This book presents a timely review of the latest advances in rhizosphere biology, which have been facilitated by the application of omics tools. It includes chapters on the use of various omics tools in rhizosphere biology, focusing on understanding plant and soil microbe interactions. The role of proteomics and metagenomics in research on symbiotic association is also discussed in detail. The book also includes chapters on the use of omics tools for the isolation of functional biomolecules from rhizospheric microorganisms. The book's respective sections describe and provide detailed information on important omics tools, such as genomics, transcriptomics, proteomics, metabolomics and meta-epigenomics. In turn, the book promotes and describes the combined use of plant biology, microbial ecology, and soil sciences to design new research strategies and innovative methods in soil biology. Lastly, it highlights the considerable potential of the rhizosphere in terms of crop productivity, bioremediation, ecological engineering, plant nutrition and health, as well as plant adaptation to stress conditions. This book offers both a practical guide and reference source for all scientists working in soil biology, plant pathology, etc. It will also benefit students studying soil microbiology, and researchers studying rhizosphere structure.

This book presents a set of modern protocols forming a solid background for who want to start or improve research programme on phytoplasmas. Chapters guide readers through detailed techniques for maintaining phytoplasma collections, border inspection, detection of different phytoplasma strains, new pipelines to produce phytoplasma genome draft, protocols for phytoplasma gene expression analyses, and methods for the investigation of the phloem tissue. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Phytoplasmas: Methods and Protocols aims to ensure successful results in the further study of this vital field.

This book examines an important paradigm shift in biology: Plants and animals, traditionally viewed as individuals, are now considered to be complex systems and host to a plethora of microorganisms. After first presenting historical aspects of microbiota research, bacterial compositions of individual microbiomes and the critical analysis of current methods, the book discusses how microbial communities inside the human body are profoundly affected by numerous factors, such as macro- and micro-nutrients, physical exercise, antibiotics, gender and age. As described by current research, the author highlights how microbiomes contribute to the fitness of the host by providing nutrients, inhibiting pathogens, aiding in the storage of fat during pregnancy, and contributing to development and behavior. The author not only focusses on prokaryotic components in microbiomes, but also addresses single-cell eukaryotes and viruses. This follow-up to the successful book The Hologenome Concept: Human, Animal and Plant Microbiota, published in 2013, provides a contemporary overview of microbiomes. It appeals to anyone working in the life sciences and biomedicine.

The new series "Microbiology Monographs" begins with two volumes on intracellular components in prokaryotes. In this first volume, "Inclusions in Prokaryotes", the components, labeled inclusions, are defined as discrete bodies resulting from synthesis of a metabolic product. Research on the biosynthesis and reutilization of the accumulated materials is still in progress, and interest in the inclusions is growing. This comprehensive volume provides historical background and comprehensive reviews of eight well-known prokaryotic inclusions.

One of the most exciting developments in the field of bacterial pathogenesis in recent years is the discovery that many pathogens utilize complex nanomachines to deliver bacterially encoded effector proteins into eukaryotic and prokaryotic target cells to modulate a variety of cellular functions for the pathogen's benefit. These protein-delivery machines include the type III secretion system (T3SS), which is widespread in nature and encoded not only by bacteria pathogenic to vertebrates or plants, but also by bacteria that are symbiotic to plants or insects. Because they are essential virulence factors for many important human pathogens, these systems are emerging as a prime target for the development of new-generation, anti-infective drugs. This book reviews our current understanding of these intriguing injection machines as well as of the closely related T3SS that serves in flagella assembly. Individual chapters focus on regulation, assembly, structure, and function of the type III secretion machine and on the evolution of the secreted effector proteins. Given its scope, this book will appeal to a broad readership, including researchers and teachers in the fields of infectious diseases, host pathogen interactions, plant and animal pathogenesis, and symbiosis.

This Microbiology Monographs volume covers the latest advances in laccase applications in bioremediation and waste valorisation. The first three chapters provide a comprehensive introduction to fungal and bacterial laccases (the two most important enzyme groups from an application viewpoint) and their practical use in bioremediation and lignocellulosic waste valorisation. Subsequent chapters discuss possible combinations of laccases and further potentially collaborating enzymes, and offer in-depth insights into laccase immobilisation for wastewater treatment and environmental biosensor applications of laccases. Lastly, the book addresses the quest for enzymes with improved and better-fitting properties, covering laccase engineering by directed and computational evolution, and novel enzymes from extreme environments. As such, it is a fascinating read for microbiologists in both industry and academia.

This comprehensive laboratory manual describes the various protocols involved in Actinobacterial research. The content is divided into fifteen major sections, each of which is further divided into sub-sections describing the respective aim, principles, materials & methods, protocol, expected results and diagrams. Readers will find essential protocols for e.g. sample collection, isolation, characterization, analysis, profiling and evaluation of Actinobacteria for various applications. Gathering all relevant protocols concerning Actinobacteria, and written by a team of experienced Actinobacterial researchers, it is the first book of its kind.

Bacteria in various habitats are subject to continuously changing environmental conditions, such as nutrient deprivation, heat and cold stress, UV radiation, oxidative stress, dessication, acid stress, nitrosative stress, cell envelope stress, heavy metal exposure, osmotic stress, and others. In order to survive, they have to respond to these conditions by adapting their physiology through sometimes drastic changes in gene expression. In addition they may adapt by changing their morphology, forming biofilms, fruiting bodies or spores, filaments, Viable But Not Culturable (VBNC) cells or moving away from stress compounds via chemotaxis. Changes in gene expression constitute the main component of the bacterial response to stress and environmental changes, and involve a myriad of different mechanisms, including (alternative) sigma factors, bi- or tri-component regulatory systems, small non-coding RNA s, chaperones, CHRIS-Cas systems, DNA repair, toxin-antitoxin systems, the stringent response, efflux pumps, alarmones, and modulation of the cell envelope or membranes, to name a few. Many regulatory elements are conserved in different bacteria; however there are endless variations on the theme and novel elements of gene regulation in bacteria inhabiting particular environments are constantly being discovered. Especially in (pathogenic) bacteria colonizing the human body a plethora of bacterial responses to innate stresses such as pH, reactive nitrogen and oxygen species and antibiotic stress are being described. An attempt is made to not only cover model systems but give a broad overview of the stress-responsive regulatory systems in a variety of bacteria, including medically important bacteria, where elucidation of certain aspects of these systems could lead to treatment strategies of the pathogens. Many of the regulatory systems being uncovered are specific, but there is also considerable cross-talk between different circuits. Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria is a comprehensive two-volume work bringing together both review and original research articles on key topics in stress and environmental control of gene expression in bacteria. Volume One contains key overview chapters, as well as content on one/two/three component regulatory systems and stress responses, sigma factors and stress responses, small non-coding RNAs and stress responses, toxin-antitoxin systems and stress responses, stringent response to stress, responses to UV irradiation, SOS and double stranded systems repair systems and stress, adaptation to both oxidative and osmotic stress, and desiccation tolerance and drought stress. Volume Two covers heat shock responses, chaperonins and stress, cold shock responses, adaptation to acid stress, nitrosative stress, and envelope stress, as well as iron homeostasis, metal resistance, quorum sensing, chemotaxis and biofilm formation, and viable but not culturable (VBNC) cells. Covering the full breadth of current stress and environmental control of gene expression studies and expanding it towards future advances in the field, these two volumes are a one-stop reference for (non) medical molecular geneticists interested in gene regulation under stress.

The book compiles the latest studies on microorganisms thriving in extreme conditions. Microbes have been found in extremely high and low temperatures, highly acidic to saline conditions, from deserts to the Dead sea, from hot-springs to underwater hydrothermal vents- the diversity is incredible. The various chapters highlight the microbial life and describe the mechanisms of tolerance to these harsh conditions, and show how an understanding of these phenomena can help us exploit the microbes in biotechnology. The theme of the book is highly significant since life in these environments can give vital clues about the origin and evolution of life on earth, as a lot of these conditions simulate the environment present billions of years ago. Additionally, the study of adaptation and survival of organisms in such environments can be important for finding life on other planets. This book shall be useful for students, researchers and course instructors interested in evolution, microbial adaptations and ecology in varied environments.

This book explores the broad and diverse biological and physiological impacts of established and newly discovered cyclic di-nucleotide second messenger signaling systems, while also providing descriptions of the intriguing biochemical characteristics of multiple turnover enzymes and receptors. The respective chapters discuss the commonalities and diversity of cyclic di-GMP, cyclic di-AMP and recently discovered cyclic GMP-AMP signaling systems in manifold Gram-negative and Gram-positive bacteria. The global human pathogens Mycobacterium tuberculosis, Vibrio cholerae, Salmonella typhimurium, Escherichia coli and Streptococcus pneumoniae, the facultative human pathogen Pseudomonas aeruginosa, global plant pathogens as exemplified by Xanthomonas campestris and Burkholderia spp., and the omnipresent probiotic Lactobacilli, as well as environmentally important photoautotrophic cyanobacteria, the multicellular Myxococcus xanthus, and chemolithotrophic Acidithiobacillus are among the representatives of the microbial kingdom that are described. In turn, the various aspects of bacterial physiology affected by these signaling systems- e.g. biofilm formation and dispersal, the cell cycle, motility, virulence, production of antimicrobials, fundamental metabolism and osmohomeostasis - are discussed in detail in the context of different microorganisms. Dedicated chapters focus on the population diversity of cyclic dinucleotide signaling systems, their tendency to be horizontally transferred, the cyclic di-GMP signaling system in the social amoeba Dictyostelium, honorary cyclic (di)nucleotides, and the development of strategies for interfering with cyclic dinucleotide signaling in order to manipulate microbial behavior. Taken together, the chapters provide an authoritative source of information for a broad readership: beginners and advanced researchers from various disciplines; individuals seeking a broad overview of cyclic di-nucleotide signaling; and those who want to learn more about specific aspects. Also featuring reviews with a forward-looking perspective, the book offers a valuable source of inspiration for future research directions.

This book focuses on the multitude of functions bacterial membrane vesicles perform in bacterial ecology and pathogenesis as well as in emerging medical and biotechnological applications. Both Gram-negative and Gram-positive bacteria produce membrane-bound nanostructures, known as membrane vesicles, which have a range of functions that include serving as delivery vehicles, providing a means of communication over both spatial and temporal scales, and contributing to bacterial survival and evolution. Topics covered in this book range from the biogenesis and composition of bacterial membrane vesicles to their abundance and biological roles in microbial ecosystems, such as marine environments. In the individual chapters, the involvement of bacterial membrane vesicles in host-pathogen interactions, promoting virulence and in facilitating the establishment of infection is explained. In addition, current knowledge regarding membrane vesicles produced by commensal bacteria and their role in the maturation of the host immune system, as well as the therapeutic potential of bacterial membrane vesicles as delivery systems and innovative nanotechnology-based therapeutics are discussed. This work appeals to a wide readership of students and researchers interested in microbial ecology, mechanism underlying pathogenesis and new avenues in applied microbiology and nanotechnology.

Pulses have played a major role in human diet and are considered a rich source of proteins. But, the major constraints in achieving the yield of pulses are the occurrences of various diseases and pests. Hence, there is a need to understand major fungal pathogens and their management strategies for sustainable agriculture. The major pulse crops in India and other Asian countries are bengal gram, pigeon pea, black gram, green gram, lentil and peas, which are attacked by several pathogens that cause considerable crop damage. Bengal gram is affected mainly by wilt (Fusarium oxysporum f. sp. ciceri), blight (Mycosphaerella pinodes) and rust (Uromyces ciceris-arietini). The main diseases of pigeon pea are wilt (Fusarium oxysporum) and Phytophtora stem blight (Phytophthora drechsleri f. sp. cajani). Powdery mildew (Erysiphe polygoni) and rust (Uromyces vicia-fabae) are the most important diseases affecting the production of pea. This volume offers details like symptoms, distribution, pathogens associated, predisposing factors and epidemiology, sources of resistance and holistic management of diseases with particular reference to those of economic importance. Several minor diseases of lentil, green gram and of black gram are discussed with their detailed and updated information. This volume provides pooled information regarding the management of major fungal phytopathogens affecting pulses.

Thermophilic Bacteria is a comprehensive volume that describes all major bacterial groups that can grow above 60-65 DegreesC (excluding the Archaea). Over 60 different species of aerobic and anaerobic thermophilic bacteria are covered. Isolation, growth methods, characterization and identification, ecology, metabolism, and enzymology of thermophilic bacteria are examined in detail, and an extensive compilation of recent biotechnological applications and the properties of many thermostable enzymes are also included. Major topics discussed in the book include a general review on thermophilic bacteria and archaea; heterotropic bacilli; the genus Thermus; new and rare genera of aerobic heterophophs, such as Saccharococcus, Rhodothermus, and Scotohermus; aerobic chemolithoautotrophic thermophilic bacteria; obligately anaerobic thermophilic bacteria; and hyperthermophilic Thermotogales and thermophilic phototrophs. Extensive bibliographies are also provided for each chapter. The vast amount of information packed into this one volume makes it essential for all microbiologists, biochemists, molecular biologists, and students interested in the expanding field of thermophilicity. Biotechnologists will find the book useful as a source of information on thermophiles or thermostable enzymes of possible industrial use.

Focuses on the aggregation of recombinant proteins in bacterial cells in the form of inclusion bodies and on their use in biotechnological and medical applications The first book devoted specifically to the topic of aggregation in bacteria, Protein Aggregation in Bacteria: Functional and Structural Properties of Inclusion Bodies in Bacterial Cells provides a large overview of protein folding and aggregation, including cell biology and methodological aspects. It summarizes, for the first time in one book, ideas and technical approaches that pave the way for a direct use of inclusion bodies in biotechnological and medical applications. Protein Aggregation in Bacteria covers: * Molecular and cellular mechanisms of protein folding, aggregation, and disaggregation in bacteria * Physiological importance and consequences of aggregation for the bacterial cell * Factors inherent to the protein sequence responsible for aggregation and evolutionary mechanisms to keep proteins soluble * Structural properties of proteins expressed as soluble aggregates and as inclusion bodies within bacterial cells both from a methodological point of view and with regard to their similarity with amyloids * Control of the structural and functional properties of aggregated proteins and use thereof in biotechnology and medicine Protein Aggregation in Bacteria is ideal for researchers in protein science, biochemistry, bioengineering, biophysics, microbiology, medicine, and biotechnology, particularly if they are related with the production of recombinant proteins and pharmaceutical science.

Did You Just Eat That? provides the answers to perennial questions about food and germs, such as whether electric hand dryers spread fewer germs than paper towels or about picking a crisp off the ground within five seconds of dropping it. The authors show how they have determined everything from how much bacteria gets transferred from sharing utensils to how many microbes live on restaurant menus. They list their materials and methods, guide the reader through their results and offer explanations of food safety and microbiology. Written with humour, this fascinating book reveals surprising answers to the weirdest and most commonly debated questions about food and germs.

Vast numbers of different prokaryotic microorganisms shape the biosphere, with diverse metabolic capabilities. Determination of genome sequences for a wide range of bacteria and archaea now requires an in-depth knowledge of prokaryotic metabolic function to give biochemical, physiological and ecological meaning to the genomic information. This new edition describes up-to-date knowledge of the key metabolic processes that occur under different conditions, and the cellular processes that determine prokaryotic roles in the environment, biotechnology and human health. Essential for students of microbiology, applied microbiology, biotechnology, genomics and systems biology, this advanced textbook covers prokaryotic structure, composition, nutrient transport, biosynthesis and growth. Newly characterised metabolic pathways are included, as well as the latest understanding of metabolic regulation and stress responses. Additionally, the link between energetics, growth and survival is discussed as well as the maintenance of genetic integrity by the bacterial immune system.

The book summarizes the achievements of the past decade in the biochemistry, bioenergetics, structural and molecular biology of respiratory processes in selected genera of the domain Bacteria along with an extensive coverage of the redox chains of extremophiles belonging to the Archaean domain. The volume is a unique piece of work since it contains a series of chapters dealing with metabolic features having important microbiological and ecological relevance such as the use of ammonium, iron, methane, sulfur and hydrogen as respiratory substrates or nitrous compounds in denitrification processes. Particular attention is also dedicated to peculiar groups of prokaryotes such as Gram positives, acetic acid bacteria, pathogens of the genera Helicobacter and Campylobacter, nitrogen fixing symbionts and free-living species, oxygenic phototrophs (Cyanobacteria) and anoxygenic (purple non-sulfur) phototrophs. The book is intended to be a long-term source of information for Ph.D. students, researchers and undergraduates from disciplines such as microbiology, biochemistry and ecology, studying basic and applied sciences, medicine and agriculture.

Spirochetes comprise a fascinating group of bacteria. Although diverse in terms of their habitat, ecology and infectivity for vertebrate and non-vertebrate hosts, they are often considered together because of their similar cellular morphologies. This volume brings together an international group of experts to provide essential insights into spirochete biology, with an emphasis on recent advances made possible by the availability of genome sequences. As such, it offers a valuable resource for microbiologists and other scientists with an interest in spirochete biology.

This book delves into the biotechnological applications of Quorum sensing (QS)- a peculiar gene-regulatory process of some microorganisms. Quorum Sensing allows a large bacterial population to work together in a coordinated manner to carry out metabolic activities, which individual bacterium cannot. The different chapters describe how, associating bioremediation process with energy generation is an economical proposal, for reducing pollution and managing biowastes. The book discusses how QS can be exploited for biotechnological applications in generating bioproducts, bioenergy, bioremediation, biosensors, health and agricultural activities. It further highlights how QS is becoming an integral part of synthetic biology for genetic circuits for producing: (i) novel products, (ii) biosensors, (iii) bioactive molecules, etc. The book is divided into different sections for a clear understanding of the applicability of QS in, the Environment, Energy, Agriculture and Health sectors.

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.

Insect-transmitted rickettsiales diseases are significant sources of morbidity and mortality all over the world. Their incidence has been increasing in recent years in large part due to climate change and the movement of animals carrying the insect vectors. Currently there are no effective vaccines against diseases caused by members of the order Rickettsiales. Rickettsiales diseases are often misdiagnosed; this book is intended to serve as a tool for their understanding and diagnosis. Rickettsiales covers the seven main genera: Anaplasma, Ehrlichia, Midichloria, Neorickettsia, Orientia, Rickettsia and Wolbachia. Discussion of each genus includes immunology and molecular biology of host-pathogen interactions, epidemiology and diagnosis, and vaccination strategies and therapies.