Genetics and Regulation of Nitrogen-Fixing Bacteria This book is the second volume of a seven-volume series, which covers all fields of research related to nitrogen fixation - from basic studies through applied aspects to environmental impacts. Volume II provides a comprehensive and detailed source of information concerning the genetics and regulation of biological nitrogen fixation in free-living prokaryotes. This preface attempts to provide the reader with some insight into how this volume originated, how it was planned, and then how it developed over the several years of its production. Once the editorial team was established, the first job was to decide which of the many free-living diazotrophs that have been subjected to genetic analysis should be included in this volume. Would we need to develop specific criteria for selection or would the organisms, in effect, select themselves? Of course, Klebsiella pneumoniae and Azotobacter vinelandii, which have served (and still serve) as the main model organisms for the genetic analysis of diazotrophy, plus some of the other bacteria described in this volume, did indeed select themselves. However, there was considerable discussion surrounding well-characterized fixing species, like Azorhizobium caulinodans and Herbaspirillum seropedicae, both of which are able to fix atmospheric N under free-living conditions.

At last, here is a graduate-level textbook that focuses on the very latest information on the molecular and cellular mechanism of several major foodborne bacterial pathogens. For the first time in the field, this book makes the link between foodborne illness and immunology. It also covers virulence genes and their regulation in the host or the food environment, pathogenicity testing models, clinical symptoms and prevention and control strategies. Unlike other textbooks this one also covers the host/parasite interaction to a level where readers have a real appreciation of the disease mechanism. It is imperative that we acquire a better understanding of foodborne pathogens. And this is what this brilliant and timely contribution to the subject offers.

Ranging from the evolution of pathogenicity to oceanic carbon cycling, the many and varied roles that bacteriophages play in microbial ecology and evolution have inspired increased interest within the scientific community. Bacteriophages: Methods and Protocols pulls together the vast body of knowledge and expertise from top international bacteriophage researchers to provide both classical and state-of-the-art molecular techniques. With its well-organized modular design, Volume 1: Isolation, Characterization, and Interactions examines a multitude of topics, including the isolation of phages, morphological and molecular characterization, and interaction with bacteria. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters consist of brief introductions to the subject, lists of the necessary materials and reagents, readily reproducible laboratory protocols, and a Notes section which details tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Bacteriophages: Methods and Protocols is a valuable reference for experienced bacteriophage researchers as well as an easily accessible introduction for newcomers to the subject.

There is currently increasing interest concerning the biology and disease caused by Acinetobacter species. Such interest, however, developed relatively slowly because of the necessity to clarify the confusing taxonomy of these organisms. Much work was needed to identify various species as members of this genus, to recognize their epidemiologic profile, their pathogenic role and their increasing importance as multi-antibiotic resistant organisms. In recent years improvement of genetic approaches, recognition of plasmids, integrons and chromosomal sources of resistance mechanisms aroused interest on the role of Acinetobacters in disease by many microbiologists and clinicians, especially internists and infectious disease specialists. In this regard, physicians are frequently confronted with extremely difficult therapeutic approaches for treatment and prevention of severe nosocomial infections due to multi antibiotic resistant Acinetobacter. Moreover, recent observations of community acquired infections have been reported, especially in patients with various risk factors such as immuno-deficiencies. Also, it is now becoming evident that Acinetobacter infections occur frequently in violent situations such as earthquake or war zones. The mechanisms of Acinetobacter virulence are becoming increasingly clear, providing new insights into their pathogenic role in community acquired infections. It is apparent the time is appropriate for detailed review of the increasing knowledge concerning important new information, both clinical and therapeutic, especially information concerning virulence, resistance mechanisms and typing of Acinetobacter spp. Many new findings are accumulating in almost an exponential manner since publication of previous books on this subject in 1991 and 1996.

Includes a revised taxonomic outline for the phyla Bacteroidetes, Planctomycetes, Chlamydiae, Spirochetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes based upon the SILVA project as well as a description of more than 153 genera in 29 families. Includes many medically important taxa.

Over the course of the past decade, there have been remarkable advances in the study of human pathogenic fungi. These developments have taken place throughout a wide range of disciplines, and have come as the result of newly available genome sequences of pathogens such as candida albicans and other model fungi. In Candida Albicans: Methods and Protocols, expert researchers explore these exciting new insights, focusing on the study of medically important fungi and Candida spp in particular. Chapters examine critical aspects of molecular methods, providing information on reporter gene assays, transformation, gene expression in vivo, and methods for large-scale gene disruption. At the same time, the work includes in-depth descriptions of disease models of candidiasis, facts about strain identification, and guidelines on the preparation of samples for proteomic investigations and tandem affinity purification. Composed in the highly successful "Methods in Molecular Biology " series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting edge, Candida Albicans: Methods and Protocols is an invaluable source of methods for investigators in the exhilarating fields of medical and molecular mycology."

PGPR have gained world wide importance and acceptance for agricultural benefits. These microorganisms are the potential tools for sustainable agriculture and the trend for the future. Scientific researches involve multidisciplinary approaches to understand adaptation of PGPR to the rhizosphere, mechanisms of root colonization, effects on plant physiology and growth, biofertilization, induced systemic resistance, biocontrol of plant pathogens, production of determinants etc. Biodiversity of PGPR and mechanisms of action for the different groups: diazotrophs, bacilli, pseudomonads, and rhizobia are shown. Effects of physical, chemical and biological factors on root colonization and the proteomics perspective on biocontrol and plant defence mechanism is discussed. Visualization of interactions of pathogens and biocontrol agents on plant roots using autofluorescent protein markers has provided more understanding of biocontrol process. Commercial formulations and field applications of PGPR are detailed.

As this book. Antibacterial Peptide Protocols, will attest, my enthusi asm for the field of antibacterial peptides is based on a conviction (and I am unashamed to say, prejudice) that these substances are in essence antibiotics produced by the host that then participate in host defense against infectious agents. Because of their capacity to exert antibiotic-like action against patho genic microorganisms (bacteria, fungi, parasites, and viruses), there is reason to believe that these agents will soon be used clinically to treat infectious diseases. In fact, in recent years, biotechnology companies have been formed for the sole purpose of developing antibacterial peptides for clinical use. It should be emphasized that antibacterial peptides will likely play a major role in the treatment of infectious diseases, particularly with the increasing prob lem of multidrug-resistant microbes and the relative dearth of new antibiotics being provided by pharmaceutical companies. The topic of this volume of Methods in Molecular Biology, the diverse methods used in research on antibacterial peptides, is thus quite timely. As the subject of antibacterial peptides develops into its own discipline (something strongly suggested by the explosion in the number of papers published over the past decade), it is essential that reliable techniques and strategies be made available not only to those of us in the field, but also to the newcomers and researchers in complementary disciplines."

Since the discovery of circadian rhythms in cyanobacteria in the late 1980s, the field has exploded with new information. The cyanobacterial model system for studying circadian rhythms, "Synechococcus elongatus," has allowed a detailed genetic dissection of the bacterial clock due to the methods currently available in molecular, structural, and evolutionary biology.

This book addresses multiple aspects of bacterial circadian programs: the history and background of the cyanobacteria and circadian rhythms in microorganisms, the molecular basis, structure, and evolution of the circadian clock, entrainment of the oscillator with the environment and the control of downstream processes by the clock, the demonstration of adaptive significance and the prokaryotic clock s remarkable stability, and mathematical and synthetic oscillator models for clock function.

Experts in the field provide a timely and comprehensive review and a stepping-stone for future work on this amazing group of microorganisms and timing."

This volume provides an overview of the latency strategies developed during the estimated 200 Myears long coevolution of Alpha-, Beta- and Gammaherpesvirinae and their host species. The main emphasis is on herpesviruses infecting humans. However, relevant cases if herpesviruses infecting animals are covered as well. Special emphasis is drawn on results on molecular mechanisms regulating latent promoters of herpesvirus genomes and signals and molecular pathways resulting in reactivation of latent viral genomes. To balance the volume, epigenetic mechanisms (DNA methylation, histone modification, chromatin structure) involved in cell type specific expression of growth-transformation-associated Gammaherpesvirus genes will also be discussed at length)

"Alginates: Biology and Applications" provides an overview of the state of art of alginate material properties, genetics and the molecular mechanisms underlying alginate biosynthesis as well as applications of tailor-made alginates in medicine, food and biotechnology.

Topics treated are: material properties of alginates, alginate production: precursor biosynthesis, polymerization and secretion, bacterial system for alginate uptake and degradation, enzymatic alginate modification, alginate gene regulation, role of alginate in bacterial biofilms, microbial production of alginates: physiology and process aspects, alginate-based blends and nano/microbeads, applications of alginates in food, alginate and its comonomer mannuronic acid: medical relevance as drugs.

Bacteria change the surface of the Earth. All kinds of bacteria reside in the biosphere, and although sometimes they may cause damage, they also help in cleaning the surface of the Earth and in the circulation of various substances. Chemolithoautotrophic bacteria in particular have a unique and intimate relationship with inorganic substances and human beings. This book covers in detail advances in the biochemistry and physiology of several chemolithoautotrophic bacteria as well as their relationship to certain environments. Included are recent findings regarding the oxidation mechanisms of ammonia, nitrite, sulfur compounds, and ferrous iron by special bacteria. The characteristics of many cytochromes are described to further advance the understanding of bacterial oxidation systems of inorganic compounds. Applications of bacteria, such as in sewage treatment and in biohydometallurgy, among others, are detailed, and bacteria considered closest to the origins of life are discussed in the final chapter.

In the context of increasing international concern for food and environmental quality, use of Plant Growth-Promoting Rhizobacteria (PGPR) for reducing chemical inputs in agriculture is a potentially important issue. PGPR are root-colonizing bacteria that exert beneficial effects on plant growth and development, but they can be also employed in the control of plant pathogens, for enhancing the efficiency of fertilizers, and for degrading xenobiotic compounds. This book provides an update by renowned international experts on the most recent advances in the ecology of these important bacteria, the application of innovative methodologies for their study, their interaction with the host plant, and their potential application in agriculture.

The book 's purpose is to explain from the development of life on earth to the evolution of diversity. It is this diversity that led, almost automatically to the development of pathogens and predators. The relationship of pathogens and host lead to the development of antibiotics and resistance mechanism. Man has extended this process and we now have a situation in which new antibiotics only are effective for a short time. If we are to create long term antibiotics we must design them with this history in mind.

Understanding antibiotic chemotherapy at the ecological level is necessary for more permanent advances in development and in the usage of antibiotic agents both old, new, and in the future.

This book is intended for students at various levels that will be the microbiology researchers in the time to come. Also microbiology professors, particularly those teaching medical microbiology as well as physicians administering antibiotics daily and researchers in the pharmaceutical industry may find this book useful.

This manual reflects practical approaches to handling bacteria in the labora- tory. It is designed to recall historical methods of bacterial genetics that have had recent developments and to present new techniques that allow full genome analysis. It has been written for microbiologists who need to group their protocols at the state of the art of a new millennium and also for scientists in other fields of life sciences who need to use bacteria for their research. Teachers, graduate students, and postdocs also will benefit from having these protocols to help them understand modern bacterial genetics. I learned so much from these contributions from my colleagues that I have no doubt about the daily usefulness of this book. April 2002 Michel Blot XII Abbreviations Acyl-HSL N-acyl homoserine lactone moi multiplicity of infection Amp or Ap ampicillin N amino C carboxy NMR nuclear magnetic resonance CIO-HSL N-decanoyl-L-homoserine lactone 3-0H-C14:1-HSL N-(3-hydroxy-7 -cis-tetra- C12-HSL N-dodecanoyl-L-homoserine lac- decanoyl)homo-serine lactone tone 3-0H-C4-HSL N-3-hydroxybutanoyl-L- C14-HSL N-tetradecanoyl-L-homoserine homoserine lactone lactone ONPG o-nitrophenyl ~-D-galactopyranoside C4-HSL N-butanoyl-L-homoserine lactone ORF open reading frame C6-HSL N-hexanoyl-L-homoserine lactone OTG I-S-octyl-~-D-thioglucoside C8-HSL N-octanoyl-L-homoserine lactone 3-oxo-CIO-HSL N-3-oxodecanoyl-L-homo- Cam or Cm chloramphenicol serine lactone CBD chitin binding domain 3-oxo-C12-HSL N-3-oxododecanoyl-L- CHEF contour clamped homogenous electric homoserine lactone field 3-oxo-C14-HSL N-3-oxotetradecanoyl-L- CI consistency index homoserine lactone CRIM conditional-replication, integration, 3-oxo-C4-HSL N-3-oxobutanoyl-L-homoser- and modular ine lactone dCTP deoxycytidine triphosphate 3-oxo-C6-HSL N-3 -oxohexanoyl-L-homoser- deg.

Cyanobacteria make a major contribution to world photosynthesis and nitrogen fixation, but are also notorious for causing nuisances such as dense and often toxic blooms' in lakes and the ocean. The Ecology of Cyanobacteria: Their Diversity in Time and Space is the first book to focus solely on ecological aspects of these organisms. Its twenty-two chapters are written by some thirty authors, who are leading experts in their particular subject. The book begins with an overview of the cyanobacteria - or blue-green algae, for those who are not specialists - then looks at their diversity in the geological record and goes on to describe their ecology in present environments where they play important roles. Why is one of the key groups of organisms in the Precambrian still one of the most important groups of phototrophs today? The importance of ecological information for rational management and exploitation of these organisms for commercial and other practical purposes is also assessed. Accounts are provided of nuisances as well as the ecology of the commercially successful Spirulina and the role of cyanobacteria in ecosystem recovery from oil pollution. Many chapters include aspects of physiology, biochemistry, geochemistry and molecular biology where these help general understanding of the subject. In addition there are three chapters dealing specifically with molecular ecology. Thirty-two pages of colour photos incorporate about seventy views and light micrographs. These features make the book valuable to a wide readership, including biologists, microbiologists, geologists, water managers and environmental consultants. The book complements the highly successful The Molecular Biology of Cyanobacteria already published by Kluwer.

Creating bacteria with modified genetic properties allows the specific investigation of these microorganisms. Electrotransformation is a highly efficient and easy to apply technique to introduce genetic material into bacterial cells. A strong electric field is used for this purpose.
In the present manual, protocols for the transformation of about 40 strains of bacteria are described. Emphasis is placed on the individual critical procedural steps, since the practical details mainly depend on the bacterial strain under investigation. This presentation together with the theoretical introductionary chapters, allows the user to modify and adapt each protocol to his/her own experiments. Bacterial strains with relevance in the food industry, biotechnology, medical and veterinary fields, agroindustry and environmental sciences are covered.

Detailed information dealing with the ecology of mycobacteria is derived from a variety of different scientific fields such as botany, biochemistry, genetics, immunology, microbiology and epidemiology. This is the first attempt to evaluate this information from an ecological point of view and to develop a strategy for the prevention of tuberculosis and other mycobacterioses based on the ecological behavior of mycobacteria, especially the potentially pathogenic species capable of either growth in the environment or provoking disease. Regarding the interests of the developing countries, special attention is paid to the ecology of Mycobacterium leprae and to the supporting effect of accompanying mycobacteria in its pathogenicity. On a more positive side, environmental mycobacteria play an important role in the ecology of moorland dragonflies. Such a book is needed for specialists working in the field of mycobacterial research, clinical laboratories, the public health service, food hygiene, the water industry and in general ecology.

This book contains the Proceedings of the Ninth International Symposium on Pho- totrophic Prokaryotes (IXth ISPP) which was held in Vienna, Austria, from September 6-12,1997. In 1973, the far-sighted efforts of Gerhart Drews, Roger Y. Stanier, and Nor- bert Pfennig launched the first ISPP as a joint forum for scientific discussion of all aspects of research on phototrophic prokaryotes, both anoxygenic and oxygenic (cyanobacteria or blue-green algae). The ISPP International Scientific Committee, a rather loose community of scientists (see page vii for a list of current members), has since been responsible for the organization of the ISPPs on a triennial basis, without any dedicated financial support from a society, membership fees, or similar. The success of the ISPPs is therefore due to the continued enthusiasm of the scientific community for such a forum, as exemplified by the rise in attendance from 79 (1 st ISPP) to more than 400 active scientists (plus depen- dants) from all five continents in Vienna. Comparing the Book of Abstracts of 1973 with that of 1997 reflects the tremendous change that has occurred in the last 25 years in scien- tific research on phototrophic prokaryotes. Two noteworthy examples of such change are the significant shift in emphasis from anoxyphototrophs to cyanobacteria and the advent of molecular genetics, culminating at the 9th ISPP in the first complete genomic DNA se- quence of a phototrophic prokaryote, viz. the cyanobacterium Synechocystis sp. PCC6803.

Since the discovery of circadian rhythms in cyanobacteria in the late 1980s, the field has exploded with new information. The cyanobacterial model system for studying circadian rhythms, "Synechococcus elongatus," has allowed a detailed genetic dissection of the bacterial clock due to the methods currently available in molecular, structural, and evolutionary biology.

This book addresses multiple aspects of bacterial circadian programs: the history and background of the cyanobacteria and circadian rhythms in microorganisms, the molecular basis, structure, and evolution of the circadian clock, entrainment of the oscillator with the environment and the control of downstream processes by the clock, the demonstration of adaptive significance and the prokaryotic clock s remarkable stability, and mathematical and synthetic oscillator models for clock function.

Experts in the field provide a timely and comprehensive review and a stepping-stone for future work on this amazing group of microorganisms and timing."

Bacterial plasmids originating in a wide range of genera are being studied from a variety of perspectives in hundreds of laboratories around the globe. These elements are well known for carrying "special" genes that confer important survival properties, frequently neces sary under atypical conditions. Classic examples of plasmid-borne genes are those provid ing bacterial resistance to toxic substances such as antibiotics, metal ions, and bacte riophage. Often included are those determining bacteriocins, which may give the bacterium an advantage in a highly competitive environment. Genes offering metabolic alternatives to the cell under nutritionally stressed conditions are also commonly found on plasmids, as are determinants important to colonization and pathogenesis. It is likely that in many, if not most, cases plasmids and their passenger determinants represent DNA acquired recently by their bacterial hosts, and it is the characteristic mobility of these elements that enables their efficient establishment in new bacterial cells by the process known as conjugation. Whereas many plasmids are fully capable of promoting their own conjugal transfer, others move only with help from coresident elements. The ability of a plasmid to establish itself in a variety of different species is com mon, and recent studies have shown that transfer can in some cases occur from bacterial cells to eukaryotes such as yeast."

Published nearly ten years ago, the first edition of Practical Atlas for Bacterial Identification broke new ground with the wealth of detail and breadth of information it provided. The second edition is poised to do the same. Differing fundamentally from the first edition, this book begins by introducing the concept of bacteria community intelligence as reflected in corrosion, plugging, and shifts in the quality parameters in the product whether it be water, gas, oil, or even air. It presents a new classification system for bacterial communities based upon their effect and activities, and not their composition. The book represents a radical departure from the classical reductionist identification of bacteria dominated by genetic and biochemical analyses of separated strains. The author takes a holistic approach based on form, function, and habitat of communities (consorms) of bacteria in real environments. He uses factors related to the oxidation-reduction potential at the site where the consorm is active and the viscosity of the bound water within that consorm to position their community structures within a two-dimensional bacteriological positioning system (BPS) that then allows the functional role to be defined. This book has an overarching ability to define bacterial activities as consorms in a very effective and applied manner useful to an applied audience involved in bacterial challenges. Organized for ease of use, the book allows readers to start with the symptom, uncover the bacterial activities, and then indentify the communities distinctly enough to allow management and control practices that minimize the damage. The broad spectrum approach, new to this edition, lumps compatible bacteria together into a relatively harmonious consortia that share a common primary purpose. It gives a big picture view of the role of bacteria not as single strains but collectively as communities and uses this information to provide key answe

Rhizosphere biology is approaching a century of investigations wherein growth-promoting rhizomicroorganisms (PGPR) have attracted special attention for their ability to enhance productivity, profitability and sustainability at a time when food security and rural livelihood are a key priority. Bio-inputs - either directly in the form of microbes or their by-products - are gaining tremendous momentum and harnessing the potential of agriculturally important microorganisms could help in providing low-cost and environmentally safe technologies to farmers.One approach to such biologically-based strategies is the use of naturally occurring products such as PGPR. Advances in PGPR Research explores recent developments and global issues in biopesticide research, presented via extended case studies and up-to-date coverage of: * Low input biofertilizers and biofungicides used for sustainable agriculture. * Molecular techniques to enhance efficacy of microbial inputs. * Intellectual property issues in PGPR research. Written by an international team of experts, this book considers new concepts and global issues in biopesticide research and evaluates the implications for sustainable productivity. It is an invaluable resource for researchers in applied agricultural biotechnology, microbiology and soil science, and also for industry personnel in these areas.

A special meeting of the Royal Society in London in 1986 marked the centenary of the first demonstration of nitrogen fixation. Currently the subject is of great practical importance because the use of nitrogenous fertilizers has resulted in unacceptable levels of water pollution; also these fertilizers are becoming steadily less economic both in cash terms and in utilization of fossil fuels for their manufacture. The number of papers published and the frequency of national and international meetings to discuss research into nitrogen fixation have both increased steadily during the 1970s and 1980s. Specialist monographs and review papers are often too detailed to be of real use to undergraduates in biology or related areas such as agriculture and forestry, and even for graduates and research workers newly entering the field of nitrogen fixation. For people in these categories, the senior author wrote The Biology of Nitrogen-fixing Organisms published by McGraw Hill in 1979. This book has similar aims. It incorporates new findings that have not only resolved some of the uncertainties reported in that earlier text hut, more importantly, it reflects the influence on the subject of recent developments in biochemistry, molecular biology, genetic engineering and other biotechnologies. We have devoted more attention to quantitative aspects of the subject, but unfortunately the many practical difficulties for accurate field assessment of nitrogen fixation and its contribution to nitrogen cycles means that many assessments are either in contlict with each other or must be accepted as tentative.

Agrobacterium is a plant pathogen which causes the "crown-gall" disease, a neoplastic growth that results from the transfer of a well-defined DNA segment ("transferred DNA", or "T-DNA") from the bacterial Ti (tumor-inducing) plasmid to the host cell, its integration into the host genome, and the expression of oncogenes contained on the T-DNA. The molecular machinery, needed for T-DNA generation and transport into the host cell and encoded by a series of chromosomal (chv) and Ti-plasmid virulence (vir) genes, has been the subject of numerous studies over the past several decades. Today, Agrobacterium is the tool of choice for plant genetic engineering with an ever expanding host range that includes many commercially important crops, flowers, and tree species. Furthermore, its recent application for the genetic transformation of non-plant species, from yeast to cultivated mushrooms and even to human cells, promises this bacterium a unique place in the future of biotechnological applications. The book is a comprehensive volume describing Agrobacterium's biology, interactions with host species, and uses for genetic engineering.