Publications by Colleges and Departments (MSU - Bozeman)
Permanent URI for this communityhttps://scholarworks.montana.edu/handle/1/3
Browse
7 results
Search Results
Item Influence of pH on 2,4,6-trinitrotoluene degradation by Yarrowia lipolytica(2010-04) Ziganshin, Ayrat M.; Naumova, R. P.; Pannier, Andy J.; Gerlach, RobinThe microbial reduction of the aromatic ring of 2,4,6-trinitrotoluene (TNT) can lead to its complete destruction. The acid-tolerant yeast Yarrowia lipolytica AN-L15 transformed TNT through hydride ion-mediated reduction of the aromatic ring (as the main pathway), resulting in the accumulation of nitrite and nitrate ions, as well as through nitro group reduction (as minor pathway), resulting in hydroxylamino- and aminoaromatics. TNT transformation depended on the yeasts' ability to acidify the culture medium through the production of organic acids. Aeration and a low medium buffer capacity favored yeast growth and resulted in rapid acidification of the medium, which influenced the rate and extent of TNT transformation. This is the first time that nitrate has been detected as a major product of microbial TNT degradation, and this work demonstrates the importance of pH on TNT biotransformation. The ability of Y. lipolytica AN-L15 to reduce the TNT aromatic ring to form TNT-hydride complexes, followed by their denitration, makes this strain a potential candidate for bioremediation of sites contaminated with explosives. (c) 2010 Elsevier Ltd. All rights reserved.Item Aerobic degradation of 2,4,6-trinitrotoluene by the yeast strain Geotrichum candidum AN-Z4(2010-04) Ziganshin, Ayrat M.; Gerlach, Robin; Naumenko, E. A.; Naumova, R. P.The yeast strain Geotrichum candidum AN-Z4 isolated from an anthropogenically polluted site was able to transform 2,4,6-trinitrotoluene (TNT) via the formation of unstable intermediate hydride Meisenheimer complexes with their subsequent destruction and accumulation of nitrite and nitrate ions as the end mineral forms of nitrogen. Aeration of the medium promoted more profound destruction of this xenobiotic by the strain G. candidum AN-Z4 than static conditions. The yeast strain was shown to produce citrate, succinate, and isocitrate, which sharply acidified the medium and influenced the TNT destruction. Two possible pathways of TNT biodegradation were confirmed experimentally: (1) via the destruction of the TNT-monohydride complex (3-H−-TNT) and (2) via the destruction of one protonated TNT-dihydride complex (3,5-2H−-TNT · H+). The strain G. candidum AN-Z4, due to its ability for TNT degradation, may be promising for bioremediation of TNT-contaminated soil and water.Item Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum(2012-06) Valenzuela, Jacob J.; Mazurie, Aurélien J.; Carlson, Ross P.; Gerlach, Robin; Cooksey, Keith E.; Peyton, Brent M.; Fields, Matthew W.BACKGROUND: Phaeodactylum tricornutum is a unicellular diatom in the class Bacillariophyceae. The full genome hasbeen sequenced (<30 Mb), and approximately 20 to 30% triacylglyceride (TAG) accumulation on a dry cell basis hasbeen reported under different growth conditions. To elucidate P. tricornutum gene expression profiles duringnutrient-deprivation and lipid-accumulation, cell cultures were grown with a nitrate to phosphate ratio of 20:1 (N:P)and whole-genome transcripts were monitored over time via RNA-sequence determination.RESULTS: The specific Nile Red (NR) fluorescence (NR fluorescence per cell) increased over time; however, theincrease in NR fluorescence was initiated before external nitrate was completely exhausted. Exogenous phosphatewas depleted before nitrate, and these results indicated that the depletion of exogenous phosphate might be anearly trigger for lipid accumulation that is magnified upon nitrate depletion. As expected, many of the genesassociated with nitrate and phosphate utilization were up-expressed. The diatom-specific cyclins cyc7 and cyc10were down-expressed during the nutrient-deplete state, and cyclin B1 was up-expressed during lipid-accumulationafter growth cessation. While many of the genes associated with the C3 pathway for photosynthetic carbonreduction were not significantly altered, genes involved in a putative C4 pathway for photosynthetic carbonassimilation were up-expressed as the cells depleted nitrate, phosphate, and exogenous dissolved inorganic carbon(DIC) levels. P. tricornutum has multiple, putative carbonic anhydrases, but only two were significantly up-expressed(2-fold and 4-fold) at the last time point when exogenous DIC levels had increased after the cessation of growth.Alternative pathways that could utilize HCO-3 were also suggested by the gene expression profiles (e.g., putativepropionyl-CoA and methylmalonyl-CoA decarboxylases).CONCLUSION: The results indicate that P. tricornutum continued carbon dioxide reduction when population growthwas arrested and different carbon-concentrating mechanisms were used dependent upon exogenous DIC levels.Based upon overall low gene expression levels for fatty acid synthesis, the results also suggest that the build-up ofprecursors to the acetyl-CoA carboxylases may play a more significant role in TAG synthesis rather than the actualenzyme levels of acetyl-CoA carboxylases per se. The presented insights into the types and timing of cellularresponses to inorganic carbon will help maximize photoautotrophic carbon flow to lipid accumulation.Item Physiological and molecular analysis of carbon source supplementation and pH stress-induced lipid accumulation in the marine diatom Phaeodactylum tricornutum(2013-03) Mus, Florence; Toussaint, Jean-Paul; Cooksey, Keith E.; Fields, Matthew W.; Gerlach, Robin; Peyton, Brent M.; Carlson, Ross P.A detailed physiological and molecular analysis of lipid accumulation under a suite of conditions including nitrogen limitation, alkaline pH stress, bicarbonate supplementation, and organic acid supplementation was performed on the marine diatom Phaeodactylum tricornutum. For all tested conditions, nitrogen limitation was a prerequisite for lipid accumulation and the other culturing strategies only enhanced accumulation highlighting the importance of compounded stresses on lipid metabolism. Volumetric lipid levels varied depending on condition; the observed rankings from highest to lowest were for inorganic carbon addition (15 mM bicarbonate), organic acid addition (15 carbon mM acetate), and alkaline pH stress (pH9.0). For all lipidaccumulating cultures except acetate supplementation, a common series of physiological steps were observed. Upon extracellular nitrogen exhaustion, culture growth continued for approximately 1.5 cell doublings with decreases in specific protein and photosynthetic pigment content. As nitrogen limitation arrested cell growth, carbohydrate content decreased with a corresponding increase in lipid content. Addition of the organic carbon source acetate appeared to activate alternative metabolic pathways for lipid accumulation. Molecular level data on more than 50 central metabolism transcripts were measured using real-time PCR. Analysis of transcripts suggested the central metabolism pathways associated with bicarbonate transport, carbonic anhydrases, and C4 carbon fixations were important for lipid accumulation. Transcriptomic data also suggested that repurposing of phospholipids may play a role in lipid accumulation. This study provides a detailed physiological and molecular-level foundation for improved understanding of diatom nutrient cycling and contributes to a metabolic blueprint for controlling lipid accumulation in diatoms.Item Effect of ferrihydrite on 2,4,6-trinitrotoluene biotransformation by an aerobic yeast(2013-09) Khilyas, I. V.; Ziganshin, Ayrat M.; Pannier, Andy J.; Gerlach, RobinThis study investigated the impact of ferrihydrite on the pathway and rate of 2,4,6-trinitrotoluene (TNT) transformation by Yarrowia lipolytica AN-L15. The presence of ferrihydrite in the culture medium decreased the rate of TNT biotransformation but resulted in the accumulation of the same TNT metabolites as in the absence of ferrihydrite, albeit at slightly different concentrations. Transformation products observed included aromatic ring reduction products, such as hydride-Meisenheimer complexes, and nitro group reduction products, such as hydroxylamino- and amino-dinitrotoluenes. Independently of the presence of ferrihydrite the subsequent degradation of the hydride complex(es) resulted in the release of nitrite followed by its conversion to nitrate and nitric oxide at the low pH values observed during yeast cultivation. Nitric oxide generation was ascertained by electron spin resonance spectroscopy. In addition, increased Fe3+-reduction was observed in the presence of TNT and Y. lipolytica. This study demonstrates that in the presence of yeast cells, TNT hydride complexes were formed at approximately the same level as in the presence of ferrihydrite, opening up the possibility of aromatic ring cleavage, instead of promoting the production of potentially toxic nitro group reduction products in the presence of iron minerals.Item Pathways of 2,4,6-trinitrotoluene transformation by aerobic yeasts(2013-08) Ziganshin, Ayrat M.; Gerlach, RobinThe production and use of various highly persistent synthetic compounds lead to environmental pollution. Among such compounds, 2,4,6-trinitrotoluene (TNT) is the one which is commonly used as an explosive. Synthesis and wide use of TNT in ammunition have resulted in the contamination of soil, air, surface water, and groundwater. TNT and its nitro group reduction products are highly toxic, potentially mutagenic and persistent contaminants which can persist in the environment for a long time (Spain et al. 2000; Stenuit et al. 2005; Smets et al. 2007; Singh et al. 2012). The U.S. Environmental Protection Agency has classified TNT as one of the most dangerous pollutants in the biosphere. Hence, remediation of TNT-contaminated sites is urgently warranted at places of its production and use (Keith and Telliard 1979; Fiorella and Spain 1997).Human exposure to TNT or its nitro group reduction metabolites can lead to the development of diseases, such as aplastic anemia, cataracts, impaired liver function and the formation of tumors in the urinary tract (Hathaway 1985; Yinon 1990; Leung et al. 1995). Hence, it is inevitable to work out strategies targeting the degradation of TNT.Decontamination of sites contaminated with explosives, especially with TNT, is possible with application of various physical, chemical, and biological methods. The main advantages of bioremediation are environmental friendliness and involvement of low cost (Rodgers and Bunce 2001).Item Fracture Sealing with Microbially-Induced Calcium Carbonate Precipitation: A Field Study(2016-04) Phillips, Adrienne J.; Cunningham, Alfred B.; Gerlach, Robin; Hiebert, Dwight Randall; Hwang, Chiachi; Lomans, B. P.; Westrich, Joseph; Mantilla, C.; Kirksey, J.; Esposito, R.; Spangler, Lee H.A primary environmental risk from unconventional oil and gas development or carbon sequestration is subsurface fluid leakage in the near wellbore environment. A potential solution to remediate leakage pathways is to promote microbially induced calcium carbonate precipitation (MICP) to plug fractures and reduce permeability in porous materials. The advantage of microbially induced calcium carbonate precipitation (MICP) over cement-based sealants is that the solutions used to promote MICP are aqueous. MICP solutions have low viscosities compared to cement, facilitating fluid transport into the formation. In this study, MICP was promoted in a fractured sandstone layer within the Fayette Sandstone Formation 340.8 m below ground surface using conventional oil field subsurface fluid delivery technologies (packer and bailer). After 24 urea/calcium solution and 6 microbial (Sporosarcina pasteurii) suspension injections, the injectivity was decreased (flow rate decreased from 1.9 to 0.47 L/min) and a reduction in the in-well pressure falloff (>30% before and 7% after treatment) was observed. In addition, during refracturing an increase in the fracture extension pressure was measured as compared to before MICP treatment. This study suggests MICP is a promising tool for sealing subsurface fractures in the near wellbore environment.