This book is a printed edition of the Special Issue "Microbial Community Modeling: Prediction of Microbial Interactions and Community Dynamics" that was published in Processes

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.

Elements move through Earth's critical zone along interconnected pathways that are strongly influenced by fluctuations in water and energy. The biogeochemical cycling of elements is inextricably linked to changes in climate and ecological disturbances, both natural and man-made. Biogeochemical Cycles: Ecological Drivers and Environmental Impact examines the influences and effects of biogeochemical elemental cycles in different ecosystems in the critical zone. Volume highlights include: Impact of global change on the biogeochemical functioning of diverse ecosystems Biological drivers of soil, rock, and mineral weathering Natural elemental sources for improving sustainability of ecosystems Links between natural ecosystems and managed agricultural systems Non-carbon elemental cycles affected by climate change Subsystems particularly vulnerable to global change The American Geophysical Union promotes discovery in Earth and space science for the benefit of humanity. Its publications disseminate scientific knowledge and provide resources for researchers, students, and professionals. Find out more about this book from this Q&A with the Author. Book Review: http://www.elementsmagazine.org/archives/e16_6/e16_6_dep_bookreview.pdf

Can physics be an appropriate framework for the understanding of ecological science? Most ecologists would probably agree that there is little relation between the complexity of natural ecosystems and the simplicity of any example derived from Newtonian physics. Though ecologists have long been interested in concepts originally developed by statistical physicists and later applied to explain everything from why stock markets crash to why rivers develop particular branching patterns, applying such concepts to ecosystems has remained a challenge. Self-Organization in Complex Ecosystems is the first book to clearly synthesize what we have learned about the usefulness of tools from statistical physics in ecology. Ricard Solé and Jordi Bascompte provide a comprehensive introduction to complex systems theory, and ask: do universal laws shape the structure of ecosystems, at least at some scales? They offer the most compelling array of theoretical evidence to date of the potential of nonlinear ecological interactions to generate nonrandom, self-organized patterns at all levels. Tackling classic ecological questions--from population dynamics to biodiversity to macroevolution--the book's novel presentation of theories and data shows the power of statistical physics and complexity in ecology. Self-Organization in Complex Ecosystems will be a staple resource for years to come for ecologists interested in complex systems theory as well as mathematicians and physicists interested in ecology.

Systems-Level Modelling of Microbial Communities: Theory and Practice introduces various aspects of modelling microbial communities and presents a detailed overview of the computational methods which have been developed in this area. This book is aimed at researchers in the field of computational/systems biology as well as biologists/experimentalists studying microbial communities, who are keen on embracing the concepts of computational modelling. The primary focus of this book is on methods for modelling interactions between micro-organisms in a community, with special emphasis on constraint-based and network-based modelling techniques. A brief overview of population- and agent-based modelling is also presented. Lastly, it covers the experimental methods to understand microbial communities, and provides an outlook on how the field may evolve in the coming years.

Teaches the application of Reactive Transport Modeling (RTM) for subsurface systems in order to expedite the understanding of the behavior of complex geological systems This book lays out the basic principles and approaches of Reactive Transport Modeling (RTM) for surface and subsurface environments, presenting specific workflows and applications. The techniques discussed are being increasingly commonly used in a wide range of research fields, and the information provided covers fundamental theory, practical issues in running reactive transport models, and how to apply techniques in specific areas. The need for RTM in engineered facilities, such as nuclear waste repositories or CO2 storage sites, is ever increasing, because the prediction of the future evolution of these systems has become a legal obligation. With increasing recognition of the power of these approaches, and their widening adoption, comes responsibility to ensure appropriate application of available tools. This book aims to provide the requisite understanding of key aspects of RTM, and in doing so help identify and thus avoid potential pitfalls. Reactive Transport Modeling covers: the application of RTM for CO2 sequestration and geothermal energy development; reservoir quality prediction; modeling diagenesis; modeling geochemical processes in oil & gas production; modeling gas hydrate production; reactive transport in fractured and porous media; reactive transport studies for nuclear waste disposal; reactive flow modeling in hydrothermal systems; and modeling biogeochemical processes. Key features include: A comprehensive reference for scientists and practitioners entering the area of reactive transport modeling (RTM) Presented by internationally known experts in the field Covers fundamental theory, practical issues in running reactive transport models, and hands-on examples for applying techniques in specific areas Teaches readers to appreciate the power of RTM and to stimulate usage and application Reactive Transport Modeling is written for graduate students and researchers in academia, government laboratories, and industry who are interested in applying reactive transport modeling to the topic of their research. The book will also appeal to geochemists, hydrogeologists, geophysicists, earth scientists, environmental engineers, and environmental chemists.

The editors have enlisted a broad range of experts, including microbial ecologists, physiologists, geneticists, biochemists, molecular biologists, and biochemical engineers, who offer practical experience not found in texts and journals. This comprehensive perspective makes MIMB a valuable "how to" resource, the structure of which resembles the sequence of operation involved in the development of a commercial biological process and product.

The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.

This volume highlights recent advances that have contributed to our understanding of spatial patterns and scale issues in microbial ecology. The book brings together research conducted at a range of spatial scales (from μm to km) and in a variety of different types of environments. These topics are addressed in a quantitative manner, and a primer on statistical methods is included. In soil ecosystems, both bacteria and fungi are discussed.