Contaminant Distributions at Typical U.S. Uranium Milling Facilities and Their Effect on Remedial Action Decisions

Past operations at uranium processing sites throughout the US have resulted in local contamination of soils and ground water by radionuclides, toxic metals, or both. Understanding the origin of contamination and how the constituents are distributed is a basic element for planning remedial action decisions. This report describes the radiological and nonradiological species found in ground water at a typical US uranium milling facility. The report will provide the audience with an understanding of the vast spectrum of contaminants that must be controlled in planning solutions to the long-term management of these waste materials

Effects of Experimental Choices and Analysis Noise on Surveys of the “Rare Biosphere”▿ †

When planning a survey of 16S rRNA genes from a complex environment, investigators face many choices including which primers to use and how to taxonomically classify sequences. In this study, we explored how these choices affected a survey of microbial diversity in a sample taken from the aerobic basin of the activated sludge of a North Carolina wastewater treatment plant. We performed pyrosequencing reactions on PCR products generated from primers targeting the V1-V2, V6, and V6-V7 variable regions of the 16S rRNA gene. We compared these sequences to 16S rRNA gene sequences found in a whole-genome shotgun pyrosequencing run performed on the same sample. We found that sequences generated from primers targeting the V1-V2 variable region had the best match to the whole-genome shotgun reaction across a range of taxonomic classifications from phylum to family. Pronounced differences between primer sets, however, occurred in the “rare biosphere” involving taxa that we observed in fewer than 11 sequences. We also examined the results of analysis strategies comparing a classification scheme using a nearest-neighbor approach to directly classifying sequences with a naïve Bayesian algorithm. Again, we observed pronounced differences between these analysis schemes in infrequently observed taxa. We conclude that if a study is meant to probe the rare biosphere, both the experimental conditions and analysis choices will have a profound impact on the observed results

Molecular Diversity of a North Carolina Wastewater Treatment Plant as Revealed by Pyrosequencing▿ †

We report the results of pyrosequencing of DNA collected from the activated sludge basin of a wastewater treatment plant in Charlotte, NC. Using the 454-FLX technology, we generated 378,601 sequences with an average read length of 250.4 bp. Running the 454 assembly algorithm over our sequences yielded very poor assembly, with only 0.3% of our sequences participating in assembly of significant contigs. Of the 117 contigs greater than 500 bp long that were assembled, the most common annotations were to transposases and hypothetical proteins. Comparing our sequences to known microbial genomes showed nonspecific recruitment, indicating that previously described taxa are only distantly related to the most abundant microbes in this treatment plant. A comparison of proteins generated by translating our sequence set to translations of other sequenced microbiomes shows a distinct metabolic profile for activated sludge with high counts for genes involved in metabolism of aromatic compounds and low counts for genes involved in photosynthesis. Taken together, these data document the substantial levels of microbial diversity within activated sludge and further establish the great utility of pyrosequencing for investigating diversity in complex ecosystems

Association Between Composition of the Human Gastrointestinal Microbiome and Development of Fatty Liver With Choline Deficiency

BACKGROUND & AIMS: Non-alcoholic fatty liver disease affects up to 30% of the U.S. population, but the mechanisms underlying this condition are incompletely understood. We investigated how diet standardization and choline deficiency influence the composition of the microbial community in the human gastrointestinal (GI) tract and the development of fatty liver under conditions of choline deficiency. METHODS: We performed a 2-month in-patient study of 15 female subjects who were placed on well-controlled diets in which choline levels were manipulated. We used 454-FLX pyrosequencing of 16S rRNA bacterial genes to characterize microbiota in stool samples collected over the course of the study. RESULTS: The compositions of the GI microbial communities changed with choline levels of diets; each individual’s microbiome remained distinct for the duration of the experiment, even though all subjects were fed identical diets. Variations between subjects in levels of Gammaproteobacteria and Erysipelotrichi were directly associated with changes in liver fat in each subject during choline depletion. Levels of these bacteria, change in amount of liver fat, and a single nucleotide polymorphism that affects choline were combined into a model that accurately predicted the degree to which subjects developed fatty liver on a choline-deficient diet. CONCLUSIONS: Host factors and GI bacteria each respond to dietary choline deficiency, although the gut microbiota remains distinct in each individual. We identified bacterial biomarkers of fatty liver that results from choline deficiency, adding to the accumulating evidence that GI microbes have a role in metabolic disorders