One of the most profound paradigms that have transformed our understanding about life over the last decades was the acknowledgement that microorganisms play a central role in shaping the past and present environments on Earth and the nature of all life forms. Each organism is the product of its history and all extant life traces back to common ancestors, which were microorganisms. Nowadays, microorganisms represent the vast majority of biodiversity on Earth and have survived nearly 4 billion years of evolutionary change. Microbial evolution occurred and continues to take place in a great variety of environmental conditions. However, we still know little about the processes of evolution as applied to microorganisms and microbial populations. In addition, the molecular mechanisms by which microorganisms communicate/interact with each other and with multicellular organisms remains poorly understood. Such patterns of microbe-host interaction are essential to understand the evolution of microbial symbiosis and pathogenesis.Recent advances in DNA sequencing, high-throughput technologies, and genetic manipulation systems have enabled studies that directly characterize the molecular and genomic bases of evolution, producing data that are making us change our view of the microbial world. The notion that mutations in the coding regions of genomes are, in combination with selective forces, the main contributors to biodiversity needs to be re-examined as evidence accumulates, indicating that many non-coding regions that contain regulatory signals show a high rate of variation even among closely related organisms. Comparative analyses of an increasing number of closely related microbial genomes have yielded exciting insight into the sources of microbial genome variability with respect to gene content, gene order and evolution of genes with unknown functions. Furthermore, laboratory studies (i.e. experimental microbial evolution) are providing fundamental biological insight through direct observation of the evolution process. They not only enable testing evolutionary theory and principles, but also have applications to metabolic engineering and human health. Overall, these studies ranging from viruses to Bacteria to microbial Eukaryotes are illuminating the mechanisms of evolution at a resolution that Darwin, Delbruck and Dobzhansky could barely have imagined. Consequently, it is timely to review and highlight the progress so far as well as discuss what remains unknown and requires future research. This book explores the current state of knowledge on the molecular mechanisms of microbial evolution with a collection of papers written by authors who are leading experts in the field.

One of the most profound paradigms that have transformed our understanding about life over the last decades was the acknowledgement that microorganisms play a central role in shaping the past and present environments on Earth and the nature of all life forms. Each organism is the product of its history and all extant life traces back to common ancestors, which were microorganisms. Nowadays, microorganisms represent the vast majority of biodiversity on Earth and have survived nearly 4 billion years of evolutionary change. Microbial evolution occurred and continues to take place in a great variety of environmental conditions. However, we still know little about the processes of evolution as applied to microorganisms and microbial populations. In addition, the molecular mechanisms by which microorganisms communicate/interact with each other and with multicellular organisms remains poorly understood. Such patterns of microbe-host interaction are essential to understand the evolution of microbial symbiosis and pathogenesis. Recent advances in DNA sequencing, high-throughput technologies, and genetic manipulation systems have enabled studies that directly characterize the molecular and genomic bases of evolution, producing data that are making us change our view of the microbial world. The notion that mutations in the coding regions of genomes are, in combination with selective forces, the main contributors to biodiversity needs to be re-examined as evidence accumulates, indicating that many non-coding regions that contain regulatory signals show a high rate of variation even among closely related organisms. Comparative analyses of an increasing number of closely related microbial genomes have yielded exciting insight into the sources of microbial genome variability with respect to gene content, gene order and evolution of genes with unknown functions. Furthermore, laboratory studies (i.e. experimental microbial evolution) are providing fundamental biological insight through direct observation of the evolution process. They not only enable testing evolutionary theory and principles, but also have applications to metabolic engineering and human health. Overall, these studies ranging from viruses to Bacteria to microbial Eukaryotes are illuminating the mechanisms of evolution at a resolution that Darwin, Delbruck and Dobzhansky could barely have imagined. Consequently, it is timely to review and highlight the progress so far as well as discuss what remains unknown and requires future research. This book explores the current state of knowledge on the molecular mechanisms of microbial evolution with a collection of papers written by authors who are leading experts in the field.

Bacteria have been the dominant forms of life on Earth for the past 3.5 billion years. They rapidly evolve, constantly changing their genetic architecture through horizontal DNA transfer and other mechanisms. Consequently, it can be difficult to define individual species and determine how they are related. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines how bacteria and other microbes evolve, focusing on insights from genomics-based studies. Contributors discuss the origins of new microbial populations, the evolutionary and ecological mechanisms that keep species separate once they have diverged, and the challenges of constructing phylogenetic trees that accurately reflect their relationships. They describe the organization of microbial genomes, the various mutations that occur, including the birth of new genes de novo and by duplication, and how natural selection acts on those changes. The role of horizontal gene transfer as a strong driver of microbial evolution is emphasized throughout. The authors also explore the geologic evidence for early microbial evolution and describe the use of microbial evolution experiments to examine phenomena like natural selection. This volume will thus be essential reading for all microbial ecologists, population geneticists, and evolutionary biologists.

Dr. Joshua Lederberg - scientist, Nobel laureate, visionary thinker, and friend of the Forum on Microbial Threats - died on February 2, 2008. It was in his honor that the Institute of Medicine's Forum on Microbial Threats convened a public workshop on May 20-21, 2008, to examine Dr. Lederberg's scientific and policy contributions to the marketplace of ideas in the life sciences, medicine, and public policy. The resulting workshop summary, Microbial Evolution and Co-Adaptation, demonstrates the extent to which conceptual and technological developments have, within a few short years, advanced our collective understanding of the microbiome, microbial genetics, microbial communities, and microbe-host-environment interactions.

Today's microorganisms represent the vast majority of biodiversity on Earth and have survived nearly 4 billion years of evolutionary change. However, we still know little about the processes of evolution as applied to microorganisms and microbial populations. Microbial evolution occurred and continues to take place in a vast variety of environmental conditions that range from anoxic to oxic, from hot to cold, from free-living to symbiotic, etc. Some of these physicochemical conditions are considered "extreme", particularly when inhabitants are limited to microorganisms. It is easy to imagine that microbial life in extreme environments is somehow more constrained and perhaps subjected to different evolutionary pressures. But what do we actually know about microbial evolution under extreme conditions and how can we apply that knowledge to other conditions? Appealingly, extreme environments with their relatively limited numbers of inhabitants can serve as good model systems for the study of evolutionary processes. A look at the microbial inhabitants of today's extreme environments provides a snapshot in time of evolution and adaptation to extreme conditions. These adaptations manifest at different levels from established communities and species to genome content and changes in specific genes that result in altered function or gene expression. But as a recent (2011) report from the American Academy of Microbiology observes: "A complex issue in the study of microbial evolution is unraveling the process of evolution from that of adaptation. In many cases, microbes have the capacity to adapt to various environmental changes by changing gene expression or community composition as opposed to having to evolve entirely new capabilities." We have learned much about how microbes are adapted to extreme conditions but relatively little is known about these adaptations evolved. How did the different processes of evolution such as mutation, immigration, horizontal (lateral) gene transfer, recombination, hybridization, genetic drift, fixation, positive and negative selection, and selective screens contribute to the evolution of these genes, genomes, microbial species, communities, and functions? What are typical rates of these processes? How prevalent are each of these processes under different conditions? This book explores the current state of knowledge about microbial evolution under extreme conditions and addresses the following questions: What is known about the processes of microbial evolution (mechanisms, rates, etc.) under extreme conditions? Can this knowledge be applied to other systems and what is the broader relevance? What remains unknown and requires future research? These questions will be addressed from several perspectives including different extreme environments, specific organisms, and specific evolutionary processes.

Molecular Mechanisms of Plant and Microbe Coexistence presents studies on the complex and manifold interactions of plants and microbes at the population, genomics and proteomics level. The role of soil microbial diversity in enhancing plant health and plant microbe beneficial symbioses is discussed. Microbial communities are shown in the light of evolution. Main topics include genome coexistence and the functional genomics and proteomics of plant-associated microbes, which could form the basis for new environmentally benign strategies to combat infectious plant diseases and regulate plant growth. Further chapters focus on the role of signaling during the different stages of plant microbe coexistence, in symbiotic or pathogenic relationships, in quorum sensing and plant viral infections. Methods for studying the interactions in the root zone complement the book, which will certainly be of relevance in the practical application to agriculture, food security and for maintaining the balance of our ecosystems.

The extent of lateral gene transfer among diverse microbes has effectively broken down the concept of species when we seek to apply it to the microbial world. This book brings together workers to try to reach an accomodation and consensus on the outline of how cellular life has evolved.

In recent decades we have come to realize that the microbial world is hugely diverse, and can be found in the most extreme environments. Fungi, single-celled protists, bacteria, archaea, and the vast array of viruses and sub-viral particles far outnumber plants and animals. Microbes, we now know, play a critical role in ecosystems, in the chemistry of atmosphere and oceans, and within our bodies. The field of microbiology, armed with new techniques from molecular biology, is now one of the most vibrant in the life sciences. In this Very Short Introduction Nicholas P. Money explores not only the traditional methods of microscopy and laboratory culture but also the modern techniques of genetic detection and DNA sequencing, genomic analysis, and genetic manipulation. In turn he demonstrates how advances in microbiology have had a tremendous impact on the areas of medicine, agriculture, and biotechnology. ABOUT THE SERIES: The Very Short Introductions series from Oxford University Press contains hundreds of titles in almost every subject area. These pocket-sized books are the perfect way to get ahead in a new subject quickly. Our expert authors combine facts, analysis, perspective, new ideas, and enthusiasm to make interesting and challenging topics highly readable.

Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.

Principles of Bacterial Pathogenesis presents a molecular perspective on a select group of bacterial pathogens by having the leaders of the field present their perspective in a clear and authoritative manner. Each chapter contains a comprehensive review devoted to a single pathogen. Several chapters include work from authors outside the pathogenesis field, providing general perspectives on the evolution, regulation, and secretion of virulence and determinants. - Explains the basic principles of bacterial pathogenesis - Covers diverse aspects integrating regulation, cellular microbiology and evolution of microbial disease of humans - Discusses current strategies for the identification of virulence determinants and the methods used by microbes to deliver virulence factors - Presents authoritative treatises of the major disease microorganisms