Browsing by Author "Bowen De León, Kara"

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Archaeal and bacterial communities in three alkaline hot springs in Heart Lake Geyser Basin, Yellowstone National Park
(2013-11) Bowen De León, Kara; Gerlach, Robin; Peyton, Brent M.; Fields, Matthew W.
The Heart Lake Geyser Basin (HLGB) is remotely located at the base of Mount Sheridan in southern Yellowstone National Park (YNP), Wyoming, USA and is situated along Witch Creek and the northwestern shore of Heart Lake. Likely because of its location, little is known about the microbial community structure of springs in the HLGB. Bacterial and archaeal populations were monitored via small subunit (SSU) rRNA gene pyrosequencing over 3 years in 3 alkaline (pH 8.5) hot springs with varying temperatures (44Â°C, 63Â°C, 75Â°C). The bacterial populations were generally stable over time, but varied by temperature. The dominant bacterial community changed from moderately thermophilic and photosynthetic members (Cyanobacteria and Chloroflexi) at 44Â°C to a mixed photosynthetic and thermophilic community (Deinococcus-Thermus) at 63Â°C and a non-photosynthetic thermophilic community at 75Â°C. The archaeal community was more variable across time and was predominantly a methanogenic community in the 44 and 63Â°C springs and a thermophilic community in the 75Â°C spring. The 75Â°C spring demonstrated large shifts in the archaeal populations and was predominantly Candidatus nitrosocaldus, an ammonia-oxidizing crenarchaeote, in the 2007 sample, and almost exclusively Thermofilum or Candidatus caldiarchaeum in the 2009 sample, depending on SSU rRNA gene region examined. The majority of sequences were dissimilar (â‰¥10% different) to any known organisms suggesting that HLGB possesses numerous new phylogenetic groups that warrant cultivation efforts.
Complete genome sequence of Pelosinus fermentans JBW45, a member of a remarkably competitive group of Negativicutes in the Firmicutes Phylum
(2015-09) Bowen De León, Kara; Utturkar, S. M.; Camilleri, Laura B.; Elias, Dwayne A.; Arkin, Adam P.; Fields, Matthew W.; Brown, S. D.; Wall, Judy D.
The genome of Pelosinus fermentans JBW45, isolated from a chromium-contaminated site in Hanford, Washington, USA, has been completed with PacBio sequencing. Nine copies of the rRNA gene operon and multiple transposase genes with identical sequences resulted in breaks in the original draft genome and may suggest genomic instability of JBW45.
Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction
(2012-10) Bowen De León, Kara; Young, Mary Lynn; Camilleri, Laura B.; Brown, S. T.; Skerker, J. M.; Deutschbauer, A. M.; Arkin, Adam P.; Fields, Matthew W.
Pelosinus fermentans JBW45 is an anaerobic, lactate-fermenting bacterium isolated from Cr(VI)-contaminated groundwater at the Hanford Nuclear Reservation 100-H site (Washington) that was collected after stimulation with a polylactate compound. The genome sequence of this organism will provide insight into the metabolic potential of a predominant population during stimulation for metal-reducing conditions.
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.