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Microbial mat communities consist of dense populations of microorganisms embedded in exopolymers and/or biomineralized solid phases, and are often found in mm-cm thick assemblages, which can be stratified due to environmental gradients such as light, oxygen or sulfide. Microbial mat communities are commonly observed under extreme environmental conditions, deriving energy primarily from light and/or reduced chemicals to drive autotrophic fixation of carbon dioxide. Microbial mat ecosystems are regarded as living analogues of primordial systems on Earth, and they often form perennial structures with conspicuous stratifications of microbial populations that can be studied in situ under stable conditions for many years. Consequently, microbial mat communities are ideal natural laboratories and represent excellent model systems for studying microbial community structure and function, microbial dynamics and interactions, and discovery of new microorganisms with novel metabolic pathways potentially useful in future industrial and/or medical applications. Due to their relative simplicity and organization, microbial mat communities are often excellent testing grounds for new technologies in microbiology including micro-sensor analysis, stable isotope methodology and modern genomics. Integrative studies of microbial mat communities that combine modern biogeochemical and molecular biological methods with traditional microbiology, macro-ecological approaches, and community network modeling will provide new and detailed insights regarding the systems biology of microbial mats and the complex interplay among individual populations and their physicochemical environment. These processes ultimately control the biogeochemical cycling of energy and/or nutrients in microbial systems. Similarities in microbial community function across different types of communities from highly disparate environments may provide a deeper basis for understanding microbial community dynamics and the ecological role of specific microbial populations. Approaches and concepts developed in highly-constrained, relatively stable natural communities may also provide insights useful for studying and understanding more complex microbial communities.
Systems biology is the study of interactions between assorted components of biological systems with the aim of acquiring new insights into how organisms function and respond to different stimuli. Although more and more efforts are being directed toward examining systems biology in complex multi-cellular organisms, the bulk of system-level analyses conducted to date have focused on the biology of microbes. In, Microbial Systems Biology: Methods and Protocols expert researchers in the field describe the utility and attributes of different tools (both experimental and computational) that are used for studying microbial systems. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microbial Systems Biology: Methods and Protocols introduces and aids scientists in using the various tools that are currently available for analysis, modification and utilization of microbial organisms.
Overview of ecological principles underlying natural and synthetic microbial communities Techniques to infer relationships in microbial communities from metagenomic sequences Detailed account of constraint-based methods to decipher metabolic interactions in microbial communities Case studies to illustrate applications of various community modelling approaches Brief outline of experimental methods to understand and characterise microbial communities
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.
Microbiologists have become interested in applying "systems biology" to understand and harness complex biological processes in microbial communities. A systems approach, which attempts to use comparative, high-throughput assays, and mathematical or computational models, has been used to generate a picture of system-wide activity that can yield insight into processes operating within a single cell. But the concept of integrating advances in genomics, proteomics, and metabolomics and incorporating them into mathematical models can also be applied to microbial ecosystems, which typically occur in consortia of related and unrelated organisms. Research on microbial communities using a system-based approach could provide a broader perspective on controls on biological processes and how they operate in and among microorganisms. The National Academies of Sciences, Engineering, and Medicine held a workshop on "Progress and Promises of Systems Microbiology" in August 2003, with the intent of providing a forum for discussion of the tools, technology, and programs that are needed to advance the study of microorganisms through a systems approach. Participants also discussed ways to encourage collaboration among scientists of different disciplines. This report summarizes the presentations and discussions from the workshop.
Microbial mat communities consist of dense populations of microorganisms embedded in exopolymers and/or biomineralized solid phases, and are often found in mm-cm thick assemblages, which can be stratified due to environmental gradients such as light, oxygen or sulfide. Microbial mat communities are commonly observed under extreme environmental conditions, deriving energy primarily from light and/or reduced chemicals to drive autotrophic fixation of carbon dioxide. Microbial mat ecosystems are regarded as living analogues of primordial systems on Earth, and they often form perennial structures with conspicuous stratifications of microbial populations that can be studied in situ under stable conditions for many years. Consequently, microbial mat communities are ideal natural laboratories and represent excellent model systems for studying microbial community structure and function, microbial dynamics and interactions, and discovery of new microorganisms with novel metabolic pathways potentially useful in future industrial and/or medical applications. Due to their relative simplicity and organization, microbial mat communities are often excellent testing grounds for new technologies in microbiology including micro-sensor analysis, stable isotope methodology and modern genomics. Integrative studies of microbial mat communities that combine modern biogeochemical and molecular biological methods with traditional microbiology, macro-ecological approaches, and community network modeling will provide new and detailed insights regarding the systems biology of microbial mats and the complex interplay among individual populations and their physicochemical environment. These processes ultimately control the biogeochemical cycling of energy and/or nutrients in microbial systems. Similarities in microbial community function across different types of communities from highly disparate environments may provide a deeper basis for understanding microbial community dynamics and the ecological role of specific microbial populations. Approaches and concepts developed in highly-constrained, relatively stable natural communities may also provide insights useful for studying and understanding more complex microbial communities.
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.
Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.
This volume contains cutting-edge reviews by world-leading experts on the systems biology of microorganisms. As well as covering theoretical approaches and mathematical modelling this book includes case studies on single microbial species of bacteria and archaea, and explores the systems analysis of microbial phenomena such as chemotaxis and phagocytosis. Topics covered include mathematical models for systems biology, systems biology of Escherichia coli metabolism, bacterial chemotaxis, systems biology of infection, host-microbe interactions, phagocytosis, system-level study of metabolism in M.
This book is based on the proceedings of the inaugural symposium "Northwest Symposium for Systems Biology". Particular focus is on identifying current breakthrough technologies and their application to important model systems. By integrating computational sciences, high-throughput technologies and quantitative biology, this book will advance the understanding of not just the function of individual genes, proteins and smaller molecules like hormones, but also how all of these molecules interact within a cell. This volume will be a collection of presentations on four topics that comprise the scope of the Genomes to Life project recently announced by the Department of Energy. They are four aspects of a system biology approach to understanding microbial communities. These topics include complex microbial systems, gene regulatory networks, molecular machines/ multiprotein complexes and computational techniques.