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Abstracts of Recent Publications
001 - Aubrey D.N.J. de Grey , Pedro J.J. Alvarez , Roscoe O. Brady, Ana Maria Cuervo, W. Gray Jerome, Perry L. McCarty, Ralph A. Nixon, Bruce E. Rittmann and Janet R. Sparrow (Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK). Medical bioremediation: Prospects for the application of microbial catabolic diversity to aging and several major age-related diseases. Ageing Research Reviews, 4 (2005), 315-338.
Several major diseases of old age, including atherosclerosis, macular degeneration and neurodegenerative diseases are associated with the intracellular accumulation of substances that impair cellular function and viability. Moreover, the accumulation of lipofuscin, a substance that may have similarly deleterious effects, is one of the most universal markers of aging in postmitotic cells. Reversing this accumulation may thus be valuable, but has proven challenging, doubtless because substances resistant to cellular catabolism are inherently hard to degrade. We suggest a radically new approach: augmenting humans' natural catabolic machinery with microbial enzymes. Many recalcitrant organic molecules are naturally degraded in the soil. Since the soil in certain environments - graveyards, for example - is enriched in human remains but does not accumulate these substances, it presumably harbours microbes that degrade them. The enzymes responsible could be identified and engineered to metabolise these substances in vivo. Here, we survey a range of such substances, their putative roles in age-related diseases and the possible benefits of their removal. We discuss how microbes capable of degrading them can be isolated, characterised and their relevant enzymes engineered for this purpose and ways to avoid potential side-effects.
Keywords: Aggregates; Lysosomes; Bioremediation; Bacteria; Catabolism; Atherosclerosis; Neurodegeneration; Maculardegeneration.

002- Kevin B. Hallberg and D. Barrie Johnson (School of Biological Sciences, Memorial Building, Deiniol Road, Bangor, LL57 2UW, UK).Microbiology of a wetland ecosystem constructed to remediate mine drainage from a heavy metal mine. Science of the Total Environment, 338 (2005), 53-66.
A pilot passive treatment plant (PPTP) was constructed to evaluate the potential of a composite wetland system to remediate acidic, metal-rich water draining the former Wheal Jane tin, in Cornwall, England. The treatment plant consists of three separate and controllable composite systems, each of which comprises a series of aerobic wetlands for iron oxidation and precipitation, a compost bioreactor for removing chalcophilic metals and to generate alkalinity, and rock filter ponds for removing soluble manganese and organic carbon. To understand the roles of microorganisms in remediating acid mine drainage (AMD) in constructed wetland ecosystems, populations of different groups of cultivatable acidophilic microbes in the various components of the Wheal Jane PPTP were enumerated over a 30-month period. Initially, moderately acidophilic iron-oxidising bacteria (related to Halothiobacillus neapolitanus) were found to be the major cultivatable microorganisms present in the untreated AMD, though later heterotrophic acidophiles emerged as the dominant group, on a numerical basis. Culturable microbes in the surface waters and sediments of the aerobic wetlands were similarly dominated by heterotrophic acidophiles, though both moderately and extremely acidophilic iron-oxidising bacteria were also present in significant numbers. The dominant microbial isolate in waters draining the anaerobic compost bioreactors was an iron- and sulfur-oxidising moderate acidophile that was closely related to Thiomonas intermedia. The acidophiles enumerated at the Wheal Jane PPTP accounted for 1% to 25% of the total microbial population. Phylogenetic analysis of 14 isolates from various components of the Wheal Jane PPTP showed that, whilst many of these bacteria were commonly encountered acidophiles, some of these had not been previously encountered in AMD and AMD-impacted environments.
Keywords: Acid mine drainage; Acidophiles; Bioremediation; Iron-oxidising bacteria; Sulfur-oxidising bacteria; Wetland; Wheal Jane.

003- Michael Kube1, Alfred Beck1, Stephen H Zinder2, Heiner Kuhl1, Richard Reinhardt1 & Lorenz Adrian3 (1 Max-Planck-Institut für Molekulare Genetik, Ihnestr. 63-73, 14195 Berlin-Dahlem, Germany, 2 Dept. of Microbiology, Cornell University, 272 Wing Hall, Ithaca, New York 14853, USA. 3 FG Technische Biochemie, Technische Universität Berlin, Seestr. 13, 13353 Berlin, Germany.ld be addressed to Lorenz Adrian, E-mail:lorenz.adrian@tu-berlin.de). chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nature Biotechnology, 23(2005), 1269-1273.
Dehalococcoides species are strictly anaerobic bacteria, which catabolize many of the most toxic and persistent chlorinated aromatics and aliphatics by reductive dechlorination and are used for in situ bioremediation of contaminated sites. Our sequencing of the complete 1,395,502 base pair genome of Dehalococcoides strain CBDB1 has revealed the presence of 32 reductive-dehalogenase-homologous (rdh) genes, possibly conferring on the bacteria an immense dehalogenating potential. Most rdh genes were associated with genes encoding transcription regulators such as two-component regulatory systems or transcription regulators of the MarR-type. Four new paralog groups of rdh-associated genes without known function were detected. Comparison with the recently sequenced genome of Dehalococcoides ethenogenes strain 195 reveals a high degree of gene context conservation (synteny) but exceptionally high plasticity in all regions containing rdh genes, suggesting that these regions are under intense evolutionary pressure.

004- Greer E. Noonburg and MD. Dr. Noonburg is (Orthopaedic Surgeon, Memorial Health University Physicians, Savannah, GA). Management of Extremity Trauma and Related Infections Occurring in the Aquatic Environment. Journal of the American Academy of Orthope- rdic Surgrons, 13 (2005) 4,243-253.
Wounds sustained in oceans, lakes, and streams are exposed to a milieu of bacteria rarely encountered in typical land-based injuries. These include Vibrio species, Aeromonas hydrophila, Pseudomonas and Plesiomonas species, Erysipelothrix rhusiopathiae, Mycobacterium marinum, and other microbes. Failure to recognize and treat these less common pathogens in a timely manner may result in significant morbidity or death. Initial antibiotic therapy should address common gram-positive and gram-negative aquatic bacteria, depending on the environment. Trauma occurring in brackish or salt water should be treated with doxycycline and cefiazidime, or a fluoroquinolone (eg, ciprofloxacin or levofloxacin). Freshwater wounds should be managed with ciprofloxacin, levofloxacin, or a third- or fourth- generation cephalosporin (eg, ceftazidime). Injuries sustained in a marine or freshwater environment may result from bites or venomous stings of aquatic organisms as well as from accidental trauma. Musculoskeletal trauma caused by venomous underwater species (eg, stingrays, stinging fish, sea urchins, and coral) requires immediate neutralization of the heat-labile toxin with immersion in nonscalding water for 30 to 90 minutes. Appropriate management of aquatic wounds requires recognition of the mechanism of injury, neutralization of venom, antibiotic administration, radiographic assessment, surgical debridement with irrigation, wound cultures, and structural repair or amputation as indicated by the severity of the injury.
Keywords: Vibrio, Aeromonas hydrophila, Pseudomonas, Plesfomonas, Mycobacterium marinum, Microbes

005- Simcha Stroes-Gascoynea. and Julia M. WestbMicrobial studies in the Canadian nuclear fuel waste management program(Atomic Energy of Canada Limited, Whiteshell Laboratories, Pinawa, Manitoba ROElLO, Canada, British Geological Survey, Keyworth, Nottingham, UK). FEMS Microbiology Reviews, 20 (1997),3-4573-590.
Atomic Energy of Canada Limited (AECL) has developed a concept for pernlanent geological disposal of used nuclear fuel in Canada. This concept, based on a multibarrier system, wo~ld involve disposal of nuclear fuel waste in titanium or copper containers, surrounded by compacted clay-based buffer and backfill materials, in a vault 500 I 000 m deep in granitic rock of the Canadian Shield. Subsurface environments will not be sterile and an experimental program was initiated in 1991 by AECL to address and quantify the potential effects of microbial action on the integrity of the disposal vault. This microbial program focuses on answering specific questions in areas such as the survival of bacteria in compacted clay-based buffer materials under relevant radiation, temperature and desiccation conditions; mobility of microbes in compacted buffer materials; the potential for microbially influenced corrosion of containers; microbial gas production in backfill material; introduction of nutrients as a result of vault excavation and operation; the presence and activity of microbes in deep granitic groundwaters; and the effects of biofilms on radionuclide migration in the geosphere. This paper summarizes the results to date from the research activities at AECL.
Keywords: Nuclear waste disposal; Radiation and desiccation effects; Microbially influenced corrosion; Radionuclide migration; Gas production.

006- Om V. Singh and Nagathihalli S. Nagaraj (Park 316, 600 N. Wolfe St, Baltimore, MD 21209, USA. Tel: 410-614-1804; Fax: 410-955-1030; E-mail: osingh1@jhmi.edu ; ovs11@yahoo.com).Transcriptomics, proteomics and interactomics: unique approaches to track the insights of bioremediation Briefings in Functional Genomics and Proteomics, 4 (2006), 355-362.
Microbial mediated bioremediation has a great potential to effectively restore contaminated environment, but the lack of information about factors regulating the growth and metabolism of various microbial communities in polluted environment often limits its implementation. Newly seeded techniques such as transcriptomics, proteomics and interactomics offer remarkable promise as tools to address longstanding questions regarding the molecular mechanisms involved in the control of mineralization pathways. During mineralization, transcript structures and their expression have been studied using high-throughput transcriptomic techniques with microarrays. Generally however, transcripts have no ability to operate any physiological response; rather, they must be translated into proteins with significant functional impact. These proteins can be identified by proteomic techniques using powerful two-dimensional polyacrylamide gel electrophoresis (2-DE). Towards the establishment of functional proteomics, the current advances in mass spectrometry (MS) and protein microarrays play a central role in the proteomics approach. Exploring the differential expression of a wide variety of proteins and screening of the entire genome for proteins that interact with particular mineralization regulatory factors would help us to gain insights into bioremediation.
Keywords: bioremediation, transcriptomics, proteomics, interactomics, pollutants, environmental cleanup.

007- Sara Di Toro, Giulio Zanaroli and Fabio Fava (DICASM, Faculty of Engineering, Alma Mater Studiorum-University of Bologna, Viale Risorgimento 2, I-40136 Bologna, Italy). Intensification of the aerobic bioremediation of an actual site soil historically contaminated by polychlorinated biphenyls (PCBs) through bioaugmentation with a non acclimated, complex source of microorganisms. Microbial Cell Factories, 5 (2006), 11.
The biotreatability of actual-site polychlorinated biphenyl (PCB)-contaminated soils is often limited by their poor content of autochthonous pollutant-degrading microorganisms. In such cases, inoculation might be the solution for a successful bioremediation. Some pure and mixed cultures of characterized PCB degrading bacteria have been tested to this purpose. However, several failures have been recorded mostly due to the inability of inoculated microbes to compete with autochthonous microflora and to face the toxicity and the scarcity of nutrients occurring in the contaminated biotope. Complex microbial systems, such as compost or sludge, normally consisting of a large variety of robust microorganisms and essential nutrients, would have better chances to succeed in colonizing degraded contaminated soils. However, such sources of microorganisms have been poorly applied in soil bioremediation and in particular in the biotreatment of soil with PCBs. Thus, in this study the effects of Enzyveba, i.e. a consortium of non-adapted microorganisms developed from composted material, on the slurry- and solid-phase aerobic bioremediation of an actual-site, aged PCB-contaminated soil were studied

008- Yuji Aso, Yukiko Miyamoto, Karen Mine Harada, Keiko Momma, Shigeyuki Kawai, Wataru Hashimoto, Bunzo Mikami & Kousaku Murata (Laboratory of Basic and Applied Molecular Biotechnology & Laboratory of Food Quality Design and Development, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan. E-mail: kmurata@kais.kyoto-u.ac.jp).Engineered membrane superchannel improves bioremediation potential of dioxin-degrading bacteria. Nature Biotechnology, 24(2006), 188-189.
Sphingomonas sp. A1 possesses specialized membrane structures termed 'superchannels' that enable the direct incorporation of macromolecules into the cell. We have engineered two related sphingomonads, the dioxin-degrading S. wittichii RW1 and the polypropylene glycol-degrading S. subarctica IFO 16058T, to incorporate this superchannel into their cell membranes. In both cases the bioremediation capability of the organisms was substantially increased pointing at the potential of this approach as a general strategy to improve bacterial degradation of hazardous compounds in the environment

009- Cindy H. Wu, Thomas K. Wood, Ashok Mulchandani, and Wilfred Chen (Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521. E-mail: Wilfred@engr.ucr.edu). Engineering Plant-Microbe Symbiosis for Rhizoremediation of Heavy Metals. Applied and Environmental Microbiology, 72 (2006), 1129-1134.
The use of plants for rehabilitation of heavy-metal-contaminated environments is an emerging area of interest because it provides an ecologically sound and safe method for restoration and remediation. Although a number of plant species are capable of hyper accumulation of heavy metals, the technology is not applicable for remediating sites with multiple contaminants. A clever solution is to combine the advantages of microbe-plant symbiosis within the plant rhizosphere into an effective cleanup technology. We demonstrated that expression of a metal-binding peptide (EC20) in a rhizobacterium, Pseudomonas putida 06909, not only improved cadmium binding but also alleviated the cellular toxicity of cadmium. More importantly, inoculation of sunflower roots with the engineered rhizobacterium resulted in a marked decrease in cadmium phytotoxicity and a 40% increase in cadmium accumulation in the plant root. Owing to the significantly improved growth characteristics of both the rhizobacterium and plant, the use of EC20-expressing P. putida endowed with organic-degrading capabilities may be a promising strategy to remediate mixed organic-metal-contaminated sites
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