This collection represents certain discoveries that were made in evolutionary and genomic microbiology during the recent ten years. We attempted to shed light on topical issues of microbial evolution and microbiome biology. In our eyes, these articles are of an excellent quality and may be helpful both for casual readers and for specialists 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.

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.

This is the story of a profound revolution in the way biologists explore life's history, understand its evolutionary processes, and reveal its diversity. It is about life's smallest entities, deepest diversity, and greatest cellular biomass: the microbiosphere. Jan Sapp introduces us to a new field of evolutionary biology and a new brand of molecular evolutionists who descend to the foundations of evolution on Earth to explore the origins of the genetic system and the primary life forms from which all others have emerged. In so doing, he examines-from Lamarck to the present-the means of pursuing the evolution of complexity, and of depicting the greatest differences among organisms. The New Foundations of Evolution takes us into a world that classical evolutionists could never have imagined: a deep phylogeny based on three domains of life and multiple kingdoms, and created by mechanisms very unlike those considered by Darwin and his followers. Evolution by leaps seems to occur regularly in the microbial world where molecular evolutionists have shown the inheritance of acquired genes and genomes are major modes of evolutionary innovation. Revisiting the history of microbiology for the first time from the perspective of evolutionary biology, Sapp shows why classical Darwinian conceptions centering on questions of the origin of species were forged without a microbial foundation, why classical microbiologists considered it impossible to know the course of evolution, and classical molecular biologists considered the evolution of the molecular genetic system to be beyond understanding. In telling this stirring story of scientific iconoclasm, this book elucidates how the new evolutionary biology arose, what methods and assumptions underpin it, and the fiery controversies that continue to shape biologists' understanding of the foundations of evolution today.

This book proposes an important new paradigm for understanding biological evolution. Shapiro demonstrates why traditional views of evolution are inadequate to explain the latest evidence, and presents an alternative. His information- and systems-based approach integrates advances in symbiogenesis, epigenetics, and saltationism, and points toward an emerging synthesis of physical, information, and biological sciences.

The Logic of Chance offers a reappraisal and a new synthesis of theories, concepts, and hypotheses on the key aspects of the evolution of life on earth in light of comparative genomics and systems biology. The author presents many specific examples from systems and comparative genomic analysis to begin to build a new, much more detailed, complex, and realistic picture of evolution. The book examines a broad range of topics in evolutionary biology including the inadequacy of natural selection and adaptation as the only or even the main mode of evolution; the key role of horizontal gene transfer in evolution and the consequent overhaul of the Tree of Life concept; the central, underappreciated evolutionary importance of viruses; the origin of eukaryotes as a result of endosymbiosis; the concomitant origin of cells and viruses on the primordial earth; universal dependences between genomic and molecular-phenomic variables; and the evolving landscape of constraints that shape the evolution of genomes and molecular phenomes. "Koonin's account of viral and pre-eukaryotic evolution is undoubtedly up-to-date. His "mega views" of evolution (given what was said above) and his cosmological musings, on the other hand, are interesting reading." Summing Up: Recommended Reprinted with permission from CHOICE, copyright by the American Library Association.

This book examines the toxicological and health implications of environmental epigenetics and provides knowledge through an interdisciplinary approach. Included in this volume are chapters outlining various environmental risk factors such as phthalates and dietary components, life states such as pregnancy and ageing, hormonal and metabolic considerations and specific disease risks such as cancer cardiovascular diseases and other non-communicable diseases. Environmental Epigenetics imparts integrative knowledge of the science of epigenetics and the issues raised in environmental epidemiology. This book is intended to serve both as a reference compendium on environmental epigenetics for scientists in academia, industry and laboratories and as a textbook for graduate level environmental health courses. Environmental Epigenetics imparts integrative knowledge of the science of epigenetics and the issues raised in environmental epidemiology. This book is intended to serve both as a reference compendium on environmental epigenetics for scientists in academia, industry and laboratories and as a textbook for graduate level environmental health courses.