Browsing by Author "Fields, Matthew W."

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Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane
(Springer Science and Business Media LLC, 2021-10) McKay, Luke J.; Smith, Heidi J.; Barnhart, Elliott P.; Schweitzer, Hannah D.; Malmstrom, Rex R.; Goudeau, Danielle; Fields, Matthew W.
Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum, and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active "Chlorobi PRB" MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. "M. paradoxum PRB" encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.
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.
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.
Autonomous metabolomics for rapid metabolite identification in global profiling
(2015-01) Benton, H. Paul; Ivanisevic, Julijana; Mahieu, N. G.; Kurczy, M. E.; Johnson, Caroline H.; Franco, Lauren C.; Rinehart, Duane; Valentine, E.; Gowda, H.; Ubhi, B. K.; Tautenhahn, R.; Gieschen, A.; Fields, Matthew W.; Patti, G. J.; Siuzdak, Gary
An autonomous metabolomic workflow combining mass spectrometry analysis with tandem mass spectrometry data acquisition was designed to allow for simultaneous data processing and metabolite characterization. Although previously tandem mass spectrometry data have been generated on the fly, the experiments described herein combine this technology with the bioinformatic resources of XCMS and METLIN. As a result of this unique integration, we can analyze large profiling datasets and simultaneously obtain structural identifications. Validation of the workflow on bacterial samples allowed the profiling on the order of a thousand metabolite features with simultaneous tandem mass spectra data acquisition. The tandem mass spectrometry data acquisition enabled automatic search and matching against the METLIN tandem mass spectrometry database, shortening the current workflow from days to hours. Overall, the autonomous approach to untargeted metabolomics provides an efficient means of metabolomic profiling, and will ultimately allow the more rapid integration of comparative analyses, metabolite identification, and data analysis at a systems biology level.
Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths
(2009-01) Hwang, Chiachi; Wu, Wei-Min; Gentry, Terry J.; Carley, Jack; Corbin, Gail A.; Carroll, Sue L.; Watson, David B.; Jardine, Phil M.; Zhou, Jizhong; Criddle, Craig S.; Fields, Matthew W.
Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5-year period. Analyses showed that the communities changed in a manner consistent with geochemical variations that occurred along temporal and spatial scales. Canonical correspondence analysis revealed that the levels of nitrate, uranium, sulfide, sulfate and ethanol were strongly correlated with particular bacterial populations. As sulfate and U(VI) levels declined, sequences representative of sulfate reducers and metal reducers were detected at high levels. Ultimately, sequences associated with sulfate-reducing populations predominated, and sulfate levels declined as U(VI) remained at low levels. When engineering controls were compared with the population variation through canonical ordination, changes could be related to dissolved oxygen control and ethanol addition. The data also indicated that the indigenous populations responded differently to stimulation for bioreduction; however, the two biostimulated communities became more similar after different transitions in an idiosyncratic manner. The strong associations between particular environmental variables and certain populations provide insight into the establishment of practical and successful remediation strategies in radionuclide-contaminated environments with respect to engineering controls and microbial ecology.
Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths
(2009-01) Hwang, Chiachi; Wu, Wei-Min; Gentry, Terry J.; Carley, Jack; Corbin, Gail A.; Carroll, Sue L.; Watson, David B.; Jardine, Phil M.; Zhou, Jizhong; Criddle, Craig S.; Fields, Matthew W.
Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5-year period. Analyses showed that the communities changed in a manner consistent with geochemical variations that occurred along temporal and spatial scales. Canonical correspondence analysis revealed that the levels of nitrate, uranium, sulfide, sulfate and ethanol were strongly correlated with particular bacterial populations. As sulfate and U(VI) levels declined, sequences representative of sulfate reducers and metal reducers were detected at high levels. Ultimately, sequences associated with sulfate-reducing populations predominated, and sulfate levels declined as U(VI) remained at low levels. When engineering controls were compared with the population variation through canonical ordination, changes could be related to dissolved oxygen control and ethanol addition. The data also indicated that the indigenous populations responded differently to stimulation for bioreduction; however, the two biostimulated communities became more similar after different transitions in an idiosyncratic manner. The strong associations between particular environmental variables and certain populations provide insight into the establishment of practical and successful remediation strategies in radionuclide-contaminated environments with respect to engineering controls and microbial ecology.
Biofilm formation in Desulfovibrio vulgaris Hildenborough is dependent upon protein filaments
(2007-11) Clark, M. E.; Edelmann, Richard E.; Duley, Matt L.; Wall, Judy D.; Fields, Matthew W.
Desulfovibrio vulgaris Hildenborough is a gram-negative sulfate-reducing bacterium (SRB), and the physiology of SRBs can impact many anaerobic environments including radionuclide waste sites, oil reservoirs and metal pipelines. In an attempt to understand D. vulgaris as a population that can adhere to surfaces, D. vulgaris cultures were grown in a defined medium and analysed for carbohydrate production, motility and biofilm formation. Desulfovibrio vulgaris wild-type cells had increasing amounts of carbohydrate into stationary phase and approximately half of the carbohydrate remained internal. In comparison, a mutant that lacked the 200 kb megaplasmid, strain DeltaMP, produced less carbohydrate and the majority of carbohydrate remained internal of the cell proper. To assess the possibility of carbohydrate re-allocation, biofilm formation was investigated. Wild-type cells produced approximately threefold more biofilm on glass slides compared with DeltaMP; however, wild-type biofilm did not contain significant levels of exopolysaccharide. In addition, stains specific for extracellular carbohydrate did not reveal polysaccharide material within the biofilm. Desulfovibrio vulgaris wild-type biofilms contained long filaments as observed with scanning electron microscopy (SEM), and the biofilm-deficient DeltaMP strain was also deficient in motility. Biofilms grown directly on silica oxide transmission electron microscopy (TEM) grids did not contain significant levels of an exopolysaccharide matrix when viewed with TEM and SEM, and samples stained with ammonium molybdate also showed long filaments that resembled flagella. Biofilms subjected to protease treatments were degraded, and different proteases that were added at the time of inoculation inhibited biofilm formation. The data indicated that D. vulgaris did not produce an extensive exopolysaccharide matrix, used protein filaments to form biofilm between cells and silica oxide surfaces, and the filaments appeared to be flagella. It is likely that D. vulgaris used flagella for more than a means of locomotion to a surface, but also used flagella, or modified flagella, to establish and/or maintain biofilm structure.
Biofilm growth mode promotes maximum carrying capacity and community stability during product inhibition syntrophy
(2014-12) Brileya, Kristen A.; Camilleri, Laura B.; Zane, Grant M.; Wall, Judy D.; Fields, Matthew W.
Sulfate-reducing bacteria (SRB) can interact syntrophically with other community members in the absence of sulfate, and interactions with hydrogen-consuming methanogens are beneficial when these archaea consume potentially inhibitory H2 produced by the SRB. A dual continuous culture approach was used to characterize population structure within a syntrophic biofilm formed by the SRB Desulfovibrio vulgaris Hildenborough and the methanogenic archaeum Methanococcus maripaludis. Under the tested conditions, monocultures of D. vulgaris formed thin, stable biofilms, but monoculture M. maripaludis did not. Microscopy of intact syntrophic biofilm confirmed that D. vulgaris formed a scaffold for the biofilm, while intermediate and steady-state images revealed that M. maripaludis joined the biofilm later, likely in response to H2 produced by the SRB. Close interactions in structured biofilm allowed efficient transfer of H2 to M. maripaludis, and H2 was only detected in cocultures with a mutant SRB that was deficient in biofilm formation (ΔpilA). M. maripaludis produced more carbohydrate (uronic acid, hexose, and pentose) as a monoculture compared to total coculture biofilm, and this suggested an altered carbon flux during syntrophy. The syntrophic biofilm was structured into ridges (∼300 × 50 μm) and models predicted lactate limitation at ∼50 μm biofilm depth. The biofilm had structure that likely facilitated mass transfer of H2 and lactate, yet maximized biomass with a more even population composition (number of each organism) when compared to the bulk-phase community. Total biomass protein was equivalent in lactate-limited and lactate-excess conditions when a biofilm was present, but in the absence of biofilm, total biomass protein was significantly reduced. The results suggest that multispecies biofilms create an environment conducive to resource sharing, resulting in increased biomass retention, or carrying capacity, for cooperative populations.
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.
Changes in microbial communities and associated water and gas geochemistry across a sulfate gradient in coal beds: Powder River Basin, USA
(2019-01) Schweitzer, Hannah D.; Ritter, Daniel J.; McIntosh, Jennifer C.; Barnhart, Elliott P.; Cunningham, Alfred B.; Vinson, David S.; Orem, William; Fields, Matthew W.
Competition between microbial sulfate reduction and methanogenesis drives cycling of fossil carbon and generation of CH4 in sedimentary basins. However, little is understood about the fundamental relationship between subsurface aqueous geochemistry and microbiology that drives these processes. Here we relate elemental and isotopic geochemistry of coal-associated water and gas to the microbial community composition from wells in two different coal beds across CH4 and SO42− gradients (Powder River Basin, Montana, USA). Areas with high CH4 concentrations generally have higher alkalinity and δ13C-DIC values, little to no SO42−, and greater conversion of coal-biodegradable organics to CH4 (based on δ13C-CH4 and δ13C-CO2 values). Wells with SO42− concentrations from 2 to 10 mM had bacterial populations dominated by several different sulfate-reducing bacteria and archaea that were mostly novel and unclassified. In contrast, in wells with SO42− concentrations <1 mM, the sequences were dominated by presumptive syntrophic bacteria as well as archaeal Methanosarcinales and Methanomicrobiales. The presence of sequences indicative of these bacteria in low SO42− methanogenic wells may suggest a syntrophic role in coal biodegradation and/or the generation of methanogenic substrates from intermediate organic compounds. Archaeal sequences were observed in all sampled zones, with an enrichment of sequences indicative of methanogens in low SO42− zones and unclassified sequences in high SO42− zones. However, sequences indicative of Methanomassiliicoccales were enriched in intermediate SO42− zones and suggest tolerance to SO42− and/or alternative metabolisms in the presence of SO42−. Moreover, sequences indicative of methylotrophic methanogens were more prevalent in an intermediate SO42− and CH4 well and results suggest an important role for methylotrophic methanogens in critical zone transitions. The presented results demonstrate in situ changes in bacterial and archaeal population distributions along a SO42− gradient associated with recalcitrant, organic carbon that is biodegraded and converted to CO2 and/or CH4.
Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer
(Elsevier BV, 2020-05) Moon, Ji-Won; Paradis, Charles J.; Joyner, Dominique C.; von Netzer, Frederick; Majumder, Erica L.; Dixon, Emma R.; Podar, Mircea; Ge, Xiaoxuan; Walian, Peter J.; Smith, Heidi J.; Wu, Xiaoqin; Zane, Grant M.; Walker, Kathleen F.; Thorgersen, Michael P.; Poole, Farris L. II; Lui, Lauren M.; Adams, Benjamin G.; De León, Kara B.; Brewer, Sheridan S.; Williams, Daniel E.; Lowe, Kenneth A.; Rodriguez, Miguel; Mehlhorn, Tonia L.; Pfiffner, Susan M.; Chakraborty, Romy; Arkin, Adam P.; Wall, Judy D.; Fields, Matthew W.; Adams, Michael W.W.; Stahl, David A.; Elias, Dwayne A.; Hazen, Terry C.
The processing of sediment to accurately characterize the spatially-resolved depth proﬁles of geophysical and geochemical properties along with signatures of microbial density and activity remains a challenge especially in complex contaminated areas. This study processed cores from two sediment boreholes from background and contaminated core sediments and surrounding groundwater. Fresh core sediments were compared by depth to capture the changes in sediment structure, sediment minerals, biomass, and pore water geochemistry in terms of major and trace elements including pollutants, cations, anions, and organic acids. Soil porewater samples were matched to groundwater level, ﬂow rate, and preferential ﬂows and compared to homogenized groundwater-only samples from neighboring monitoring wells. Groundwater analysis of nearby wells only revealed high sulfate and nitrate concentrations while the same analysis using sediment pore water samples with depth was able to suggest areas high in sulfate-and nitrate-reducing bacteria based on their decreased concentration and production of reduced by-products that could not be seen in the groundwater samples. Positive correlations among porewater content, total organic carbon, trace metals and clay minerals revealed a more complicated relationship among contaminant, sediment texture, groundwater table, and biomass. The ﬂuctuating capillary interface had high concentrations of Fe and Mn-oxides combined with trace elements including U, Th, Sr, Ba, Cu, and Co. This suggests the mobility of potentially hazardous elements, sediment structure, and biogeochemical factors are all linked together to impact microbial communities, emphasizing that solid interfaces play an important role in determining the abundance of bacteria in the sediments.
Comparative metagenomics reveals impact of contaminants on groundwater microbiomes
(2015-10) Hemme, C. L.; Tu, Qichao; Shi, Zhou; Qin, Yujia; Gao, W.; Deng, Ye; VanNostrand, J. D.; Wu, Liyou; He, Zhili; Chain, P. S.; Fields, Matthew W.; Rubin, E. M.; Tiedje, J. M.; Hazen, Terry C.; Arkin, Adam P.; Zhou, Jizhong
To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion ( >55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. These results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.
Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia
(2018-04) Carlson, Ross P.; Beck, Ashley E.; Phalak, Poonam; Fields, Matthew W.; Gedeon, Tomas; Hanley, Luke; Harcombe, W. R.; Henson, Michael A.; Heys, Jeffrey J.
Resource scarcity is a common stress in nature and has a major impact on microbial physiology. This review highlights microbial acclimations to resource scarcity, focusing on resource investment strategies for chemoheterotrophs from the molecular level to the pathway level. Competitive resource allocation strategies often lead to a phenotype known as overflow metabolism; the resulting overflow byproducts can stabilize cooperative interactions in microbial communities and can lead to cross-feeding consortia. These consortia can exhibit emergent properties such as enhanced resource usage and biomass productivity. The literature distilled here draws parallels between in silico and laboratory studies and ties them together with ecological theories to better understand microbial stress responses and mutualistic consortia functioning.
Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds
(2016-11) Hwang, Chiachi; Copeland, Alex; Lucas, Susan; Lapidus, Alla; Barry, Kerrie; Detter, John C.; Glavina del Rio, Tijana; Hammon, Nancy; Israni, Sanjay; Dalin, Eileen; Tice, Hope; Pitluck, S.; Chertkov, Olga; Brettin, Tom; Bruce, David; Han, C.; Schmutz, Jeremy; Larimer, F.; Land, M. L.; Hauser, Loren; Kyrpides, Nikos; Mikhailova, Natalia; Ye, Qi; Zhou, Jizhong; Richardson, Paul; Fields, Matthew W.
Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.
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.
Comprehensive bioimaging with fluorinated nanoparticles using breathable liquids
(2015-01) Kurczy, M. E.; Zhu, Zheng-Jiang; Ivanisevic, Julijana; Schuyler, A. M.; Lalwani, K.; Santidrian, A. F.; David, J. M.; Giddabasappa, A.; Roberts, A. J.; Olivos, H. J.; O'Brien, P. J.; Franco, Lauren C.; Fields, Matthew W.; Paris, L. P.; Friedlander, M.; Johnson, Caroline H.; Epstein, A. A.; Gendelman, H. E.; Wood, Malcolm R.; Felding, B. H.; Patti, G. J.; Spiker, M. E.; Siuzdak, Gary
Fluorocarbons are lipophobic and non-polar molecules that exhibit remarkable biocompatibility, with applications in liquid ventilation and synthetic blood. The unique properties of these compounds have also enabled mass spectrometry imaging of tissues where the fluorocarbons act as a Teflon-like coating for nanostructured surfaces to assist in desorption/ionization. Here we report fluorinated ?gold nanoparticles (f-AuNPs) designed to facilitate nanostructure imaging mass spectrometry. Irradiation of f-AuNPs results in the release of the fluorocarbon ligands providing a driving force for analyte desorption. The f-AuNPs allow for the mass spectrometry analysis of both lipophilic and polar (central carbon) metabolites. An important property of AuNPs is that they also act as contrast agents for X-ray microtomography and electron microscopy, a feature we have exploited by infusing f-AuNPs into tissue via fluorocarbon liquids to facilitate multimodal (molecular and anatomical) imaging.
Cr(VI) reduction and physiological toxicity are impacted by resource ratio in Desulfovibrio vulgaris
(2018-03) Franco, Lauren C.; Steinbeisser, Sadie; Zane, Grant M.; Wall, Judy D.; Fields, Matthew W.
Desulfovibrio spp. are capable of heavy metal reduction and are well-studied systems for understanding metal fate and transport in anaerobic environments. Desulfovibrio vulgaris Hildenborough was grown under environmentally relevant conditions (i.e., temperature, nutrient limitation) to elucidate the impacts on Cr(VI) reduction on cellular physiology. Growth at 20 °C was slower than 30 °C and the presence of 50 μM Cr(VI) caused extended lag times for all conditions, but once growth resumed the growth rate was similar to that without Cr(VI). Cr(VI) reduction rates were greatly diminished at 20 °C for both 50 and 100 μM Cr(VI), particularly for the electron acceptor limited (EAL) condition in which Cr(VI) reduction was much slower, the growth lag much longer (200 h), and viability decreased compared to balanced (BAL) and electron donor limited (EDL) conditions. When sulfate levels were increased in the presence of Cr(VI), cellular responses improved via a shorter lag time to growth. Similar results were observed between the different resource (donor/acceptor) ratio conditions when the sulfate levels were normalized (10 mM), and these results indicated that resource ratio (donor/acceptor) impacted D. vulgaris response to Cr(VI) and not merely sulfate limitation. The results suggest that temperature and resource ratios greatly impacted the extent of Cr(VI) toxicity, Cr(VI) reduction, and the subsequent cellular health via Cr(VI) influx and overall metabolic rate. The results also emphasized the need to perform experiments at lower temperatures with nutrient limitation to make accurate predictions of heavy metal reduction rates as well as physiological states in the environment.
Cultivation of a native alga for biomass and biofuel accumulation in coal bed methane production water
(2016-11) Hodgkiss, Logan H.; Nagy, J.; Barnhart, Elliott P.; Cunningham, Alfred B.; Fields, Matthew W.
Coal bed methane (CBM) production has resulted in thousands of ponds in the Powder River Basin of low-quality water in a water-challenged region. A green alga isolate, PW95, was isolated from a CBM production pond, and analysis of a partial ribosomal gene sequence indicated the isolate belongs to the Chlorococcaceae family. Different combinations of macro- and micronutrients were evaluated for PW95 growth in CBM water compared to a defined medium. A small level of growth was observed in unamended CBM water (0.15 g/l), and biomass increased (2-fold) in amended CBM water or defined growth medium. The highest growth rate was observed in CBM water amended with both N and P, and the unamended CBM water displayed the lowest growth rate. The highest lipid content (27%) was observed in CBM water with nitrate, and a significant level of lipid accumulation was not observed in the defined growth medium. Growth analysis indicated that nitrate deprivation coincided with lipid accumulation in CBM production water, and lipid accumulation did not increase with additional phosphorus limitation. The presented results show that CBM production wastewater can be minimally amended and used for the cultivation of a native, lipid-accumulating alga.
Draft Genome Sequence of Methanothermobacter thermautotrophicus WHS, a Thermophilic Hydrogenotrophic Methanogen from Washburn Hot Springs in Yellowstone National Park, USA
(American Society for Microbiology, 2021-02) McKay, Luke K.; Klingelsmith, Korinne B.; Deutschbauer, Adam M.; Inskeep, William P.; Fields, Matthew W.
A thermophilic methanogen was enriched in coculture from Washburn Hot Springs (Yellowstone National Park, USA), grown on carbon dioxide and hydrogen, and subsequently sequenced. The reconstructed 1.65-Mb genome sequence for Methanothermobacter thermautotrophicus WHS contributes to our understanding of hydrogenotrophic, CO2-reducing methanogenesis in geothermal ecosystems.
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.