This Volume describes methods for investigating microbes in their natural environment and how to obtain representative samples and preserve them for subsequent analyses. Chapters are arranged according to the environments under investigation, which include: oil reservoirs, fracking fluids, aquifers, coal beds, oil sands and their tailing ponds, lakes, rivers, leaves, polar seas and ice, the sea-surface microlayer, mud flats, microbialites, and deep-sea fauna. A variety of downstream analytical procedures are described, including: nucleic-acid extraction and preparation for high-throughput sequencing, fluorescence in-situ hybridisation, and cultivation of aerobic and anaerobic hydrocarbon-degrading microbes. Though most chapters focus on hydrocarbon-rich environments, many of the approaches used are generic, and as such will be of value to researchers embarking on studies of microbes and their processes in the field. 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.

Bacterial genomics is a mature research interdisciplinary field, which is approached by ecologists, geneticists, bacteriologists, molecular biologists and evolutionary biologists working in medical, industrial and basic science. Thanks to the large diffusion of bacterial genome analysis, Bacterial Pangenomics: Methods and Protocols is able to provide the most recent methodologies about the study of bacterial pangenomes by covering the three major areas: the experimental methods for approaching bacterial pangenomics, the bio informatic pipelines for analysis and annotation of sequence data and finally the methods for inferring functional and evolutionary features from the pangenome. Written in the 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 protocols and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Bacterial Pangenomics: Methods and Protocols will serve as a field guide for both qualified bacterial genomics investigators who want to update their technical knowledge, for less experienced researchers who want to start working with bacterial genomics and pangenomics, as well as serving as a manual and supplemental textbook for graduate students of genomics and bioinformatics.

This volume provides a comprehensive coverage of the principal extreme soil ecosystems of natural and anthropogenic origin. Extreme soils oppose chemical or physical limits to colonization by most soil organisms and present the microbiologist with exciting opportunities.

Described here are a range of fascinating environments from permafrost to Martian soils. The book includes chapters on basic research in addition to applications in biotechnology and bioremediation.

Salt is an essential requirement of life. Already from ancient times (e. g. , see the books of the Bible) its importance in human life has been known. For example, salt symbolizes destruction (as in Sodom and Gomorra), but on the other hand it has been an ingredient of every sacrifice during the Holy Temple periods. Microbial life in concentrated salt solutions has fascinated scientists since its discovery. Recently there have been several international meetings and books devoted entirely to halophiles. This book includes the proceedings of the "Halophiles 2004" conference held in Ljubljana, Slovenia, in September 2004 (www. u- lj. si/~bfbhaloph/index. html). This meeting was attended by 120 participants from 25 countries. The editors have selected presentations given at the meeting for this volume, and have also invited a number of contributions from experts who had not been present in Ljubljana. This book complements "Halophilic Microorganisms", edited by A. Ventosa and published by Springer-Verlag (2004), "Halophilic Microorganism and their Environments" by A. Oren (2002), published by Kluwer Academic Publishers as volume 5 of "Cellular Origins, Life in Extreme Habitats and Astrobiology" (COLE), and "Microbiology and Biogeochemistry of Hypersaline Environments" edited by A. Oren, and published by CRC Press, Boca Raton (1999). Salt-loving (halophilic) microorganisms grow in salt solutions above seawater salinity (~3. 5% salt) up to saturation ranges (i. e. , around 35% salt). High concentrations of salt occur in natural environments (e. g.

We might think of them as living on the very edge of existence. Referred to as extremophiles, these microorganisms exhibit the most radical capacity for adaptation in those harsh environments that are just barely conducive to the existence of cellular life. Unlocking the mechanisms and understanding the evolutionary development that allows these simple organisms to thrive can teach us much about microbiology in extremis. Highly diverse, these microorganisms are found nearly everywhere. One example, thermophiles are microorganisms that thrive at temperatures above the mesophilic range of 25-40 degrees C. Until recently, due to their extreme environment, the study of thermophiles was limited. However with the advent of new tools, particularly genetic analysis, remarkable strides have been made. Thermophiles: Biology and Technology at High Temperatures presents a cogent summary of the progress made in studying these extremophiles. Discover how thermophiles demonstrate extremes that indicate a lack of evolutionary constraints Much is being learned from the study of thermophiles, especially our understanding of biology at the molecular level and the genetic mechanisms that permit adaptation. Included in this volume is a discussion of protective strategies of thermophiles, including their thermostability, which allow them to maintain functional proteins. It also investigates whether hyperthermophiles employ protein phosphorylation-dephosphryation as a molecular regulatory mechanism, and provides significant clues regarding the synthesis of protein. By studying this extreme example, its subtle, yet exaggerated response mechanisms, and its development over the course of many short-lived generations, we may begin to understand the mechanisms in diseases linked to improper protein folding, and also begin to more fully understand the ingenious design of DNA, and all that such an understanding implies regarding the survival of human life in a rapidly changing environment.

The NATO Advanced Research Workshop from which this book derives was conceived during Biotec-88, the Second Spanish Conference on Biotechnology, held at Barcelona in June 1988. The President of the Conference, Dr. Ricardo Guerrero, had arranged sessions on bacterial polymers which included lectures by five invited participants who, together with Dr. Guerrero, became the Organizing Committee for a projected meeting that would focus attention upon the increasing international importance of novel biodegradable polymers. The proposal found favour with the NATO Science Committee and, with Dr. R. Clinton Fuller and Dr. Robert W. Lenz as the co-Directors, Dr. Edwin A. Dawes as the Proceedings Editor, and Dr. Hans G. Schlegel, Dr. Alexander J.B. Zehnder and Dr. Ricardo Guerrero as members of the Organizing Committee, the meeting quickly took shape. To Dr. Guerrero we owe the happy choice of Sitges for the venue, a pleasant coastal resort 36 kilometres from Barcelona, which proved ideal. The sessions were held at the Palau de Maricel in appropriately impressive surroundings, and invaluable local support was provided by Mr. Jordi Mas-Castella and by Ms. Merce Piqueras. Much of the preparatory work fell upon the broad shoulders of Mr. Edward Knee, whose efforts are deeply appreciated. The Organizing Committee hopes that this Workshop will prove to be the first of a series which will aim to keep abreast of a rapidly expanding and exciting area of research that is highly relevant to environmental and industrial interests.

This book provides readers with information on the factors underlying the emergence of infectious diseases originating in animals and spreading to people. The One Health concept recognizes the important links between human, animal, and environmental health and provides an important strategy in epidemic mitigation and prevention. The essential premise of the One Health concept is to break down the silos among the different health professions and promote transdisciplinary collaborations. These concepts are illustrated with in-depth analyses of specific zoonotic agents and with examples of the successes and challenges associated with implementing One Health. The book also highlights some of the challenges societies face in confronting several specific zoonotic diseases. A chapter is included on comparative medicine to demonstrate the broad scope of the One Health concept. Edited by a team including the One Health Initiative pro bono members, the book is dedicated to those studying zoonotic diseases and comparative medicine in both human and veterinary medicine, to those involved in the prevention and control of zoonotic infections and to those in the general public interested in the visionary field of One Health.

Antimicrobial resistance is recognised among the world’s most challenging problems. Despite its global spread, Africa, specifically sub-Saharan Africa, is the most affected by this malaise. Poor living conditions and inadequate access to sanitation and potable water supplies are among contributing factors that have influenced a high disease burden on the continent, requiring extensive antimicrobials. Weak health systems and the absence of firm policies further aggravate the problem, as the use of antimicrobials is mostly unregulated. The increasing demand for animal protein to meet the starving populations’ demands has also influenced the use of these antimicrobials, including those banned on other continents, for food animal production. The ripple effect of indiscriminate use in humans and animals is the massive discharge of antimicrobials, their residues, antimicrobial-resistant microorganisms and their associated genes into the environment.  This 14-chapter unique masterpiece presents the AMR problem in African, addressing the various compartments of the One Health – humans, animals, and the environment, to illustrate the need for concerted efforts in the fight against AMR, especially in Africa. Authors from the four cardinal points present diverse aspects of AMR in Africa, starting with behavioural and social drivers of AMR in Africa. Antimicrobial stewardship in an African context is also discussed. AMR in humans is presented through studies on antibiotic-resistant neonates and nontyphoidal Salmonella infections and the clinical relevance of the genetics of viral resistance. Topics on AMR in mastitis, biosecurity in animal farming and the linkage between disinfectants and AMR are discussed. The environmental dimension of AMR is discussed, notably in the aquatic environment, and its implication for aquaculture and irrigation and using nanomaterials to treat polluted waters from such environments are highlighted. Finally, Africa’s rich floral diversity is portrayed as an eco-friendly and cost-effective approach to combat AMR. Hopefully, the work presented will spur greater collaboration between scientists, environmental, animal and human health practitioners, the general population, and policymakers to assimilate and implement the One Health approach to combating AMR, rather than working in silos on their various sectors

Leishmania parasites cause a diverse group of diseases endemic to many tropical and subtropical regions of the world. This volume seeks to bring together recent research on cell and molecular biology of Leishmania with chapters on the host response to infection, the current epidemiology of leishmaniasis, explanations of the many different species, vector control, and strategies for vaccine development and drug treatment. Leishmania, volume four of World Class Parasites, is written for researchers, students and scholars who enjoy reading research that has a major impact on human health, or agricultural productivity, and against which we have no satisfactory defense. It is intended to supplement more formal texts that cover taxonomy, life cycles, morphology, vector distribution, symptoms and treatment. It integrates vector, pathogen and host biology and celebrates the diversity of approach that comprises modern parasitological research.

Allelochemicals play a great role in managed and natural ecosystems. Apart from plant growth, allelochemicals also may influence nutrient dynamics, mycorrhizae, soil chemical characteristics, and microbial ecology. Synergistic action of various factors may better explain plant growth and distribution in natural systems. The book emphasizes the role of allelochemicals in shaping the structure of plant communities in a broader ecological perspective. The book addresses the following questions: (1) How do allelochemicals influence different components of the ecosystem in terms of shaping community structure? (2) Why is it difficult to demonstrate interference by allelochemicals (i.e., allelopathy) in a natural system in its entirety? Despite a large amount of existing literature on allelopathy, why are ecologists still skeptical about the existence of allelopathy in nature? (3) Why are there only scarce data on aquatic ecosystems? (4) What role do allelochemicals play in microbial ecology?.....

This volume focuses on blocking disease transmission and the ecological perspective of pathogens and pathogenic processes. The chapters on blocking transmission cover the environmental safety of space flight, biocides and biocide resistance, as well as infection control in healthcare facilities. The book also offers insights into the ecological aspects of infectious disease, introducing the reader to the role of indigenous gut microbiota in maintaining human health and current discussions on environmentally encountered bacterial and fungal pathogens including species that variously cause the necrotizing skin disease Buruli ulcer and coccidioidomycosis. Further, it explores the influenza A virus as an example for understanding zoonosis. It is a valuable resource for microbiologists and biomedical scientists alike.

The past decade has witnessed an explosion of information on the molecular biology of insect viruses and a frenzy of activity in applying this information to medicine and agriculture. Genetically engineered baculoviruses are presently being tested for commercial use as pesticides, and the study of such viruses is also revealing remarkable insights into basic cellular processes such as apoptosis. This comprehensive volume provides readers with knowledge of basic and applied baculovirology so that current literature in the field can be appreciated.

Principles of Virology, the leading virology textbook in use, is an extremely valuable and highly informative presentation of virology at the interface of modern cell biology and immunology. This text utilizes a uniquely rational approach by highlighting common principles and processes across all viruses. Using a set of representative viruses to illustrate the breadth of viral complexity, students are able to under-stand viral reproduction and pathogenesis and are equipped with the necessary tools for future encounters with new or understudied viruses. This fifth edition was updated to keep pace with the ever-changing field of virology. In addition to the beloved full-color illustrations, video interviews with leading scientists, movies, and links to exciting blogposts on relevant topics, this edition includes study questions and active learning puzzles in each chapter, as well as short descriptions regarding the key messages of references of special interest. Volume I: Molecular Biology focuses on the molecular processes of viral reproduction, from entry through release. Volume II: Pathogenesis and Control addresses the interplay between viruses and their host organisms, on both the micro- and macroscale, including chapters on public health, the immune response, vaccines and other antiviral strategies, viral evolution, and a brand new chapter on the therapeutic uses of viruses. These two volumes can be used for separate courses or together in a single course. Each includes a unique appendix, glossary, and links to internet resources. Principles of Virology, Fifth Edition, is ideal for teaching the strategies by which all viruses reproduce, spread within a host, and are maintained within populations. This edition carefully reflects the results of extensive vetting and feedback received from course instructors and students, making this renowned textbook even more appropriate for undergraduate and graduate courses in virology, microbiology, and infectious diseases.

This concise yet comprehensive text surveys the field of bacterial metabolism in terms useful to students and researchers. Emphasis is on those metabolic reactions occurring only in bacteria. Thus, the book describes in detail the energy metabolism of the various groups of bacteria. In addition it examines pathways used by bacteria for the degradation of organic compounds, the synthesis of cellular consituents, the regulation of bacterial metabolism and the fixation of molecular nitrogen. The general arrangement of the first edition has been retained. However, it has been thoroughly revised and updated in recognition of the rapid progress of research in this field. Readers will also appreciate the increased emphasis on membrane-associated processes. From the review of the second edition: "If there is a better textbook in its fields, I'm not aware of it, and I feel the book deserves a place on the shelf of any serious student of microbiology." -ASM News

Filamentous fungi have long been known for their ability to produce an enormous range of unusual chemical compounds known as secondary metabolites, many of which have potentially useful antibiotic or pharmacological properties. Recent focus on fungal genomics coupled with advances in detection and molecular manipulation techniques has galvanized a revitalization of this field. Fungal Secondary Metabolism: Methods and Protocols is aimed at providing the key methodologies currently in use and necessary for accessing and exploiting the natural product information provided by the genomes of this large and varied kingdom. Written by active researchers in the field, the chapters deal with all the steps necessary, from optimization of fungal culture conditions for metabolite production, through rapid genome sequencing and bioinformatics, and genetic manipulations for functional analysis, to detection and testing of metabolites. In addition, chapters on basic science address approaches to the genetic regulation, protein biochemistry, and cellular localization of the biosynthetic pathways. Written in the highly successful Methods in Molecular Biology (TM) 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. Practical and hands-on, Fungal Secondary Metabolism: Methods and Protocols encourages new investigators to enter the field and expands upon the expertise and range of skills of those already researching fungal natural products.

This book provides an essential update on the startling array of novel insecticidal toxins and drugs produced by the fascinating bacterium Photorhabdus. The respective chapters describe everything from the detailed molecular biology of the 'Toxin complexes' or Tc's to the complexity of insect immune response in relation to both the bacterium and its nematode vector. The volume covers both primary (toxin production and regulation) and secondary (natural product synthesis and regulation) metabolism and emphasises the potential use of toxins and drugs in both agriculture and medicine. It also discusses in detail two totally novel quorum sensing mechanisms and the likely role of LuxR solos in sensing the presence of different bacterial hosts. Lastly, the book explores the unique case of P. asymbiotica, which seems to have evolved the ability to infect both insects and humans. This synthesis proves that Photorhabdus truly does offer a 'gold mine' for the discovery of novel insecticidal proteins and novel natural products with potential uses in agriculture and medicine alike.

The genome sequences of several pseudomonads have become available in recent years and researchers are beginning to use the data to make new discoveries about this bacterium. This concise volume reviews the most current and topical aspects of Pseudomonas molecular biology and genomics and is aimed at a readership of research scientists, graduate students and other specialists. Renowned international authors have contributed chapters on diverse topics including taxonomy, genome diversity, oligonucleotide usage, polysaccharides, pathogenesis, virulence, biofilms, antibiotic resistance and iron uptake. In addition an entire chapter is devoted to the genetic tools being developed to take full advantage of the wealth of information generated by the genome sequencing efforts. This book is essential reading for anyone involved in Pseudomonas research.

Bacteria occupy a unique position in the living world. They are amongst the first inhabitants of planet earth, and have survived until the present day. Adaptation, adjustment, and accommodation are the hallmarks of their strategy for survival. Their structural simplicity, and yet independent lifestyle, has provided a baseline model system on which every branch of modern biology have been founded. This includes the fields of molecular genetics and recombinant DNA technology. Bacteria have been at the heart of developments in the field of biotechnology where today many microbial and eukaryotic (including human) metabolites have found industrial applications. Amenable to all modern tools and techniques, bacteriology has developed an interface with all other branches of biology, often providing the major leads and clues. In the present era of genomics, now that many microbial genomes have been sequenced, bacteria are destined to provide new information that will further our understanding of life and biological processes.
This book contains exhaustive information on almost all aspects of bacteria. The book deals exclusively with bacteria and includes the entire gamut of bacteriology. It will be useful to graduate and post-graduate levels but also to established researchers. The book is organized in such a way that it will give the reader an overview of our current understanding of bacteria. It will explain the categories under which various types have been grouped and describe the versatile range of metabolic processes which can be found in these microbial organisms. Their metabolic regulation, capacity to change and keep evolving and their pivotal role in natural processes arehighlighted. Research on bacteria, especially genetic engineering, will have far reaching applications in the future.

This book discusses the commercialization of biofuels and the Brazilian government policies for the promotion of renewable energy program in Brazil, which could be a learning module for several countries for implementing biofuels policy to improve their socioeconomic status and make them energy independent.

Researchers in academia and industries, policy makers, and economic analysts will be assisted by important source of information in their ongoing research and future perspectives.

This book will benefit graduate and postgraduate students of chemical and biochemical engineering, forestry, microbiology, biochemistry, biotechnology, applied chemistry, environmental science, sustainable energy, and biotech business disciplines by signifying the applied aspects of bioenergy production from various natural sources and their implications. Graduate and postgraduate students as well as postdoctoral researchers will find clear concepts of feedstock analysis, feedstock degradation, microbial fermentation, genetic engineering, renewable energy generation and storage, climate changes, and techno-economic analysis of biofuels production technologies.

This comprehensive study of poultry meat safety offers readers the most up-to-date information on food safety concerns in poultry meat production. Chapters address recent topics of interest such as organic poultry production, antimicrobial resistant pathogens in poultry, antibiotic usage in poultry production, and pre- and post- harvest approaches to improving poultry meat safety. The last couple of decades have observed a significant increase in poultry meat production in the US. However, poultry meat is a potential source of foodborne pathogens such as Salmonella, Campylobacter spp. and pathogenic Escherichia coli (APEC linked to human infections), leading to economic losses to the poultry industry and impacting public health. Advances in knowledge in microbiology, molecular biology, immunology and "omics" fields have intensified efforts to improve the microbiological safety of poultry by targeting virulence mechanisms of the pathogens, developing vaccines and improving gut health in chickens. Moreover, due to the emergence of multidrug resistance in poultry-borne pathogens, and growth of organic poultry production, there exists significant interest for developing natural strategies for controlling pathogens in chickens. This edited volume provides insight into these strategies and covers other material of interest to food microbiologists, public health personnel, and poultry scientists. Readers of various backgrounds will appreciate its incorporation of recent developments not covered in other publications on the subject.

Research on the interaction between plants and microbes continues to attract increasing attention, both within the field as well as in the scientific community at large. Many of the major scientific journals have recently reviewed various aspects of the field. Several papers dealing with plant-microbe interactions have been featured on the covers of scientific publications in the past several months, and the lay press have recently presented feature articles of this field. An additional sign of the interest in this field is that the International Society of Molecular Plant-Microbe Interactions has almost 500 members. This book is a collection of the papers that were given at the Sixth Inlernational Symposium on the Molecular Genetics of Plant-Microbe Interactions which was held in Seattle, Washington in July, 1992. Approximately 650 scientists attended and approximately 50 lectures covering the topics of Agrobacterium-plant interactions, Rhizobium-plant interactions, bacteria-plant interactions, fungal-plant interactions and new aspects of biotechnology were presented. In addition, many sessions were devoted to the plant response to the microbe. Over 400 posters were presented of which the authors of 20 were selected to give an oral presentation. These papers are included in this volume as well. The symposium also included speakers whose research interests are not directly related to plant-microbe interactions but who are at the cutting edge of research areas that impact on the theme of the symposium. These individuals kindly agreed to summarize their talks and their papers are also included.

This book review series presents current trends in modern biotechnology. The aim is to cover all aspects of this interdisciplinary technology where knowledge, methods and expertise are required from chemistry, biochemistry, microbiology, genetics, chemical engineering and computer science. Volumes are organized topically and provide a comprehensive discussion of developments in the respective field over the past 3-5 years. The series also discusses new discoveries and applications. Special volumes are dedicated to selected topics which focus on new biotechnological products and new processes for their synthesis and purification. In general, special volumes are edited by well-known guest editors. The series editor and publisher will however always be pleased to receive suggestions and supplementary information. Manuscripts are accepted in English.

The promotion of a high level of food safety and quality is of major importance world-wide. Aspects of food quality such as genetically modified organisms (GMOs), food allergens and food authentication have become increasingly important while food-borne diseases caused by bacteria, viruses and parasites continue to be a significant problem. The application of real-time PCR is one of the most promising advances in food safety and quality providing rapid, reliable and quantitative results. In recent years real-time PCR has become a valuable alternative to traditional detection methods in the agricultural and food industries. The advantages of quantitative real-time PCR include speed, an excellent detection limit, selectivity, specificity, sensitivity and the potential for automation.