This completely revised edition explores novel discoveries in bacterial genomic research, with a focus on technical and computational improvements as well as methods used for bacterial pangenome analysis, which relies on microbiome studies and metagenomic data. Beginning with up-to-date sequencing methods, the book continues with sections covering methods for deep phylogenetic analysis, the role of metagenomic data in understanding the genomics of the many yet uncultured bacteria, progress in genome-to-phenome inference, as well as computational genomic tools. Written for the highly successful Methods in Molecular Biology series, chapters include the type of practical detail necessary for reproducible results in the lab. Authoritative and up-to-date, Bacterial Pangenomics: Methods and Protocols, Second Edition serves as an ideal guide for both highly qualified investigators in bacterial genomics and for less experienced researchers, including students and teachers, who could use a reference for approaching genomic analysis and genome data.

This edited volume covers all aspects of the latest research in the field of soil formation and its functioning, soil diversity, soil proteomics, the impact of anthropogenic activities on the pedosphere, plant-microbe interactions in the pedosphere, and factors influencing the formation and functioning of the soils. In the pedosphere, all forms of soils possess a particular type of structure and different organic and mineral components. Thus, the pedosphere as a whole plays a significant role in providing unique habitats for a vast diversity of life forms, developing a link between geological and biological substances circulation in the terrestrial ecosystems. In the processes making available vital mineral elements to plants and supporting human health as various trace elements in the lithosphere are accessed by people through the formation of soils and such soils are utilized for food production. With the depth of information on different aspects of soil, this extensive volume is a valuable resource for the researchers in the area of soil science, agronomy, agriculture, scientists in academia, crop consultants, policymakers, government from diverse disciplines, and graduate and post-graduate students in the area of soil and environmental science.

This book covers recent advances and future trends in yeast synthetic biology, providing readers with an overview of computational and engineering tools, and giving insight on important applications. Yeasts are one of the most attractive microbial cell factories for the production of a wide range of valuable products, including pharmaceuticals, nutraceuticals, cosmetics, agrochemicals and biofuels. Synthetic biology tools have been developed to improve the metabolic engineering of yeasts in a faster and more reliable manner. Today, these tools are used to make synthetic pathways and rewiring metabolism even more efficient, producing products at high titer, rate, and yield. Split into two parts, the book opens with an introduction to rational metabolic pathway prediction and design using computational tools and their applications for yeast systems and synthetic biology. Then, it focuses on the construction and assembly of standardized biobricks for synthetic pathway engineering in yeasts, yeast cell engineering and whole cell yeast-based biosensors. The second part covers applications of synthetic biology to produce diverse and attractive products by some well-known yeasts. Given its interdisciplinary scope, the book offers a valuable asset for students, researchers and engineers working in biotechnology, applied microbiology, metabolic engineer ing and synthetic biology.

Biodegradation and Detoxification of Micropollutants in Industrial Wastewater summarizes the occurrence and source of micropollutants through various industrial wastewaters. It covers the type of micropollutants, their effects, and emerging detection and treatment methods. The book has 11 chapters, and throughout each chapter, it presents the fate and effects of micropollutants, quantitative and qualitative analysis of micropollutants in industrial wastewaters, and treatment of micropollutants through conventional and advanced wastewater treatment technologies.

Agricultural Nanobiotechnology: Biogenic Nanoparticles, Nanofertilizers and Nanoscale Biocontrol Agents presents the most up-to-date advances in nanotechnology to improve the agriculture and food industry with novel nanotools for the controlling of rapid disease diagnostic and enhancement of the capacity of plants to absorb nutrients and resist environmental challenges. Highlighting the emerging nanofertilizers, nanopesticides and nanoherbicides that are being widely explored in order to overcome the limitations of conventional agricultural supplements, the book provides important insights to enable smart, knowledge-driven selection of nanoscale agricultural biomaterials, coupled with suitable delivery approaches and formulations will lead to promising agricultural innovation using nanotechnology. Agricultural Nanobiotechnology: Biogenic Nanoparticles, Nanofertilizers and Nanoscale Biocontrol Agents explores emerging innovations in nanobiotechnology for agriculture, food, and natural resources to address the challenges of food security, sustainability, susceptibility, human health, and healthy life. The book is ideal for the multidisciplinary scientists whose goal is to see the use of nanomaterials in agriculture to reduce the amount of spread chemicals, minimize nutrient losses in fertilization and to generate increased yield through pest and nutrient management.

This volume contains material first presented at an international workshop on the 'Use of Microorganisms to Combat Pollution', held in Israel, May 10--18, 1992. The workshop was sponsored by the Bat-Sheva de Rothschild Foundation for the Advancement of Science and included microbiologists, biochemists and geneticists from universities, environmental agencies and the military. Each of the contributors to this volume is an ack nowledged expert on the treatment of one or more types of pollution using microorganisms or their enzymes. This book differs from most published symposia proceedings in the breadth of coverage of each subject. Most of the chapters are divided into three parts: (a) A general presentation of the source and toxicity of the pollutant, (b) a review of the current state-of-the-science on the biodegradation of that pollutant and (c) the authors' unique research experiences on the problem. In several examples, the authors have presented data from both laboratory studies and field trials. Thus, the book contains not only the theoretical background on the biodegradation of pollutants, but also practical experiences in applying this knowledge to solving significant pollution problems."

This second edition provides new and updated chapters describing the utility and attributes of different tools that are used for studying microbial systems. Chapters detail a number of methods, including in silico system level analyses by MetaFlux, Kbase genome-scale model builder, COBRA toolbox, NanoSIP, and PAMMS. 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, Microbial Systems Biology: Methods and Protocols, Second Edition aims to introduce and aid scientists in using the various tools that are currently available for analysis, modification, and utilization of microbial organisms.

The 12th meeting on Frankia and Actinorhizal Plants that took place in Carry-le-Rouet, France in June 2001 was the opportunity for scientists to communicate about latest developments on this symbiosis that concerns a wide range of dicotyledonous plants, initiates ecological successions and is used in a number of countries to protect crops from winds or improve soil status. Selected papers on plant ecology, Frankia's genetics or physiology, and host plants' genetics or physiology are published in this special Plant & Soil issue.

This Volume describes methods for simulating natural environments by using reproducible and controllable meso- and microcosm experiments to analyse hydrocarbon-degrading microorganisms and to test hypotheses. It presents important aspects of the preparation of experimental set-ups, hydrocarbon application and sampling, and features protocols for experiments with different types of samples, such as biofilms, aquatic systems (e.g. groundwater, streams), and sediments, including oscillating oxic-anoxic mesocosms, as well as for in-situ experimentation in subtidal and deep sediments. Two chapters are dedicated to cultivation under high-pressure conditions, and several chapters include protocols for processing samples for downstream chemical, microbial or activity analyses. Several of the approaches presented are generic and will benefit anyone embarking on designing meso- and microcosm experiments. < Hydrocarbon and Lipid Microbiology Protocols There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Clinical Microbiology, Volume 664 in the Methods in Enzymology series, highlights new advances in the field with this new volume presenting interesting chapters on a variety of topics, including Synthesis of chemical probes to study bacterial adenylating enzymes, Fluoroquinolone-derived fluorescent probes for studies of bacterial penetration and efflux, Combining informatics with ABPP to identify serine hydrolyses in bacteria, A Ligand Selection Strategy Identifies Chemical Probes Targeting the Proteases of SARS-CoV-2, Activity-based probes for bacterial histidine kinases, Metabolomic approaches to enzyme function and pathway discovery, Identification of bile salt hydrolase activity in gut microbiota, and much more. Other chapters cover Multiplex fluorescence screening and identification using multiplex TMT, Customized Peptidoglycan Surfaces to Investigate Innate Immune Recognition via SPR, Site-Specific Siderocalin Binding to Ferric and Ferric-Free Enterobactin As Revealed by Mass Spectrometry, Proteomics of short-chain fatty acid probes in Salmonella, Development and application of highly sensitive labeling reagents for amino acids, and a variety of other timely topics.

This contributed volume compiles the latest developments in the field of microbial enzymology. It focuses on topics such as distribution of microbial enzymes in natural habitats, microbial enzymes in environmental sustainability, and environmental disturbances on microbial enzymes, which are organized into three parts, respectively. Ranging from micro-scale studies to macro, it covers a huge domain of microbial enzymes and their interplay between the components of the environment. Overall, the book portrays the importance of microbial enzyme technology and its role in solving the problems in modern-day life. The book is a ready reference for practicing students and researchers in environmental engineering, chemical engineering, agricultural engineering, and other allied fields.

This book presents a comprehensive view on mycotoxins of agricultural as well as non-agricultural environments and their health effects in humans and animals. Mycotoxins have immunosuppressive effects; but some of them can cause cancers, mutagenicity, neurotoxicity, liver and kidney damage, birth defects, DNA damage and respiratory disorders. The problem of mycotoxins is long-lasting and their direct or indirect exposures to humans and animals must be further discussed. The first chapter will cover the historical perspective of mycotoxins along with timeline while the second one will provide overview including classification of mycotoxins and mycotoxicoses. The comprehensive information/ literature on traditional, emerging and mushroom mycotoxins will be given in chapters 3, 4 and 5 respectively. Chapter 6 will deal with mycotoxins co-occurrence poisoning whereas new and masked mycotoxins will be described in chapter 7. The important aspects of mycotoxin studies like extraction, characterization and analysis and management strategies will be summarized in 8 and 9 chapters. The last chapter of the book will cover the recent developments in toxicokinetic studies of mycotoxins. The book will have the most up-to-date information and recent discoveries to deliver accurate data and to illustrate essential points to a wide range of readers including mycologists, clinicians, agricultural scientists, chemists, veterinarians, environmentalists and food scientists.

The beetle genus Agrilus has over 3000 species which makes it the most numerous in the Animal Kingdom. Many species are serious pests of plants with high invasive potential. Among them, the notoriously known Agrilus planipennis invaded from Asia to North America where it killed tens of millions of ash trees, caused regulatory agencies to enforce quarantines and cost municipalities, property owners, nursery operators and forest products industries tens of millions of dollars. The monograph provides coherent, comprehensive and critical review on all known host plants for more than 680 Agrilus species. All host plants have assigned the confidence index from 0-3 based on the evaluated reliability which eliminates false records. All original and subsequent references for particular plants are cited at each Agrilus species. Data are organized from both, insect and plant viewpoints. Results are analyzed and illustrated by graphs and diagrams. The main impact of the monograph is seen in entomology, phytopathology, forestry, agriculture ecology and biocontrol.

Soil is an important but often neglected element of the climate system. It is the second largest carbon store, or 'sink', after the oceans. Despite being a fundamental resource that supports all kinds of life on Earth, concerns related to soil are often not included as an important environmental issue. Climate changes put soil under pressure. The increasing concentration of carbon dioxide in our atmosphere may cause the microbes in the soil to work faster to break down organic matter, potentially releasing even more carbon dioxide. The soil moisture content is being constantly affected by rising temperatures and changes in precipitation patterns and future projections show that this may continue. This book presents current environmental issues and their remedies for soil which are mainly based on soil degradation, soil pollution and the effect of climate change on the soil. Adding xenobiotic chemicals or other alterations in the natural soil environment for agricultural, industrial or urban purposes result in a decline in the soil quality due to improper use or poor management, which is a serious environmental problem. The book is divided into five parts - soil science, soil physics, soil chemistry, soil biology and soil environment. The first part "Soil Science" serves as the introduction to the book and discusses some common topics such as soil formation, mineralogy, taxonomy, quality and analytical techniques. The second part "Soil Physics" is mainly concerned with the physical properties and processes of soil and their association with effects on air, water and temperature. Soil Chemistry, the third part, discusses the chemical reactions and processes between inorganic and organic components. The fourth part "Soil Biology" explains the biological properties and processes of the soil, with special concern to microbial diversity and its effect on the ecology. Lastly, the fifth part "Soil Environment" discusses the current environmental problems such as climate change and soil pollution, including processes to mitigate these issues through carbon sequestration, nutrient management and land management.

Advanced Biosensors for Virus Detection: Smart Diagnostics to Combat Against the SARS-CoV2 Pandemic covers the development of biosensor-based approaches for the diagnosis and prognosis of viral infections, specifically coronaviruses. The book discusses wide-ranging topics of available biosensor-based technologies and their application for early viral detection. Sections cover the emergence of SARS-CoV, MERS-CoV and SARS-CoV2, the global health response, the impact on affected populations, state-of-the art biomarkers, and risk factors. Specific focus is given to COVID-19, with coverage of genomic profiling, strain variation and the pathogenesis of SARS-CoV2. In addition, current therapeutics, nano-abled advancements and challenges in the detection of SARS-CoV2 and COVID-19 management are discussed, along with the role of nanomaterials in the development of biosensors and how biosensors can be scaled up for clinical applications and commercialization.

In this Journey to Microbial Worlds we present the diversity of microorganisms, from the state of fossil microbes in Archaean age rocks to the possibilities of extraterrestrial life. This volume discusses the extremophiles living in harsh environments (from our anthropocentric point) and describes them in considerable detail. Some chapters also review topics such as symbiosis, bacterial luminescence, methanogens, and petroleum-grown cells. The final chapters of this book shed new light on astrobiology and speculate on extremophiles as candidates for extraterrestrial life. All chapters are updated to the latest research level.

This book is a collection of scholarly articles presenting the research results of work carried out under the supervision of Prof. Saroj Bhosle, a microbiologist at Goa University, India.The objective of this volume is to document the comprehensive ecological knowledge of eubacteria isolated from diverse coastal ecosystems of Goa, little explored for microbiological studies. These ecosystems need to be properly tapped in order to reveal potential bacteria yet to be exploited. The topics of this book are particularly relevant to researchers and students in the field of microbiology with an interest in the varied aspects of eubacteria. They provide academic insight for scientific communities in Goa and the rest of the world.

Viral Vectors for Gene Therapy: Methods and Protocols consists of 30 ch- ters detailing the use of herpes viruses, adenoviruses, adeno-associated viruses, simple and complex retroviruses, including lentiviruses, and other virus systems for vector development and gene transfer. Chapter cont- butions provide perspective in the use of viral vectors for applications in the brain and in the central nervous system. Viral Vectors for Gene Therapy: Methods and Protocols contains step-by-step methods for successful rep- cation of experimental procedures, and should prove useful for both experienced investigators and newcomers in the field, including those beginning graduate study or undergoing postdoctoral training. The "Notes" section contained in each chapter provides valuable troublesho- ing guides to help develop working protocols for your laboratory. With Viral Vectors for Gene Therapy: Methods and Protocols, it has been my intent to develop a comprehensive collection of modern molecular methods for the construction, development, and use of viral vectors for gene transfer and gene therapy. I would like to thank the many chapter authors for their contributions. They are all experts in various aspects of viral vectors, and I appreciate their efforts and hard work in developing comprehensive chapters. As editor, it has been a privilege to preview the development of Viral Vectors for Gene Therapy: Methods and Protocols, and to acquire insight into the various methodological approaches from the many different contri- tors.

Development in Wastewater Treatment Research and Processes: Microbial Degradation of Xenobiotics through Bacterial and Fungal Approach covers the active and applicable role that bacteria and fungi play in the degradation of xenobiotic compounds from the environment. The book gives up-to-date information on recent advancements in the field of environmental xenobiotics and how they disturb a plant's metabolism. The book also gives information on aerobic and anaerobic degradation of xenobiotic compounds through bacteria or fungi and/or a combined approach. Finally, the book covers the characteristics of environmental microbiology, biochemical engineering, agricultural microbiology, environmental engineering, and soil bioremediation.

Rhizosphere Engineering is a guide to applying environmentally sound agronomic practices to improve crop yield while also protecting soil resources. Focusing on the potential and positive impacts of appropriate practices, the book includes the use of beneficial microbes, nanotechnology and metagenomics. Developing and applying techniques that not only enhance yield, but also restore the quality of soil and water using beneficial microbes such as Bacillus, Pseudomonas, vesicular-arbuscular mycorrhiza (VAM) fungi and others are covered, along with new information on utilizing nanotechnology, quorum sensing and other technologies to further advance the science. Designed to fill the gap between research and application, this book is written for advanced students, researchers and those seeking real-world insights for improving agricultural production.

This volume explores the latest techniques used to study Mycobacterium ulcerans, and more specifically M. ulcerans disease (Buruli ulcer). The chapters in this book are organized into three parts and cover methods for the detection of M. ulcerans and the analysis of host-pathogen interaction; the quantification and characterization of mycolactone, the macrolide toxin of M. ulcerans; and drug development against M. ulcerans. 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, Mycobacterium ulcerans: Methods and Protocols is a valuable resource that helps scientists advance their research on Buruli ulcer, which is still an under-researched field in infection biology.

This self contained book presents a comprehensive overview of the past, present and future of the galactose regulon of yeast, the classical model system of molecular biologists. The book starts with a brief historical overview on yeast research. This is followed by molecular genetics of the galactose regulon, isolation of genes and testing of the hypotheses. Contemporary topics including genomics, evolution, binary and graded responses, and stochasticity are all addressed.

The creation of plant-based foods is one of the most rapidly advancing areas in the modern food industry. Many consumers are adopting more plant-based foods in their diets because of concerns about global warming and its devastating impacts on the environment and biodiversity. In addition, consumers are adopting plant-based diets for ethical and health reasons. As a result, many food companies are developing plant-based analogs of animal-based foods like dairy, egg, meat, and seafood products. This is extremely challenging because of the complex structure and composition of these animal-based foods. Next-Generation Plant-based Foods: Design, Production and Properties presents the science and technology behind the design, production, and utilization of plant-based foods. Readers will find a review of ingredients, processing operations, nutrition, quality attributes, and specific plant-based food categories such as milk and dairy products, egg and egg products, meat and seafood products, providing the fundamental knowledge required to create the next generation of healthier and more sustainable plant-based food alternatives.

The vast explosion of high-resolution molecular data in the past few years has provided an unprecedented glimpse into the microbial world. This book synthesises current viewpoints and knowledge on microbial ecological theory.