do this fascinating stuff that you do?”

Darwin placed heavy emphasis on geographic divergence as a determining factor in the evolution of diversity and speciation. A number of essays in the book examine this precept from a microbial point of view. Rachel Whitaker (“A New Age of Naturalists”) examines the role of bacteriophage as determinants of the adaptation of the extremophilic Archaon Sulfolobus. Paul Rainey (“The Evolution of Diversity and the Emergence of Rules Governing Phenotypic Evolution”) describes the adaptive radiation of Pseudomonas fluorescens in static and shaken lab cultures, and found their evolution strikingly similar to Darwin’s description of adaptive radiation of fınches in the Galapagos. And Johannes Sikorski (“A Glimpse Into Microevolution in Nature. Adaptation and Speciation of Bacillus simplex from Evolution Canyon”) not only recounts his own evolution from a creationist Christian to an evolutionary microbiologist, but also describes the existence of phenotypic and genetic diversity in 1,000 stains of Bacillus simplex isolated from two geographically separated canyons in Israel, each with two facing slopes of widely different environments.

Each of the essays is preceded by an often ideosyncratic mini-biography of its author. As I read them I longed to meet each of their authors. It often astonishes me that not everyone wants to be a biologist—a puzzlement that is reinforced by this wonderful book—and what a bargain it is at $14.95.

Microbe Magazine

Reviewer: Martin Dworkin, Microbe Reviews Editor, University of Minnesota, Minneapolis

Review Date: August 2012

Journal of Microbiology and Biology Education (JMBE)

30 May 2013

MICROORGANISMS ENHANCE UNDERSTANDING OF EVOLUTION

Microbes and Evolution: The World That Darwin Never Saw is a paperback collection of essays written by eminent researchers. Very short essays provide compelling reading with substantial factual and hypothetical information. The authors cover a broad diversity of interesting and useful topics, revealing personal interests and how their scientific research fits into and, in some cases, changed their lives. The authors write passionately and with excitement inviting everyone to join in their research journeys. The book is a great reference source of expertly written essays with detailed, succinct background information, most with additional readings, and some with figures and illustrations. There is also a helpful index for navigating to topics of interest. The collection of short essays can easily be used by educators in many disciplines. For example, it can be used to prepare students for discussions about how evolution relates to DNA, and allows them to compare Darwin’s phenotypic studies to a modern view of genotypic research, now made easy using bioinformatics and genomic techniques. Many authors use simple analogies to explain the workings of evolution, comparing it to a software program continually being upgraded, and overuse of antibiotics to running too quickly and too soon, instead of setting a slow, consistent pace. The essays bring up many important questions posed by authors concerning evolutionary processes related to their research.

Additionally, essays document the role of microbes as the first life form, initiating explosive development of aerobic organisms, and microbial roles in endosymbiosis. The authors pay homage to Darwin’s seminal work, pointing out questions Darwin could not answer but can now be answered. Students skeptical of macroevolution may understand essays on “test tube evolution” describing random mutation and selection in varied environmental conditions, and observing microevolution in short periods of time and not eons. Another essay addresses the power of reverse genetics to determine gene additions and deletions, providing pathways for commensals to evolve into pathogens. Writings cover core concepts such as how the species definition relates to prokaryotes, horizontal gene transfer and leaps in rapid diversification, and classifications in the tree of life, all of which Darwin did not discover.

While some essays may start discussion on practical topics such as increased antibiotic resistance, pathogenicity islands and virulence, and co-evolution of host/parasite and immune system, the collection may also serve to stimulate debate and hypothesis-generation. Essays on using metagenomics to study microbial interactions in unique natural environments and to catalogue entire ecosystems of microbes could preface debate about disrupting environmental microbial ecosystems, agriculture, biofilms, and the human microbiome. The role of viruses in evolution and the impact of their absence on the tree of life are presented, as well as the role of pseudogenes in driving co-evolution, genome reduction, and host restriction in parasitic relationships. Authors describe small core genomes of certain bacteria, such as E. coli or Prochlorococcus, and the large available gene pool resulting in diversification into new strains. Compelling essays discuss altruistic bacteria, the role of non-coding RNAs in multiple phenotypic expressions of the same genes, and long-term stationary-phase mutants that live continuously. Other essays bring forward the implications of interkingdom conjugation, and the role of transformation as means of obtaining nutrients rather than a need for new genetic material. In total, students are reminded that humans depend on microbial life for survival, and that these organisms live with us in continuous evolutionary flux and refinement. Authors point out that microbes have shown us it is better not to kill everything but to live together for survival—an important concept for students of any discipline. The collection suggests that our understanding of evolution might have been very different if Darwin had started studying microbes.

Journal of Microbiology & Biology Education (JMBE)

Reviewer: Deborah V. Harbour, College of Southern Nevada, Las Vegas, NV

Review Date: December 2012

Microbiology Today

03 March 2013

Initially stimulated by the bicentenary of Darwin's birth, this collection of essays discusses how microbes fit evolution as Darwin would have understood it. There are good examples of classical Darwinian evolution and cases where we have to bend our ideas somewhat.

Metaphor is a powerful tool for conveying concepts to a lay audience. Unfortunately, it ends up being confusing when the metaphor shifts every few pages. This is not, then, a book to be read from cover to cover, at least not in one sitting. It is also unclear at whom this book is aimed. Many chapters would be clear to any intelligent reader, but others seem to be written for an audience of microbiologists or molecular biologists. That said, there are some excellent essays in this collection and I shall use ideas from it when teaching the concept of microbiology to general biologists.

Society for General Microbiology: Microbiology Today

Reviewer: David Roberts, The Natural History Museum

Review Date: 2012

CHOICE

03 December 2012

Biologists have a long history of using the microbial world as a ready-made laboratory for the exploration and testing of evolutionary theory. The editors of this volume, inspired by the 200th anniversary of Darwin's birth and the 150th anniversary of the publication of The Origin of Species, have assembled a fascinating, entertaining, and informative collection of scientific essays that focuses on the burgeoning field of microbial ecology and evolution.

Written by leading researchers, the essays address the most current research, and they will certainly be of great use to other researchers in the field. However, the stated purpose of this book was to make microbial ecology and evolution more accessible to general readers, and in this, the editors have succeeded. Many of the essays have interesting, eye-catching titles, and most of the researchers/contributors include personal vignettes that relate how they arrived at their particular fields of research, including wrong turns and serendipitous events. Each essay is accompanied by a short but useful list of references for further reading, and the book includes a complete index.

Summing Up: Highly recommended. All readership levels.

CHOICE Current Reviews for Academic Libraries

SCIENCE AND TECHNOLOGY Biology

Vol. 50 No. 04

Reviewer: R. K. Harris, William Carey University

Review Date: December 2012

Reprinted with permission from CHOICE http://www.cro2.org, copyright by the American Library Association.

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