About the Course
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Welcome
to the Theoretical and Practical Molecular Approaches for In Situ Biodegradation Course information center. This course is sponsored by the United States-European Commission Task Force on Biotechnology Research. The Joint US-EC Short Course on Environmental Biotechnology is designed for several purposes. One of the central tenets is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that will set the groundwork for future overseas collaborative interactions. The course is also designed to give the scientists hands-on experience in modern, up-to-date biotechnological methods for the analysis of microbes and their activities pertinent to the remediation of pollutants in the environment. The University of Oklahoma (OU) is an excellent place to host such a short course since it has a strong microbiology faculty with expertise in many areas of environmental biotechnology. It is particularly strong in the area of anaerobic microbiology and the associated techniques will be taught to the students in the course. Equally important, OU is within two miles of a model municipal landfill study site operated by the United States Geological Survey. The alluvial aquifer underlying the now closed landfill will serve as a backdrop for many of the exercises conducted in the short course. It provides an excellent opportunity to study the spatial variability associated with various biogeochemical processes and samples from the aquifer can be used to investigate the metabolic fate of contaminants under defined redox conditions. The lessons learned from studying the landfill will be extrapolated to at least one other system. To that end, we are in contact with the Nature Conservancy to obtain access to the tallgrass prairie, the largest protected remnant of tallgrass prairie left on earth. Oil and gas collection and separation facilities are common on the preserve and several examples of associated environmental problems are known. There is ongoing hydrocarbon biodegradation research on preserve property so there is the opportunity to avoid some of the sensitivities typically associated with approaching energy producing industries. The students will investigate oil field issues such as corroding pipelines or storage tanks or even historical environmental releases of petroleum. The students will thus relate their findings to real environmental issues and at the same time, learn how energy is produced, transported, stored, used, and occasionally spilled in modern society.The course will cover multiple topics in environmental biotechnology. This includes chemical, microbiological, and molecular analyses of sediments and/or waters, contaminant assessment, enrichment culture establishment, gene probing, PCR amplification, cloning, microbe identification based on 16S rRNA sequence determination, metabolite profiling, and microarray analyses. Each of these topics is explained in more detail in the next section. This proposal contains a list of objectives with a time line to show what the students will be doing each day as well as how the experiments interrelate to one another. It is envisioned that each day will begin with a 30 to 60 minute lecture by one of the instructors, covering the principles behind the experiments for that day. A seminar will be held at the end of the day by a distinguished scientist, covering a research area related to what the students are doing in the course. This scientist will then have dinner and spend the evening and the next morning with the students to promote interaction and discussions.
The course will focus on alkanes as a model substrate for investigating and illustrating biodegradative processes. This group of hydrocarbons is chosen as a model substrate for the following reasons: (1) there is a considerable knowledge base related to alkane biodegradation both in natural and in engineered systems; (2) alkanes are quantitatively the most numerous hydrocarbons, are regularly released in the environment and are amenable to microbial attack under a variety of terminal electron accepting conditions, (3) the course instructors have extensive experience investigating alkane biodegradation, both in the laboratory as well as in the field; (4) existing enrichments and pure cultures are available to ensure the success of the course exercises and (5) the objectives and tasks outlined for this two week course can be accomplished using a readily degradable and relative water soluble alkane such as hexane as a model substrate. It should be noted, however, that the course will not focus exclusively on alkanes. The principles of biodegradation transcend the particular model substrates we may employ. The distinguished guest scientists who will be invited as seminar speakers and will serve as consultants to the students will be asked to present issues of biodegradability in complex environmental matrices related to other groups of hydrocarbons and even other environmental contaminants, such as halogenated solvents, highly chlorinated dioxins, and nitroaromatic compounds, to name a few.
Rationale
The Specific Aim of this course is to train molecular
microbiologists and microbial ecologists in state-of-the art techniques in
biodegradation research and in situ bioremediation. In order to accomplish this
Course Directors have structured the course to include a mixture of
field-related and laboratory-related exercises. In the laboratory, the students
will learn through a combination of practical lectures, hands-on exercises that
introduce the techniques of molecular biology as applied to environmental
matrices, and one-on-one consultation with distinguished experts in the field of
environmental microbiology and biotechnology. Having a national research site
within two miles of the laboratory allows students the luxury of hands on
sampling, and if mistakes are made or samples lost, the prospect of redoing the
exercise is realistic.
The course instructors are eminently well-qualified to organize and coordinate a
Theoretical and Practical Course on Molecular Approaches for In Situ
Biodegradation. They are experts in the topics to be covered, having published
extensively in the fields of molecular biology, biodegradation, environmental
microbiology, environmental biochemistry, and bioremediation, and they have had
extensive experience as teachers and consultants. In addition, all instructors
have had significant experience in on-site field remediation activities.