Browsing by Author "Gerlach, Robin"

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Addressing wellbore integrity and thief zone permeability using microbially-induced calcium carbonate precipitation (MICP): A field demonstration
(Elsevier BV, 2020-02) Kirkland, Catherine M.; Thane, Abby; Hiebert, Randy; Hyatt, Robert; Kirksey, Jim; Cunningham, Alfred B.; Gerlach, Robin; Spangler, Lee; Philips, Adrienne J.
Microbially-induced calcium carbonate precipitation (MICP) is an emerging biotechnology for wellbore integrity applications including sealing defects in wellbore cement and modifying the permeability of rock formations. The goal of this field demonstration was to characterize a failed waterflood injection well and provide proof of principle that MICP can reduce permeability in the presence of oil using conventional oilfield fluid delivery methods. We compared well logs performed at the time the well was drilled with ultrasonic logs, sonic cement evaluation, and temperature logs conducted after the well failed. Analysis of these logs suggested that, rather than entering the target waterflood formation, injectate was traveling through defects in the well cement to a higher permeability sandstone layer above the target formation. Sporosarcina pasteurii cultures and urea-calcium media were delivered 2290 ft (698 m) below ground surface using a 3.75 gal (14.2 L) slickline dump bailer to promote mineralization in the undesired flow paths. By Day 6 and after 25 inoculum and 49 calcium media injections, the injectivity [gpm/psi] had decreased by approximately 70%. This demonstration shows that 1) common well logs can be used to identify scenarios where MICP can be employed to reduce system permeability, remediate leakage pathways, and improve waterflood efficiency, and 2) MICP can occur in the presence of hydrocarbons.
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-Hâˆ’-TNT) and (2) via the destruction of one protonated TNT-dihydride complex (3,5-2Hâˆ’-TNT Â· 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.
Algal amendment enhances biogenic methane production from coals of different thermal maturity
(Frontiers Media SA, 2023-03) Platt, George A.; Davis, Katherine J.; Schweitzer, Hannah D.; Smith, Heidi J.; Fields, Matthew W.; Barnhart, Elliott P.; Gerlach, Robin
The addition of small amounts of algal biomass to stimulate methane production in coal seams is a promising low carbon renewable coalbed methane enhancement technique. However, little is known about how the addition of algal biomass amendment affects methane production from coals of different thermal maturity. Here, we show that biogenic methane can be produced from five coals ranging in rank from lignite to low-volatile bituminous using a coal-derived microbial consortium in batch microcosms with and without algal amendment. The addition of 0.1 g/l algal biomass resulted in maximum methane production rates up to 37 days earlier and decreased the time required to reach maximum methane production by 17–19 days when compared to unamended, analogous microcosms. Cumulative methane production and methane production rate were generally highest in low rank, subbituminous coals, but no clear association between increasing vitrinite reflectance and decreasing methane production could be determined. Microbial community analysis revealed that archaeal populations were correlated with methane production rate (p = 0.01), vitrinite reflectance (p = 0.03), percent volatile matter (p = 0.03), and fixed carbon (p = 0.02), all of which are related to coal rank and composition. Sequences indicative of the acetoclastic methanogenic genus Methanosaeta dominated low rank coal microcosms. Amended treatments that had increased methane production relative to unamended analogs had high relative abundances of the hydrogenotrophic methanogenic genus Methanobacterium and the bacterial family Pseudomonadaceae. These results suggest that algal amendment may shift coal-derived microbial communities towards coal-degrading bacteria and CO2-reducing methanogens. These results have broad implications for understanding subsurface carbon cycling in coal beds and the adoption of low carbon renewable microbially enhanced coalbed methane techniques across a diverse range of coal geology.
Anomalous fluid transport in porous media induced by biofilm growth
(2004-11) Seymour, Joseph D.; Gage, Justin P.; Codd, Sarah L.; Gerlach, Robin
Magnetic resonance measurements of the transition from normal to anomalous hydrodynamic dispersion in porous media due to biological activity are presented. Fractional advection-diffusion equations are shown to provide models for the measured impact of biofilm growth on porous media transport dynamics.
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.
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.
Bacterial transport issues related to subsurface biobarriers
(1999) Sharp, Robert R.; Gerlach, Robin; Cunningham, Alfred B.
Bacterially induced calcium carbonate precipitation and strontium coprecipitation in a porous media flow system
(2013-02) Lauchnor, Ellen G.; Schultz, Logan N.; Bugni, S.; Mitchell, Andrew C.; Cunningham, Alfred B.; Gerlach, Robin
Strontium-90 is a principal radionuclide contaminant in the subsurface at several Department of Energy sites in the Western U.S., causing a threat to groundwater quality in areas such as Hanford, WA. In this work, we used laboratory-scale porous media flow cells to examine a potential remediation strategy employing coprecipitation of strontium in carbonate minerals. CaCO3 precipitation and strontium coprecipitation were induced via ureolysis by Sporosarcina pasteurii in two-dimensional porous media reactors. An injection strategy using pulsed injection of calcium mineralization medium was tested against a continuous injection strategy. The pulsed injection strategy involved periods of lowered calcite saturation index combined with short high fluid velocity flow periods of calcium mineralization medium followed by stagnation (no-flow) periods to promote homogeneous CaCO3 precipitation. By alternating the addition of mineralization and growth media the pulsed strategy promoted CaCO3 precipitation while sustaining the ureolytic culture over time. Both injection strategies achieved ureolysis with subsequent CaCO3 precipitation and strontium coprecipitation. The pulsed injection strategy precipitated 71âˆ’85% of calcium and 59% of strontium, while the continuous injection was less efficient and precipitated 61% of calcium and 56% of strontium. Over the 60-day operation of the pulsed reactors, ureolysis was continually observed, suggesting that the balance between growth and precipitation phases allowed for continued cell viability. Our results support the pulsed injection strategy as a viable option for ureolysis-induced strontium coprecipitation because it may reduce the likelihood of injection well accumulation caused by localized mineral plugging while Sr coprecipitation efficiency is maintained in field-scale applications.
Bayesian estimation and uncertainty quantification in models of urea hydrolysis by E. coli biofilms
(Informa UK Limited, 2021-02) Jackson, Benjamin D.; Connolly, James M.; Gerlach, Robin; Klapper, Issac; Parker, Albert E.
Urea-hydrolysing biofilms are crucial to applications in medicine, engineering, and science. Quantitative information about ureolysis rates in biofilms is required to model these applications. We formulate a novel model of urea consumption in a biofilm that allows different kinetics, for example either first order or Michaelis-Menten. The model is fit it to synthetic data to validate and compare two approaches: Bayesian and nonlinear least squares (NLS), commonly used by biofilm practitioners. The shortcomings of NLS motivate the Bayesian approach where a simple Markov Chain Monte Carlo (MCMC) sampler is applied. The model is then fit to real data of influent and effluent urea concentrations from experiments on biofilms of Escherichia coli. Results from synthetic data aid in interpreting results from real data, where first order and Michaelis-Menten kinetic models are compared. The method shows potential for general applications requiring biofilm kinetic information.
Biofilm enhanced subsurface sequestration of supercritical CO2
(2009-01) Mitchell, Andrew C.; Phillips, Adrienne J.; Hiebert, Dwight Randall; Gerlach, Robin; Cunningham, Alfred B.
In order to develop subsurface CO2 storage as a viable engineered mechanism to reduce the emission of CO2 into the atmosphere, any potential leakage of injected supercritical CO2 (SC-CO2) from the deep subsurface to the atmosphere must be reduced. Here, we investigate the utility of biofilms, which are microorganism assemblages firmly attached to a surface, as a means of reducing the permeability of deep subsurface porous geological matrices under high pressure and in the presence of SC-CO2, using a unique high pressure (8.9 MPa), moderate temperature (32 Â°C) flow reactor containing 40 millidarcy Berea sandstone cores. The flow reactor containing the sandstone core was inoculated with the biofilm forming organism Shewanella fridgidimarina. Electron microscopy of the rock core revealed substantial biofilm growth and accumulation under high-pressure conditions in the rock pore space which caused >95% reduction in core permeability. Permeability increased only slightly in response to SC-CO2 challenges of up to 71 h and starvation for up to 363 h in length. Viable population assays of microorganisms in the effluent indicated survival of the cells following SC-CO2 challenges and starvation, although S. fridgidimarina was succeeded by Bacillus mojavensis and Citrobacter sp. which were native in the core. These observations suggest that engineered biofilm barriers may be used to enhance the geologic sequestration of atmospheric CO2.
Biofilm reactors for the treatment of used water in space:potential, challenges, and future perspectives
(Elsevier BV, 2023-12) Espinosa-Ortiz, Erika J.; Gerlach, Robin; Peyton, Brent M.; Roberson, Luke; Yeh, Daniel H.
Water is not only essential to sustain life on Earth, but also is a crucial resource for long-duration deep space exploration and habitation. Current systems in space rely on the resupply of water from Earth, however, as missions get longer and move farther away from Earth, resupply will no longer be a sustainable option. Thus, the development of regenerative reclamation water systems through which useable water can be recovered from “waste streams” (i.e., used waters) is sorely needed to further close the loop in space life support systems. This review presents the origin and characteristics of different used waters generated in space and discusses the intrinsic challenges of developing suitable technologies to treat such streams given the unique constrains of space exploration and habitation (e.g., different gravity conditions, size and weight limitations, compatibility with other systems, etc.). In this review, we discuss the potential use of biological systems, particularly biofilms, as possible alternatives or additions to current technologies for water reclamation and waste treatment in space. The fundamentals of biofilm reactors, their advantages and disadvantages, as well as different reactor configurations and their potential for use and challenges to be incorporated in self-sustaining and regenerative life support systems in long-duration space missions are also discussed. Furthermore, we discuss the possibility to recover value-added products (e.g., biomass, nutrients, water) from used waters and the opportunity to recycle and reuse such products as resources in other life support subsystems (e.g., habitation, waste, air, etc.).
Biofilms in porous media
(2000) Bouwer, Edward J.; Rijnaarts, Huub H. M.; Cunningham, Alfred B.; Gerlach, Robin
Biogenic coal-to-methane conversion efficiency decreases after repeated organic amendment stimulation
(2018-01) Davis, Katherine J.; Barnhart, Elliott P.; Fields, Matthew W.; Gerlach, Robin
Addition of organic amendments to coal-containing systems can increase the rate and extent of biogenic methane production for 60−80 days before production slows or stops. Understanding the effect of repeated amendment additions on the rate and extent of enhanced coal-dependent methane production is important if biological coal-to-methane conversion is to be enhanced on a commercial scale. Microalgal biomass was added at a concentration of 0.1 g/L to microcosms with and without coal on days 0, 76, and 117. Rates of methane production were enhanced after the initial amendment but coal-containing treatments produced successively decreasing amounts of methane with each amendment. During the first amendment period, 113% of carbon added as amendment was recovered as methane, whereas in the second and third amendment periods, 39% and 32% of carbon added as amendment was recovered as methane, respectively. Additionally, algae-amended coal treatments produced ∼38% more methane than unamended coal treatments and ∼180% more methane than amended coal-free treatments after one amendment. However, a second amendment addition resulted in only an ∼25% increase in methane production for coal versus noncoal treatments and a third amendment addition resulted in similar methane production in both coal and noncoal treatments. Successive amendment additions appeared to result in a shift from coal-to-methane conversion to amendment-to-methane conversion. The reported results indicate that a better understanding is needed of the potential impacts and efficiencies of repeated stimulation for enhanced coal-to-methane conversion.
Biogeochemical elimination of chromium (VI) contaminated water
(2002-01) Nyman, Jennifer L.; Caccavo, Frank; Cunningham, Alfred B.; Gerlach, Robin
Ferrous iron [Fe(II)] reductively transforms heavy metals in contaminated groundwater, and the bacterial reduction of indigenous ferric iron [Fe(II)] has been proposed as a means of establishing redox reactive barriers in the subsurface. The reduction of Fe(III) to Fe(II) can be accomplished by stimulation of microbially produced Fe(II) can chemically react with contaminants such as Cr(VI) to form insoluble Cr(III) precipitates. The DMRB Shewanella algae BrY reduced highly soluble Cr(VI) to insoluble Cr(III). Once the chemical Cr(VI) reduction capacity of the Fe(II)/Fe(III) couple in the experimental systems was exhausted, the addition of S. algae BrY allowed for the repeated reduction of Fe(III) to Fe(II), which again reduced Cr(VI) to Cr(III). The research presented herein indicates that a biological process using DMRB allows the establishment of biogeochemical cycle that facilitates chromium production. Such a system could provide a means for establishing and maintaining remedial redox reactive zones on Fe(III)- bearing subsurface environments.
Biological treatment of selenium-laden wastewater containing nitrate and sulfate in an upflow anaerobic sludge bed reactor at pH 5.0
(2018-11) Tan, Lea Chua; Nancharaiah, Yarlagadda V.; Lu, Shipeng; van Hullebusch, Eric D.; Gerlach, Robin; Lens, Piet N. L.
This study investigated the removal of selenate (SeO42−), sulfate (SO42−) and nitrate (NO3−) at different influent pH values ranging from 7.0 to 5.0 and 20 °C in an upflow anaerobic sludge blanket (UASB) reactor using lactate as an electron donor. At pH 5.0, the UASB reactor showed a 20–30% decrease in reactor performance compared to operation at pH 5.5 to 7.0, reaching removal efficiencies of 79%, 15%, 43% and 61% for NO3−, SO42−, Setotal and Sediss, respectively. However, the reactor stability was an issue upon lowering the pH to 5.0 and further experiments are recommended. The sludge formed during low pH operation had a fluffy, floc-like appearance with filamentous structure, possibly due to the low polysaccharide (PS) to protein (PN) ratio (0.01 PS/PN) in the soluble extracellular polymeric substances (EPS) matrix of the biomass. Scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) analysis of the sludge confirmed Se oxyanion reduction and deposition of Se0 particles inside the biomass. Microbial community analysis using Illumina MiSeq sequencing revealed that the families of Campylobacteraceae and Desulfomicrobiaceae were the dominant phylotypes throughout the reactor operation at approximately 23% and 10% relative abundance, respectively. Furthermore, approximately 10% relative abundance of both Geobacteraceae and Spirochaetaceae was observed in the granular sludge during the pH 5.0 operation. Overall, this study demonstrated the feasibility of UASB operation at pH values ranging from 7.0 to 5.0 for removing Se and other oxyanions from wastewaters.
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, Robin
Inorganic 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.
Carbon-dependent chromate toxicity mechanism in an environmental Arthrobacter isolate
(2018-08) Field, Erin K.; Blaskovich, John P.; Peyton, Brent M.; Gerlach, Robin
Arthrobacter spp. are widespread in soil systems and well-known for their Cr(VI) reduction capabilities making them attractive candidates for in situ bioremediation efforts. Cellulose drives carbon flow in soil systems; yet, most laboratory studies evaluate Arthrobacter-Cr(VI) interactions solely with nutrient-rich media or glucose. This study aims to determine how various cellulose degradation products and biostimulation substrates influence Cr(VI) toxicity, reduction, and microbial growth of an environmental Arthrobacter sp. isolate. Laboratory culture-based studies suggest there is a carbon-dependent Cr(VI) toxicity mechanism that affects subsequent Cr(VI) reduction by strain LLW01. Strain LLW01 could only grow in the presence of, and reduce, 50 μM Cr(VI) when glucose or lactate were provided. Compared to lactate, Cr(VI) was at least 30-fold and 10-fold more toxic when ethanol or butyrate was the sole carbon source, respectively. The addition of sulfate mitigated toxicity somewhat, but had no effect on the extent of Cr(VI) reduction. Cell viability studies indicated that a small fraction of cells were viable after 8 days suggesting cell growth and subsequent Cr(VI) reduction may resume. These results suggest when designing bioremediation strategies with Arthrobacter spp. such as strain LLW01, carbon sources such as glucose and lactate should be considered over ethanol and butyrate.
Cellular cycling, carbon utilization, and photosynthetic oxygen production during bicarbonate-induced triacylglycerol accumulation in a Scenedesmus sp.
(2013-11) Gardner, Robert D.; Lohman, Egan J.; Cooksey, Keith E.; Gerlach, Robin; Peyton, Brent M.
Microalgae are capable of synthesizing high levels of triacylglycerol (TAG) which can be used as precursor compounds for fuels and specialty chemicals. Algal TAG accumulation typically occurs when cellular cycling is delayed or arrested due to nutrient limitation, an environmental challenge (e.g., pH, light, temperature stress), or by chemical addition. This work is a continuation of previous studies detailing sodium bicarbonate-induced TAG accumulation in the alkaline chlorophyte Scenedesmus sp. WC-1. It was found that upon sodium bicarbonate amendment, bicarbonate is the ion responsible for TAG accumulation; a culture amendment of approximately 15 mM bicarbonate was sufficient to arrest the cellular cycle and switch the algal metabolism from high growth to a TAG accumulating state. However, the cultures were limited in dissolved inorganic carbon one day after the amendment, suggesting additional carbon supplementation was necessary. Therefore, additional abiotic and biotic experimentation was performed to evaluate in- and out-gassing of CO2. Cultures to which 40â€“50 mM of sodium bicarbonate were added consumed DIC faster than CO2 could ingas during the light hours and total photosynthetic oxygen production was elevated as compared to cultures that did not receive supplemental inorganic carbon.
Cellular Cycling, Carbon Utilization, and Photosynthetic Oxygen Production During Bicarbonate-Induced Triacylglycerol Accumulation in a Scenedesmus Sp.
(2013-11) Gardner, Robert D.; Lohman, Egan J.; Cooksey, Keith E.; Gerlach, Robin
Microalgae are capable of synthesizing high levels of triacylglycerol (TAG) which can be used as precursor compounds for fuels and specialty chemicals. Algal TAG accumulation typically occurs when cellular cycling is delayed or arrested due to nutrient limitation, an environmental challenge (e.g., pH, light, temperature stress), or by chemical addition. This work is a continuation of previous studies detailing sodium bicarbonate-induced TAG accumulation in the alkaline chlorophyteScenedesmus sp. WC-1. It was found that upon sodium bicarbonate amendment, bicarbonate is the ion responsible for TAG accumulation; a culture amendment of approximately 15 mM bicarbonate was sufficient to arrest the cellular cycle and switch the algal metabolism from high growth to a TAG accumulating state. However, the cultures were limited in dissolved inorganic carbon one day after the amendment, suggesting additional carbon supplementation was necessary. Therefore, additional abiotic and biotic experimentation was performed to evaluate in- and out-gassing of CO2. Cultures to which 40–50 mM of sodium bicarbonate were added consumed DIC faster than CO2 could ingas during the light hours and total photosynthetic oxygen production was elevated as compared to cultures that did not receive supplemental inorganic carbon.
Chromium elimination with microbially reduced iron: redox-reactive biobarriers
(1999) Gerlach, Robin; Cunningham, Alfred B.; Caccavo, Frank