Expert scientists critically review the current and most recent advances in the genomics and molecular biology of mycobacteria. The focus is on the topical and most relevant aspects and the authors aim to give readers an insight into the current understan

This volume discusses various basic and advanced methods and protocols that have been proven to be successful among certain bacterial species, or a family of species, in type III secretion systems (T3S system). The chapters in this book cover topics such as: site-directed mutagenesis and its application in studying the interactions of T3S components; use of transcriptional control to increase expression and secretion of heterologous proteins in T3S systems; fractionation techniques to examine effector translocation; detecting immune responses to T3S systems; mouse immunization with purified needle proteins from T3S systems and the characterization of the immune responses to these proteins; and detection of protein interactions in T3S systems using yeast 2-hybrid analysis. 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. Practical and comprehensive, Type 3 Secretion Systems: Methods and Protocols is a valuable resource for anyone interested in learning about the fascinating and ever-changing T3S systems.

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.

Based on the thesis that insights into both evolution and ecology can be obtained through the study of microorganismsm, Microbial Ecology examines microbiology through the lens of evolutionary ecology. Measured from a microbial perspective, this text covers such topics as optimal foraging, genome, reduction, novel evolutionary mechanisms, bacterial speciation, and r and K selection. Numerous aspects of microbial existence are also discussed and include: species competition, predation, parasitism, mutualism, microbial communication through quorum sensing and other . The result is a context for understanding microbes in nature and a framework for microbiologists working in industry, medicine, and the environment.
* Applies evolutionary ecological concepts to microbes
* Addresses individual, population and community ecology
* Presents species concepts and offers insights on the origin of life and modern microbial ecology
* Examines topics such as species interactions, nutrient cycling, quorum sensing and cheating

This book provides a comprehensive overview of the benefits of biofertilizers as an alternative to chemical fertilizers and pesticides. Agricultural production has increased massively over the last century due to increased use of chemical fertilizers and pesticides, but these gains have come at a price. The chemicals are not only expensive; they also reduce microbial activity in agricultural soils and accumulate in the food chain, with potentially harmful effects for humans. Accordingly, it is high time to explore alternatives and to find solutions to overcome our increasing dependence on these chemicals. Biofertilizers, which consist of plant remains, organic matter and microorganisms, might offer an alternative. They are natural, organic, biodegradable, eco-friendly and cost-effective. Further, the microbes present in the biofertilizers are important, because they produce nutrients required for plant growth (e.g., nitrogen, phosphorus, potassium), as well as substances essential for plant growth and development (e.g., auxins and cytokinins). Biofertilizers also improve the physical properties, fertility and productivity of soil, reducing the need for chemical fertilizers while maintaining high crop yield. This makes biofertilizers a powerful tool for sustainable agriculture and a sustainable environment. The book covers the latest research on biofertilizers, ranging from beneficial fungal, bacterial and algal inoculants; to microbes for bioremediation, wastewater treatment; and recycling of biodegradable municipal, agricultural and industrial waste; as well as biocontrol agents and bio-pesticides. As such, it offers a valuable resource for researchers, academics and students in the broad fields of microbiology 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.

With an ever-increasing human population, the demand placed upon the agriculture sector to supply more food is one of the greatest challenges for the agrarian community. In order to meet this challenge, environmentally unfriendly agroch- icals have played a key role in the green revolution and are even today commonly recommended to circumvent nutrient de?ciencies of the soils. The use of ag- chemicals is, though, a major factor for improvement of plant production; it causes a profound deteriorating effect on soil health (soil fertility) and in turn negatively affects the productivity and sustainability of crops. Concern over disturbance to the microbial diversity and consequently soil fertility (as these microbes are involved in biogeochemical processes), as well as economic constraints, have prompted fun- mental and applied research to look for new agro-biotechnologies that can ensure competitive yields by providing suf?ciently not only essential nutrients to the plants but also help to protect the health of soils by mitigating the toxic effects of certain pollutants. In this regard, the role of naturally abundant yet functionally fully unexplored microorganisms such as biofertilizers assume a special signi?cance in the context of supplementing plant nutrients, cost and environmental impact under both conventional practices and derelict environments. Therefore, current devel- ments in sustainability involve a rational exploitation of soil microbial communities and the use of inexpensive, though less bio-available, sources of plant nutrients, which may be made available to plants by microbially-mediated processes.

Beginning with the basics of lactic acid bacteria and stress response, then working into specific fields of research and current developments, "Stress Responses of Lactic Acid Bacteria" will serve as an essential guidebook to researchers in the field, industry professionals, and advanced students in the area.

The exploration of stress responses in lactic acid bacteria began in the early 90s and revealed the differences that exist between LAB and the classical model microorganisms. A considerable amount of work has been performed on the main genera / species of LAB regarding the genes implicated and their actual role and regulation, and the mechanisms of stress resistance have also been elucidated. Recent genome and transcriptome analyses complement the proteome and genetic information available today and shed a new light on the perception of and the responses to stress by lactic acid bacteria.

Magnetotactic bacteria (MTB) synthesize intracellular nano-sized minerals of magnetite and/or greigite magnetosomes for magnetic orientation. They play important roles in global iron cycling and sedimentary magnetism, and have a broad range of potential applications in both biotechnological and biomedical fields. However, because the majority of MTB in nature remain unculturable, our understanding of these specific bacteria remains fairly limited. This thesis describes the development of a novel approach for effectively collecting, purifying and characterizing uncultivated magnetotactic bacteria. The diversity, genomic information and rock magnetic properties of various uncultivated MTB are investigated and characterized using a combination of biological and geophysical methods. The results will lead to a better understanding of the biogeography and biomineralization mechanisms of MTB in nature, and improve our knowledge of the contributions of MTB to biogeochemical cycles of elements and sedimentary magnetism. Dr. Wei Lin works at the Institute of Geology and Geophysics, Chinese Academy of Sciences, China

"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.

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 text attempts 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 behaviour 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.

Bioethanol has been recognized as a potential alternative to petroleum-derived transportation fuels. Even if cellulosic biomass is less expensive than corn and sugarcane, the higher costs for its conversion make the near-term price of cellulosic ethanol higher than that of corn ethanol and even more than that of sugarcane ethanol. Conventional process for bioethanol production from lignocellulose includes a chemical/physical pre-treatment of lignocellulose for lignin removal, mostly based on auto hydrolysis and acid hydrolysis, followed by saccharification of the free accessible cellulose portions of the biomass. The highest yields of fermentable sugars from cellulose portion are achieved by means of enzymatic hydrolysis, currently carried out using a mix of cellulases from the fungus Trichoderma reesei. Reduction of (hemi)cellulases production costs is strongly required to increase competitiveness of second generation bioethanol production. The final step is the fermentation of sugars obtained from saccharification, typically performed by the yeast Saccharomyces cerevisiae. The current process is optimized for 6-carbon sugars fermentation, since most of yeasts cannot ferment 5-carbon sugars. Thus, research is aimed at exploring new engineered yeasts abilities to co-ferment 5- and 6-carbon sugars. Among the main routes to advance cellulosic ethanol, consolidate bio-processing, namely direct conversion of biomass into ethanol by a genetically modified microbes, holds tremendous potential to reduce ethanol production costs. Finally, the use of all the components of lignocellulose to produce a large spectra of biobased products is another challenge for further improving competitiveness of second generation bioethanol production, developing a biorefinery.

Implications of Resource-Ratio Theory for Microbial Ecology; V.H. Smith. 13C Tracer Methodology in Microbial Ecology with Special Reference to Primary Production Processes in Aquatic Environments; T. Hama, et al. Sex in Ciliates; F. Dini, D. Nyberg. Microbial Ecology in Lake Ciso; C. PedroAlio, R. Guerrero. Biological Activities of Symbiotic and Parasitic Protists in Low Oxygen Environments; A.G. Williams, D. Lloyd. Polymorphism in Bacteria; P.B. Rainey, et al. Decomposition of Shoots of a Saltmarsh Grass; S.Y. Newell. Dynamics of Autotrophic Picoplankton in Marine and Freshwater Ecosystems; T. Weisse. Bacterial Growth Rates and Production As Determined by [3HMethyl]thymidine? R.D. Robarts, T. Zohary. Index.

Pseudomonas volume 7 collects some of the most relevant and emerging issues in the biology of these microorganisms, and a number of other important issues that were not collected in the previous volumes. The first six volumes of the Pseudomonas series covered the biology of pseudomonads in a wide range of contexts, including the niches they inhabit, the taxonomic relations among its members of this group, the molecular biology of gene expression in different niches and under different environmental conditions, the analysis of virulence in plants, animal and human pathogens, as well as the determinants that make some of these strains of interesting for biotechnological applications. This seventh volume covers the following topics: The history of the biology of Pseudomonas The use of Pseudomonas as biological agents New trends in the molecular biology of these microorganisms Pseudomonas and the immune system of insects and animals This book will be of use to researchers working on these bacteria, particularly those studying medical aspects of Pseudomonas, and their use as a means to control pathogens or to stimulate plant growth. This volume is also interesting for those studying the physiology, genetics, molecular biology of Pseudomonas and those using novel-omics approaches to understand bacteria of the genus Pseudomonas.

This book provides useful information on microbial physiology and metabolism. The key aspects covered are prokaryotic diversity, growth physiology, basic metabolic pathways and their regulation, metabolic diversity with details of various unique pathways. Another focus area is stress physiology with details on varying environmental stresses, signal transduction, adaptation and survival. For instructional purposes, the book provides case studies, interesting facts, techniques etc. which help in showcasing the inter-disciplinary nature and bridge the gap between various aspects of applied microbiology.

This book describes the vast variety of xenobiotics, such as pesticides, antibiotics, antibiotic resistance genes, agrochemicals and other pollutants, their interactions with the soil environment, and the currently available strategies and techniques for soil decontamination and bioremediation. Topics covered include: transport mechanisms of pollutants along the Himalayas; use of earthworms in biomonitoring; metagenomic strategies for assessing contaminated sites; xenobiotics in the food chain; phyto-chemical remediation; biodegradation by fungi; and the use of enzymes and potential microbes in biotransformation. Accordingly, the book offers a valuable guide for scientists in the fields of environmental ecology, soil and food sciences, agriculture, and applied microbiology.

This book describes how genomics has revolutionized our understanding of agriculturally important plant-associated fungi and oomycetes. It illustrates some fundamental discoveries about these eukaryotic microbes with regard to the overall structure of their genomes, their lifestyles and the molecular mechanisms that form the basis of their interactions with plants. Genomics has provided new insights into fungal lifestyles and led to practical advances in plant breeding and crop protection, such as predictions about the spread and evolution of new pathogens.This volume focuses on fungi and oomycetes that are typical dicot plant pathogens and includes: Sclerotinia sclerotiorum, Botrytis cinerea, Alternaria sp.,Verticillium alfalfae and Verticillium dahliae, Fusarium oxysporum, Phytophthora capsici, Phytophthora sojae, Phytophthora ramorum, Phytophthora infestans, Hyaloperonospora arabidopsidis.

The currently available means of combating fungal infections are weak and clumsy. The application of fungal genomics offers an unparalleled opportunity to develop novel antifungal drugs. Interestingly, several novel antifungal drug targets have already been identified and validated. However, it is premature to expect a novel antifungal agent in clinical setting as drug discovery programs are still in their infancy. In addition to classical and genomic approaches to drug discovery, treasure trove based on natural products and phytomedicine can provide a multitude of alternative modes of combating fungal infection. This book incisively addresses essential topics on various aspects pertaining to fungal diseases in human and animals, their reservoir, fungal pathogenesis, their management and recent advances in their treatment. Issues of antifungal drug toxicity, especially nephrotoxicity, are also discussed. The development of resistance in fungal pathogens, including multidrug resistance and its mechanism, is dealt with in two chapters. Diverse diagnostic approaches to fungal infections are also reviewed. The combinational drug strategies used in combating invasive fungal infections are addressed in detail. The management of pulmonary mycoses in stem cell transplantation is also given special focus. Novel antifungal drugs (synthetic and herbal), fungal vaccines, and metabolic pathways as drug targets are discussed in detail in three different chapters. Subsequently the roles of innate immunity, cytokine therapy and immunomodulators in the treatment of fungal infections are elaborated upon. As novel drug delivery systems have a great potential for modifying the pharmacokinetics of medications, the last chapter takes this fact into consideration in its examination of state-of-the-art delivery systems in controlling fungal infections.

This volume presents a collection of methods that have contributed to the current understanding of bacterial persisters. Chapters in the book detail general guidelines for measuring persister levels in bacterial cultures, strategies to enrich and resuscitate persister subpopulations, single-cell approaches for visualizing and characterizing persisters, omics techniques and cellular and animal models for studying persistence. 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, Bacterial Persistence: Methods and Protocols, Second Edition aims to be a useful practical guide to researchers to help further their study in this field.

Until late 1960s the coronaviruses were not recognized as pathogens responsible for human diseases (common cold), and it has been in 2003 when human coronaviruses (HCoVs) recalled worldwide attention with the emergence of the severe and acute respiratory syndrome (SARS), produced by a coronavirus (SARS-CoV) that has infected more than 8000 people, killing about ten percent of them in 32 countries. The increase of research on coronaviruses has soon lead to the discovery of another human coronavirus (HCoV-NL63) which is prevalent in 7% of hospital patients and has been associated with bronchiolitis and, possibly, conjunctivitis.

This book discusses the latest research and new techniques in the field of lactic acid bacteria, including comparative genomics, transcriptomics, proteomics and metabolomics. It also introduces the omics and functional evaluation in detail and shows the links between lactic acid bacteria and gut health and host immunity. Summarizing the biotechnological advances in lactic acid bacteria for food and health, it is a valuable resource for researchers and graduate students in the fields of food microbiology, bioengineering, food science, nutrition and health.

Since its early days in the 1990s, the Quorum Sensing (QS) field has grown from a few dozen laboratories, investigating the pathways, proteins, and chemicals that facilitate signaling in bacteria, to hundreds of groups that have integrated evolutionary biology, computer science, mathematics, engineering, and metagenomics to create an ever-expanding and dynamic field. In Quorum Sensing: Methods and Protocols, expert researchers provide an in-depth set of diverse protocols that span this broad area of study. Broken into three detailed sections, the volume covers the detection, isolation, and characterization of the QS signals made by both Gram- and Gram+ bacteria, determination of the function of QS signals in vivo, and the development of QS disruption strategies. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and expert tips on troubleshooting and avoiding known experimental pitfalls. Comprehensive and cutting-edge, Quorum Sensing: Methods and Protocols serves as an invaluable collection of easily accessible techniques for scientists seeking to further our knowledge about bacterial communication and its relation to humanity.

This updated monograph deals with methanogenic endosymbionts of anaerobic protists, in particular ciliates and termite flagellates, and with methanogens in the gastrointestinal tracts of vertebrates and arthropods. Further chapters discuss the genomic consequences of living together in symbiotic associations, the role of methanogens in syntrophic degradation, and the function and evolution of hydrogenosomes, hydrogen-producing organelles of certain anaerobic protists. Methanogens are prokaryotic microorganisms that produce methane as an end-product of a complex biochemical pathway. They are strictly anaerobic archaea and occupy a wide variety of anoxic environments. Methanogens also thrive in the cytoplasm of anaerobic unicellular eukaryotes and in the gastrointestinal tracts of animals and humans. The symbiotic methanogens in the gastrointestinal tracts of ruminants and other "methanogenic" mammals contribute significantly to the global methane budget; especially the rumen hosts an impressive diversity of methanogens. This makes this updated volume an interesting read for scientists and students in Microbiology and Physiology.

Bioaugmentation, biostimulation and biocontrol approaches using microbial inoculants, biofertilizers, biochemicals and organic amendments improve soil biology, fertility and crop productivity by providing plant growth-promoting nutrients and suppressing soil-borne diseases and plant-parasitic nematodes. Our knowledge of microbial diversity and its function in soils has been increased tremendously due to the availability of a wealth of data gained through recent advances in the development of molecular methods and metagenomics for the evaluation of microbial diversity and functions in the rhizosphere environment of soil. Chapters dealing with the application of biofertilizers and organic amendments are contributed by experts - authorities in the area of soil science including microbiology and molecular biology - from academic institutions and the industry.

This book presents a detailed discussion on the direct interactions of plants and microorganisms in the rhizosphere environment. It includes fifteen chapters, each focusing on a specific component of plant-microbe interactions, such as the influence of plants on the root microbiome, and the downstream effects of rhizosphere microbial dynamics on carbon and nutrient fluxes in the surroundings. As such, the book helps readers gain a better understanding of diversity above the ground, and its effect on the microbiome and its functionality.