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Endosymbiosis In Statu Nascendi: Close Phylogenetic RelationshipBetween Obligately Endosymbiotic and Obligately Free-LivingPolynucleobacter Strains (Betaproteobacteria)

Description: Bacterial strains affiliated to the phylogenetically shallowsubcluster C (PnecC) of the 28 Polynucleobacter cluster, which ischaracterized by a minimal 16S rRNA gene sequence similarity of approx.98.5 percent, have been reported to occur as obligate endosymbionts of 30ciliates (Euplotes spp.), as well as to occur as free-living cells in thepelagic zone of freshwater habitats. We investigated if these two groupsof closely related bacteria represent 32 strains fundamentally differingin lifestyle, or if they simply represent different stages of afacultative endosymbiotic lifestyle. The phylogenetic analysis of 16SrRNA gene and 16S34 23S ITS sequences of five endosymbiont strains fromtwo different Euplotes species and 40 pure culture strains demonstratedhost-species-specific clustering of the endosymbiont 36 sequences withinthe PnecC subcluster. The sequences of the endosymbionts showedcharacteristics indicating an obligate endosymbiotic lifestyle.Cultivation experiments 38 revealed fundamental differences inphysiological adaptations, and determination of the genome sizesindicated a slight size reduction in endosymbiotic strains. We concludethat the 40 two groups of PnecC bacteria represent obligately free-livingand obligately endosymbiotic strains, respectively, and do not representdifferent stages of the same complex lifecycle. 42 These closely relatedstrains occupy completely separated ecological niches. To our bestknowledge, this is the closest phylogenetic relationship between obligateendosymbionts and 44 obligately free-living bacteria everrevealed.
Date: July 21, 2006
Creator: Vannini, Claudia; Pockl, Matthias; Petroni, Giulio; Wu, Qinglong; Lang, Elke; Stackebrandt, Erko et al.
Partner: UNT Libraries Government Documents Department

Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community

Description: Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.
Date: February 15, 2010
Creator: Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.; Fields, Matthew W.; Wu, Liyou; Barua, Soumitra et al.
Partner: UNT Libraries Government Documents Department

Adaptation of the Biolog Phenotype MicroArrayTM Technology to Profile the Obligate Anaerobe Geobacter metallireducens

Description: The Biolog OmniLog? Phenotype MicroArray (PM) plate technology was successfully adapted to generate a select phenotypic profile of the strict anaerobe Geobacter metallireducens (G.m.). The profile generated for G.m. provides insight into the chemical sensitivity of the organism as well as some of its metabolic capabilities when grown with a basal medium containing acetate and Fe(III). The PM technology was developed for aerobic organisms. The reduction of a tetrazolium dye by the test organism represents metabolic activity on the array which is detected and measured by the OmniLog(R) system. We have previously adapted the technology for the anaerobic sulfate reducing bacterium Desulfovibrio vulgaris. In this work, we have taken the technology a step further by adapting it for the iron reducing obligate anaerobe Geobacter metallireducens. In an osmotic stress microarray it was determined that the organism has higher sensitivity to impermeable solutes 3-6percent KCl and 2-5percent NaNO3 that result in osmotic stress by osmosis to the cell than to permeable non-ionic solutes represented by 5-20percent ethylene glycol and 2-3percent urea. The osmotic stress microarray also includes an array of osmoprotectants and precursor molecules that were screened to identify substrates that would provide osmotic protection to NaCl stress. None of the substrates tested conferred resistance to elevated concentrations of salt. Verification studies in which G.m. was grown in defined medium amended with 100mM NaCl (MIC) and the common osmoprotectants betaine, glycine and proline supported the PM findings. Further verification was done by analysis of transcriptomic profiles of G.m. grown under 100mM NaCl stress that revealed up-regulation of genes related to degradation rather than accumulation of the above-mentioned osmoprotectants. The phenotypic profile, supported by additional analysis indicates that the accumulation of these osmoprotectants as a response to salt stress does not occur in G.m. and response to stress must occur by other ...
Date: May 17, 2010
Creator: Joyner, Dominique; Fortney, Julian; Chakraborty, Romy & Hazen, Terry
Partner: UNT Libraries Government Documents Department

Earth Sciences Division Research Summaries 2002-2003

Description: Research in earth and atmospheric sciences is becoming increasingly important in light of the energy, climate change, and environmental issues facing the United States and the world. The development of new energy resources other than hydrocarbons and the safe disposal of nuclear waste and greenhouse gases (such as carbon dioxide and methane) are critical to the future energy needs and environmental safety of this planet. In addition, the cleanup of many contaminated sites in the U.S., along with the preservation and management of our water supply, remain key challenges for us as well as future generations. Addressing these energy, climate change, and environmental issues requires the timely integration of earth sciences' disciplines (such as geology, hydrology, oceanography, climatology, geophysics, geochemistry, geomechanics, ecology, and environmental sciences). This integration will involve focusing on fundamental crosscutting concerns that are common to many of these issues. A primary focus will be the characterization, imaging, and manipulation of fluids in the earth. Such capabilities are critical to many DOE applications, from environmental restoration to energy extraction and optimization. The Earth Sciences Division (ESD) of the Ernest Orlando Lawrence Berkeley National Laboratory (Berkeley Lab) is currently addressing many of the key technical issues described above. In this document, we present summaries of many of our current research projects. While it is not a complete accounting, it is representative of the nature and breadth of our research effort. We are proud of our scientific efforts, and we hope that you will find our research useful and exciting. Any comments on our research are appreciated and can be sent to me personally. This report is divided into five sections that correspond to the major research programs in the Earth Sciences Division: (1) Fundamental and Exploratory Research; (2) Nuclear Waste; (3) Energy Resources; (4) Environmental Remediation Technology; and (5) ...
Date: November 1, 2003
Creator: Bodvarsson, G.S.
Partner: UNT Libraries Government Documents Department

Development And Evaluation Of Stable Isotope And Fluorescent Labeling And Detection Methodologies For Tracking Injected Bacteria During In Situ Bioremediation

Description: This report summarizes the results of a research project conducted to develop new methods to label bacterial cells so that they could be tracked and enumerated as they move in the subsurface after they are introduced into the groundwater (i.e., during bioaugmentation). Labeling methods based on stable isotopes of carbon (13C) and vital fluorescent stains were developed. Both approaches proved successful with regards to the ability to effectively label bacterial cells. Several methods for enumeration of fluorescently-labeled cells were developed and validated, including near-real time microplate spectrofluorometry that could be performed in the field. However, the development of a novel enumeration method for the 13C-enriched cells, chemical reaction interface/mass spectrometry (CRIMS), was not successful due to difficulties with the proposed instrumentation. Both labeling methodologies were successfully evaluated and validated during laboratory- and field-scale bacterial transport experiments. The methods developed during this research should be useful for future bacterial transport work as well as other microbial ecology research in a variety of environments. A full bibliography of research articles and meeting presentations related to this project is included (including web links to abstracts and full text reprints).
Date: December 17, 2003
Creator: Fuller, Mark E. & Onstott, Tullis C.
Partner: UNT Libraries Government Documents Department