The Center has carried out an "industrial outreach" effort since its formation with funding from the Michigan Strategic Fund (MSF). Over this period, we have had numerous successes in bringing the expertise of Michigan State University into partnership with other sectors of the state economy: business, industry and government. As a part of this endeavor we have come to better understand how university resources, especially research centers, can contribute to technological and economic development. This process parallels a national trend to merge research and what is termed knowledge transfer into an integrated program that not only develops new information, but actively disseminates it and facilitates its use. In addition, by engaging researchers in the knowledge transfer process, they are better able to target their research on the needs of users, and ultimately, of society. The overriding goal is to expedite the process whereby the nation benefits from scientific discoveries as they are translated into new products and services in the marketplace, and a stronger scientific foundation for political decision-making.
1. Bioremediation. The Schoolcraft bioaugmentation effort has successfully completed its third phase which was a full-scale field research and demonstration project. The approach was to use a biocurtain colonized by Pseudomonas stutzeri KC through which the carbon tetrachloride contaminant plume passed. Closely spaced wells were used for tracer studies, base addition to achieve the correct pH level, inoculation, and for weekly introduction of substrates to sustain long-term degradation of carbon tetrachloride. Carbon tetrachloride was removed to regulatory levels. The next phase is to test a cheap means of introducing the electron donor, especially to reduce operation personnel costs. Use of a solid carbon source will be tested in 1999.
A pilot scale evaluation of the use of slow release solid phase nutrient(s) to support bioaugmentation with Pseudomonas stutzeri strain KC was also conducted at the Schoolcraft site. The inoculum, a carbon source (vegetable shortening), a phosphate source and the base (NaOH) needed for pH adjustment were absorbed into the pore space of heat fractured clay beads (hydroponic plant growth media). This mixture was then packed with # 5 drilling sand into nylon sachets and introduced directly into the saturated, CT contaminated zone by drilling with oversized augers to the impacted depth of the aquifer, gravity dropping the sachets around a 4" well and then removing the augers. This resulted in the formation of a PKC colonized bed, containing required nutrients surrounding a well. Two of these beds were created 5 ft apart, normal to the aquifer flow, and spanning 20 ft vertical height. Nutrients and base to sustain 60 days of operation were contained in the beds, and an above ground system to deliver supplemental nutrients was constructed. Within 24 days of inoculation, CT levels had decreased downstream of the treatment zone by approximately 40%. The maximum CT degradation (50-60%) was observed 60 days after inoculation, at which point the solid phase base began to be depleted. Liquid phase addition of base, acetate and a liquid phase re-inoculation are planned for the final 6 months of this experiment.
The Schoolcraft CT evaluation is completing the last six months of a 4 year Michigan Department of Environmental Quality supported field trial. The plume, however is but one of the nine contaminant plumes located in the vicinity of Schoolcraft, MI. Two of the contaminant plumes, Plume G (PCE/TCE) and Plume F (hexavalent chromium and arsenic) are co-mingled and present a mixed waste treatment challenge. Working with the MDEQ a two year study of remediation options for these plumes will be conducted. Intrinsic remediation, biostimulation of reducing conditions and dechlorinators, bioaugmentation with halorespiring microbes and biological generation of reducing conditions for chromium fixation will be evaluated in a series of laboratory and pilot field tests.
The Bachman Road site in Oscoda, Michigan - on the shore of Lake Huron - has ground water contaminated with chlorinated ethenes and petroleum hydrocarbons in four separate plumes. CME, in collaboration with the University of Michigan's (UM) Hazardous Substance Research Center, has been contracted by the state of Michigan Department of Environmental Quality to evaluate the effectiveness of innovative technologies for the remediation of chlorinated ethenes. Phase I, funded at $800,000, was successfully completed in early 1999 and a Phase II site characterization and pilot scale design and testing is underway. CME personnel are responsible for leading microbial halorespiration studies in cooperation with UM project-members, Peter Adriaens and Babu Fathepure. EFX, a bioremediation company, is involved in the challenging task of scaling up the production of the anaerobic halorespiring organisms. This technology and know-how is critical to transitioning chloroethene respiration to commercial practice.
We have been informed of acceptance of our proposal for a project involving an industrial brine pond with approximately one million cubic yards of sediments containing hydrates of iron oxide, iron chlorates, iron chlorides, calcium chlorides, and magnesium hydroxide. The pond water varies between 1 and 3% total dissolved solids (TDS), a salt concentration too high for most aquatic plants and wildlife. We have proposed to devise a diffusive barrier to reduce salt release, control hydraulic flushing and construct a salt-tolerant wetland ecosystem. It is estimated that this approach will reduce closure costs by 50 to 90%. Critical research issues involve the development of low-cost diffusion barriers, how to establish and maintain a functional and diverse ecosystem with sufficient salt-tolerance, and whether the system can tolerate occasional inputs of carbon, nutrients, and metals if the hydraulic regime involves use of the system as a municipal combined sewer overflow (CSO) equilization basin. Work is expected to begin this fall.
Additional activities in the bioremediation portion of the knowledge transfer program of the center include regular consultation with representatives of all the major economic and political sectors on site contamination and remediation issues. We have regular interaction with the State of Michigan, Department of Environmental Quality, Emergency Response Division on the technical aspects of regulatory issues. We have provided advice on how the current state of scientific understanding affects both the need for new regulations and interpretation of existing regulations. We have also worked with industrial, consulting and other governmental concerns. In coordination with the Great Lakes and Mid-Atlantic Center for Hazardous Substance Research, we have worked with communities having hazardous waste problems, with federal and regional EPA officials involved in community involvement, and municipal officials under interested in "brownfields redevelopment" projects.
2. Microbial Informatics. Technical Publishing Activities - During the third quarter of 1999, Bergey's Manual Trust and Springer-Verlag, NY entered into a long term agreement to publish the Second Edition of Bergey's Manual of Systematic Bacteriology in print and electronic form. An essential component of the agreement was the use of SGML (standard generalized markup language) and XML (extended markup language) to make the content more manageable and reusable in the future. Although SGML/XML have not been widely used in the production of scientific publications to date, adoption of this approach was based on two fundamental points. First, SGML is widely used in the production and maintenance of complex technical documents in the automotive, aerospace, telecommunications and computer industries, thus, there is a wealth of expertise that can be drawn upon to expedite usage in the scientific arena. Secondly, SGML is an industry standard and development is governed by international working groups/committees that guarantee both software and hardware independence. This latter point is critical to ensure that our information remains usable and accessible in the future. This technology also allows the publication in a variety of formats (print, custom print editions, CD-ROM, and web based versions) with little or no further modification of the underlying content. It also makes our content more accessible to end-users as the search space can be limited to a defined set of tags that have predefined microbiological relevance (eg. gene sequences, phenotypic characteristics, ecological information, nomenclature, etc).
Collaborative work (Bergey's Manual Trust, Springer-Verlag and Mulberry Technologies) on developing an open, XML compliant document type definition (DTD) began during the fourth quarter of 1998 and was completed by the second quarter of 1999. In the first version of the DTD, approximately 250 elements and attributes were defined that are specific to our scientific domain. Tagging of manuscripts from the first volume began in April of 1999 and the first set of galley proofs were produced in September. Work on the first volume will be competed by the end 1999 with publication scheduled for March 2000 (ISBN 0-387-987771-1). Funding for this activity is provided through publication royalties and a pre-publication grant from Springer-Verlag to Bergey's Manual Trust. Additional support, in the form of reduced license fees and software discounts have been provided by ArborText, Inc., Ann Arbor, MI. (SGML/XML editor, DTD editor) and Chrystal Software, San Diego, CA (SGML based document repository).
Updating the RDP - In conjunction with Bergey's publishing efforts, we have been actively collaborating with other faculty and staff affiliated with the Ribosomal Database Project at MSU. This database serves as one of the principal sources of aligned small ribosomal subunit sequences. As described in the 1998 annual report, the RDP is of special importance to Bergey's Manual Trust as it serves as the principal organizational device for our content and will, in turn, serve as a means for our world-wide readership to traverse the Second Edition of the Manual of Systematic Bacteriology. Over the past year Bergey's and RDP staff have been updating the sequence database, increasing the number of reference sequences by a factor of four (approximately 750 type strains to approximately 2800), and preparing small phylogenetic trees for presentation in print and electronic form. Funding for a portion of this activity was provided from the Michigan Strategic Fund to support RDP personnel and equipment costs.
B. Future Plans
1. Bioremediation. The following activities are planned for the balance of our funding cycle (MSF funding expires in June 2000). We will continue our emphasis on developing new remediation technologies using integrated field and laboratory, research and demonstration projects. We will do this by working with a variety of stakeholders - regulatory agencies, industries, consulting firms, and technology vendors - to identify sites, projects, and sources of funding where a collaborative effort will be beneficial to all participants. Three additional activities are also proposed under the remediation initiative. First, we will continue to work with State agencies in a consulting capacity on remediation issues. This will help ensure that cost-effective technologies are employed so that the need to address contamination does not place an unnecessary financial burden on site owners. Second, we will work with communities having hazardous substance problems to understand the issues and participate effectively in the decision-making process. This should serve to facilitate the remediation process and reduce the costly delays that result in highly adversarial situations. To do this we will work to integrate CME expertise with the existing GLMAC Technical Outreach Services to Communities (TOSC) program. Third, we will work with local government officials addressing brownfields redevelopment projects. It is our goal to provide technical assistance aimed at improving the scientific basis for environmental decisions affecting the development process. Critical in this regard are questions related to the effectiveness of natural attenuation and the risks associated with containment technologies. This will be accomplished in conjunction with the existing GLMAC Technical Assistance to Brownfields (TAB) program, and the newly-established Victor Institute for Responsible Land Development at MSU.
By the conclusion of the Industrial Outreach Program, we are seeking to have in place both the resources and institutional framework to continue and expand our remediation efforts. Tentatively designated the Environmental Experiment Station (EES) we envision an organization that will oversee a set of core laboratories that have broad capability to support field operations, perform high-volume, rapid-turn-around sample analysis, and conduct pilot testing of new technologies. These facilities will complement existing research laboratories and be dedicated to environmental technology development activities. In addition, EES would have expertise in the business aspects of technology development, in the form of staff who can provide assistance to technology development projects on issues of costs, market considerations, regulatory acceptance, and legal aspects. Under the current program, we have selected Dr. Michael Dybas, Co-lead Principal Investigator, to work with Dr. Voice to develop a full scientific and business plan for EES, and to develop funding sufficient to support core operations.
2. Bioinformatics. A new initiative has arisen from the Bergey's - RDP informatics collaboration: the creation of a fully annotated, hierarchical list of procaryotic taxa. Since 1980, the number of validly named procaryotic species has increased from 1742 to 4599. Furthermore, there have been a significant number of name changes, usually precipitated by phylogenetic studies. As of July 1999, there were 5298 valid names for the 4599 validly named species. In some instances, given species have borne three or more distinct names and at least one has undergone four name changes and currently bears the same name it began with more than ten years ago. While these changes are usually the result of significant new findings, they can lead to considerable confusion in the community at large. To that end, we have begun developing an XML compliant DTD that will provide the community with essential (sequence and culture collection accession numbers) in a concise and easily transported format. This DTD will also provide: a.) links to the suite of phylogenetic trees mentioned above and b.) links to synonyms and basonyms that so as to allow users to sequentially track name changes across time.
There is a pressing need for a list of this type that is carefully maintained and made freely available via the World Wide Web. For instance, it is not uncommon to find phylogenetic trees appearing in print bearing replicates of the same species under different names. Nomenclatural changes also have tremendous impact on many commercial activities that fall under the purview of various regulatory agencies (eg. D.O.T., Department of Commerce, the USDA, the US Post Office, the EPA, the FDA, the International Airline Transport Association, etc.). At present, we have already identified and confirmed over 22,000 culture collection deposits in 79 different repositories. We have also identified and confirmed almost 2800 16S rRNA sequences that are at least 1000 nucleotides long and contain less than 0.1% ambiguous data.
While this effort has taken somewhat longer than anticipated, it is clear that there is a need for scrupulously edited data in an electronic form. Clearly, the sequence databases do not provide adequate control over the quality of submitted data and many of the records are never updated by either the originators or the database managers. Furthermore, this information is not available during the editorial review process, thus we are now witnessing an accumulation of erroneous information in the peer-reviewed literature. To that end, we have reprioritized the scope of our collaborative work and available resources have been redirected to this support this project. Our objective is to distribute the first version of the annotated outline via the web, using XML capable browsers, by the first quarter of 2000. Outside support is being sought to sustain this activity as it is deemed critical to future efforts.
An Industrial Advisory Panel provides strategic guidance to the Center's research program. The panel includes representatives from large and small companies in various industrial sectors including Pharmacia-Upjohn, Envirogen, Dow, Immunom, 3M, Shell Oil, Nalco, Procter and Gamble, Delmonte, the U.S. Environmental Protection Agency, the Michigan Department of Environmental Quality, and the Michigan Strategic Fund.
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