In recent years, rapid technological advances and changes in agricultural management have taken place. These have yielded benefits to society but have also generated new and significant environmental problems. Novel questions and challenges relating to agricultural practice and soil microbial ecology, ecotoxicology, biotechnology, and bioremediation must be addressed. As a consequence, the fields of soil microbiology and biochemistry have been highlighted.
This book provides a modern, authoritative, and comprehensive collection of methods for the study of soil microbiology and biochemistry. Classical and modern, aerobic and anerobic, laboratory and field-based methods are presented. Detailed techniques are given, but in addition the theoretical basis behind such methodology is described, so that the origins and principles of the techniques are clear to the reader. Particular emphasis has been placed on uniform, simple, and clear presentation of the different methods.
With respect to bioremediation of soils, this work provides a unique bridge between general and applied soil microbiology and biochemistry, presenting an integrated discussion of concepts, theories, and methods. This book will be essential for all scientists and students actively involved in natural and environmental sciences and engineering, and for those working in industry, authorities, and consulting companies.
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* Uniform and clear presentation of the different methods.
* Bridges the gap between general and applied soil microbiology.
* Maintains a balanced discussion of concepts, theories, and methods.
* Essential reading for all scientists and students involved in natural and environmental sciences and anyone working in the industry.

The books in this acclaimed series are the most detailed, up-to-date accounts of the field available. Volume 3 explores the oncogenic potential shared by retroviruses of different species, the widespread presence of retrovirues in nature, and the role of retroviruses in normal development and pathogenesis.

Cold-adapted microorganisms play a major role in nutrient turnover and primary biomass production in cold ecosystems and have important applications in biotechnology and in the study of food spoilage microorganisms. Divided into three main sections, the book covers the major aspects of biodiversity in cold ecosystems, the physiology and molecular adaptation mechanisms, and the various biomolecules related to cold adaptation.

This volume gives an insight into what a group of contemporary plankton biologists think about the utility, virtues, strengths and theoretical and practical weaknesses of J.H. Connell's Intermediate Disturbance Hypothesis within the context of phytoplankton ecology. The sequence of papers in this volume moves from particular case studies to more general and finally theoretical approaches.

Epigenetic modification of cellular genomes is a fascinating means of regulating tissue- and cell type-specific gene expression in all developmental stages of the life of an organism. Carefully orchestrated processes, such as DNA methylation and a plenitude of specific histone modifications secure the faithful transmission of gene expression patterns to progeny cells. Upon chronic infection, the epigenetic cellular balance can become disrupted and, in the long run, through the epigenetic reprogramming of host cell genomes, contribute to the malignant conversion of formerly healthy cells, in many cases preceded by the establishment of an epigenetic field of cancerization. The present volume undertakes to highlight the interactions of infectious pathogens and their effector molecules with the epigenetic regulatory machinery of the cell. Clearly, the recent take-off of epigenetics research did not leave Research on Infectious Diseases and Infection-Associated Cancer untouched. This resulted in a great many of clinically relevant data on understanding the molecular mechanisms of chronic infectious disease. Infectious pathogen- and disease-specific epigenetic alterations are already being used for the early detection of malignant disease and for the prediction of chemotherapy resistance or response to treatment.

The aim of Plant Virology Protocols is to provide a source of infor- tion to guide the reader through the wide range of methods involved in gen- ating transgenic plants that are resistant to plant viruses. To this end, we have commissioned a wide-ranging list of chapters that will cover the methods required for: plant virus isolation; RNA extraction; cloning coat p- tein genes; introduction of the coat protein gene into the plant genome; and testing transgenic plants for resistance. The book then moves on to treatments of the mechanisms of resistance, the problems encountered with field testing, and key ethical issues surrounding transgenic technology. Although Plant Virology Protocols deals with the cloning and expression of the coat protein gene, the techniques described can be equally applied to other viral genes and nucleotide sequences, many of which have also been shown to afford protection when introduced into plants. The coat protein has, however, been the most widely applied, and as such has been selected to illustrate the techniques involved. Plant Virology Protocols has been divided into six major sections, c- taining 55 chapters in total.

This volume provides state-of-the-art and novel methods on antibiotic isolation and purification, identification of antimicrobial killing mechanisms, and methods for the analysis and detection of microbial adaptation strategies. Antibiotics: Methods and Protocols guides readers through chapters on production and design, mode of action, and response and susceptibility. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Antibiotics: Methods and Protocols aims to inspire scientific work in the exciting field of antibiotic research.

1 2 MARCEL B. ROBERFROID AND GLENN R. GIBSON 1 Universite Catholique de Louvain, Department of Pharmaceutical Sciences, Avenue Mounier 73, B-1200 Brussels, BELGIUM 2 Food Microbial Sciences Unit, Department of Food Science and Technology, The University of Reading, Reading, UK It is clear that diet fulfils a number of important human requirements. These include the provision of sufficient nutrients to meet the requirements of essential metabolic pathways, as well as the sensory (and social) values associated with eating. It is also evident that diet may control and modulate various body functions in a manner that can reduce the risk of certain diseases. This very broad view of nutrition has led to the development of foodstuffs with added "functionality." Many different definitions of functional foods have arisen. Most of these complicate the simple issue that a functional food is merely a dietary ingredient(s) that can have positive properties above its normal nutritional value. Other terms used to describe such foods include vitafoods, nutraceuticals, pharmafoods, foods for specified health use, health foods, designer foods, etc. Despite some trepidation, the concept has recently attracted much interest through a vast number of articles in both the popular and scientific media.

The book summarizes the latest research and developments in dairy biotechnology and engineering. It provides a strategic approach for readers relating to fundamental research and practical work with lactic acid bacteria. The book covers every aspect from identification, ecology, taxonomy and industrial use. All contributors are experts who have substantial experience in the corresponding research field. The book is intended for researchers in the human, animal, and food sciences related to lactic acid bacteria. Dr. Heping Zhang is a Professor at the Key Laboratory of Dairy Biotechnology and Engineering Ministry of Education, Inner Mongolia Agricultural University, China. Dr. Yimin Cai works in Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Japan.

Since penicillin and salvarsan were discovered, a number of new drugs to combat infectious diseases have been developed, but at the same time, the number of multi-resistant microorganism strains is increasing. Thus, the design of new and effective antibacterial, antiviral and antifungal agents will be a major challenge in the next years. This book reviews the current state-of-the-art in antimicrobial research and discusses new strategies for the design and discovery of novel therapies. Topics covered include the use of genetic engineering, genome mining, manipulation of gene clusters, X-ray and neutron scattering as well as the antimicrobial effects of essential oils, antimicrobial agents of plant origin, beta-lactam antibiotics, antimicrobial peptides, and cell-wall-affecting antifungal antibiotics.

Microorganisms are capable of producing a wide variety of biopolymers. Homopolymer peptides, which are made up of only a single type of amino acid, are far less ubiquitous. The only two amino-acid homopolymers known to occur in nature are presented in this volume. Poly-epsilon-L-lysine is a polycationic peptide and exhibits antimicrobial activity against a wide spectrum of microorganisms. It is both safe and biodegradable and is therefore used as a food preservative in several countries. In addition, there has been great interest in medical and other applications of poly-lysine and its derivatives. In contrast, poly-gamma-glutamic acid is an unusual anionic polypeptide. It is also water soluble, biodegradable, edible, non-toxic and non-immunogenic and can be chemically modified to introduce various drugs. These features are very useful for pharmaceutical and biomedical applications. Poly-glutamic acid is also a highly attractive as a food ingredient.

McCoy's guide to the maintenance and management of cooling water systems and the bacteria that live in them. Includes studies and testing of microbicides and other microorganisms that infest re-circulating cooling water systems and factors influencing their health and growth. Tests biological oxidation processes as a way of reusing treated effluents as an important method of water conservation in the petroleum refining and chemical processing industries. Explores practical methods for controlling microorganisms in cooling water; including working with chlorine dioxide as a microbicide. Methods are given for identifying and evaluating toxicants and bacteria that lead to fouling and staining of cooling water systems.

The tropical plant family Pandanaceae comprises three genera, Freycinetia, Pandanus and Sararanga. One-hundred and fourteen genera and 226 species of fungi were found on dead leaves of Pandanaceae collected in Australia, Brunei Darussalam, Fiji, Hawaii, Hong Kong, Malaysia, Mauritius, Nepal, New Zealand, Niue, Philippines, Seychelles, Vanuatu and Vietnam. Taxonomic issues within each fungus genus are discussed and reference made to preceding work. All species are written up with bibliographic details, relevant measurements of the current specimens, known habitat and distribution, collection details, and a discussion on taxonomic conclusions. New taxa (4 genera, 35 species) are fully described and illustrated, each with a plate showing relevant macro- and microscopic details. Keys and/or synoptic tables are provided to all species in 28 genera. In addition, details on almost 700 species of fungi described and recorded worldwide from the Pandanaceae are listed.

In response to low iron availability in the environment most microorganisms synthesize iron chelators, called siderophores. Bacteria and fungi produce a broad range of structurally diverse siderophores, which all show a very high affinity for ferric ions.

"Microbial Siderophores" presents an up-to-date overview of the chemistry, biology and biotechnology of these iron chelators. Following an introduction to the structure, functions and regulation of fungal siderophores, several chapters focus on siderophores of pseudomonads. Here, the technique of siderotyping, which has proved to be a rapid, accurate and inexpensive tool for pseudomonad characterization and identification, is described. Further, the biological significance of siderophores of symbiotic fungi and the possible role of siderophores in pathogenesis are discussed. In addition to methodological approaches, chapters on the biotechnological production of siderophores and their application in promoting human and plant health are included.

Applied Microbiology and Molecular Biology in Oil Field Systems addresses the major problems microbes cause in oil fields, (e.g. biocorrosion and souring) and how beneficial microbial activities may be exploited (e.g. MEOR and biofuels). The book describes theoretical and practical approaches to specific Molecular Microbiological Methods (MMM), and is written by leading authorities in the field from both academia and industry. The book describes how MMM can be applied to faciliate better management of oil reservoirs and downstream processes. The book is innovative in that it utilises real industrial case studies which gives useful technical and scientific information to researchers, engineers and microbiologists working with oil, gas and petroleum systems. Content Level Professional/practitioner

Fundamentals of Plant Virology is an introductory student text covering all of modern plant virology. The author, Dr. R.E.F. Matthews, has written this coursebook based on his classic and comprehensive Plant Virology, Third Edition. Four introductory chapters review properties of viruses and cells and techniques used in their study. Five chapters are devoted to current knowledge of all major plant viruses and related pathogens. Seven chapters describe biological properties such as transmission, host response, disease, ecology, control, classification, and evolution of plant viruses. A historical and future overview concludes the text. Fundamentals of Plant Virology is a carefully designed instructional format for a plant virology course. It is also an invaluable resource for students of plant pathology and plant molecular biology.
Key Features
* Summarizes knowledge on all aspects of plant virology
* Condenses all essential material from Plant Virology 3/e
* Compares basic properties of cells and viruses
* Outlines principles of gene manipulation technology
* Discusses serological techniques including monoclonal antibodies
* Geared to student level course

This Volume presents a comprehensive series of generic protocols for the genetic and genomic analysis of prokaryotic isolates. Genetic methods for functional analyses employ the latest cloning vectors, gene fusion methods and transposon mutagenesis systems, as well as systems for introducing protease-cleavage sequences into permissive sites in proteins under investigation. Genomic methods described include protocols for transcriptomics, shotgun proteomics, interactomics, metabolic profiling, and lipidomics. Bioinformatic tools for genome annotation, transcriptome display and the integration of transcriptomic data into genome-scale metabolic reconstructions are described. Protocols for 13C-based metabolic flux determinations and analysis of the hierarchical and metabolic regulation of fluxes through pathways are included. The Volume thus enables investigators to functionally analyse an isolate over the entire cellular range spanning the gene, the genome, the transcript repertoire, the proteome, the interactome, the metabolic network with its nodes and their regulatory hierarchies, and the metabolic fluxes and their physiological controls. Hydrocarbon and Lipid Microbiology Protocols There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

This volume describes recent advances in the bioconversion of lignocellulosics. It starts with two articles on genetics and properties of cellulases and their re- tion kinetics and mechanisms. The cost of cellulases has been a hindrance to large scale use of enzymatic hydrolysis. Two articles on cellulase production by submerged fermentation and by solid state fementation are included to describe the state of the art in this area. Dilute acid hydrolysis of cellulose continues to be of interest as well as potentially useful. The most recent advances in this area is also covered. A great deal of progress has been made in genetic engineering for improved regulation of xylose fermentation by yeasts. An article on genetically engineered Saccharomyces for simulteaneous fermentation of glucose and xylose describes the importance advances made in production of fuel ethanol from lignocellulosic biomass. In recent years, there has been increasing interests in recycling and the reuse of scrap paper as well as environment considerations. A contribution is presented which describes the research perspectives in that area. Finally, recent advances in the use of lignocellulosic biomass for the p- duction of ethanol and organic acids are presented in two articles. Renewable resources are inevitably of great importance in the years to come. There is a never-ending search for better living conditions for human beings. The more resource materials can be recycled, the richer we will be.

This book should be of interest to students of animal ecology; ecology.

The ability to predict the behavior of fermentation systems enhances the possibility of optimizing their performance. Mathematical equations of model systems represent a tool for this and the most recent advances in computer hardware and software have made the approach more effective than previous simplistic attempts. The current knowledge of biochemical microbial pathways and the experience in optimization of chemical reactors combined with extremely powerful and accessible computers, loaded with easy to use software and mathematical routines, are changing the way processes are being developed and operated.

This book has been written for all those who work with microbial cultures, providing a useful, quick and contemporary re-education for practitioners and students alike, breaking through interdisciplinary barriers. Biologists, engineers and biochemists will benefit from the methods of microbial process description and optimization based on mathematical equations. The basic techniques of modeling the bio-system are summarized in Part I. The useful concept of mass balancing is introduced in Part II for those who are not used to this simple and very useful engineering tool. An extensive and descriptive case study of a selected fermentation bio-process in Part III elucidates further the concepts of very pragmatic mathematical modeling of bioreactor systems.

The volume outlines how to simply develop mathematical models of microbial systems and demonstrates their power to: guide and minimize the experimental work; check the consistency of experimental results; predict the behavior of the bio-system and analyze biocatalytic processes; diagnose the anomalies in the microbial culture behavior and optimize the performance of bioreactors.

Part of a review series that looks at trends in modern biology. This book covers aspects of bioprocessing and biotransformation, where knowledge, methods and expertise are required from chemistry, biochemistry, microbiology, genetics, chemical engineering and computer science.

This book discusses the practical applications of quorum sensing inhibitors for both human and plant health. Quorum sensing inhibitors that disrupt microbial biofilms can be employed to treat bacterial infections. The book describes the various bioactive molecules that can serve as quorum sensing inhibitors to combat deadly bacterial infections, in addition to several synthetic quorum sensing inhibitors. Quorum sensing is the mechanism through which bacteria develop antibiotic resistance. Intended to provide a clearer understanding of the practical applications of quorum sensing inhibitors, the book details how the problem of antibiotic resistance can be countered through the intelligent application of quorum sensing inhibitors.

Next Generation Sequencing: Chemistry, Technology and Applications, by P. Hui Application of Next Generation Sequencing to Molecular Diagnosis of Inherited Diseases, by W. Zhang, H. Cui, L.-J.C. Wong Clinical Applications of the Latest Molecular Diagnostics in Noninvasive Prenatal Diagnosis, by K.C.A. Chan The Role of Protein Structural Analysis in the Next Generation Sequencing Era, by W.W. Yue, D.S. Froese, P.E. Brennan Emerging Applications of Single-Cell Diagnostics, by M. Shirai, T. Taniguchi, H. Kambara Mass Spectrometry in High-Throughput Clinical Biomarker Assays: Multiple Reaction Monitoring, by C.E. Parker, D. Domanski, A.J. Percy, A.G. Chambers, A.G. Camenzind, D.S. Smith, C.H. Borchers Advances in MALDI Mass Spectrometry in Clinical Diagnostic Applications, by E.W.Y. Ng, M.Y.M. Wong, T.C.W. Poon Application of Mass Spectrometry in Newborn Screening: About Both Small Molecular Diseases and Lysosomal Storage Diseases, by W.-L. Hwu, Y.-H. Chien, N.-C. Lee, S.-F. Wang, S.-C. Chiang, L.-W. Hsu

This book is highly recommended on the basis of the following points:

- The editors are highly regarded in the field of mycorrhizal biology and one is co-author of the most comprehensive textbook on mycorrhizas;
- Chapters by international experts based on invited presentations at the 3rd International Conference on Mycorrhizas, supplemented by invited chapters on special topics;
- Mycorrhizas are being increasingly recognised as ubiquitous plant/fungal symbioses, with the potential to influence the function and ecology of around 90% of all land plants; perhaps the most common and also ancient terrestrial symbioses in existence;
- This book has a broad coverage of biology of symbioses between mycorrhizal fungi and plants, especially ecto- and arbuscular mycorrhizas (other recent texts have focused mainly on arbuscular mycorrhizal symbioses);
- Forward-looking review chapters by keynote speakers including an overview of research challenges for the future;
- Up-to-date research focus;
- Coverage includes: molecular diversity and detection of mycorrhizal fungi; cellular and molecular interactions between the symbionts; physiology of the interactions; implications of the symbioses for ecosystem processes, including agriculture;
- Several complementary chapters on some topics, ensuring that different perspectives are presented (recent edited volumes have had a smaller group of authors and hence narrower focus);
- Readership from advanced undergraduate students in biology (particularly plant science), postgraduate students and researchers in universities and government agencies.

This Volume presents key microscopy and imaging methods for revealing the structure and ultrastructure of environmental and experimental samples, of microbial communities and cultures, and of individual cells. Method adaptations that specifically address problems concerning the hydrophobic components of samples are highlighted and discussed. The methods described range from electron microscopy and light and fluorescence microscopy, to confocal laser-scanning microscopy, and include experimental set-ups for the analysis of interfacial processes like microbial growth and activities at hydrocarbon:water interfaces, biofilms and microbe:mineral interfaces. Three forms of fluorescence in situ hybridization - CARD-FISH, MAR-FISH and Two-pass TSA-FISH - are described for the ecophysiological analysis of functionally active microbes in samples. The methods presented will enable readers to obtain an ultrastructural picture of, and identify the key functional microbes in, samples under investigation. This in turn will constitute a key framework for the interpretation of information from other experimental approaches, such as physicochemical analyses and genomic investigations. Hydrocarbon and Lipid Microbiology ProtocolsThere are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.