Genomic Adaptation For Organohalide Respiration Of Vinyl Chloride And Other Priority Pollutants By The Anaerobic Bacterium Dehalococcoides
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| Author | : Paul Joseph McMurdie (II.) |
| Publisher | : Stanford University |
| Total Pages | : 174 |
| Release | : 2011 |
| Genre | : |
| ISBN | : |
Vinyl chloride (VC) is a widespread groundwater pollutant and Group 1 carcinogen. Microbial respiration of VC is both critical for complete remediation of chloroethenes in situ, and a unique physiology only observed by certain strains of Dehalococcoides. Two different genes independently encoding VC respiration in Dehalococcoides, vcrA and bvcA, were identified previously, each a member of the diverse family of reductive dehalogenase homologous genes, or rdhA. In this thesis I report that vcrA and bvcA are among a subset of putative 'foreign' rdhA with a low GC3 codon usage that favors the nucleotide T, even though tRNAs recognizing T-ending codons are categorically absent in Dehalococcoides genomes. Comparative genomics of the first two complete genome sequences of microorganisms able to respire VC, Dehalococcoides strains VS and BAV1, reveals that vcrA and bvcA are both located within recently integrated, but different, genomic islands (GIs). These islands have different predicted integration sites and different relative positions in the genome, suggesting that bvcA and vcrA were acquired independently and through different mechanisms. In particular, the vcrA-containing GI appears to have integrated at the single-copy tmRNA encoding gene, ssrA, along with many other homologous elements that site-specifically integrate/excise at ssrA -- some of which contain other rdhA. A detailed analysis of these 'ssrA-GIs' in Dehalococcoides identifies the precise position of insertion as well as a conserved module of syntenic integration-associated genes that includes the likely ssrA-specific integrase. Further analysis of (meta)genomic data, as well as targeted sequencing from 4 additional VC-respiring cultures, provided a total of 8 syntenic vcr-GIs from independently derived cultures. Evolutionary estimates for the age of divergence of these 8 vcrA sequences is not confidently distinguishable from the first industrial synthesis of chlorinated ethenes approximately 100 years ago. By contrast, the estimated age of divergence of Dehalococcoides strains far precedes industrial civilization. Overall, ssrA-GIs appear to be a major contributor to the second of two high plasticity regions, genetically dynamic regions that interrupt an otherwise stable, syntenic, and streamlined Dehalococcoides genome -- among the smallest of any free living microorganism. The apparent compartmentalization of Dehalococcoides genome dynamics within specialized regions may enhance opportunistic adaptation to (new) organohalide respiratory niches while protecting a core genome that is highly adapted to life in the anoxic subsurface, exemplified here by the recent site-specific acquisition of VC reductase genes.
| Author | : Lorenz Adrian |
| Publisher | : Springer |
| Total Pages | : 620 |
| Release | : 2016-08-03 |
| Genre | : Science |
| ISBN | : 3662498758 |
This book summarizes the current state of knowledge concerning bacteria that use halogenated organic compounds as respiratory electron acceptors. The discovery of organohalide-respiring bacteria has expanded the range of electron acceptors used for energy conservation, and serves as a prime example of how scientific discoveries are enabling innovative engineering solutions that have transformed remediation practice. Individual chapters provide in-depth background information on the discovery, isolation, phylogeny, biochemistry, genomic features, and ecology of individual organohalide-respiring genera, including Dehalococcoides, Dehalogenimonas, Dehalobacter, Desulfitobacterium and Sulfurospirillum, as well as organohalide-respiring members of the Deltaproteobacteria. The book introduces readers to the fascinating biology of organohalide-respiring bacteria, offering a valuable resource for students, engineers and practitioners alike.
| Author | : Hans F. Stroo |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 421 |
| Release | : 2012-10-02 |
| Genre | : Technology & Engineering |
| ISBN | : 1461441153 |
This volume provides a review of the past 10 to 15 years of intensive research, development and demonstrations that have been on the forefront of developing bioaugmentation into a viable remedial technology. This volume provides both a primer on the basic microbial processes involved in bioaugmentation, as well as a thorough summary of the methodology for implementing the technology. This reference volume will serve as a valuable resource for environmental remediation professionals who seek to understand, evaluate, and implement bioaugmentation.
| Author | : T. Satyanarayana |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 827 |
| Release | : 2012-01-02 |
| Genre | : Science |
| ISBN | : 940072229X |
Microbes and their biosynthetic capabilities have been invaluable in finding solutions for several intractable problems mankind has encountered in maintaining the quality of the environment. They have, for example, been used to positive effect in human and animal health, genetic engineering, environmental protection, and municipal and industrial waste treatment. Microorganisms have enabled feasible and cost-effective responses which would have been impossible via straightforward chemical or physical engineering methods. Microbial technologies have of late been applied to a range of environmental problems, with considerable success. This survey of recent scientific progress in usefully applying microbes to both environmental management and biotechnology is informed by acknowledgement of the polluting effects on the world around us of soil erosion, the unwanted migration of sediments, chemical fertilizers and pesticides, and the improper treatment of human and animal wastes. These harmful phenomena have resulted in serious environmental and social problems around the world, problems which require us to look for solutions elsewhere than in established physical and chemical technologies. Often the answer lies in hybrid applications in which microbial methods are combined with physical and chemical ones. When we remember that these highly effective microorganisms, cultured for a variety of applications, are but a tiny fraction of those to be found in the world around us, we realize the vastness of the untapped and beneficial potential of microorganisms. At present, comprehending the diversity of hitherto uncultured microbes involves the application of metagenomics, with several novel microbial species having been discovered using culture-independent approaches. Edited by recognized leaders in the field, this penetrating assessment of our progress to date in deploying microorganisms to the advantage of environmental management and biotechnology will be widely welcomed.
| Author | : Surajit Das |
| Publisher | : Academic Press |
| Total Pages | : 715 |
| Release | : 2018-09-20 |
| Genre | : Science |
| ISBN | : 0128148500 |
Microbial Diversity in the Genomic Era presents insights on the techniques used for microbial taxonomy and phylogeny, along with their applications and respective pros and cons. Though many advanced techniques for the identification of any unknown bacterium are available in the genomics era, a far fewer number of the total microbial species have been discovered and identified to date. The assessment of microbial taxonomy and biosystematics techniques discovered and practiced in the current genomics era with suitable recommendations is the prime focus of this book. - Discusses the techniques used for microbial taxonomy and phylogeny with their applications and respective pros and cons - Reviews the evolving field of bacterial typing and the genomic technologies that enable comparative analysis of multiple genomes and the metagenomes of complex microbial environments - Provides a uniform, standard methodology for species designation
| Author | : Max M. Häggblom |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 702 |
| Release | : 2007-05-08 |
| Genre | : Science |
| ISBN | : 0306480115 |
Halogenated organic compounds constitute one of the largest groups of environmental chemicals. The industrial production of new halogenated organic compounds has increased throughout the last century peaking in the 1960s, and continuing in widespread use today. Organohalides are integral to a variety of industrial applications, including use as solvents, degreasing agents, biocides, pharmaceuticals, plasticizers, hydraulic and heat transfer fluids, and intermediates for chemical synthesis, to name a few. It is important to recognize the beneficial aspects of halogenated organic compounds, as well as their potentially deleterious impact on the environment and health. Recognition ofthe adverse environmental effects ofmanytypes oforganohalide compounds has led to efforts to reduce or eliminate the most problematic ones. Although organohalide compounds are typically considered to be anthropogenic industrial compounds, they have their counterpart in several thousands of natural biogenic and geogenic organohalides, representing most classes of organic chemicals. Natural sources account for a significant portion of the global organohalogen budget. This volume authored by recognized experts in the field provides a current perspective on how both natural and synthetic organohalides are formed and degraded, and how these processes are incorporated into a global halogen cycle. The focus is on microbial processes, since these play a major role both in the production and degradation, i. e. , cycling of halogenated organic compounds inthe environment. This book is organized into five parts. Part I, Introduction, provides a global perspective on the issues of organohalides and their fate in the environment.
| Author | : Hans F. Stroo |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 807 |
| Release | : 2010-09-10 |
| Genre | : Technology & Engineering |
| ISBN | : 1441914013 |
In the late 1970s and early 1980s, our nation began to grapple with the legacy of past disposal practices for toxic chemicals. With the passage in 1980 of the Comprehensive Envir- mental Response, Compensation, and Liability Act (CERCLA), commonly known as Sup- fund, it became the law of the land to remediate these sites. The U. S. Department of Defense (DoD), the nation’s largest industrial organization, also recognized that it too had a legacy of contaminated sites. Historic operations at Army, Navy, Air Force, and Marine Corps facilities, ranges, manufacturing sites, shipyards, and depots had resulted in widespread contamination of soil, groundwater, and sediment. While Superfund began in 1980 to focus on remediation of heavily contaminated sites largely abandoned or neglected by the private sector, the DoD had already initiated its Installation Restoration Program in the mid-1970s. In 1984, the DoD began the Defense Environmental Restoration Program (DERP) for contaminated site assessment and remediation. Two years later, the U. S. Congress codified the DERP and directed the Secretary of Defense to carry out a concurrent program of research, development, and demonstration of innovative remediation technologies. As chronicled in the 1994 National Research Council report, “Ranking Hazardous-Waste Sites for Remedial Action,” our early estimates on the cost and suitability of existing techn- ogies for cleaning up contaminated sites were wildly optimistic. Original estimates, in 1980, projected an average Superfund cleanup cost of a mere $3.
| Author | : M. Vasanthy |
| Publisher | : Springer Nature |
| Total Pages | : 604 |
| Release | : 2021-10-23 |
| Genre | : Science |
| ISBN | : 3030724417 |
This volume describes the identification of emerging organic pollutants, mainly from industrial sources, their associated toxicological threats, and the latest green methods and biotechnological solutions to abate harmful impacts on people and the environment. The chapters present reviews on current applied toxicology research, occupational health hazards and green remedial solutions for pollution control in terrestrial and aquatic environments, with the aim of raising public awareness of these issues and providing chemists, toxicologists and environmental scientists with the knowledge to combat organic pollutants through sustainable means. Readers will learn about the multi-dimensional applications of materials and processes which harvest energy out of environmental remediation technologies, as well as the roles of biotechnology and nanotechnology in addressing high pollutant load. Specific attention is paid to technologies that draw energy through wastewater remediation, as this covers the primary means by which organic pollutants are introduced into the environment from industry and other sources. The book will be of use to pollution control boards, industry regulators, and students and researchers in the fields of biotechnology, biomedical science, hydrology and water chemistry.
| Author | : Robert J. Steffan |
| Publisher | : Springer |
| Total Pages | : 0 |
| Release | : 2019-08-22 |
| Genre | : Science |
| ISBN | : 9783319504322 |
In this book international experts discuss the state-of-the-art in the biological degradation of hydrocarbons to meet remedial or disposal goals. The work focuses on practical applications, often on globally important scales including the remediation of some of the world’s largest crude oil spills. Other related chapters discuss important implications of microbial transformation of hydrocarbons, including treatment of high fat processing wastes, impacts of microbial biodegradation activity on industrial processes, and the implications of microbial oil degradation in relation to modern oil extraction processes like hydraulic fracturing of shales and extraction of oil sands.
| Author | : Gaurav Saxena |
| Publisher | : Springer |
| Total Pages | : 447 |
| Release | : 2019-06-29 |
| Genre | : Science |
| ISBN | : 9811318913 |
Achieving environmental sustainability with rapid industrialization is a major challenge of current scenario worldwide. As globally evident, industries are the key economic drivers, but are also the major polluters as untreated/partially treated effluents discharged from the industries is usually thrown into the aquatic resources and also dumped unattended. Industrial effluents are considered as the major sources of environmental pollution as these contains highly toxic and hazardous pollutants, which reaches far off areas due to the medium of dispersion and thus, create ecological nuisance and health hazards in living beings. Hence, there is an urgent to find ecofriendly solution to deal with industrial waste, and develop sustainable methods for treating/detoxifying wastewater before its release into the environment. Being a low cost and eco-friendly clean technology, bioremediation can be a sustainable alternative to conventional remediation technologies for treatment and management of industrial wastes to protect public health and environment. Therefore, this book (Volume I) covers the bioremediation of different industrial wastes viz. tannery wastewater, pulp and paper mill wastewater, distillery wastewater, acid mine tailing wastes, and many more; which are lacking in a comprehensive manner in previous literature at one place. A separate chapter dedicated to major industries and type of waste produced by them is also included. This book will appeal to students, researchers, scientists, industry persons and professionals in field of microbiology, biotechnology, environmental sciences, eco-toxicology, environmental remediation and waste management and other relevant areas, who aspire to work on the biodegradation and bioremediation of industrial wastes for environmental safety.
