Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog

The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, Minnesota, USA. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing, expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14-17 μmol CH4 g dry wt soil-1 d-1. Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25-36% after 8 -14 days. Phylogenetic analysis of the 13C-enriched DNA fractions revealed the active methanotrophs were dominated by the genera Methylocystis (Type II; Alphaproteobacteria), Methylomonas, and Methylovulum (Type I; Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers which attenuated rapidly with depth, indicating the highest methane consumption was associated with the 0-10 cm depth interval. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed the dominant active methanotrophs were Methylocystis and Methylomonas. Although Type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate members of the genera Methylomonas and Methylovulum (Type I) can significantly contribute to aerobic methane oxidation in these ecosystems

An Integrated Assessment of Geochemical and Community Structure Determinants of Metal Reduction Rates in Subsurface Sediments

Summary of Results to Date: Our current research represents a joint effort between Oak Ridge National Laboratory (ORNL), Florida State University (FSU), and the University of Tennessee. ORNL will serve as the lead institution with Dr. A.V. Palumbo responsible for project coordination, integration, and deliverables. This project was initiated in November, 2004, in the Integrative Studies Element of the NABIR program. The overall goal of our project is to provide an improved understanding of the relationships between microbial community structure, geochemistry, and metal reduction rates

An Integrated Assessment of Geochemical and Community Structure Determinants of Metal Reduction Rates in Subsurface Sediments

This project represented a joint effort between Oak Ridge National Laboratory (ORNL), the University of Tennessee (UT), and Florida State University (FSU). ORNL served as the lead in-stitution with Dr. A.V. Palumbo responsible for project coordination, integration, and deliver-ables. In situ uranium bioremediation is focused on biostimulating indigenous microorganisms through a combination of pH neutralization and the addition of large amounts of electron donor. Successful biostimulation of U(VI) reduction has been demonstrated in the field and in the laboratory. However, little data is available on the dynamics of microbial populations capable of U(VI) reduction, and the differences in the microbial community dynamics between proposed electron donors have not been explored. In order to elucidate the potential mechanisms of U(VI) reduction for optimization of bioremediation strategies, structure-function relationships of microbial populations were investigated in microcosms of subsurface materials cocontaminated with radionuclides and nitrate from the Oak Ridge Field Research Center (ORFRC), Oak Ridge, Tennessee

Impacts of Mineralogy and Competing Microbial Respiration Pathways on the Fate of Uranium in Contaminated Groundwater

This is a field-oriented project designed to elucidate the microbiological and geochemical factors controlling U(VI) reduction/immobilization in subsurface environments at the NABIR FRC. Efforts focused on acidic sediments, (1) to characterize the dominant minerals likely to limit U speciation, (2) to directly quantify microbial respiration processes controlling U subsurface chemistry, and (3) to identify and enumerate the responsible organisms. Results indicate that the activities and growth of bacteria are limited in this acidic subsurface. The relevant geochemical parameters have now been characterized, and respiration rates quantified

Biostimulation of Iron Reduction and Uranium Immobilization: Microbial and Mineralogical Controls

This project represented a joint effort between Florida State University (FSU), Rutgers University (RU), and the University of Illinois (U of I). FSU served as the lead institution and Dr. J.E. Kostka was responsible for project coordination, integration, and deliverables. This project was designed to elucidate the microbial ecology and geochemistry of metal reduction in subsurface environments at the U.S. DOE-NABIR Field Research Center at Oak Ridge, Tennessee (ORFRC). Our objectives were to: 1) characterize the dominant iron minerals and related geochemical parameters likely to limit U(VI) speciation, 2) directly quantify reaction rates and pathways of microbial respiration (terminal-electron-accepting) processes which control subsurface sediment chemistry, and 3) identify and enumerate the organisms mediating U(VI) transformation. A total of 31 publications and 47 seminars or meeting presentations were completed under this project. One M.S. thesis (by Nadia North) and a Ph.D. dissertation (by Lainie Petrie-Edwards) were completed at FSU during fall of 2003 and spring of 2005, respectively. Ph.D. students, Denise Akob and Thomas Gihring have continued the student involvement in this research since fall of 2004. All of the above FSU graduate students were heavily involved in the research, as evidenced by their regular attendance at PI meetings and ORFRC workshops

The bacterial composition within the Sarracenia purpurea model system: local scale differences and the relationship with the other members of the food web

The leaves of the carnivorous pitcher plant, Sarracenia purpurea, contain a microscopic aquatic food web that is considered a model system in ecological research. The species identity of the intermediate and top trophic level of this food web, as well the detritivore midge, are highly similar across the native geographic range of S. purpurea and, in some cases, appear to have co-evolved with the plant. However, until recently, the identity, geographic variation, and diversity of the bacteria in the bottom trophic level of this food web have remained largely unknown. This study investigated bacterial community composition inside the leaves of S. purpurea to address: 1) variation in bacterial communities at the beginning of succession at the local scale in different areas of the plant’s native geographic range (southern and mid-regional sites) and 2) the impacts of bacterial consumers and other members of the aquatic food web (i.e., insects) on bacterial community structure. Communities from six leaves (one leaf per plant) from New York and Florida study sites were analyzed using 16S ribosomal RNA gene cloning. Each pitcher within each site had a distinct community; however, there was more overlap in bacterial composition within each site than when communities were compared across sites. In contrast, the identity of protozoans and metazoans in this community were similar in species identity both within a site and between the two sites, but abundances differed. Our results indicate that, at least during the beginning of succession, there is no strong selection for bacterial taxa and that there is no core group of bacteria required by the plant to start the decomposition of trapped insects. Co-evolution between the plant and bacteria appears to not have occurred as it has for other members of this community

DBEndo: a web-based endodontic case management tool

BACKGROUND: The success of endodontic treatment depends-among many other factors-on good documentation. Paper-based records are often difficult to read or incomplete and commercially available tools focus on billing. An electronic record captures the state of treatment at all times. Databases are a common tool in everyday life. RESULTS: Here, we present a database created for the Charite-Universitatsmedizin Berlin, Germany. Through consistent digital documentation, data analytics of patients, root canal anatomies, instrumentation techniques, efficacy of chemical disinfection, root filling techniques, and corresponding recall success rates, which needed extensive research before, are now easy to perform. Tables and even graphics and data analystics are only one click away and can be exported to other programs. CONCLUSIONS: DBEndo is a database to store and visualise internally, as well as to share endodontic cases online. For academic use we provide the database including all forms and some anonymous data for free at: http://dbendo.charite.de . Through easy import and export of the data, the system is open and flexible

Decomposition of fractional quantum Hall states: New symmetries and approximations

We provide a detailed description of a new symmetry structure of the monomial (Slater) expansion coefficients of bosonic (fermionic) fractional quantum Hall states first obtained in Ref. 1, which we now extend to spin-singlet states. We show that the Haldane-Rezayi spin-singlet state can be obtained without exact diagonalization through a differential equation method that we conjecture to be generic to other FQH model states. The symmetry rules in Ref. 1 as well as the ones we obtain for the spin singlet states allow us to build approximations of FQH states that exhibit increasing overlap with the exact state (as a function of system size). We show that these overlaps reach unity in the thermodynamic limit even though our approximation omits more than half of the Hilbert space. We show that the product rule is valid for any FQH state which can be written as an expectation value of parafermionic operators.Comment: 22 pages, 8 figure