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Author : Woo Jun Sul
Publisher :
ISBN 13 :
Total Pages : 348 pages
Book Rating : 4.3/5 (129 download)
Download or read book Microbial Community Analysis Assessed by Pyrosequencing of RRNA Gene written by Woo Jun Sul and published by . This book was released on 2009 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Francis Martin
Publisher : Springer Nature
ISBN 13 : 1071628712
Total Pages : 370 pages
Book Rating : 4.0/5 (716 download)
Download or read book Microbial Environmental Genomics (MEG) written by Francis Martin and published by Springer Nature. This book was released on 2022-12-15 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Experimental Factors Affecting PCR-based Estimates of Microbial Species Richness and Evenness written by and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield greater than two orders of magnitude more sensitivity than traditional PCR-cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCRbased community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness number of species and evenness relative abundance of species by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1-V2 or V8 regions, using amplicons ranging n length from 352 to 1443 bp. Our results demonstrate that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.
Author : Tae Jin Park
Publisher : Open Dissertation Press
ISBN 13 : 9781361024539
Total Pages : 154 pages
Book Rating : 4.0/5 (245 download)
Download or read book MICROBIAL COMMUNITY ECOLOGY IN written by Tae Jin Park and published by Open Dissertation Press. This book was released on 2017-01-26 with total page 154 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "Microbial Community Ecology in Bioelectrochemical Systems (BESs) Using 16S Ribosomal RNA (rRNA) Pyrosequencing" by Tae Jin, Park, 朴台鎮, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Microbial community ecology in bioelectrochemical systems (BES) has provided useful information on the fundamental understanding of microbial community structure and function for bioenergy production. With rapidly developing high-throughput DNA sequencing technologies coupled with bioinformatics tools, the deep sequencing has become a popular tool to provide better understanding complex interactions occurring in bioenergy-producing microbial communities in BES. In this thesis, I analyzed the microbial community from variable characteristics of BESs including microbial fuel cell (MFC) media solutions enriched by Rhodopseudomonas sp, methanogenic biocathodes inoculated with different inoculum sources, newly designed MFCs under nitrogen-rich conditions and alkaline MFCs, using 16S rRNA gene pyrosequencing. My results indicated: 1) a syntrophic relationship between Rhodopseudomonas and hydrogenotrophic microbes could exist in the acetate-fed MFCs under light conditions. Observations suggested that high power densities obtained from the light-induced MFC reactors might be explained by not only the enrichment of Rhodopseudomonas palustris but also its respective syntrophic assosociates; 2) Major groups of unknown bacteria in the phyla Firmicutes and Bacteroidetes originated from the biocathodes with different inoculum sources including the sludge (BIS) and effluent of acetate-fed microbial fuel cell (BIE), suggesting them to be involved in hydrolysis, acidogenesis and acetogenesis. They could play an important role in CO2 production for methane generation by three major hydrogenotrophic methanogens identified as Methanobacterium, Methanocorpusculum and Methanobacterium. Their specific roles in the reduction of CO2 to methane may be due to external power and/or H2 used as electron donors; 3) the additional electrode-like biocathode in the newly designed nitrogen-rich MFCs showed inhibition of true nitrifiers as the potential exoelectrogen in the anode biofilm. The dominance of Geobacter in the additional electrode-like biocathode could be mainly involved in denitrification processes; 4) The Desulfuromonas species was the most prevalent bacterial species in pH10 and 11 MFC reactors with its abundance trend consistent with higher levels of power density. It was suggested that the possibility of their activities might be related to the amount of electricity generated. The dominant Desulfuromonas of pH10 and 11 MFC reactors could outcompete other exoelectrogens for acetate and this resulted in lower bacterial diversity and linking their abundance values with higher power generation. Overall, these distinct microbial community compositions provided useful information for a better understanding of microbial interactions and functions associated with the different operating conditions of electricity and methane generation in BESs. DOI: 10.5353/th_b5543986 Subjects: Microbial biotechnology Microbial genomics Bioelectrochemistry
Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309449839
Total Pages : 318 pages
Book Rating : 4.3/5 (94 download)
Download or read book Microbiomes of the Built Environment written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-10-06 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: People's desire to understand the environments in which they live is a natural one. People spend most of their time in spaces and structures designed, built, and managed by humans, and it is estimated that people in developed countries now spend 90 percent of their lives indoors. As people move from homes to workplaces, traveling in cars and on transit systems, microorganisms are continually with and around them. The human-associated microbes that are shed, along with the human behaviors that affect their transport and removal, make significant contributions to the diversity of the indoor microbiome. The characteristics of "healthy" indoor environments cannot yet be defined, nor do microbial, clinical, and building researchers yet understand how to modify features of indoor environmentsâ€"such as building ventilation systems and the chemistry of building materialsâ€"in ways that would have predictable impacts on microbial communities to promote health and prevent disease. The factors that affect the environments within buildings, the ways in which building characteristics influence the composition and function of indoor microbial communities, and the ways in which these microbial communities relate to human health and well-being are extraordinarily complex and can be explored only as a dynamic, interconnected ecosystem by engaging the fields of microbial biology and ecology, chemistry, building science, and human physiology. This report reviews what is known about the intersection of these disciplines, and how new tools may facilitate advances in understanding the ecosystem of built environments, indoor microbiomes, and effects on human health and well-being. It offers a research agenda to generate the information needed so that stakeholders with an interest in understanding the impacts of built environments will be able to make more informed decisions.
Author : Erko Stackebrandt
Publisher :
ISBN 13 :
Total Pages : 370 pages
Book Rating : 4.3/5 (91 download)
Download or read book Nucleic Acid Techniques in Bacterial Systematics written by Erko Stackebrandt and published by . This book was released on 1991-04-19 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of a series whose aim is to identify specialist areas in microbiology and to provide up-to-date methodological information for laboratory microbiologists, active researchers and graduate students. This volume addresses nucleic acid techniques in bacterial systematics.
Author : Brian Douglas Robertson
Publisher : Caister Academic Press Limited
ISBN 13 : 9781908230027
Total Pages : 0 pages
Book Rating : 4.2/5 (3 download)
Download or read book Systems Microbiology written by Brian Douglas Robertson and published by Caister Academic Press Limited. This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology is the study of the dynamic interactions of more than one component in a biological system in order to understand and predict the behavior of the system as a whole. Systems biology is a rapidly expanding discipline fuelled by the 'omics' era and new technological advances that have increased the precision of data. A focus on simple single cell organisms, such as bacteria, aids tractability and means that systems microbiology is a rapidly maturing science. Recommended for all microbiology laboratories, this book contains cutting-edge reviews by world-leading experts on the systems biology of microorganisms. As well as covering theoretical approaches and mathematical modeling, the book includes case studies on single microbial species of bacteria and archaea, and it explores the systems analysis of microbial phenomena, such as chemotaxis and phagocytosis. The topics covered include: the mathematical models for systems biology * systems biology of Escherichia coli metabolism * bacterial chemotaxis * systems biology of infection * host-microbe interactions * phagocytosis * system-level study of metabolism in Mycobacterium tuberculosis * systems biology of Sulfolobus.
Author : Peter Goos
Publisher : John Wiley & Sons
ISBN 13 : 1119976162
Total Pages : 249 pages
Book Rating : 4.1/5 (199 download)
Download or read book Optimal Design of Experiments written by Peter Goos and published by John Wiley & Sons. This book was released on 2011-06-28 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This is an engaging and informative book on the modern practice of experimental design. The authors' writing style is entertaining, the consulting dialogs are extremely enjoyable, and the technical material is presented brilliantly but not overwhelmingly. The book is a joy to read. Everyone who practices or teaches DOE should read this book." - Douglas C. Montgomery, Regents Professor, Department of Industrial Engineering, Arizona State University "It's been said: 'Design for the experiment, don't experiment for the design.' This book ably demonstrates this notion by showing how tailor-made, optimal designs can be effectively employed to meet a client's actual needs. It should be required reading for anyone interested in using the design of experiments in industrial settings." —Christopher J. Nachtsheim, Frank A Donaldson Chair in Operations Management, Carlson School of Management, University of Minnesota This book demonstrates the utility of the computer-aided optimal design approach using real industrial examples. These examples address questions such as the following: How can I do screening inexpensively if I have dozens of factors to investigate? What can I do if I have day-to-day variability and I can only perform 3 runs a day? How can I do RSM cost effectively if I have categorical factors? How can I design and analyze experiments when there is a factor that can only be changed a few times over the study? How can I include both ingredients in a mixture and processing factors in the same study? How can I design an experiment if there are many factor combinations that are impossible to run? How can I make sure that a time trend due to warming up of equipment does not affect the conclusions from a study? How can I take into account batch information in when designing experiments involving multiple batches? How can I add runs to a botched experiment to resolve ambiguities? While answering these questions the book also shows how to evaluate and compare designs. This allows researchers to make sensible trade-offs between the cost of experimentation and the amount of information they obtain.
Download or read book Size Matters written by and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.
Author : Dinesh K. Maheshwari
Publisher : Springer Science & Business Media
ISBN 13 : 3642336396
Total Pages : 502 pages
Book Rating : 4.6/5 (423 download)
Download or read book Bacteria in Agrobiology: Disease Management written by Dinesh K. Maheshwari and published by Springer Science & Business Media. This book was released on 2013-01-11 with total page 502 pages. Available in PDF, EPUB and Kindle. Book excerpt: The future of agriculture greatly depends on our ability to enhance productivity without sacrificing long-term production potential. The application of microorganisms, such as the diverse bacterial species of plant growth promoting bacteria (PGPB), represents an ecologically and economically sustainable strategy. The use of these bio-resources for the enhancement of crop productivity is gaining importance worldwide. "Bacteria in Agrobiology: Disease Management" discusses various aspects of biological control and disease suppression using bacteria. Topics covered include: fluorescent pseudomonads; siderophore-producing PGPR; pseudomonas inoculants; bacillus-based biocontrol agents; bacterial control of root and tuber crop diseases; fungal pathogens of cereals; soil-borne fungal pathogens; peronosporomycete phytopathogens; and plant parasitic nematodes.
Author : Diana Elizabeth Marco
Publisher : Frontiers Media SA
ISBN 13 : 2889458148
Total Pages : 674 pages
Book Rating : 4.8/5 (894 download)
Download or read book Using Genomics, Metagenomics and Other "Omics" to Assess Valuable Microbial Ecosystem Services and Novel Biotechnological Applications written by Diana Elizabeth Marco and published by Frontiers Media SA. This book was released on 2019-05-15 with total page 674 pages. Available in PDF, EPUB and Kindle. Book excerpt: Most ecosystem services and goods human populations use and consume are provided by microbial populations and communities. Indeed, numerous provisioning services (e.g. food and enzymes for industrial processes), regulating services (e.g. water quality, contamination alleviation and biological processes such as plant-microbial symbioses), and supporting services (e.g. nutrient cycling, agricultural production and biodiversity) are mediated by microbes. The fast development of metagenomics and other meta-omics technologies is expanding our understanding of microbial diversity, ecology, evolution and functioning. This enhanced knowledge directly translates into the emergence of new applications in an unlimited variety of areas across all microbial ecosystem services and goods. The varied topics addressed in this Research Topic include the development of innovative industrial processes, the discovery of novel natural products, the advancement of new agricultural methods, the amelioration of negative effects of productive or natural microbiological processes, as well as food security and human health, and archeological conservation. The articles compiled provide an updated, high-quality overview of current work in the field. This body of research makes a valuable contribution to the understanding of microbial ecosystem services, and expands the horizon for finding and developing new and more efficient biotechnological applications.
Author : Salom Gnana Thanga Vincent
Publisher : Elsevier
ISBN 13 : 0128151668
Total Pages : 206 pages
Book Rating : 4.1/5 (281 download)
Download or read book Microbial Communities in Coastal Sediments written by Salom Gnana Thanga Vincent and published by Elsevier. This book was released on 2021-06-02 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: A concise reference on the structural composition and function of microbial communities in coastal environments, especially in relation to natural and anthropogenic impacts. Microbial Communities in Coastal Sediments presents twenty years of coastal microbiology research, grounding it as a vital development in the field of microbial ecology. It is the first book to focus exclusively on the complex microbial ecology and its function in rest of the marine environment. The book outlines the structure, function, and assessment of microbial communities in marine sediments while exploring practical methods of assessment. It is an invaluable resource to aquatic microbiologists, marine ecologists, marine microbiologists, aquatic researchers, and graduate students in this field. Microbial Communities in Coastal Sediments begins with an examination of nutrient sources in the coastal context with a focus on organic matter inputs. The quantity and quality of organic matter in coastal sediments and their impacts on the composition and formation of microbial communities is discussed. The book explores the consequences of anthropogenic changes and human activity on microbial ecology and nutrient cycling. Sections on nutrient availability, green house gas production and biodegradation of persistent organic pollutants provide essential details. Molecular research techniques and methods for assessing microbial community structure and function in coastal sediments are also covered. Explores the interplay of physicochemical and biological features of coastal ecosystems on microbial community composition to provide a template of comparison for field research Includes unique figures, schematic diagrams and photographs related to microbial processes of coastal ecosystem to clearly represent different aspects of microbial structure and functions Provides analytical methods and detailed molecular techniques for qualitative and quantitative analyses of microbial community structure
Author : P. Fratamico
Publisher : Elsevier Inc. Chapters
ISBN 13 : 0128089822
Total Pages : 46 pages
Book Rating : 4.1/5 (28 download)
Download or read book Advances in microbial food safety written by P. Fratamico and published by Elsevier Inc. Chapters. This book was released on 2013-07-31 with total page 46 pages. Available in PDF, EPUB and Kindle. Book excerpt: Omic technologies, including genomics, proteomics and metabolomics, are used to study pathogen behavior at the molecular level and develop improved pathogen detection and typing systems. Omic technologies analyze complete or nearly complete expressions of cell functions. DNA sequencing has resulted in complete genomes of foodborne pathogens. Omic-based technologies explore biological processes in a quantitative and integrative manner. They facilitate identification of genes and proteins that contribute to survival and persistence in food and other environments, that play a role in pathogenesis and that are targets for detection methods and control strategies. Challenges that remain are performing genomic and proteomic studies in food and other complex matrices and interpreting and analyzing the data produced from these investigations to enhance food safety.
Author : Rebekah Ruth Helton
Publisher :
ISBN 13 :
Total Pages : 222 pages
Book Rating : 4.3/5 (129 download)
Download or read book Assessment of the Microbial Communities Derived from Two Tetrachloroethene (PCE)-contaminated Aquifers written by Rebekah Ruth Helton and published by . This book was released on 2000 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Karen E. Nelson
Publisher : Springer
ISBN 13 : 9781461446743
Total Pages : 1528 pages
Book Rating : 4.4/5 (467 download)
Download or read book Encyclopedia of Metagenomics written by Karen E. Nelson and published by Springer. This book was released on 2015-02-18 with total page 1528 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Wojtek Krzanowski
Publisher : OUP Oxford
ISBN 13 : 0191053945
Total Pages : 609 pages
Book Rating : 4.1/5 (91 download)
Download or read book Principles of Multivariate Analysis written by Wojtek Krzanowski and published by OUP Oxford. This book was released on 2000-09-28 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is an introduction to the principles and methodology of modern multivariate statistical analysis. It is written for the user and potential user of multivariate techniques as well as for students coming to the subject for the first time. The author's emphasis is problem-orientated and he is at pains to stress geometrical intuition in preference to algebraic manipulation. Mathematical sections that are not essential for a practical understanding of the techniques are clearly indicated so that they may be skipped by the non-specialist. Discrete and mixed variable techniques are presented as well as continuous variable techniques to give a comprehensive coverage of the subject. This updated edition includes a new appendix which traces developments that have taken place in the years since the publication of the first edition and which clarifies some issues raised by readers of the original text. References to about 60 recent books and articles supplement the material in this appendix. Overall, this volume provides an up-to-date and readable practical account of the subject, both for students of statistics and for research workers in subjects as diverse as anthropology, education, industry, medicine and taxonomy. The new edition includes a survey of the most recent developments in the subject.
Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309106761
Total Pages : 170 pages
Book Rating : 4.3/5 (91 download)
Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
