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.

The 21st century has witnessed a complete revolution in the understanding and description of bacteria in eco- systems and microbial assemblages, and how they are regulated by complex interactions among microbes, hosts, and environments. The human organism is no longer considered a monolithic assembly of tissues, but is instead a true ecosystem composed of human cells, bacteria, fungi, algae, and viruses. As such, humans are not unlike other complex ecosystems containing microbial assemblages observed in the marine and earth environments. They all share a basic functional principle: Chemical communication is the universal language that allows such groups to properly function together. These chemical networks regulate interactions like metabolic exchange, antibiosis and symbiosis, and communication. The National Academies of Sciences, Engineering, and Medicine's Chemical Sciences Roundtable organized a series of four seminars in the autumn of 2016 to explore the current advances, opportunities, and challenges toward unveiling this "chemical dark matter" and its role in the regulation and function of different ecosystems. The first three focused on specific ecosystemsâ€"earth, marine, and humanâ€"and the last on all microbiome systems. This publication summarizes the presentations and discussions from the seminars.

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.

Special features of this second edition are: complete coverage of all aspects of microbiology; a newly updated and expanded treatment of microbial physiology and metabolism; a completely new approach to presenting the biology of eukaryotic microorganisms; updated information on genetics and genomics; a more extensive, phylogenetic approach to microbial diversity; a revised up-to-date section on microbial structure and function that reflects current concepts and techniques; expanded treatment of microbial diseases; recent information about the taxonomy, evolution, and speciation of Bacteria and Archaea; a new section on energetics covering both chemical and light energy conservation; expanded and updated treatment of immunology; chapters on the popular area of beneficial symbioses and on human host-microbe interactions; separate chapters on industrial microbiology and applied and environmental microbiology.

Microbial systems in extreme environments and in the deep biosphere may be analogous to potential life on other planetary bodies and hence may be used to investigate the possibilities of extraterrestrial life. This book examines the mode and nature of links between geological processes and microbial activities and their significance for the origin and evolution of life on the Earth and possibly on other planets. This is a truly interdisciplinary science with societal relevance.

The marvelous microbes that made life on Earth possible and support our very existence For almost four billion years, microbes had the primordial oceans all to themselves. The stewards of Earth, these organisms transformed the chemistry of our planet to make it habitable for plants, animals, and us. Life's Engines takes readers deep into the microscopic world to explore how these marvelous creatures made life on Earth possible—and how human life today would cease to exist without them. Paul Falkowski looks "under the hood" of microbes to find the engines of life, the actual working parts that do the biochemical heavy lifting for every living organism on Earth. With insight and humor, he explains how these miniature engines are built—and how they have been appropriated by and assembled like Lego sets within every creature that walks, swims, or flies. Falkowski shows how evolution works to maintain this core machinery of life, and how we and other animals are veritable conglomerations of microbes. A vibrantly entertaining book about the microbes that support our very existence, Life's Engines will inspire wonder about these elegantly complex nanomachines that have driven life since its origin. It also issues a timely warning about the dangers of tinkering with that machinery to make it more "efficient" at meeting the ever-growing demands of humans in the coming century.

"Microcosmos is nothing less than the saga of the life of the planet. Lynn Margulis and Dorion Sagan have put it all together, literally, in this extraordinary book, which is unlike any treatment of evolution for a general readership that I have encountered before. A fascinating account that we humans should be studying now for clues to our own survival."—From the Foreword by Dr. Lewis Thomas Microcosmos brings together the remarkable discoveries of microbiology in the later decades of the 20th century and the pioneering research of Dr. Margulis to create a vivid new picture of the world that is crucial to our understanding of the future of the planet. Addressed to general readers, the book provides a beautifully written view of evolution as a process based on interdependency and their interconnectedness of all life on the planet.

A powerful framework for understanding how natural selection shapes adaptation and biological design Design and diversity are the two great challenges in the study of life. Microbial Life History draws on the latest advances in microbiology to describe the fundamental forces of biological design and apply these evolutionary processes to a broad diversity of traits in microbial metabolism and biochemistry. Emphasizing how to formulate and test hypotheses of adaptation, Steven Frank provides a new foundation for exploring the evolutionary forces of design. He discusses the economic principles of marginal valuations, trade-offs, and payoffs in risky and random environments; the social aspects of conflict and cooperation; the demographic aspects of age and spatial heterogeneity; and the engineering control theory principles by which systems adjust to environments. Frank then applies these evolutionary principles to the biochemistry of microbial metabolism, providing the first comprehensive link between the forces that shape biological design and cellular energetics. Tracing how natural selection sculpts metabolism, Microbial Life History provides new perspectives on the life histories of organisms, from growth rate and survival to dispersal and defense against attack. Along the way, this incisive book addresses the conceptual and philosophical challenges confronting evolutionary biologists and other practitioners who study biological design and seek to apply its lessons.

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.

Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.