Molecular Microbial Ecology Manual


Book Description

For a long time microbial ecology has been developed as a distinct field within Ecology. In spite of the important role of microorganisms in the environment, this group of 'invisible' organisms remained unaccessable to other ecologists. Detection and identification of microorganisms remain largely dependent on isolation techniques and characterisation of pure cul tures. We now realise that only a minor fraction of the microbial com munity can be cultivated. As a result of the introduction of molecular methods, microbes can now be detected and identified at the DNA/RNA level in their natural environment. This has opened a new field in ecology: Molecular Microbial Ecology. In the present manual we aim to introduce the microbial ecologist to a selected number of current molecular techniques that are relevant in micro bial ecology. The first edition of the manual contains 33 chapters and an equal number of additional chapters will be added this year. Since the field of molecular ecology is in a continuous progress, we aim to update and extend the Manual regularly and will invite anyone to depo sit their new protocols in full detail in the next edition of this Manual. We hope this book finds its place where it was born: at the lab bench! Antoon D.L. Akkermans, Jan Dirk van Elsas and Frans J. de Bruijn March 1995 Molecular Microbial Ecology Manual 1.3.6: 1-8, 1996. © 1996 Kluwer Academic Publishers.




Handbook of Molecular Microbial Ecology II


Book Description

The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds. Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This second volume, Metagenomics in Different Habitats, covers such topics as: Viral genomes Metagenomics studies in a variety of habitats, including marine environments and lakes, soil, and human and animal digestive tracts Other habitats, including those involving microbiome diversity in human saliva and functional intestinal metagenomics; diversity of archaea in terrestrial hot springs; and microbial communities living at the surface of building stones Biodegradation Biocatalysts and natural products A special feature of this book is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Such studies in a variety of habitats are described here, which present a large number of different system-dependent approaches in greatly differing habitats. Handbook of Molecular Microbial Ecology II is an invaluable reference for researchers in metagenomics, microbial ecology, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; and professionals in molecular microbiology and bioinformatics.




Manual of Environmental Microbiology


Book Description

The single most comprehensive resource for environmental microbiology Environmental microbiology, the study of the roles that microbes play in all planetary environments, is one of the most important areas of scientific research. The Manual of Environmental Microbiology, Fourth Edition, provides comprehensive coverage of this critical and growing field. Thoroughly updated and revised, the Manual is the definitive reference for information on microbes in air, water, and soil and their impact on human health and welfare. Written in accessible, clear prose, the manual covers four broad areas: general methodologies, environmental public health microbiology, microbial ecology, and biodegradation and biotransformation. This wealth of information is divided into 18 sections each containing chapters written by acknowledged topical experts from the international community. Specifically, this new edition of the Manual Contains completely new sections covering microbial risk assessment, quality control, and microbial source tracking Incorporates a summary of the latest methodologies used to study microorganisms in various environments Synthesizes the latest information on the assessment of microbial presence and microbial activity in natural and artificial environments The Manual of Environmental Microbiology is an essential reference for environmental microbiologists, microbial ecologists, and environmental engineers, as well as those interested in human diseases, water and wastewater treatment, and biotechnology.




Handbook of Molecular Microbial Ecology I


Book Description

The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds. Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This first volume, Metagenomics and Complementary Approaches, covers such topics as: Background information on DNA reassociation and use of 16 rRNA and other DNA fingerprinting approaches Species designation in microbiology Metagenomics: Introduction to the basic tools with examples Consortia and databases Bioinformatics Computer-assisted analysis Complementary approaches—microarrays, metatranscriptomics, metaproteomics, metabolomics, and single cell analysis A special feature of this volume is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Handbook of Molecular Microbial Ecology I is an invaluable reference for researchers in metagenomics, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; molecular microbial ecologists; and professionals in molecular microbiology and bioinformatics.




Handbook of Molecular Microbial Ecology I


Book Description

The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds. Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This first volume, Metagenomics and Complementary Approaches, covers such topics as: Background information on DNA reassociation and use of 16 rRNA and other DNA fingerprinting approaches Species designation in microbiology Metagenomics: Introduction to the basic tools with examples Consortia and databases Bioinformatics Computer-assisted analysis Complementary approaches—microarrays, metatranscriptomics, metaproteomics, metabolomics, and single cell analysis A special feature of this volume is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Handbook of Molecular Microbial Ecology I is an invaluable reference for researchers in metagenomics, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; molecular microbial ecologists; and professionals in molecular microbiology and bioinformatics.




Handbook of Soil Sciences (Two Volume Set)


Book Description

An evolving, living organic/inorganic covering, soil is in dynamic equilibrium with the atmosphere above, the biosphere within, and the geology below. It acts as an anchor for roots, a purveyor of water and nutrients, a residence for a vast community of microorganisms and animals, a sanitizer of the environment, and a source of raw materials for co




Handbook of Fermented Food and Beverage Technology Two Volume Set


Book Description

Fermented food can be produced with inexpensive ingredients and simple techniques and makes a significant contribution to the human diet, especially in rural households and village communities worldwide. Progress in the biological and microbiological sciences involved in the manufacture of these foods has led to commercialization and heightened int




Methods for General and Molecular Microbiology


Book Description

A first source for traditional methods of microbiology as well as commonly used modern molecular microbiological methods. • Provides a comprehensive compendium of methods used in general and molecular microbiology. • Contains many new and expanded chapters, including a section on the newly important field of community and genomic analysis. • Provides step-by-step coverage of procedures, with an extensive list of references to guide the user to the original literature for more complete descriptions. • Presents methods for bacteria, archaea, and for the first time a section on mycology. • Numerous schematics and illustrations (both color and black and white) help the reader to easily understand the topics presented.




Genomic Approaches in Earth and Environmental Sciences


Book Description

The first comprehensive synthesis of genomic techniques in earth sciences The past 15 years have witnessed an explosion of DNA sequencing technologies that provide unprecedented insights into biology. Although this technological revolution has been driven by the biomedical sciences, it also offers extraordinary opportunities in the earth and environmental sciences. In particular, the application of "omics" methods (genomics, transcriptomics, proteomics) directly to environmental samples offers exciting new vistas of complex microbial communities and their roles in environmental and geochemical processes. This unique book fills the gap where there exists a lack of resources and infrastructure to educate and train geoscientists about the opportunities, approaches, and analytical methods available in the application of omic technologies to problems in the geosciences. Genomic Approaches in Earth and Environmental Sciences begins by covering the role of microorganisms in earth and environmental processes. It then goes on to discuss how omics approaches provide new windows into geobiological processes. It delves into the DNA sequencing revolution and the impact that genomics has made on the geosciences. The book then discusses the methods used in the field, beginning with an overview of current technologies. After that it offers in-depth coverage of single cell genomics, metagenomics, metatranscriptomics, metaproteomics, and functional approaches, before finishing up with an outlook on the future of the field. The very first synthesis of an important new family of techniques Shows strengths and limitations (both practical and theoretical) of the techniques Deals with both theoretical and laboratory basics Shows use of techniques in a variety of applications, including various aspects of environmental science, geobiology, and evolution Genomic Approaches in Earth and Environmental Sciences is a welcome addition to the library of all earth and environmental scientists and students working within a wide range of subdisciplines.




Microbial Enzymes


Book Description

Comprehensive discussion of production and purification strategies for microbial enzymes important to various industries, from food and beverages to pharmaceuticals Microbial Enzymes provides expert insight into diverse aspects of microbial enzymes, highlighting strategies for their production, purification, and manipulation, elucidating eco-friendly industrial applications, and discussing several production processes, such as the production of cellulose and non-synthetic indigo dye. This book emphasizes recent technological interventions in microbial enzyme technology like metagenomics, system biology, molecular biology, genomics, directed evolution, and bioinformatics. The important microbial enzymes highlighted in this book include xylanases, ureases, methane monooxygenase, polyhydroxyalkanoates, pectinases, peroxidases, α-L-rhamnosidase, alkane hydroxylases, laccases, proteases, gallic acid decarboxylase, chitinases, beta-glucosidase, lipases, inulinases, tannase, mycozyme, ACC deaminase, ligninolytic enzymes, and many more. Novel treatment methods involving strains of microorganisms with desirable properties applicable in the process of bioremediation through mitigating climate concern, increasing green production technology, improving agriculture productivity, and providing a means of earning a livelihood are discussed. Readers will also gain state-of-the-art background knowledge on existing technologies and their current challenges and future prospects. Contributed to by leading experts in the field and edited by four highly qualified academics, Microbial Enzymes explores important topics including: Strategies for the discovery and enhancement of enzyme function, and potentials of system biology to better understand the kinetics of industrially important enzymes Production and therapeutic applications of monoclonal antibodies in cancer and other diseases, and characterization of tannase as a virulence factor Opportunities to produce enzymes through food waste and byproducts, and recent developments in computational tools Use of Omics tools in the discovery of fungal enzymes and secondary metabolites Microbial Enzymes is a thorough and highly practical reference on the subject for students, scientists, biotechnologists, microbiologists, and policymakers working in environmental microbiology, biotechnology, and environmental sciences.