Download or read book Functional Genomics of the Bacterial Degradation of the Emerging Water Contaminants written by Christopher Michael Sales and published by . This book was released on 2012 with total page 1024 pages. Available in PDF, EPUB and Kindle. Book excerpt: The emerging water contaminants 1,4-dioxane and N-nitrosodimethylamine (NDMA) are toxic and classified as probable human carcinogens. Both compounds are persistent in the environment and are highly mobile in groundwater plumes due to their hydrophilic nature. The major source of 1,4-dioxane is due to its use as a stabilizer in the chlorinated solvent 1,1,1-trichloroethane. The presence of NDMA as a water contaminant is related to the release of rocket fuels and its formation in the disinfection of water and wastewater. Prior studies have demonstrated that bacteria expressing monooxygenases are capable of degrading 1,4-dioxane and NDMA. While growth on 1,4-dioxane as a sole carbon and energy source has been reported in Pseudonocardia dioxanivorans CB1190 and Pseudonocardia benzenivorans B5, it is also co-metabolically degradable by a variety of monooxygenase-expressing strains. In contrast, NDMA has only been observed to biodegrade co-metabolically after growth on some monooxygenase-inducing substrates. The fastest rates of NDMA degradation occur in Rhodococcus sp. RR1 and Mycobacterium vaccae JOB5 after growth on propane. Pathways have been proposed for 1,4-dioxane biodegradation in P. dioxanivorans and for NDMA biodegradation in propane-induced Rhodococcus sp. RR1 based only on identified intermediates. The overall goal of this dissertation is to gain a better understanding of the genes and biological pathways responsible for degradation of 1,4-dioxane and NDMA. Due to the lack of molecular sequence information for organisms capable of growth on 1,4-dioxane, the genome of P. dioxanivorans strain CB1190 was sequenced in this study. The genome has a total size of 7,440,794 bp and consists of four replicons: a circular chromosome, a circular plasmid pPSED01, an unclosed circular plasmid pPSED02, and a linear plasmid pPSED03. Analysis of this genome sequence revealed the presence of eight multicomponent monooxygenases: a propane monooxygenase, a phenol monooxygenase, a 4-hydroxyphenylacetate monooxygenase, four aromatic (toluene) monooxygenases, and a tetrahydrofuran (THF) monooxygenase. A total of 92 genes identified as putative dioxygenases were identified. Protein-encoding genes involved in transport systems, signal transduction systems, secretion systems, and heavy-metal and antibiotic resistance were identified. The presence of pathways for carbon and nitrogen metabolism was examined. A complete Calvin-Benson-Bassham carbon fixation pathway was found and a number of carboxylases that function in other carbon fixation pathways were identified. Although P. dioxanivorans has been reported to fix nitrogen, no nitrogenase genes were found. The genome sequence of P. dioxanivorans was compared to other sequenced genomes of members in the family Pseudonocardiaceae, including Amycolatopsis mediterranei S699, Amycolatopsis mediterranei U32, Pseudonocardia sp. P1, Pseudonocardia sp. P2, Saccharomonaspora azurea NA-128, Saccharomonospora paurometabolica YIM 9007, Sacharomonospora viridis DSM43017, Saccharopolyspora erythraea NRRL2338, and Saccharopolyspora spinosa NRRL18395. Genome-aided approaches were employed to identify the protein-encoding genes involved in the metabolic degradation of 1,4-dioxane in P. dioxanivorans. These approaches included whole genome expression microarray transcriptomics, quantitative reverse transcriptase PCR (qRT-PCR), enzyme assays, and heterologous expression clones. Genes differentially expressed during growth on 1,4-dioxane, glycolate (a previously identified degradation intermediate), and pyruvate (control) were analyzed to determine genes differentially expressed and involved in the metabolism of 1,4-dioxane. Based on the differentially expressed genes, the 1,4-dioxane degradation pathway was revised and annotated with the enzymes known to catalyze specific transformation steps. Up-regulation of genes were confirmed and quantified by qRT-PCR. Transcriptional analyses, isotopic tracer analyses with 1,4-[U-13C]-dioxane, and glyoxylate carboligase enzymatic activity assays confirmed the role of glyoxylate as a central intermediate in the degradation of 1,4-dioxane. Specifically, transcriptional analyses indicated that the THF monooxygenase, encoded by thmADBC, is up-regulated during growth on 1,4-dioxane and THF. Furthermore, Rhodococcus jostii RHA1 clones heterologously expressing the P. dioxanivorans genes thmADBC demonstrated 1,4-dioxane and THF degradation activity. A surprising result with the THF monooxygenase expressing clones was the accumulation of the intermediate [beta]-hydroxyethoxyacetic acid (HEAA). This result, combined with the non-inhibitory effect of acetylene on HEAA degradation by 1,4-dioxane grown P. dioxanivorans indicates that a monooxygenase is not involved in the transformation of HEAA as previously hypothesized. Transcriptomic microarray analysis of THF- and succinate-grown cells led to the first proposed THF metabolic degradation pathway for P. dioxanivorans. A novel finding of this transcriptomic microarray analysis was the identification of an alcohol dehydrogenase up-regulated during growth on THF that could catalyze the conversion of 2-hydroxytetrahydrofuran to [gamma]-butyrolactone. The genome sequence of Rhodococcus jostii RHA1 was utilized to determine the propane-induced monooxygenase responsible for NDMA degradation. The degradation of NDMA was characterized in R. jostii RHA1 grown on propane and on non-inducing substrates (LB medium, soy broth, and pyruvate). Propane enhanced the removal rate of NDMA by nearly two orders of magnitude compared to constitutive degradation during growth on non-inducing substrate. Transcriptomic microarray and qRT-PCR analyses demonstrated that propane elicits the up-regulation of a propane monooxygenase gene cluster. Genetic knockouts of the prmA gene encoding the large hydroxylase component of the propane monooxygenase were unable to grow on propane and degrade NDMA. These results indicate that the propane monooxygenase is responsible for NDMA degradation by R. jostii and explain the enhanced co-metabolic degradation of NDMA in the presence of propane. With the newly gained knowledge of the role of propane monooxygenase in NDMA degradation, oligonucleotide degenerate primers targeting prmA were designed and were identify and quantify the presence of propane monooxygenase genes in Rhodoccocus sp. RR1 and M. vaccae JOB5. A homolog to prmA was found in Rhodoccocus sp. RR1 but not in M. vaccae JOB5. The prmA gene in Rhodococcus sp. RR1 was up-regulated during growth on propane relative to pyruvate. Characterization of the kinetics of propane-enhanced NDMA degradation showed that Rhodococcus sp. RR1 and M. vaccae possess similar maximum transformation rates (44 ± 5 and 28 ± 3 mg NDMA(mg protein)-1h-1, respectively). However, a comparison of half saturation constants (Ks, n) and NDMA degradation in the presence of propane revealed pronounced differences between the strains. The Ks, n for Rhodococcus sp. RR1 was 36 ± 10 mg NDMA L-1 while the propane concentration needed to inhibit NDMA rates by 50% (Kinh) occurred at 7,700 mg propane L-1 (R2 = 0.9669). In contrast, M. vaccae had a markedly lower affinity for NDMA verses propane with a calculated Ks, n of 2,200 ± 1,000 mg NDMA L-1 and Kinh of 120 mg propane L-1 (R2 = 0.9895). Differences between the propane monooxygenases in Rhodococcus sp. RR1 and the unidentified enzyme(s) in M. vaccae may explain the disparities in NDMA degradation and inhibition kinetics between these strains.
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.
Download or read book Onsite Wastewater Treatment Systems Manual written by and published by . This book was released on 2002 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This manual contains overview information on treatment technologies, installation practices, and past performance."--Introduction.
Download or read book Microbial Biodegradation and Bioremediation written by Surajit Das and published by Elsevier. This book was released on 2014-07-01 with total page 641 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbial Biodegradation and Bioremediation brings together experts in relevant fields to describe the successful application of microbes and their derivatives for bioremediation of potentially toxic and relatively novel compounds. This single-source reference encompasses all categories of pollutants and their applications in a convenient, comprehensive package. Our natural biodiversity and environment is in danger due to the release of continuously emerging potential pollutants by anthropogenic activities. Though many attempts have been made to eradicate and remediate these noxious elements, every day thousands of xenobiotics of relatively new entities emerge, thus worsening the situation. Primitive microorganisms are highly adaptable to toxic environments, and can reduce the load of toxic elements by their successful transformation and remediation. - Describes many novel approaches of microbial bioremediation including genetic engineering, metagenomics, microbial fuel cell technology, biosurfactants and biofilm-based bioremediation - Introduces relatively new hazardous elements and their bioremediation practices including oil spills, military waste water, greenhouse gases, polythene wastes, and more - Provides the most advanced techniques in the field of bioremediation, including insilico approach, microbes as pollution indicators, use of bioreactors, techniques of pollution monitoring, and more
Download or read book Ecological Engineering for Wastewater Treatment written by Carl Etnier and published by CRC Press. This book was released on 2013-10-23 with total page 480 pages. Available in PDF, EPUB and Kindle. Book excerpt: The new science of ecological engineering is winning increasing acceptance all over the world. Established industrial economies like Sweden and the United States are investing more in it as initial skepticism and regulatory hurdles are giving way to burgeoning investments by companies and municipalities, increased research activity, and great inter
Download or read book Microbial Biodegradation written by Eduardo Díaz and published by . This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In this timely book expert international authors critically review all of the most important topics in this exciting field. Although other books covering this are currently available, this book is unique in that it is the first to review the area from a molecular biology and genomics perspective. Topics covered include: aerobic and anaerobic biodegradation of aromatic compounds, molecular detection methods (e.g. microautoradiography, mRNA analyses, etc.), genome-based predictive modelling, elucidation of regulatory networks, bioavailability, chemotaxis and transport issues, functional genomic.
Download or read book Microbial Degradation of Xenobiotics written by Shree Nath Singh and published by Springer Science & Business Media. This book was released on 2011-10-07 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Our interest in the microbial biodegradation of xenobiotics has increased many folds in recent years to find out sustainable ways for environmental cleanup. Bioremediation and biotransformation processes harness the naturally occurring ability of microbes to degrade, transform or accumulate a wide range of organic pollutants. Major methodological breakthroughs in recent years through detailed genomic, metagenomic, proteomic, bioinformatic and other high-throughput analyses of environmentally relevant microorganisms have provided us unprecedented insights into key biodegradative pathways and the ability of organisms to adapt to changing environmental conditions. The degradation of a wide spectrum of organic pollutants and wastes discharged into the environment by anthropogenic activities is an emerging need today to promote sustainable development of our society with low environmental impact. Microbial processes play a major role in the removal of recalcitrant compounds taking advantage of the astonishing catabolic versatility of microorganisms to degrade or transform such compounds. New breakthroughs in sequencing, genomics, proteomics, bioinformatics and imaging are generating vital information which opens a new era providing new insights of metabolic and regulatory networks, as well as clues to the evolution of degradation pathways and to the molecular adaptation strategies to changing environmental conditions. Functional genomic and metagenomic approaches are increasing our understanding of the relative importance of different pathways and regulatory networks to carbon flux in particular environments and for particular compounds. New approaches will certainly accelerate the development of bioremediation technologies and biotransformation processes in coming years for natural attenuation of contaminated environments
Download or read book Transgenic Plant Technology for Remediation of Toxic Metals and Metalloids written by M.N.V. Prasad and published by Academic Press. This book was released on 2018-11-20 with total page 566 pages. Available in PDF, EPUB and Kindle. Book excerpt: Transgenic Plant Technology for Remediation of Toxic Metals and Metalloids covers all the technical aspects of gene transfer, from molecular methods, to field performance using a wide range of plants and diverse abiotic stress factors. It describes methodologies that are well established as a key resource for researchers, as well as a tool for training technicians and students. This book is an essential reference for those in the plant sciences, forestry, agriculture, microbiology, environmental biology and plant biotechnology, and those using transgenic plant models in such areas as molecular and cell biology, developmental biology, stress physiology and phytoremediation. Provides in-depth coverage of transgenic plant technology for environmental problems Discusses background and an introduction to techniques and salient protocols using specific plants systems Includes emerging strategies for application of transgenic plans in remediation
Download or read book Prokaryotic Genomics written by Michel Blot and published by Birkhäuser. This book was released on 2013-12-01 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Prokaryotic Genomics provides molecular microbiologists in particular and researchers working with bacteria in general with the most important established recipes needed for their work. The volume covers both revisited classical methods and new tools for global analysis such as genomics or proteomics. It is written for those in need of a bench manual to complete their experiments and for those wanting to understand the modern tools used in microbiology.
Download or read book Microbiological Sensors for the Drinking Water Industry written by Tapio Katko and published by IWA Publishing. This book was released on 2019-02-15 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book addresses the interdisciplinary area of water quality monitoring and binds together interests and competences within sensing technology, system behaviour, business needs, legislation, education, data handling, and artificial response algorithms.
Download or read book Toxicity and Waste Management Using Bioremediation written by Rathoure, Ashok K. and published by IGI Global. This book was released on 2015-12-02 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioremediation is an emerging field of environmental research. The objective of a bioremediation process is to immobilize contaminants (reactants) or to transform them into chemical products that do not pose a risk to human health and the environment. Toxicity and Waste Management Using Bioremediation provides relevant theoretical and practical frameworks and the latest empircal research findings on the remediation of contaminated soil and groundwater using bioorganisms. Focusing on effective waste treatment methodologies and management strategies that lead to improved human and environmental health, this timely publication is ideal for use by environmenal scientists, biologists, policy makers, graduate students, and scholars in the fields of environmental science, chemistry, and biology.
Download or read book Genomics Approach to Bioremediation written by Vineet Kumar and published by John Wiley & Sons. This book was released on 2023-02-22 with total page 565 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomics Approach to Bioremediation Provides insights into the various aspects of microbial genomics and biotechnology for environmental cleanup In recent years, the application of genomics to biodegradation and bioremediation research has led to a better understanding of the metabolic capabilities of microorganisms, their interactions with hazardous and toxic chemical compounds, and their adaptability to changing environmental conditions. Genomics Approach to Bioremediation: Principles, Tools, and Emerging Technologies provides comprehensive and up-to-date information on cutting-edge technologies and approaches in bioremediation and biodegradation of environmental pollutants. Edited by prominent researchers in the field, this authoritative reference examines advanced genomics technologies, next-generation sequencing (NGS), and state-of-the-art bioinformatics tools while offering valuable insights into the unique functional attributes of different microbial communities and their impact on the removal of chemical contaminants. Each chapter includes numerous high-quality illustrations, detailed tables, extensive references, and step-by-step descriptions of various microbial metabolic pathways of degradation and biotransformation of environments containing various inorganic, metallic, organometallic, and organic hydrocarbon contaminants. Describes methodologies and underlying theory for the remediation, detoxification, and degradation of contaminated environments Covers new genomics technologies that address nutrient removal, resource recovery, and other major trends in environmental cleanup Highlights recent advances in microbial biotechnological approaches including the latest description of the relationship between microbes and the environment focusing on their impact on ecosystem services Offers perspectives on energy saving, production, sustainability, and community involvement Discusses current challenges and future directions in the field of bioremediation Genomics Approach to Bioremediation: Principles, Tools, and Emerging Technologies is an essential resource for biochemical and environmental engineers, environmental microbiologists, academic researchers, process and treatment plant managers, policymakers, and industry professionals working in the areas of microbial degradation, bioremediation, and phytoremediation.
Download or read book Soil Bioremediation written by Javid A. Parray and published by John Wiley & Sons. This book was released on 2021-03-22 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: SOIL BIOREMEDIATION A practical guide to the environmentally sustainable bioremediation of soil Soil Bioremediation: An Approach Towards Sustainable Technology provides the first comprehensive discussion of sustainable and effective techniques for soil bioremediation involving microbes. Presenting established and updated research on emerging trends in bioremediation, this book provides contributions from both experimental and numerical researchers who provide reports on significant field trials. Soil Bioremediation instructs the reader on several different environmentally friendly bioremediation techniques, including: Bio-sorption Bio-augmentation Bio-stimulation Emphasizing molecular approaches and biosynthetic pathways of microbes, this one-of-a-kind reference focuses heavily on the role of microbes in the degradation and removal of xenobiotic substances from the environment and presents a unique management and conservation perspective in the field of environmental microbiology. Soil Bioremediation is perfect for undergraduate students in the fields of environmental science, microbiology, limnology, freshwater ecology and microbial biotechnology. It is also invaluable for researchers and scientists working in the areas of environmental science, environmental microbiology, and waste management.
Download or read book Biochemistry of microbial degradation written by Colin Ratledge and published by Springer. This book was released on 2012-10-25 with total page 590 pages. Available in PDF, EPUB and Kindle. Book excerpt: Life on the planet depends on microbial activity. The recycling of carbon, nitrogen, sulphur, oxygen, phosphate and all the other elements that constitute living matter are continuously in flux: microorganisms participate in key steps in these processes and without them life would cease within a few short years. The comparatively recent advent of man-made chemicals has now challenged the environment: where degradation does not occur, accumulation must perforce take place. Surprisingly though, even the most recalcitrant of molecules are gradually broken down and very few materials are truly impervious to microbial attack. Microorganisms, by their rapid growth rates, have the most rapid turn-over of their DNA of all living cells. Consequently they can evolve altered genes and therefore produce novel enzymes for handling "foreign" compounds - the xenobiotics - in a manner not seen with such effect in other organisms. Evolution, with the production of micro-organisms able to degrade molecules hitherto intractable to breakdown, is therefore a continuing event. Now, through the agency of genetic manipulation, it is possible to accelerate this process of natural evolution in a very directed manner. The time-scale before a new microorganism emerges that can utilize a recalcitrant molecule has now been considerably shortened by the application of well-understood genetic principles into microbiology. However, before these principles can be successfully used, it is essential that we understand the mechanism by which molecules are degraded, otherwise we shall not know where best to direct these efforts.
Download or read book Review of the Department of Energy s Genomics GTL Program written by National Research Council and published by National Academies Press. This book was released on 2006-04-19 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: The U.S. Department of Energy (DOE) promotes scientific and technological innovation to advance the national, economic, and energy security of the United States. Recognizing the potential of microorganisms to offer new energy alternatives and remediate environmental contamination, DOE initiated the Genomes to Life program, now called Genomics: GTL, in 2000. The program aims to develop a predictive understanding of microbial systems that can be used to engineer systems for bioenergy production and environmental remediation, and to understand carbon cycling and sequestration. This report provides an evaluation of the program and its infrastructure plan. Overall, the report finds that GTL's research has resulted in and promises to deliver many more scientific advancements that contribute to the achievement of DOE's goals. However, the DOE's current plan for building four independent facilities for protein production, molecular imaging, proteome analysis, and systems biology sequentially may not be the most cost-effective, efficient, and scientifically optimal way to provide this infrastructure. As an alternative, the report suggests constructing up to four institute-like facilities, each of which integrates the capabilities of all four of the originally planned facility types and focuses on one or two of DOE's mission goals. The alternative infrastructure plan could have an especially high ratio of scientific benefit to cost because the need for technology will be directly tied to the biology goals of the program.
Download or read book Wastewater Treatment Reactors written by Maulin P. Shah and published by Elsevier. This book was released on 2021-05-17 with total page 644 pages. Available in PDF, EPUB and Kindle. Book excerpt: Wastewater Treatment Reactors: Microbial Community Structure analyzes microbial community structure in relation to changes in physico-chemical parameters, the gene content (metagenome) or gene expression (metatranscriptome) of microbial communities in relation to changes in physico-chemical parameters, physiological aspects of microbial communities, enrichment cultures or pure cultures of key species in relation to changes in physico-chemical parameters, and modeling of potential consequences of changes in microbial community structure or function for higher trophic levels in a given habitat. As several studies have been carried out to understand bulking phenomena and the importance of environmental factors on sludge settling characteristics, which are thought to be strongly influenced by flocculation, sludge bulking, foaming and rising, this book is an ideal resource on the topics covered. Presents the state-of-the-art techniques and applications of omics tools in wastewater treatment reactors (WWTRs) Describes both theoretical and practical knowledge surrounding the fundamental roles of microorganisms in WWTRs Points out the reuse of treated wastewater through emerging technologies Covers the economics of wastewater treatment and the development of suitable alternatives in terms of performance and cost effectiveness Discusses cutting-edge molecular biological tools Gives in-depth knowledge to study microbial community structure and function in wastewater treatment reactors
Download or read book Indicators for Waterborne Pathogens written by National Research Council and published by National Academies Press. This book was released on 2004-06-19 with total page 329 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent and forecasted advances in microbiology, molecular biology, and analytical chemistry have made it timely to reassess the current paradigm of relying predominantly or exclusively on traditional bacterial indicators for all types of waterborne pathogens. Nonetheless, indicator approaches will still be required for the foreseeable future because it is not practical or feasible to monitor for the complete spectrum of microorganisms that may occur in water, and many known pathogens are difficult to detect directly and reliably in water samples. This comprehensive report recommends the development and use of a "tool box" approach by the U.S Environmental Protection Agency and others for assessing microbial water quality in which available indicator organisms (and/or pathogens in some cases) and detection method(s) are matched to the requirements of a particular application. The report further recommends the use of a phased, three-level monitoring framework to support the selection of indicators and indicator approaches.Â
