Browsing by Author "Ramsay, Bradley D."

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Enhanced coal-dependent methanogenesis coupled with algal biofuels: Potential water recycle and carbon capture
(2017-02) Barnhart, Elliott P.; Davis, Katherine J.; Varonka, Matthew; Orem, William; Cunningham, Alfred B.; Ramsay, Bradley D.; Fields, Matthew W.
Many coal beds contain microbial communities that can convert coal to natural gas (coalbed methane). Native microorganisms were obtained from Powder River Basin (PRB) coal seams with a diffusive microbial sampler placed downhole and used as an inoculum for enrichments with different nutrients to investigate microbially-enhanced coalbed methane production (MECoM). Coal-dependent methanogenesis more than doubled when yeast extract (YE) and several less complex components (proteins and amino acids) were added to the laboratory microcosms. Stimulated coal-dependent methanogenesis with peptone was 86% of that with YE while glutamate-stimulated activity was 65% of that with YE, and a vitamin mix had only 33% of the YE stimulated activity. For field application of MECoM, there is interest in identifying cost-effective alternatives to YE and other expensive nutrients. In laboratory studies, adding algal extract (AE) with lipids removed stimulated coal-dependent methanogenesis and the activity was 60% of that with YE at 27 d and almost 90% of YE activity at 1406 d. Analysis of British Thermal Unit (BTU) content of coal (a measure of potential energy yield) from long-term incubations indicated > 99.5% of BTU content remained after coalbed methane (CBM) stimulation with either AE or YE. Thus, the coal resource remains largely unchanged following stimulated microbial methane production. Algal CBM stimulation could lead to technologies that utilize coupled biological systems (photosynthesis and methane production) that sustainably enhance CBM production and generate algal biofuels while also sequestering carbon dioxide (CO2).
Evaluation and remediation of bulk soap dispensers for biofilm
(2012-01) Lorenz, Lindsey A.; Ramsay, Bradley D.; Goeres, Darla M.; Fields, Matthew W.; Zapka, Carrie A.; Macinga, David R.
Recent studies evaluating bulk soap in public restroom soap dispensers have demonstrated up to 25% of open refillable bulk-soap dispensers were contaminated with ~6 log10(CFU ml-1) heterotrophic bacteria. In this study, plastic counter-mounted, plastic wall-mounted and stainless steel wall-mounted dispensers were analyzed for suspended and biofilm bacteria using total cell and viable plate counts. Independent of dispenser type or construction material, the bulk soap was contaminated with 4â€“7 log10(CFU ml-1) bacteria, while 4â€“6 log10(CFU cm-2) biofilm bacteria were isolated from the inside surfaces of the dispensers (n=6). Dispenser remediation studies, including a 10 min soak with 5000 mg 1-1 sodium hypochlorite, were then conducted to determine the efficacy of cleaning and disinfectant procedures against established biofilms. The testing showed that contamination of the bulk soap returned to pre-test levels within 7â€“14 days. These results demonstrate biofilm is present in contaminated bulk-soap dispensers and remediation studies to clean and sanitize the dispensers are temporary.
High-quality draft genome sequence of Desulfovibrio carbinoliphilus FW-101-2B, an organic acid-oxidizing sulfate-reducing bacterium isolated from uranium(VI)-contaminated groundwater
(2015-03) Ramsay, Bradley D.; Hwang, Chiachi; Woo, Hannah L.; Carroll, Sue L.; Lucas, Susan; Han, Jie; Lapidus, Alla; Cheng, J. F.; Goodwin, L. A.; Pitluck, S.; Peters, L.; Chertkov, Olga; Held, B; Detter, John C.; Han, C.; Tapia, R.; Land, M. L.; Hauser, Loren; Kyrpides, Nikos; Ivanova, N. N.; Mikhailova, Natalia; Pagani, I.; Woyke, Tanja; Arkin, Adam P.; Dehal, P.; Chivian, D.; Criddle, Craig S.; Wu, Wei-Min; Chakraborty, R.; Hazen, Terry C.; Fields, Matthew W.
Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing d-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.
Investigation of coal-associated bacterial and archaeal populations from a diffusive microbial sampler (DMS)
(2013-08) Barnhart, Elliott P.; Bowen De León, Kara; Ramsay, Bradley D.; Cunningham, Alfred B.; Fields, Matthew W.
The Powder River Basin (PRB) in southeastern Montana and northeastern Wyoming contains massive coal deposits with biologically generated coal bed methane (CBM). The microbial ecology of an area within a coal bed influenced by recent groundwater recharge was sampled with a diffusive microbial sampler (DMS). The DMS contained native coal material and was incubated in situ (57 m depth) to allow colonization of the coal particles. Pyrotag sequence analyses of SSU rRNA gene sequences from the coal contained within the post-incubation DMS detected methylotrophic and hydrogenotrophic methanogenic archaea along with diverse bacterial communities. Microbial enrichments (coal or acetate/H2) were established from the DMS, and the enriched bacterial and archaeal communities were characterized via clone library analysis. The in situ bacterial communities were more diverse than the archaeal communities, and the archaeal populations differed between coal incubated in situ and in laboratory enrichments. In addition, bacterial diversity was higher for laboratory enrichments with coal compared to enrichments without coal. The elucidation of relationships between microorganisms involved in coal degradation and metabolite (acetate, H2) utilization within coal-dependent microbial communities is crucial to understanding and improving in situ coal bed methane production.
Quality-score refinement of SSU rRNA gene pyrosequencing differs across gene region for environmental samples
(2012-04) Bowen De León, Kara; Ramsay, Bradley D.; Fields, Matthew W.
Due to potential sequencing errors in pyrosequencing data, species richness and diversity indices of microbial systems can be miscalculated. The â€œtraditionalâ€ sequence refinement method is not sufficient to account for overestimations (e.g., length, primer errors, ambiguous nucleotides). Recent in silico and single-organism studies have revealed the importance of sequence quality scores in the estimation of ecological indices; however, this is the first study to compare quality-score stringencies across four regions of the SSU rRNA gene sequence (V1V2, V3, V4, and V6) with actual environmental samples compared directly to corresponding clone libraries produced from the same primer sets. The nucleic acid sequences determined via pyrosequencing were subjected to varying quality-score cutoffs that ranged from 25 to 32, and at each quality-score cutoff, either 10 or 15%of the nucleotides were allowed to be below the cutoff. When species richness estimates were compared for the tested samples, the cutoff values of Q2715%, Q3010%, and Q3215% for V1V2, V4, and V6, respectively, estimated similar values as obtained with clone libraries and Sanger sequencing. The most stringent Q tested (Q3210%) was not enough to account for species richness inflation of the V3 region pyrosequence data. Results indicated that quality-score assessment greatly improved estimates of ecological indices for environmental samples (species richness and Î±-diversity) and that the effect of qualityscore filtering was region-dependent.