Microbial Environmental Genomics Meg

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Microbial Environmental Genomics (MEG)

Francis Martin,Stephane Uroz
Microbial Environmental Genomics MEG Book PDF

Author : Francis Martin,Stephane Uroz
Publisher : Springer Nature
Page : 370 pages
File Size : 55,9 Mb
Release : 2022-12-15
Category : Science
ISBN : 9781071628713

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Microbial Environmental Genomics (MEG) by Francis Martin,Stephane Uroz Pdf

This volume guides researchers on how to characterize, image rare, and hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment. Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.

Microbial Genomics in Sustainable Agroecosystems

Vijay Tripathi,Pradeep Kumar,Pooja Tripathi,Amit Kishore
Microbial Genomics in Sustainable Agroecosystems Book PDF

Author : Vijay Tripathi,Pradeep Kumar,Pooja Tripathi,Amit Kishore
Publisher : Springer Nature
Page : 285 pages
File Size : 53,8 Mb
Release : 2019-11-05
Category : Science
ISBN : 9789811387395

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Microbial Genomics in Sustainable Agroecosystems by Vijay Tripathi,Pradeep Kumar,Pooja Tripathi,Amit Kishore Pdf

In recent decades, significant advances in new methodologies like DNA sequencing and high-throughput sequencing have been used to identify microorganisms and monitor their interactions with different environments. Microbial genomics techniques are opening new approaches to microbiology by revealing how microorganisms affect human beings and the environment. This book covers four major areas: 1) Environmental microbial genomics, 2) Microbial genomics in human health, 3) Microbial genomics in crop improvement and plant health protection, and 4) Genome analysis of microbial pathogens. Within these areas, the topics addressed include: microbial genome diversity, evolution, and microbial genome sequencing; bioinformatics and microarray-based genomic technologies; functional genomics of bioremediation of soil and water from organic and inorganic pollutants and carbon management; functional genomics of microbial pathogens and relevant microorganisms; functional genomics of model microorganisms; and applied functional genomics. Given its scope, the book offers a comprehensive source of information on the latest applications of microorganisms and microbial genomics to enhance the sustainability of agriculture and the environment.

Environmental Microbiology

Eugene L. Madsen
Environmental Microbiology Book PDF

Author : Eugene L. Madsen
Publisher : John Wiley & Sons
Page : 592 pages
File Size : 40,5 Mb
Release : 2015-07-06
Category : Science
ISBN : 9781118439586

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Environmental Microbiology by Eugene L. Madsen Pdf

New and expanded for its second edition, Environmental Microbiology: From Genomes to Biogeochemistry¸ Second Edition, is a timely update to a classic text filled with ideas, connections, and concepts that advance an in-depth understanding of this growing segment of microbiology. Core principles are highlighted with an emphasis on the logic of the science and new methods-driven discoveries. Numerous up-to-date examples and applications boxes provide tangible reinforcement of material covered. Study questions at the end of each chapter require students to utilize analytical and quantitative approaches, to define and defend arguments, and to apply microbiological paradigms to their personal interests. Essay assignments and related readings stimulate student inquiry and serve as focal points for teachers to launch classroom discussions. A companion website with downloadable artwork and answers to study questions is also available. Environmental Microbiology: From Genomes to Biogeochemistry, Second Edition, offers a coherent and comprehensive treatment of this dynamic, emerging field, building bridges between basic biology, evolution, genomics, ecology, biotechnology, climate change, and the environmental sciences.

Environmental Genomics

C. Cristofre Martin
Environmental Genomics Book PDF

Author : C. Cristofre Martin
Publisher : Springer Science & Business Media
Page : 363 pages
File Size : 50,8 Mb
Release : 2008-01-18
Category : Science
ISBN : 9781588297778

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Environmental Genomics by C. Cristofre Martin Pdf

Here is a manual for an environmental scientist who wishes to embrace genomics to answer environmental questions. The volume covers: gene expression profiling, whole genome and chromosome mutation detection, and methods to assay genome diversity and polymorphisms within a particular environment. This book provides a systematic framework for determining environmental impact and ensuring human health and the sustainability of natural populations.

The New Science of Metagenomics

National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications
The New Science of Metagenomics Book PDF

Author : National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications
Publisher : National Academies Press
Page : 170 pages
File Size : 55,8 Mb
Release : 2007-06-24
Category : Science
ISBN : 9780309106764

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The New Science of Metagenomics by National Research Council,Division on Earth and Life Studies,Board on Life Sciences,Committee on Metagenomics: Challenges and Functional Applications Pdf

Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

Metagenomics and Microbial Ecology

Surajit De Mandal,Amrita Kumari Panda,N. Senthil Kumar,Satpal Singh Bisht,Fengliang Jin
Metagenomics and Microbial Ecology Book PDF

Author : Surajit De Mandal,Amrita Kumari Panda,N. Senthil Kumar,Satpal Singh Bisht,Fengliang Jin
Publisher : CRC Press
Page : 266 pages
File Size : 45,9 Mb
Release : 2021-11-29
Category : Nature
ISBN : 9781000482232

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Metagenomics and Microbial Ecology by Surajit De Mandal,Amrita Kumari Panda,N. Senthil Kumar,Satpal Singh Bisht,Fengliang Jin Pdf

Microorganisms comprise the greatest genetic diversity in the natural ecosystem, and characterization of these microbes is an essential step towards discovering novel products or understanding complex biological mechanisms. The advancement of metagenomics coupled with the introduction of high-throughput, cost-effective NGS technology has expanded the possibilities of microbial research in various biological systems. In addition to traditional culture and biochemical characteristics, omics approaches (metagenomics, metaproteomics, and metatranscriptomics) are useful for analyzing complete microbial communities and their functional attributes in various environments. Metagenomics and Microbial Ecology: Techniques and Applications explores the most recent advances in metagenomics research in the landscape of next-generation sequencing technologies. This book also describes how advances in sequencing technologies are used to study invisible microbes as well as the relationships between microorganisms in their respective environments. Features: Covers a wide range of concepts, investigations, and technological advancement in metagenomics at the global level. Highlights the novel and recent approaches to analyze microbial diversity and its functional attributes. Features a range of chapters that present an introduction to the field and functional insight into various ecosystems.

Metagenomics for Microbiology

Jacques Izard,Maria Rivera
Metagenomics for Microbiology Book PDF

Author : Jacques Izard,Maria Rivera
Publisher : Academic Press
Page : 188 pages
File Size : 54,7 Mb
Release : 2014-11-07
Category : Science
ISBN : 9780124105089

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Metagenomics for Microbiology by Jacques Izard,Maria Rivera Pdf

Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.

Soil Microbiome of the Cold Habitats

Puja Gupta,Mohd. Shahnawaz
Soil Microbiome of the Cold Habitats Book PDF

Author : Puja Gupta,Mohd. Shahnawaz
Publisher : CRC Press
Page : 267 pages
File Size : 52,6 Mb
Release : 2023-09-28
Category : Medical
ISBN : 9781000933253

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Soil Microbiome of the Cold Habitats by Puja Gupta,Mohd. Shahnawaz Pdf

This book focuses on cold habitat microbes as a potential source of elite enzymes and secondary metabolites to meet the growing demands of the pharmaceutical, food and biotechnological industries. Microbes living in such extremely cold conditions are reported to produce various biomolecules with potential biotechnological applications. The book overviews recent research trends to discover such important biomolecules and also suggests future research directions to discover such elite novel biomolecules. Salient features: Covers studies on various biotic communities and abiotic components of the soil of terrestrial habitats with a focus on cold habitats Discusses various 'Omic' approaches: metagenomics and meta-transcriptomics Lists adaptation strategies adopted by cold-adapted microbes Highlights various biotechnological and industrially important biomolecules produced by cold-adapted microbes Explores the role of microbial biofilm in the degradation of microplastics in cold habitats

Microbial Symbionts

Dhanasekaran Dharumadurai
Microbial Symbionts Book PDF

Author : Dhanasekaran Dharumadurai
Publisher : Elsevier
Page : 966 pages
File Size : 49,7 Mb
Release : 2022-09-25
Category : Science
ISBN : 9780323993357

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Microbial Symbionts by Dhanasekaran Dharumadurai Pdf

Microbial Symbionts: Functions and Molecular Interactions on Host focuses on microbial symbionts of plants, animals, insects and molecular methods in the identification of microbial symbionts. The book describes the molecular mechanism and interactions of symbiosis of microbiome in plants, animals and humans. It brings the latest techniques for identification, localization and functional characterization of host-associated microbes and explains the role/importance of microbial symbionts. This comprehensive reference covers a wide range of symbiotic microorganisms used for basic and advanced techniques associated with the isolation, characterization and identification of microbial symbiotic microorganisms and their functions and molecular interactions on the host. The book will also helps users plan and execute experiments with appropriate knowledge rather than experimental trial and error in a wide range of disciplines, including Microbiology, Biotechnology, Botany and Zoology. Provides basic knowledge and working protocols for a wide range of disciplines like Microbiology, Biotechnology, Botany and Zoology Presents the most current information in symbiotic microbiome and holobiome Includes color photos pertaining to techniques

Encyclopedia of Metagenomics

Karen E. Nelson
Encyclopedia of Metagenomics Book PDF

Author : Karen E. Nelson
Publisher : Springer
Page : 1528 pages
File Size : 55,8 Mb
Release : 2015-02-18
Category : Science
ISBN : 1461446740

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Encyclopedia of Metagenomics by Karen E. Nelson Pdf

Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production, and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP; http://nihroadmap.nih.gov/hmp/) which has become a world-wide effort, and the Global Ocean Sampling (GOS) surveys; http://www.jcvi.org/cms/research/projects/gos/overview/). The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

The Science and Applications of Microbial Genomics

Institute of Medicine,Board on Global Health,Forum on Microbial Threats
The Science and Applications of Microbial Genomics Book PDF

Author : Institute of Medicine,Board on Global Health,Forum on Microbial Threats
Publisher : National Academies Press
Page : 429 pages
File Size : 53,6 Mb
Release : 2013-05-02
Category : Science
ISBN : 9780309268196

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The Science and Applications of Microbial Genomics by Institute of Medicine,Board on Global Health,Forum on Microbial Threats Pdf

Over the past several decades, new scientific tools and approaches for detecting microbial species have dramatically enhanced our appreciation of the diversity and abundance of the microbiota and its dynamic interactions with the environments within which these microorganisms reside. The first bacterial genome was sequenced in 1995 and took more than 13 months of work to complete. Today, a microorganism's entire genome can be sequenced in a few days. Much as our view of the cosmos was forever altered in the 17th century with the invention of the telescope, these genomic technologies, and the observations derived from them, have fundamentally transformed our appreciation of the microbial world around us. On June 12 and 13, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to discuss the scientific tools and approaches being used for detecting and characterizing microbial species, and the roles of microbial genomics and metagenomics to better understand the culturable and unculturable microbial world around us. Through invited presentations and discussions, participants examined the use of microbial genomics to explore the diversity, evolution, and adaptation of microorganisms in a wide variety of environments; the molecular mechanisms of disease emergence and epidemiology; and the ways that genomic technologies are being applied to disease outbreak trace back and microbial surveillance. Points that were emphasized by many participants included the need to develop robust standardized sampling protocols, the importance of having the appropriate metadata, data analysis and data management challenges, and information sharing in real time. The Science and Applications of Microbial Genomics summarizes this workshop.

Handbook of Molecular Microbial Ecology I

Frans J. de Bruijn
Handbook of Molecular Microbial Ecology I Book PDF

Author : Frans J. de Bruijn
Publisher : John Wiley & Sons
Page : 1155 pages
File Size : 51,6 Mb
Release : 2011-10-14
Category : Science
ISBN : 9781118010495

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Handbook of Molecular Microbial Ecology I by Frans J. de Bruijn Pdf

The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds. Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This first volume, Metagenomics and Complementary Approaches, covers such topics as: Background information on DNA reassociation and use of 16 rRNA and other DNA fingerprinting approaches Species designation in microbiology Metagenomics: Introduction to the basic tools with examples Consortia and databases Bioinformatics Computer-assisted analysis Complementary approaches—microarrays, metatranscriptomics, metaproteomics, metabolomics, and single cell analysis A special feature of this volume is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Handbook of Molecular Microbial Ecology I is an invaluable reference for researchers in metagenomics, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; molecular microbial ecologists; and professionals in molecular microbiology and bioinformatics.

Handbook of Molecular Microbial Ecology II

Frans J. de Bruijn
Handbook of Molecular Microbial Ecology II Book PDF

Author : Frans J. de Bruijn
Publisher : John Wiley & Sons
Page : 632 pages
File Size : 43,5 Mb
Release : 2011-10-14
Category : Science
ISBN : 9781118010532

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Handbook of Molecular Microbial Ecology II by Frans J. de Bruijn Pdf

The premiere two-volume reference on revelations from studying complex microbial communities in many distinct habitats Metagenomics is an emerging field that has changed the way microbiologists study microorganisms. It involves the genomic analysis of microorganisms by extraction and cloning of DNA from a group of microorganisms, or the direct use of the purified DNA or RNA for sequencing, which allows scientists to bypass the usual protocol of isolating and culturing individual microbial species. This method is now used in laboratories across the globe to study microorganism diversity and for isolating novel medical and industrial compounds. Handbook of Molecular Microbial Ecology is the first comprehensive two-volume reference to cover unculturable microorganisms in a large variety of habitats, which could not previously have been analyzed without metagenomic methodology. It features review articles as well as a large number of case studies, based largely on original publications and written by international experts. This second volume, Metagenomics in Different Habitats, covers such topics as: Viral genomes Metagenomics studies in a variety of habitats, including marine environments and lakes, soil, and human and animal digestive tracts Other habitats, including those involving microbiome diversity in human saliva and functional intestinal metagenomics; diversity of archaea in terrestrial hot springs; and microbial communities living at the surface of building stones Biodegradation Biocatalysts and natural products A special feature of this book is the highlighting of the databases and computer programs used in each study; they are listed along with their sites in order to facilitate the computer-assisted analysis of the vast amount of data generated by metagenomic studies. Such studies in a variety of habitats are described here, which present a large number of different system-dependent approaches in greatly differing habitats. Handbook of Molecular Microbial Ecology II is an invaluable reference for researchers in metagenomics, microbial ecology, microbiology, and environmental microbiology; those working on the Human Microbiome Project; microbial geneticists; and professionals in molecular microbiology and bioinformatics.

Forest Microbiology

Fred O Asiegbu,Andriy Kovalchuk
Forest Microbiology Book PDF

Author : Fred O Asiegbu,Andriy Kovalchuk
Publisher : Academic Press
Page : 438 pages
File Size : 43,6 Mb
Release : 2021-07-09
Category : Nature
ISBN : 9780128225431

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Forest Microbiology by Fred O Asiegbu,Andriy Kovalchuk Pdf

Forest Microbiology, Volume One: Tree Microbiome: Phyllosphere, Endosphere and Rhizosphere places an emphasis on the microbiology of leaves, needles, stems, roots, litter and soil. This comprehensive title is split into five sections, including the phyllosphere microbiome, endosphere, rhizosphere, archaea, viruses in forest ecosystem and microbiota of forest nurseries and tree pests, challenges and potentials. Microbial communities associated with various host trees and different tree tissues are compared, and generalists and specialists among tree-associated microbes are identified. In addition, biotic and abiotic factors determining the composition and the structure of forest tree microbial communities are presented, along with the concept of microbial ‘hubs.' Together, the book's editors have 25 years’ worth of experience teaching and conducting research on forest microbiology, making this an essential read for any scientist interested in the forest microbiome. Addresses the microbiology of living organs of forest trees including needles, leaves, stems and roots Highlights the potential impact of microbiota inhabiting forest trees on the health and fitness of, and disease progression in, forest biomes Focuses on the phyllosphere, endosphere and rhizosphere forest microbiome

Encyclopedia of Metagenomics

Karen E. Nelson
Encyclopedia of Metagenomics Book PDF

Author : Karen E. Nelson
Publisher : Springer
Page : 727 pages
File Size : 53,6 Mb
Release : 2015-01-22
Category : Science
ISBN : 1489974792

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Encyclopedia of Metagenomics by Karen E. Nelson Pdf

Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP) which has become a world-wide effort and the Global Ocean Sampling (GOS) surveys. The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.