Methane and its oxidation product, methanol, have occupied an important position in the chemical industry for many years: the former as a feedstock, the latter as a primary chemical from which many products are produced. More recently, the role played by methane as a potent "greenhouse" gas has aroused considerable attention from environmentalists and clima tologists alike. This role for C compounds has, of course, been quite 1 incidental to the myriad of microorganisms on this planet that have adapted their life-styles to take advantage of these readily available am bient sources. Methane, a renewable energy source that will always be with us, is actually a difficult molecule to activate; so any microorganism that can effect this may point the way to catalytic chemists looking for con trollable methane oxidation. Methanol, formed as a breakdown product of plant material, is also ubiquitous and has also encouraged the growth of prokaryotes and eukaryotes alike. In an attempt to give a balanced view of how microorganisms have been able to exploit these simple carbon sources, we have asked a number ofleading scientists (modesty forbids our own inclusion here) to contribute chapters on their specialist areas of the subject."

This Volume presents relevant single-cell and single-molecule approaches in the study of microbes producing and utilizing hydrocarbons and lipids. While generically applicable for all microorganisms, the approaches described are, wherever possible, adapted to the field of study of hydrocarbon and lipid microbiology. The methods include basic procedures for isolating single cells by means of microfluidics and flow cytometry, and their cultivation in arrays as pure clones; for isolating, amplifying and sequencing single-cell genomes and transcriptomes; and for analysing single-cell metabolomes by means of Raman spectroscopy. Single-molecule approaches include the use of protein:fluorescent dye fusions for protein localization and methods for the production of cell division protostructures and lipid monolayers. Methods for the functional analysis of single cells include detection of metabolically active (protein-synthesizing) cells in environmental samples by bioorthogonal non-canonical amino acid tagging, Raman spectroscopy combined with stable isotope labelling and fluorescent in situ hybridisation, and visualization of single cells participating in gene transfer activity. Lastly, protocols are presented for single-cell biotechnological applications, including biofuel production. 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.

This Volume presents protocols for systems and synthetic biology applications in the field of hydrocarbon and lipid microbiology. It complements another Volume that describes generic protocols for wet experimental and computer-based systems and synthetic biology studies. The protocols in this Volume demonstrate how to employ systems and synthetic biology approaches in the design of microbes for the production of esters, isoprenoids, hydrophobic polymers, rhamnolipid biosurfactant, and peptide antimicrobial and thioether-stabilised molecules. Also presented is a protocol for the engineering of transcription factor-based biosensors for intracellular products, and another for the creation of a synthetic hydroxylase with novel activity for the selective oxyfunctionalisation of linear alkanes. 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.

Coronaviruses were recognized as a group of enveloped, RNA viruses in 1968 and accepted by the International Committee on the Taxonomy of Viruses as a separate family, the Coronaviridae, in 1975. By 1978, it had become evident that the coronavirus genomic RNA was infectious (i. e., positive strand), and by 1983, at least the framework of the coronavirus replication strategy had been per ceived. Subsequently, with the application of recombinant DNA techniques, there have been remarkable advances in our understanding of the molecular biology of coronaviruses, and a mass of structural data concerning coronavirus genomes, mRNAs, and pro teins now exists. More recently, attention has been focused on the role of essential and accessory gene products in the coronavirus replication cyde and a molecular analysis of the structure-function relation ships of coronavirus proteins. Nevertheless, there are still large gaps in our knowledge, for instance, in areas such as the genesis of coronavirus subgenomic mRNAs or the function of the coronavirus RNA-dependent RNA polymerase. The diseases caused by coronaviruses have been known for much longer than the agents themselves. Possibly the first coronavirus-related disease to be recorded was feline infectious peritonitis, as early as 1912. The diseases associ ated with infectious bronchitis virus, transmissible gastroenteritis virus, and murine hepatitis virus were all well known before 1950."

Having experienced unprecedented growth since the turn of the millennium, the dramatic expansion of resources and techniques in fungal genomics is poised to fundamentally redefine the study of fungal biology. In "Fungal Genomics: Methods and Protocols," expert researchers explore the three most likely fronts upon which the field will advance: the sequencing of more and more fungal genomes, the mining of sequenced genomes for useful information, and most importantly, the use of genomics sequences to provide a foundation for powerful techniques to explain biological processes. Much of the book is dedicated to explaining established and emerging genomics-based technologies in filamentous fungi, including gene expression profiling techniques, techniques for fungal proteomics as well as various case studies that could be adapted to a wide range of fungi. Written in the highly successful "Methods in Molecular Biology " series format, protocol chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step laboratory protocols, and key unpublished tips, potential pitfalls, common mistakes, and special considerations based on the unique experiences of the contributors.

Authoritative and cutting-edge, "Fungal Genomics: Methods and Protocols" provides fungal biologists at any stage of their careers a user-friendly resource for fungal genomics, especially as readers branch out into unfamiliar but exciting new areas of study."

Nitrogen fixation is currently of great practical importance because the use of nitrogenous fertilizers has resulted in unacceptable levels of water pollution and the fact that these fertilizers are becoming steadily less economic both in cash terms and in utilization of fossil fuels for their manufacture. This book aims to present new findings in the field of nitrogen fixation and to reflect the influence on the subject of recent developments in biochemistry, molecular biology, genetic engineering and other biotechnologies. The book includes quantitative aspects of the subject, but the many practical difficulties for accurate field assessment of nitrogen fixation and its contribution to nitrogen cycles means that many assessments are either in conflict with each other or must be accepted as tentative. Although this book is concerned essentially with how nitrogen-fixing organisms function and why they are of practical importance, rather than with details of laboratory or field techniques, an appendix deals with the main methods of measurement of nitrogen fixation and some of the problems that must be faced.

Infectious diseases caused by bacteria remain a leading cause of death worldwide. Many of the antibiotics developed to combat bacterial infections have been rendered almost impotent due to the rapid evolution and spread of antibiotic resistance. A common and major resistance mechanism, the efflux system, enables bacteria to extrude structurally divers antimicrobials, facilitating survival in toxic environments. This book reviews the most important current research and summarizes the most spectacular discoveries in the field.

Adhesion plays a major role in the bacterial lifestyle. Bacteria can adhere to organic and inorganic surfaces, to each other, and of course to host cells during pathogenesis. The focus of this book is: how are such adhesion phenomena best studied? Microbial genetics experiments have greatly enhanced our knowledge of what bacterial factors are involved in adhesion. For numerous reasons, though, biochemical and structural biology knowledge of the molecular interactions involved in adhesion are limited. One major problem has been a lack of interdisciplinary research and understanding in the field. On the one hand, the microbiologists lack detailed knowledge of the biophysical possibilities and have limited access to the frequently expensive instrumentation involved while on the other hand, the experts in these methods frequently do not have access to the biological materials, nor do they necessarily understand the biological questions to be answered. The purpose of this book is thus to overcome this gap in communication between researchers in biology, chemistry and physics and to display the many ways and means to investigate bacterial adhesion. We hope to stimulate new and ground-breaking research.

This is a work on the role of fungi in processed and unprocessed foods. In addition to offering practical and applied information on fungi associated with food and beverages this second edition now covers poisonous mushrooms. Topics include water activity, specific commodities, fungi and metabolities as human dietary components, health hazards and mycotoxin producers, and mycotoxin and fungal contaminant detection.

Harnessing the sun s energy via photosynthesis is at the core of sustainable production of food, fuel, and materials by plants, algae, and cyanobacteria. Photosynthesis depends on photoprotection against intense sunlight, starting with the safe removal of excess excitation energy from the light-harvesting system, which can be quickly and non-destructively assessed via non-photochemical quenching of chlorophyll fluorescence (NPQ). By placing NPQ into the context of whole-organism function, this book aims to contribute towards identification of plant and algal lines with superior stress resistance and productivity. By addressing agreements and open questions concerning photoprotection s molecular mechanisms, this book contributes towards development of artificial photosynthetic systems. A comprehensive picture from single molecules to organisms in ecosystems, and from leading expert s views to practical information for non-specialists on NPQ measurement and terminology is presented."

In the 100 years since the legume-Rhizobium symbiotic nitrogen fixation interaction was first described, interest in this field has grown rapidly. The types of studies have been cyclical in nature, involving a cross-section of disciplines. The availability of cheap nitrogenous fertilizers caused much of the biological nitrogen fixation research to become more theoretical in the developed world. The high cost of energy, coupled with environmental concerns and the interest in sustainable agriculture, has stimulated research in symbiotic nitrogen fixation. The development of modern genetic techniques has resulted in interdisciplinary research on plant-microbe interactions controlling nitrogen fixation. This has resulted in a better understanding of environmental factors influencing the nodulation process, chemical signalling between the symbiotic partners and the nature of the specificity between host plant and microsymbiotant. This volume summarizes the diverse research efforts in biological nitrogen fixation by presenting a collection of papers in the areas of physiology and metabolism, taxonomy and evolution, genetics and ecology.

Fungal nanotechnology has great prospects for developing new products with industrial, agricultural, medicinal, and consumer applications in a wide range of sectors. The fields of chemical engineering, agri-food, biochemistry, pharmaceuticals, diagnostics, and medical device development all employ fungal products, with fungal nanomaterials currently used in applications ranging from drug development to the food industry and agricultural biotechnology. Fungal agents are an environmentally friendly, clean, non-toxic agent for the synthesis of metal nanoparticles and employ both intracellular and extracellular methods. The simplicity of scaling up and downstream processing and the presence of fungal mycelia which afford an increased surface area provide key advantages. In addition, the large spectrum of synthesized nanoparticle morphologies and the substantially faster biosynthesis rate in cell-free filtrate (due to the higher amount of proteins secreted in fungi) make this a particularly enticing route. Understanding the diversity of fungi in assorted ecosystems, as well as their interactions with other microorganisms, animals, and plants, underpins real and innovative technological developments and the applications of metal nanoparticles in many disciplines including agriculture, catalysis, and biomedical biosensors. Importantly, biogenic fungal nanoparticles show significant synergistic characteristics when combined with antibiotics and fungicides to offer substantially greater resistance to microbial growth and applications in nanomedicine ranging from topical ointments and bandages for wound healing to coated stents.

Modern approaches to microbial classification and identification, particularly those based on nucleic acid analysis, have raised the awareness and interest of microbiologists in systematics during the past decade. The extended scope of the subject has revolutionized microbial ecology with the demonstration of uncultivable microorganisms as a major component of the biosphere and evolution, with the ribosomal RNA phylogenetic tree as the basis of current classifications. However, advances in microbial systematics have also had enormous impact on other, diverse aspects of microbiology such as animal pathogenicity, plant-microbe interactions and relationships with food. In this book, we survey and discuss in depth the contribution of modern taxonomic approaches to our understanding of the microbiology of these various systems. The book does not concentrate on methods - these have been well reported elsewhere - instead it provides a unique insight into the application and value of modern systematics in diverse branches of microbiology. It will be of value to microbiologists at both research and technical levels who need to appreciate the range of organisms with which they work and the diversity within them. It will also be of value to teachers and students of microbiology courses who want to understand how systematics can enhance microbiology beyond the routine of classification, nomenclature, and identification.

This book illustrates the major trends in applied microbiology research with immediate or potential industrial applications. The papers proposed reflect the diversity of the application fields. New microbial developments have been done as well in the food and health sectors than in the environmental technology or in the fine chemical production. All the microbial genera are involved : yeast, fungi and bacteria. The development of biotechnology in parallel with the industrial microbiology has enabled the application of microbial diversity to our socio-economical world. The remarkable properties of microbes, inherent in their genetic and enzymatic material, allow a wide range of applications that can improve our every day life. Recent studies for elucidating the molecular basis of the physiological processes in micro-organisms are essential to improve and to control the metabolic pathways to overproduce metabolites or enzymes of industrial interest. The genetic engineering is of course one of the disciplines offering new horizons for the " fantastic microbial factory " . Studies of the culture parameter incidence on the physiology and the morphology are essential to control the response of the micro-organisms before its successful exploitation at the industrial scale. For this purpose, fundamental viewpoints are necessary. Development of novel approaches to characterise micro-organisms would also facilitate the understanding of the inherent metabolic diversity of the microbial world, in terms of adaptation to a wide range of biotopes and establishment of microbial consortia.

Use of Microbes for the Alleviation of Soil Stresses, Volume 2: Alleviation of Soil Stress by PGPR and Mycorrhizal Fungi describes the most important details and advances related to the alleviation of soil stresses by PGPR and mycorrhizal fungi. Comprised of eleven chapters, the book reviews the role of arbuscular mycorrhizal fungi in alleviation of salt stress, the role of AM fungi in alleviating drought stress in plants, the impact of biotic and abiotic stressors and the use of mycorrhizal fungi to alleviate compaction stress on plant growth. Written by experts in their respective fields, Use of Microbes for the Alleviation of Soil Stresses, Volume 2: Alleviation of Soil Stress by PGPR and Mycorrhizal Fungi is a comprehensive and valuable resource for researchers and students interested in the field of microbiology and soil stresses.

Legionellosis is a disease of significant medical and public interest. Legionella is commonly found in aquatic habitats where its ability to survive and to multiply within different protozoa equips the bacterium to be transmissible and pathogenic to humans. In addition, Legionella has become a favored model system to analyze the mechanisms of bacterial survival, acquisition of nutrients, and intracellular replication. Following the recent publication of the genome sequences of four L. pneumophila strains, it is now feasible to investigate the whole genome in silico, the transcriptome via micro arrays, and the proteome by two-dimensional gel electrophoresis. Research in the fields of clinical features, diagnosis, treatment, and epidemiology continues to generate new data. The topics covered by this volume range from the history of the identification of Legionella and clinical disease treatment, to the microbe's gene expression and secretion systems, as well as its strategies for intracellular multiplication and nutrient acquisition. The main focus of the book is the current state of many of the most critical features of Legionella. Internationally renowned authors have contributed chapters describing and discussing the latest research findings with an emphasis on molecular aspects. The editors and authors have produced an excellent book that will be an extremely useful reference source. This comprehensive publication is aimed at readers with teaching or research interests in microbiology, genetics, genomics, infectious diseases, or clinical research.

The Preface to the first edition of this book explained the reasons for the publication of a comprehensive text on the rumen and rumen microbes in 1988. The microbes of the ruminant's forestomach and those in related organs in other animals and birds provide the means by which herbivorous animals can digest and obtain nutriment from vegetation. In turn, humans have relied, and still do rely, on herbivores for much of their food, clothing and motive power. Herbivores also form the food of carnivorous animals and birds in the wild. The importance of the rumen microorganisms is thus apparent. But, while a knowledge of rumen organisms is not strictly neces sary for the normal, practical feeding of farm animals, in recent years there has been much more emphasis on increasing the productivity of domesti cated animals and in rearing farm animals on unusual feedstuffs. Here, a knowledge of the reactions of the rumen flora, and the limits to these reactions, can be invaluable. In addition, anaerobic rumen-type microor ganisms are found in the intestines of omnivores, including humans, and can be implicated in diseases of humans and animals. They are also found in soils and natural waters, where they playa part in causing pollution and also in reducing it, while the same organisms confined in artificial systems are essential for the purification of sewage and other polluting and toxic wastes."

Biological fixation of nitrogen by organisms and associations other than those concerned in the legume-Rhizobium symbiosis has attracted increasing attention since the firstintemationalworkshop on the theme at Piracicaba, Brasil, in 1979. Approximately 150 scientists gathered on September 2-8, 1984, at the Hanasaari Cultural Centre near Helsinki, Finland, for the third international meeting on nitrogen fixation with non-legumes. Forty-two papers and 39 posters were presented; 32 of the papers have been broughttogetherin this publication. The Symposium was generously sponsored by the FinnishNational Fund for Research and Development (SITRA) in connection with a large project on biological nitrogenfixation and utilization ofnitrogen extending from 1980 to 1985. The Symposium was organized jointly by SITRA, which dealt with all practical matters very efficiently and with impressive concern for the welfare of the participants, and Societas Biochemica, Biophysica et Microbiologica Fenniae, the society of Finnish microbiologists, which made valuable contributions on scientific matters. As in the previous symposium at Banff, Canada, in 1982 the programme did not involve parallel sessions~ all participants had the opportunity of listening to all presentations. Consequently, the FIN- NIF Symposium profited from a steady audience and the consistency this gave to the discussions. In view of the growing interest in N-fixation with non-legumes and the continuous broadening of the field, such an arrangement may not be possible in the future. I thank all participants for their contributionsto both oral sessions and poster presentations, and hope that this publication will become a frequently quoted source of knowledge.

There is a marked and most unfortunate dichotomy in the studies of avian eggs and hence in the application of new findings in commerce. Thus over the past twenty years there has been a renewed interest in the contribu tions of various parts of an egg to embryo development. This is best illustrated by those studies that have explored the diffusion of respiratory gases across the shell and at long last have provided a fundamental definition of a previously nebulous term, porosity. The activity in this general area has led in the past four years to the publication of three major books dealing with many aspects of egg structure, function and embryogenesis. When brows ing over these books, two developments are evident. First, the advantages that are to be gained by comparative studies. Thus it is now common to see within a single book articles concerned with the eggs of a range of avian species as well as those of reptiles. Second, it is evident that zoologists and physiologists as well as those employed in large breeding firms are all contributing to an improvement of our knowledge of the egg's role in the breeding biology of birds. Comparative studies are a very uncommon feature of studies concerned with bacterial infection of eggs."

This book provides a survey of recent advances in the development of antibiofilm agents for clinical and environmental applications. The fact that microbes exist in structured communities called biofilms has slowly become accepted within the medical community. We now know that over 80% of all infectious diseases are biofilm-related; however, significant challenges still lie in our ability to diagnose and treat these extremely recalcitrant infections.

Written by experts from around the globe, this book offers a valuable resource for medical professionals seeking to treat biofilm-related disease, academic and industry researchers interested in drug discovery and instructors who teach courses on microbial pathogenesis and medical microbiology.

This text is an overall view of nematology because I believe the science should be treated as a unified discipline. The differences in the biological habits of nematodes do not justify the separation of plant nematologists and animal nematologists, since the separation is not a reflection of any difIerences inherent to nematodes. Therefore, the book is arranged with a format that in the beginning chapters illustrates the similarities and se- quence of development of morphological characters among nematodes regardless of their biological habits. The later chapters illustrate the in- tegration of the evolutionary development of the parasitie habit from related free-living forms. Nematology is probably the last major discipline to establish its inde- pendence from the parent science of zoology. This natural evolvement of nematology has occurred because of the overwhelming accumulation of sophisticated information and research that reflects the unique relation- ships of nematodes to other forms of plant and animal life as weH as their relationships in other facets of the environment. N ematodes are inverte- brate animals that, like insects, are unusual in their great numbers and varieties, their smaH size (generally microscopic), their high degree of internal organization, and their virtually ubiquitous distribution. They oc- cupy almost every ecological niehe, often causing disease of humans, other animals, and plants. These activities often result in debility, death, or in the impairment and loss of food supply with consequent loss to producers and consumers.

In this second volume in the series The Retroviridae, the readers are treated to up-to-date reviews on these viruses, which are found in a variety of animal species. The volume begins with important observations on the general fea tures of retrovirus entry into cells as determined by the viral envelope glyco proteins and the cell surface receptors (Chapter 1). Aspects of this virus-cell interaction form the basis for the variety of biologic effects associated with this virus family. A timely review of the oncogenic feline viruses is included next (Chapter 2). These viruses, along with the avian and murine retroviruses (Volume 1, Chapters 6 and 7), have provided valuable insight into cancer induction in other animal species, including humans. Two other major groups of retroviruses, the lentiviruses and the spuma viruses, are introduced in the present volume. Initially these groups, along with oncoviruses, were the three subfamilies in the Retroviridae. This com plex virus family has now been reclassified into seven separate genera (Vol ume 1, Chapter 2). Equine infectious anemia virus is the prototype for a lentivirus (Chapter 5). One of the first viruses discovered in nature (1904), it was only relatively recently recognized as a retrovirus. Lentiviruses are asso ciated primarily with immunologic disorders such as autoimmunity and AIDS (Chapters 3-5), but their association with neurologic disease is also well established (Chapters 4 and 5, and future volumes)."

Not another textbook, but a valuable tool for doctors and microbiologists wanting to know how to set up a PCR diagnostic microbiology laboratory according to current regulatory standards and perform assays supplied with patient clinical diagnostic criteria and easy to follow protocols. Whether laboratories are using commercial kits or in-house methods developed in their own laboratories or adopted from published methods, all clinical microbiology laboratories need to be able to understand, critically evaluate, perform and interpret these tests according to rigorous and clinically appropriate standards and international guidelines. The cost and effort of development and evaluation of in-house tests is considerable and many laboratories do not have the resources to do so. This compendium is a vehicle to improve and maintain the clinical relevance and high quality of diagnostic PCR. It is a unique collection of; guidelines for PCR laboratory set up and quality control, test selection criteria, methods and detailed step by step protocols for a diagnostic assays in the field of molecular microbiology. The structure of the book provides the PCR fundamentals and describes the clinical aspects and diagnosis of infectious disease. This is followed by protocols divided into; bacteria, virus, fungi and parasites, and susceptibility screens. The inclusion of medical criteria and interpretation adds value to the compendium and benefits clinicians, scientists, researchers and students of clinical diagnostic microbiology

"Mycobacterium tuberculosis" is one of the most notorious pathogens on earth, causing the death of approximately 1.5 million people annually. A major problem in the fight against tuberculosis is the emergence of strains that have acquired resistance to all available antibiotics. One key to the success of "M. tuberculosis" as a pathogen is its ability to circumvent host immune responses at different levels. This is not only a result of the special makeup of "M. tuberculosis" in terms of genetic diversity and DNA metabolism and its possession of specialized secretion systems, but also of its ability to hijack the host s innate immune defence mechanisms.

In this volume, researchers from different disciplines provide a topical overview of the diverse mechanisms that contribute to the virulence of "M. tuberculosis," ranging from their genetic, metabolic and molecular makeup, as well as the complex strategies these bacteria utilize to escape immune destruction within infected hosts."