I assume that you already know a good deal of microbiology. In this book, I frequently use the word "we" by which I mean "you and I." Together we are going to consider bacteriology from a broader perspective and we will think our way through the important biological problems that are frequently just skipped over in every microbiology course. My most important reason for writing this book is to make accessible the relevant thinking from fields of science other than microbiology that are important to microbiology. The book is written for people that have already have a fascination with bacteria, but can see that their background for understanding is far complete. This book consists of topics that are largely omitted from microbiology textbooks and includes some mathematics, physics, chemistry, and evolutionary biology. It contains a good deal of my own work, both experimental and theoretical, together with a lot of speculation. If ten times bigger, it would be a full text book on microbial physiology. A third of the microbial physiology is covered by the recent is no longer treated even in textbook by White (2000). Another third current specialized tests and is greatly underrepresented in text books.

Strategies of Bacterial Interaction with Eukaryotic Cells *Tobias A. Oelschlaeger and Jorg Hacker 1. BENEFICIAL BACTERIAL-HOST INTERACTIONS Already during birth and soon thereafter mammals are colonized by bacte- ria belonging to the resident microbial flora. Cutaneous and mucosal sur- faces and the gastrointestinal tract are the areas which become colonized. These indigenous or autochthonous bacteria have a variety of beneficial effects on their hosts. They play a protective role by bacterial antagonism in fighting infections (Hoszowski and Truszczynski, 1997; Hentges, 1979). Pro- duction of vitamin K is another essential contribution of the resident microbial flora to the health of the host (Hill, 1997). Even more important, studies with germ-free animals demonstrated the involvement of the microbial flora on the development of the immune system. Such animals have underdeveloped and relatively undifferentiated lymphoid tissues and low concentrations of serum immune globulins ( Cebra et at., 1998). They TOBIAS A. OELSCHLAEGER and JORG HACKER Institut filr Molekulare lnfektionsbiologie, Universitiit Wiirzburg, 97070 Wiirzburg, Germany. *Corresponding author; Phone: (0)931-312150; FAX: (0)931-312578; E-mail: [email protected] xxix Tobias A. Oelschlaeger and Jorg Hacker also show defects in specific immune responsiveness and in nonspecific resistance induced by endotoxin, which may account for their lowered resis- tance. A more typical example of symbiotic interaction of bacteria with a host are bacteria like Ruminococcus in the gut of ruminants, essential for degradation of cellulose (Hobson, 1988). The closest benefical bacterial-host interactions are those of intracellular symbiotic bacteria and their host cells.

J. M. Olson Institute of Biochemistry Odense University OK-5230 Odense M, Denmark Green photosynthetic bacteria have traditionally included only green sulfur bacteria (Chlorobiaceae) and green filamentous bacteria (Chloro- flexaceae) , but in this volume are included also the recently-discovered heliobacteria (Gram-positive line), whose reaction centers are strikingly similar to those of the green sulfur bacteria. Two important papers on reaction centers (not included in this volume) have been published recently. Nitschke et al. (1987) have discovered 2 early electron acceptors (Fe-S centers) in the reaction center of Chlorobium limicola, and Shiozawa et al. (1987) have shown that the reaction center of Chloroflexus aurantiacus contains 2 (rather than 3) polypeptides of Mr = 24 and 24.5 kOa respectively. This volume begIns with papers describing structures on the molecular and macromolecular level and events on a picosecond time scale. It ends with papers describing organisms and populations, and events on time scales of hours, days and weeks. The scope of the volume covers biophysics, biochemistry, physiology, ecology, taxonomy and phylogeny. There is only one paper (Ormerod, 1988) dealing with genetics, an area which ought to receive much more attention in the near future.

Seeming sometimes more like science fiction than science, anaerobic bacteria have been at the center of a number of exciting new discoveries. This volume discusses and explains the diversity of metabolism, modes of protein transport, molecular biology and physiology of these unusual microbes. It has practical applications ranging from wastewater treatment to clinical diagnosis and treatment of medical conditions.

Sulfur is one of the most versatile elements in life. This book provides, for the first time, in-depth and integrated coverage of the functions of sulfur in phototrophic organisms including bacteria, plants and algae. It bridges gaps between biochemistry and cellular biology of sulfur in these organisms, and of biology and environments dominated by them. The book therefore provides a comprehensive overview of plant sulfur relations from genome to environment.

This volume collects new information on the genomics of saprophytic soil Pseudomonas, as well as functions related to genomic islands. It explores life styles in different settings and sheds further insights on the wide metabolic potential of this microbe for the removal of pollutants and production of added-value products. This volume also explores how Pseudomonas responds and reacts to environmental signals, including detection of cell density.

For both volumes:
Expert investigators describe not only the classic methods, but also the many novel techniques they have perfected for the transfer of large DNAs into the cells of both microbes and animals via large-insert recombinant DNAs. Volume 1 presents readily reproducible techniques for library construction, physical mapping, and sequencing.. An accompanying volume, Volume 2: Functional Studies, provides a wide variety of methods and applications for functional analysis of the DNA-transformed organisms. Besides protocols, each chapter includes scientific reviews, software tools, database resources, genome sequencing strategies, and illustrative case studies.

Genetic investigations and manipulations of bacteria and bacteriophage have made vital contributions to our basic understanding of living cells and to the development of molecular biology and biotechnology. This volume is a survey of the genetics of bacteria and their viruses, and it provides students with a comprehensive introduction to this rapidly changing subject. The book is written for upper level undergraduates and beginning graduate students, particularly those who have had an introductory genetics course.

The fifth edition has been extensively revised to reflect recent advances in the field. The book now has a reader-friendly look, with end-of-chapter questions, "Thinking Ahead" and "Applications" boxes to challenge students comprehension and insights. A complete glossary of commonly used terms has been revised and expanded.

This volume covers major aspects of Crimean-Congo hemorrhagic fever (CCHF) and the virus which causes it. Chapters are written by leading experts in their fields and detail historical, public health, epidemiological, and clinical aspects of CCHF and the genetics and molecular biology of the virus. Additional chapters focus on disease control, tick vectors and infection among animals, both natural and experimental.

Approximately 60% of all hospital-associated infections, over one million cases per year, are due to biofilms that have formed on indwelling medical devices. Device-related biofilm infections increase hospital stays and add over one billion dollars/year to U.S. hospitalization costs. Since the use and the types of indwelling medical devices commonly used in modern healthcare are continuously expanding, especially with an aging population, the incidence of biofilm infections will also continue to rise. The central problem with microbial biofilm infections of foreign bodies is their propensity to resist clearance by the host immune system and all antimicrobial agents tested to date. In fact, compared to their free floating, planktonic counterparts, microbes within a biofilm are 50 - 500 times more resistant to antimicrobial agents. Therefore, achieving therapeutic and non-lethal dosing regimens within the human host is impossible. The end result is a conversion from an acute infection to one that is persistent, chronic, and recurrent, most often requiring device removal in order to eliminate the infection. This text will describe the major types of device-related infections, and will explain the host, pathogen, and the unique properties of their interactions in order to gain a better understanding of these recalcitrant infections.

Env1r0nmenta1 ha5 m1cr0610109y emer9ed an extreme1y act1ve, - and 1mp0rtant area 0f re5earch dur1n9 the few year5 and ha5 cha1- 1en9ed 50me 10n9-he1d 0f F0r examp1e, the num6er5 0f c010ny-f0rm1n9 un1t5 06ta1ned 0n a9ar med1a have way5 6een a55umed t0 ref1ect the num6er5 0f 6acter1a pre5ent any 91ven 5amp1e. H0wever, n0w kn0wn that many 6acter1a the 1a60rat0ry ad0pt unu5ua1 d0rmant 5tate5 when 5u6jected t0 the nutr1ent-1- c0nd1t10n5 1ted c0mm0n many ec05y5tem5, wh1ch, turn, make5 the5e 6- ter1a t0 cu1ture. 7h15 0ur current t0 cu1ture the va5t maj0r1ty 0f6acter1a kn0wn t0 re51de natura1 env1r0nment5. Kn0- ed9e 0f the pre5ence 0f 50me 5pec1e5 a natura1 env1r0nment can 6e 0f cru- 1mp0rtance, w1th part1cu1ar1y re5pect t0 detect10n 0f path09en1c 0r t0 m0n1t0r1n9 the fate and 0f man1pu1ated 9enet1ca11y 0r9an15m5 w1th1n ec05y5tem5. 7heref0re, there ha5 6een much eff0rt 9enerated t0 dev- new and n0ve1 meth0d5 f0r detect10n, and rec0very 0f cr00r9an15m5 fr0m natura1 ha61tat5. Centra1 t0 many 0f the5e meth0d5 ha5 6een the deve10pment and ap- 0f the techn14ue5 0f 610109y m01ecu1ar t0 env1r0nmenta1 09y. 7he5e have re5u1ted d1rect 0fm1cr061a1 6a5ed 0n DNA w1th0ut the need f0r any cu1ture. 7here n0 d0u6t that w0u1d n0t have 6een w1th0ut the rev01ut10n c0mputer techn01- 09y that ha5 t0 the deve10pment 0f data6a5e5 acce55161e h19h1y 0f va5t am0unt5 0f 1nf0rmat10n. M01ecu1ar meth0d5 have 6een harne55ed and exp101ted a150 the deve10pment 0f meth0d5 that ena61e rap1d and aut0mated 0f m1cr00r9an15m5 fr0m natura1 env1r0nment5.

Research on bacterial adhesion and its significance is a major field involving many different aspects of nature and human life, such as marine science, soil and plant ecology, most importantly, the biomedical field. The adhesion ofbacteria to the food industry, and human tissue surfaces and implanted biomaterial surfaces is an important step in the patho genesis of infection. Handbook 0/ Bacterial Adhesion: Principles, Methods, and Applications is an outgrowth of the editors' own quest for information on laboratory techniques for studying bacte rial adhesion to biomaterials, bone, and other tissues and, more importantly, a response to significant needs in the research community. This book is designed to be an experimental guide for biomedical scientists, biomaterials scientists, students, laboratory technicians, or anyone who plans to conduct bacterial adhesion studies. More specifically, it is intended for all those researchers facing the chal lenge of implant infections in such devices as orthopedic prostheses, cardiovascular devices or catheters, cerebrospinal fluid shunts or extradural catheters, thoracic or abdominal catheters, portosystemic shunts or bile stents, urological catheters or stents, plastic surgical implants, oral or maxillofacial implants, contraceptive implants, or even contact lenses. It also covers research methods for the study of bacterial adhesion to tis sues such as teeth, respiratory mucosa, intestinal mucosa, and the urinary tract. In short, it constitutes a handbook for biomechanical and bioengineering researchers and students at all levels."

The new series "Microbiology Monographs" begins with two volumes on intracellular components in prokaryotes. In this second volume, "Complex Intracellular Structures in Prokaryotes," the components, labeled complex intracellular structures, encompass a multitude of important cellular functions. Continuing and newly initiated research will provide a clearer understanding of the complex intracellular structures known at present and will bring to light surprising new ones as well.

This volume details recent developments in magnetotactic bacteria research. It includes reviews on the formation and organization of magnetosomes, the genes controlling magnetosome biomineralization, and new cryogenic techniques to visualize novel cytoskeleton structures. Coverage also describes potential nanobiotechnological applications of the magnetosome crystals.

Our knowledge of the biochemistry and biophysics of dinitrogen fixa tion has developed rapidly in the 15 years since the first N2-fixing enzyme system was successfully extracted from a bacterium. This peri od has produced a literature that now describes the N2 fixation reac tion and the nitrogenase enzyme itself in sophisticated terms, though a detailed reaction mechanism at the chemical level has not yet emerged. It is the purpose of the present monograph to present an in-depth re view, analysis, and integration of this research as is possible with a non-contributed publication and to relate this work to considera tions of N2 fixation that reach beyond the confines of the biochem ist's laboratory. The first section is directed as much toward the general science read er as toward the specialist. It covers the agricultural origins of man's interest in N2 fixation and also pertinent areas of taxonomy, physiology, and evolution. Ecological aspects of the subject include a comprehensive evaluation of the nitrogen cycle leading to a sub stantially greater estimate of the rate of global N2 fixation than previous ones. The treatment is of a survey fashion, in part to pro vide a general over-view of N2 fixation and in part to provide context for the biochemistry and biophysics that follow in the second section."

w. KlingmUller Lehrstuhl fUr Genetik, Universitat Bayreuth, UniversitatsstraBe 30, 8580 Bayreuth, FRG th th On September 6 and 7 1983 the second workshop on "Azospirillum: Genetics, Physiology, Ecology" took place at the University of Bayreuth, west Germany, organized by the genetics department. There were about 50 participants, who came from German research institutions, from other European countries, from Israel, Egypt and North and South America. The first such workshop had taken place two years ago in Bayreuth too, hence the organizers could draw on the experiences then obtained. Azospirilla have, during the past ten years, found an ever increasing scientific interest, because first, these soil bacte ria carry the genetic information for binding molecular nitrogen from the air, and second, they live in close vicinity to the roots of several grain crops and forage grasses. By exploitation of these two properties, it is hoped to develop inoculation pro cedures that result in yield increases in agriculture, in par ticular in soils poor in nitrogen. The reports on the first afternoon focussed, as a result of the Bayreuth research interest, on the genetic basis and the regulation of nitrogen fixation in Azospirillum. Here, mainly by application of most modern gene technological approaches, considerable progress in the understanding of the situation has been made, and was documented in the corresponding reports."

Environmental concerns regarding continuous use of synthetic dyes saw a revival in the demand for natural dyes as natural dyes exhibit better biodegradability and generally have a higher compatibility with the environment. However, one of the limitations on the use of natural dyes or pigments is the low extraction yield factors (a few grams of pigment per kg of dried raw material). Therefore, the exploitation of other biological sources such as fungi, bacteria and cell cultures offers interesting alternative. Microbial pigments such as from bacterial origins offer the advantage in terms of production compared to pigments extracted from vegetables or animals, due to its simple cell and fast culturing technique. This book offers interesting insight into initial works carried out to demonstrate the potential use of bacterial pigment as colorant for various applications.

W. Klingmuller Lehrstuhl fur Genetik, Universitat Bayreuth, UniversitatsstraBe 30, 8580 Bayreuth, FRG Growth of higher plants, particularly agricultural crops, de pends on combined nitrogen. To obtain high yields, combined nitrogen has to be supplied as fertilizer. However, the che- cal production of nitrogen fertilizers is very energy consuming and costly. In underdeveloped countries there is in addition the problem of how to get such fertilizer and how to distribute it. Efforts to replace chemical nitrogen fertilizers by other means of nitrogen fertilization are therefore important. Some bacteria have the capability to use molecular nitrogen from the atmosphere. Such nitrogen is thus transformed into a bound form. Responsible for this capability is a gene group they carry, the nif genes, and an enzyme system, they produce, nitrogenase. An example for such bacteria are rhizobia, which grow in symbioses with leguminous plants, and in their root nodules bind molecular nitrogen. The host plant takes advantage of this. Less well known, but being studied with increasing intensity, are the so called Azospirillum bacteria. They too bind molecular nitrogen. But, in contrast to rhizobia, they do not form nodules on the roots of legumes, but live in loose associations with the roots of other plants, for instance maize, wheat, rice or other grain crops. By exploiting the capabilities of these bacteria it can be hoped to find a way for supplying biologically bound nit- gen to grain crops."

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.

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.

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."

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.

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)