Scholarly Work - Center for Biofilm Engineering
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Item Application of molecular techniques to elucidate the influence of cellulosic waste on the bacterial community structure at a simulated low level waste site(2010-03) Field, E. K.; D'Imperio, Seth; Miller, A. R.; VanEngelen, Michael R.; Gerlach, Robin; Lee, Brady D.; Apel, William A.; Peyton, Brent M.Low-level radioactive waste sites, including those at various U.S. Department of Energy (DOE) sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a non-radioactive model low-level waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rRNA gene clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both methods revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more Operational Taxonomic Units (OTUs), and therefore relative diversity, than the clone libraries. Diversity indices suggest that diversity is lowest in the Fill (F) and Fill Waste (FW) layers and greater in the Wood Waste (WW) and Waste Clay (WC) layers. Principal coordinates analysis and lineage specific analysis determined that Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose degrading microorganisms suggests the FW layer is an enrichment environment for these organisms. These results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system.Item Influence of pH and inorganic phosphate on toxicity of zinc to Arthrobacter sp. isolated from heavy-metal-contaminated sediments(2010-10) Moberly, James G.; Staven, A.; Sani, Rajesh K.; Peyton, Brent M.Because of its high solubility over a wide range of pH conditions, zinc is found in many natural and human-impacted systems. Zinc speciation is critical in assessing zinc toxicity to microorganisms because it varies considerably with pH and is dependent on other aqueous constituents. Combined results of thermodynamic modeling, statistical analysis, and batch culture studies using Arthrobacter sp. JM018 suggest that the toxic species may not be solely limited to the free ion, but also includes ZnHPO40(aq). Cellular uptake of ZnHPO40(aq) through the inorganic phosphate transporter (Pit family), which requires a neutral metal phosphate complex for phosphate transport, may explain the observed toxicity. Based on visual MINTEQ (v3.0) modeling, at 50 μM total zinc, ZnHPO40(aq) constitutes 33, 70, and 76% of the neutral metal phosphate pool at pH 6, 7, and 8, respectively. At 50 μM total zinc, cultures supplied with organic phosphate (glycerol-3-phosphate) show no significant response to pH (p=0.13) while inhibition of inorganic phosphate-supplemented cultures, whose neutral metal phosphates are increasingly dominated by ZnHPO40(aq), show significant pH dependence (p=9.45 x 10-7). Using sodium to decrease the distribution of ZnHPO40(aq) in the neutral metal phosphate pool also decreased the pH dependent toxicity, further supporting this mechanism.These findings show the important role of minor zinc species in organism toxicity and have wider implications because the Pit inorganic phosphate transport system is widely distributed in Bacteria, Archaea, and Eukarya.Item Comparison of CO2 and bicarbonate as inorganic carbon sources for triacylglycerol and starch accumulation in Chlamydomonas reinhardtii(2013-01) Gardner, Robert D.; Lohman, Egan J.; Gerlach, Robin; Cooksey, Keith E.; Peyton, Brent M.Microalgae are capable of accumulating high levels of lipids and starch as carbon storage compounds. Investigation into the metabolic activities involved in the synthesis of these compounds has escalated because these compounds can be used as precursors for food and fuel. Here, we detail the results of a comprehensive analysis of Chlamydomonas reinhardtii using high or low inorganic carbon concentrations and speciation between carbon dioxide and bicarbonate, and the effects these have on inducing lipid and starch accumulation during nitrogen depletion. High concentrations of CO2 (5%;v/v) produced the highest amount of biofuel precursors, transesterified to fatty acid methyl esters, but exhibited rapid accumulation and degradation characteristics. Low CO2 (0.04%;v/v) caused carbon limitation and minimized triacylglycerol (TAG) and starch accumulation. High bicarbonate caused a cessation of cell cycling and accumulation of both TAG and starch that was more stable than the other experimental conditions. Starch accumulated prior to TAG and then degraded as maximum TAG was reached. This suggests carbon reallocation from starch-based to TAG-based carbon storage.Item Nutrient resupplementation arrests bio-oil accumulation in Phaeodactylum tricornutum(2013-08) Valenzuela, Jacob J.; Carlson, Ross P.; Gerlach, Robin; Cooksey, Keith E.; Peyton, Brent M.; Bothner, Brian; Fields, Matthew W.Phaeodactylum tricornutum is a marine diatom in the class Bacillariophyceae and is important ecologically and industrially with regards to ocean primary production and lipid accumulation for biofuel production, respectively. Triacylglyceride (TAG) accumulation has been reported in P. tricornutum under different nutrient stresses, and our results show that lipid accumulation can occur with nitrate or phosphate depletion. However, greater lipid accumulation was observed when both nutrients were depleted as observed using a Nile Red assay and fatty acid methyl ester (FAME) profiles. Nitrate depletion had a greater effect on lipid accumulation than phosphate depletion. Lipid accumulation in P. tricornutum was arrested upon resupplementation with the depleted nutrient. Cells depleted of nitrogen showed a distinct shift from a lipid accumulation mode to cellular growth post resupplementation with nitrate, as observed through increased cell numbers and consumption of accumulated lipid. Phosphate depletion caused lipid accumulation that was arrested upon phosphate resupplementation. The cessation of lipid accumulation was followed by lipid consumption without an increase in cell numbers. Cells depleted in both nitrate and phosphate displayed cell growth upon the addition of both nitrate and phosphate and had the largest observed lipid consumption upon resupplementation. These results indicate that phosphate resupplementation can shut down lipid accumulation but does not cause cells to shift into cellular growth, unlike nitrate resupplementation. These data suggest that nutrient resupplementation will arrest lipid accumulation and that switching between cellular growth and lipid accumulation can be regulated upon the availability of nitrogen and phosphorus.Item An efficient and scalable extraction and quantification method for algal derived biofuel(2013-09) Lohman, Egan J.; Gardner, Robert D.; Halverson, L.; Macur, Richard E.; Peyton, Brent M.; Gerlach, RobinMicroalgae are capable of synthesizing a multitude of compounds including biofuel precursors and other high value products such as omega-3-fatty acids. However, accurate analysis of the specific compounds produced by microalgae is important since slight variations in saturation and carbon chain length can affect the quality, and thus the value, of the end product. We present a method that allows for fast and reliable extraction of lipids and similar compounds from a range of algae, followed by their characterization using gas chromatographic analysis with a focus on biodiesel-relevant compounds. This method determines which range of biologically synthesized compounds is likely responsible for each fatty acid methyl ester (FAME) produced; information that is fundamental for identifying preferred microalgae candidates as a biodiesel source. Traditional methods of analyzing these precursor molecules are time intensive and prone to high degrees of variation between species and experimental conditions. Here we detail a new method which uses microwave energy as a reliable, single-step cell disruption technique to extract lipids fromlive cultures of microalgae. After extractable lipid characterization (including lipid type (free fatty acids, mono-, di- or tri-acylglycerides) and carbon chain length determination) by GC–FID, the same lipid extracts are transesterified into FAMEs and directly compared to total biodiesel potential by GC–MS. This approach provides insight into the fraction of total FAMEs derived from extractable lipids compared to FAMEs derived fromthe residual fraction (i.e. membrane bound phospholipids, sterols, etc.). This approach can also indicate which extractable lipid compound, based on chain length and relative abundance, is responsible for each FAME. This method was tested on three species of microalgae: the marine diatom Phaeodactylum tricornutum, the model Chlorophyte Chlamydomonas reinhardtii, and the freshwater green alga Chlorella vulgaris. The method is shown to be robust, highly reproducible, and fast, allowing for multiple samples to be analyzed throughout the time course of culturing, thus providing time-resolved information regarding lipid quantity and quality. Total time from harvesting to obtaining analytical results is less than 2 h.Item 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 (44°C, 63°C, 75°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 44°C to a mixed photosynthetic and thermophilic community (Deinococcus-Thermus) at 63°C and a non-photosynthetic thermophilic community at 75°C. The archaeal community was more variable across time and was predominantly a methanogenic community in the 44 and 63°C springs and a thermophilic community in the 75°C spring. The 75°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 (≥10% different) to any known organisms suggesting that HLGB possesses numerous new phylogenetic groups that warrant cultivation efforts.Item Growth, nitrogen utilization and biodiesel potential for two chlorophytes grown on ammonium, nitrate or urea(2013-03) Eustance, E. O.; Gardner, Robert D.; Moll, Karen M.; Menicucci, Joseph A. Jr.; Gerlach, Robin; Peyton, Brent M.Nitrogen removal from wastewater by algae provides the potential benefit of producing lipids for biodiesel and biomass for anaerobic digestion. Further, ammonium is the renewable form of nitrogen produced during anaerobic digestion and one of the main nitrogen sources associated with wastewater. The wastewater isolates Scenedesmus sp. 131 and Monoraphidium sp. 92 were grown with ammonium, nitrate, or urea in the presence of 5 % CO2, and ammonium and nitrate in the presence of air to optimize the growth and biofuel production of these chlorophytes. Results showed that growth on ammonium, in both 5 % CO2 and air, caused a significant decrease in pH during the exponential phase, causing growth inhibition due to the low buffering capacity of the medium. Therefore, biological buffers and pH controllers were utilized to prevent a decrease in pH. Growth on ammonium with pH control (synthetic buffers or KOH dosing) demonstrated that growth (rate and yield), biodiesel production, and ammonium utilization, similar to nitrate- and urea-amended treatments, can be achieved if sufficient CO2 is available. Since the use of buffers is economically limited to laboratory-scale experiments, chemical pH control could bridge the gap encountered in the scale-up to industrial processes.Item Carbon partitioning in lipids synthesized by Chlamydomonas reinhardtii when cultured under three unique inorganic carbon regimes(2014-07) Lohman, Egan J.; Gardner, Robert D.; Halverson, L.; Peyton, Brent M.; Gerlach, RobinInorganic carbon is a fundamental component for microalgal lipid biosynthesis. Understanding how the concentration and speciation of dissolved inorganic carbon (DIC) influences lipid metabolism in microalgae may help researchers optimize the production of these high value metabolites. Using relatively straight forward methods for quantifying free fatty acids (FFAs), mono- (MAG), di- (DAG), tri-acylglycerides (TAG), and total cellular fatty acids (FAME), lipid profiles over time were established for Chlamydomonas reinhardtii when grown under three unique inorganic carbon regimes. Specifically, cultures sparged with atmospheric air were compared to cultures which were sparged with 5% CO2 (v/v) and cultures supplemented with 50 mM NaHCO3 just prior to medium nitrogen depletion. All three conditions exhibited similar lipid profiles prior to nitrogen depletion in the medium, with FFA and MAG being the predominant lipid metabolites. However, these precursors were quickly reallocated into DAG and subsequently TAG after nitrogen depletion. C16 DAG did not accumulate significantly in any of the treatments, whereas the C18 DAG content increased throughout both exponential growth and stationary phase. C16 and C18 TAG began to accumulate after nitrogen depletion, with C16 TAG contributing the most to overall TAG content. C16 fatty acids exhibited a shift towards saturated C16 fatty acids after nitrogen depletion. Results provide insight into inorganic carbon partitioning into lipid compounds and how the organism's lipid metabolism changes due to N-deplete culturing and inorganic carbon source availability. The methodologies and findings presented here may be adapted to other organisms with high industrial relevance.