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Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments

Description: The aim of this study was to enrich and identify psychrotolerant phenanthrenedegrading bacteria from polluted Baltic Sea sediments. Polyaromatic hydrocarbon (PAH)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the DNA of replicating cells. The bromodeoxyuridine-incorporated DNA was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16S rRNA gene cloning and sequencing to identify bacterial populations that were growing. In addition, degradation genes were quantified in the bromodeoxyuridine-incorporated DNA by real-time PCR. Phenanthrene concentrations decreased after 2 months of incubation in the phenanthrene-enriched sediments and this reduction correlated to increases in copy numbers of xylE and phnAc dioxygenase genes. Representatives of Exiguobacterium, Schewanella,Methylomonas, Pseudomonas, Bacteroides and an uncultured Deltaproteobacterium and a Gammaproteobacterium dominated the growing community in the phenanthrene spiked sediments. Isolates that were closely related to three of these bacteria (two pseudomonads and an Exiguobacterium sp.) could reduce phenanthrene concentrations in pure cultures and they all harbored phnAc dioxygenase genes. These results confirm that this combination of culture-based and molecular approaches was useful for identification of actively growing bacterial species with a high potential for phenanthrene degradation.
Date: May 1, 2008
Creator: Edlund, A. & Jansson, J.
Partner: UNT Libraries Government Documents Department

Mn, Fe, Zn and As speciation in a fast-growing ferromanganese marine nodule

Description: The speciation of Mn, Fe, As and Zn in a fast-growing (0.02mm/yr), shallow-marine ferromanganese nodule has been examined by micro X-ray fluorescence, micro X-ray diffraction, and micro X-ray absorption spectroscopy. This nodule exhibits alternating Fe-rich and Mn-rich layers reflecting redox variations in water chemistry. Fe occurs as two-line ferrihydrite. The As is strictly associated with Fe and is mostly pentavalent, with an environment similar to that of As sorbed on or coprecipitated with synthetic ferrihydrite. The Mn is in the form of turbostratic birnessite with {approx} 10 percent trivalent manganese in the layers and probably {approx} 8 percent corner-sharing metal octahedra in the interlayers. The Zn is enriched on the rim of the nodule, associated with Mn. The Zn is completely (>90 percent) tetrahedrally coordinated and sorbed in the interlayers of birnessite on vacant layer Mn sites. The Zn and Mn species are similar to ones found in soils, suggesting common structural principles, despite the differing formation conditions in these systems.
Date: April 1, 2004
Creator: Marcus, Matthew A.; Manceau, Alain & Kersten, Michael
Partner: UNT Libraries Government Documents Department

Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

Description: Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179 mV, -64 mV and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labeled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labeled DNA and DNA from reverse transcription PCR (rt-PCR) showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.
Date: May 15, 2008
Creator: Jansson, Janet; Edlund, Anna; Hardeman, Fredrik; Jansson, Janet K. & Sjoling, Sara
Partner: UNT Libraries Government Documents Department

A Novel Chemical Nitrate Destruction Process

Description: Nitrates represent one of the most significant pollutant discharged to the Baltic Sea by the Sliiamae hydrometallurgical plant. This article contains a brief overview of the existing nitrate destruction technologies followed by the description of a new process developed by the authors. The new chemical process for nitrate destruction is cost effective and simple to operate. It converts the nitrate to nitrogen gas which goes to the atmosphere.
Date: March 1, 1999
Creator: Dziewinski, J. & Marczak, S.
Partner: UNT Libraries Government Documents Department

Krafting an agreement: Negotiations to reduce pollution from the Nordic pulp industry, 1985--1989

Description: International environmental accords frequently contain obligations that may be easily satisfied by their signatories. Observers have speculated why it is in a state`s interests to sign agreements that lack strict conditions, but policy analysts lack a coherent model explaining how such agreements are formalized. Knowledge, values, and authority are key forces that elucidate how environmental accords are developed with provisions that are easily executable. This dissertation examines the formulation of Helsinki Commission recommendations to reduce emissions of organochlorines from Nordic kraft pulp mills. The kraft pulp industry, the largest industrial pollution emitter to the Baltic Sea, is also a crucial foreign exchange earner for both Sweden and Finland. Hence, Swedes and Finns were the most active participants in regional negotiations to reduce organochlorine emissions. Key variable analysis explains how obstacles in various regional negotiations were overcome, and how parties constructed a recommendation with obligations that could be easily accommodated. The two sides never agreed about the level of risk posed by organochlorines in the marine environment. This problem influenced the strictness of pollution limits specified in the final agreement. But, the parties overcame formidable obstacles in the negotiations, including: (1) concerns about costs to industry and competitive disadvantages in the pulp and paper sector; (2) disagreement about technologies to combat the problem; and (3) domestic rule-making schedules that were out of sync.
Date: May 1, 1996
Creator: Auer, M.R.
Partner: UNT Libraries Government Documents Department

Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

Description: Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.
Date: May 17, 2010
Creator: Wu, Liyou; Yi, T. Y.; Van Nostrand, Joy & Zhou, Jizhong
Partner: UNT Libraries Government Documents Department