Laura J. Crossey

Molecular Characterization of the Diversity and Distribution of a Thermal Spring Microbial Community by Using rRNA and Metabolic Genes

ABSTRACT The diversity and distribution of a bacterial community from Coffee Pots Hot Spring, a thermal spring in Yellowstone National Park with a temperature range of 39.3 to 74.1°C and pH range of 5.75 to 6.91, were investigated by sequencing cloned PCR products and quantitative PCR (qPCR) of 16S rRNA and metabolic genes. The spring was inhabited by three Aquificae genera—Thermocrinis, Hydrogenobaculum, and Sulfurihydrogenibium—and members of the Alpha-, Beta-, and Gammaproteobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, and candidate division OP5. The in situ chemical affinities were calculated for 41 potential metabolic reactions using measured environmental parameters and a range of hydrogen and oxygen concentrations. Reactions that use oxygen, ferric iron, sulfur, and nitrate as electron acceptors were predicted to be the most energetically favorable, while reactions using sulfate were expected to be less favorable. Samples were screened for genes used in ammonia oxidation (amoA, bacterial gene only), the reductive tricarboxylic acid (rTCA) cycle (aclB), the Calvin cycle (cbbM), sulfate reduction (dsrAB), nitrogen fixation (nifH), nitrite reduction (nirK), and sulfide oxidation (soxEF1) by PCR. Genes for carbon fixation by the rTCA cycle and nitrogen fixation were detected. All aclB sequences were phylogenetically related and spatially correlated to Sulfurihydrogenibium 16S rRNA gene sequences using qPCR (R2 = 0.99). This result supports the recent finding of citrate cleavage by enzymes other than ATP citrate lyase in the rTCA cycle of the Aquificaceae family. We briefly consider potential biochemical mechanisms that may allow Sulfurihydrogenibium and Thermocrinis to codominate some hydrothermal environments.

Organic-Inorganic Interactions and Sandstone Diagenesis

The maturation of organic material in hydrocarbon source rocks and inorganic diagenetic reactions in reservoir sandstones are a natural consequence when a prism of sedimentary rocks is buried. We can predict the distribution of porosity and permeability enhancement in potential hydrocarbon reservoirs by integrating the reaction processes characterizing the progressive diagenesis of a reservoir/source rock system. A variety of observations suggests that the organic solvents needed to increase aluminosilicate and carbonate solubilities in sandstones can be generated either by thermal or oxidative cracking of carbonylic or phenolic groups from kerogen in adjacent source rocks. For example, nuclear magnetic resonance (NMR) spectra of kerogen show that peripheral carbonylic and phenolic groups are released from the kerogen molecule before liquid hydrocarbons are generated. Experimental data indicate these water-soluble organic species can significantly affect the stability of both carbonates and aluminosilicates. Water-soluble organic acid anions (carboxylic) have been observed in oil-field waters in concentrations up to 10,000 ppm, and they commonly dominate the alkalinity in the fluid phase from 80° to 120°C. We can model the integration of organic and inorganic diagenetic reactions by constructing a series of potential reaction pathways with increasing temperature for a system that includes aluminosilicates, carbonates, organic chelate species (carboxylic and phenolic), and CO2. The important chemical divides in these diagenetic flow diagrams are dependent on temperature, the nature of the pH buffer (carbonate species or organic acid anion species), and the relationship between organic acid anions and PCO2 (P = partial pressure). Forward predictive capabilities result when this general diagenetic model is placed in a time-temperature framework. The detailed organic and inorganic geochemistry and the general thermal scenario used in the time-temperature ana ysis must be basin specific. Casting the diagenetic history of a sandstone into this type of process-oriented model helps us move from a descriptive mode to a predictive mode of analysis. Two types of information result: (1) general optimum conditions for porosity and permeability enhancement in sandstones are delineated and (2) specifically, the degree and potential for porosity and permeability enhancement are determined. Predictive models have been developed for several tectonic settings, including rift or pull-apart basins and intermontane or Laramide basins. From these reconstructions, we can forward-predict the porosity-enhancing potential of a diagenetic system based on an understanding of the reaction process in a time-temperature framework.

Model for tectonically driven incision of the younger than 6 Ma Grand Canyon

Accurate models for the incision of the Grand Canyon must include characterization of tectonic influences on incision dynamics such as active faulting and mantle to surface fluid interconnections. These young tectonic features support other geologic data that indicate that the Grand Canyon has been carved in the past 6 Ma. New U-Pb dates on speleothems are reinterpreted here in terms of improved geologic constraints and understanding of the modern aquifer. The combined data suggest that Grand Canyon incision rates have been relatively steady since 3–4 Ma. Differences in rates in the eastern (175–250 m/Ma) and western (50–80 m/Ma) Grand Canyon are explained by Neogene fault block uplift across the Toroweap-Hurricane system. Mantle tomography shows an abrupt step in mantle velocities near the Colorado Plateau edge, and geodynamic modeling suggests that upwelling asthenosphere is driving uplift of the Colorado Plateau margin relative to the Basin and Range. Our model for dynamic surface uplift in the past 6 Ma contrasts with the notion of passive incision of the Grand Canyon due solely to river integration and geomorphic response to base-level fall.

Chuar Group of the Grand Canyon: record of breakup of Rodinia, associated change in the global carbon cycle, and ecosystem expansion by 740 Ma

The Chuar Group (approximately 1600 m thick) preserves a record of extensional tectonism, ocean-chemistry fluctuations, and biological diversification during the late Neoproterozoic Era. An ash layer from the top of the section has a U-Pb zircon age of 742 +/- 6 Ma. The Chuar Group was deposited at low latitudes during extension on the north-trending Butte fault system and is inferred to record rifting during the breakup of Rodinia. Shallow-marine deposition is documented by tide- and wave-generated sedimentary structures, facies associations, and fossils. C isotopes in organic carbon show large stratigraphic variations, apparently recording incipient stages of the marked C isotopic fluctuations that characterize later Neoproterozoic time. Upper Chuar rocks preserve a rich biota that includes not only cyanobacteria and algae, but also heterotrophic protists that document increased food web complexity in Neoproterozoic ecosystems. The Chuar Group thus provides a well-dated, high-resolution record of early events in the sequence of linked tectonic, biogeochemical, environmental, and biological changes that collectively ushered in the Phanerozoic Eon.

Mantle-driven dynamic uplift of the Rocky Mountains and Colorado Plateau and its surface response: Toward a unified hypothesis

The correspondence between seismic velocity anomalies in the crust and mantle and the differential incision of the continental-scale Colorado River system suggests that significant mantle-to-surface interactions can take place deep within continental interiors. The Colorado Rocky Mountain region exhibits low-seismic-velocity crust and mantle associated with atypically high (and rough) topography, steep normalized river segments, and areas of greatest differential river incision. Thermochronologic and geologic data show that regional exhumation accelerated starting ca. 6–10 Ma, especially in regions underlain by low-velocity mantle. Integration and synthesis of diverse geologic and geophysical data sets support the provocative hypothesis that Neogene mantle convection has driven long-wavelength surface deformation and tilting over the past 10 Ma. Attendant surface uplift on the order of 500–1000 m may account for ∼25%–50% of the current elevation of the region, with the rest achieved during Laramide and mid-Tertiary uplift episodes. This hypothesis highlights the importance of continued multidisciplinary tests of the nature and magnitude of surface responses to mantle dynamics in intraplate settings.

Impact crater lakes on Mars

The robotic search for life on Mars centers on identifying accessible environments where the biological catalyst, water, has existed. The formation of large impact craters on Mars (>65 km diameter) may have resulted in the creation of ice-covered impact crater lakes, which would not freeze for thousands of years, even under present climatic conditions. Water could be supplied from deep confined aquifers penetrated by the impact craters, without the need for surface melt water. Freezing of the lakes is postponed owing to heat from impact generated melt-bearing deposits, from impact-related uplift of hotter rocks from depth, and from the latent heat of freezing of a deep crater lake. Abundant morphologic evidence for ancient crater lakes has not been found in Viking images, except for craters associated with outflow channels. However ice-covered crater lakes could have formed, and further searches for evidence of these lakes are warranted. The lake deposits from dissected impact craters may represent one of the best targets for future surface exobiology investigations or sample return missions from Mars.

Dissected hydrologic system at the Grand Canyon: Interaction between deeply derived fluids and plateau aquifer waters in modern springs and travertine

Geochemical study of water and gas discharging from the deeply incised aquifer system at the Grand Canyon, Arizona, provides a paradigm for understanding complex groundwater mixing phenomena, and Quaternary travertines deposited from cool springs provide a paleohydrologic record of this mixing. Geochemical data show that springs have marked compositional variability: those associated with active travertine accumulations (deeply derived endogenic waters) are more saline, richer in CO2, and elevated in 87Sr/86Sr relative to springs derived dominantly from surface recharge of plateau aquifers (epigenic waters). Endogenic waters and associated travertine are preferentially located along basement-penetrating faults. We propose a model whereby deeply derived fluids are conveyed upward via both magmatism and seismicity. Our model is supported by: (1) gas analyses from spring waters with high He/Ar and He/N2 and 3He/4He ratios indicating the presence of mantle-derived He; (2) large volumes of travertine and CO2-rich gases in springs recording high CO2 fluxes; and (3) 87Sr/86Sr in these springs that indicate circulation of waters through Precambrian basement. Geochemical trends are explained by mixing of epigenic waters of the Colorado Plateau aquifers with different endogenic end-member waters in different tectonic subprovinces. Endogenic waters are volumetrically minor but have significant effects on water chemistry. They are an important and largely unrecognized component of the hydrogeochemistry and neotectonics of the southwestern United States.

Degassing of mantle-derived CO2 and He from springs in the southern Colorado Plateau region - Neotectonic connections and implications for groundwater systems

Groundwaters of the southern Colorado Plateau–Arizona Transition Zone region are a heterogeneous mixture of chemically diverse waters including meteoric (epigenic) fluids, karst-aquifer waters, and deeply sourced (endogenic) fluids. We investigate the composition of travertine-depositing CO 2 -rich springs to determine the origin, transport, and mixing of these various components. The San Francisco Mountain recharge area has little surface flow. Instead, waters discharge through major springs hundreds of kilometers away. About 70% (9340 L/s) of the total recharge (13,500 L/s) discharges 100 km to the north in the incised aquifer system at Grand Canyon. Most of this water (85%; 8070 L/s) emerges through two travertine-depositing karst spring systems: Blue Springs (6230 L/s) and Havasu Springs (1840 L/s). About 30% of recharge (4150 L/s) flows to the south and discharges along NW-striking faults in the Arizona Transition Zone, forming the base flow for the Verde River. Geochemical data define regional mixing trends between meteoric recharge and different endogenic end members that range from bicarbonate waters to sulfate waters. Water quality in the region is dictated by the percentage and character of the endogenic inputs that cause a measurable degradation of groundwater quality for water supply. Sources for the high CO 2 include dissolution of limestone and dolostone (C carb ) and “external carbon” (C external ). C external is computed as the bicarbonate alkalinity (dissolved inorganic carbon [DIC]) minus the C carb (C external = DIC - C carb ). C external is deconvolved using carbon isotopes into biogenically derived sedimentary carbon (C organic ) and deep CO 2 inputs (C endogenic ). Measured δ 13 C values are −17‰ to +3‰ versus Pee Dee Belemnite (PDB). Assuming δ 13 C carb = +2‰, δ 13 C organic = −28‰, and δ 13 C endogenic = −5‰, water chemistry mixing models indicate that an average of 42% of the total DIC comes from dissolution of carbonate rocks, 25% from organic carbon, including soil-respired CO 2 ,and 33% from deep (endogenic) sources. Helium isotope values ( 3 He/ 4 He) in gases dissolved in spring waters in the southern Colorado Plateau region range from 0.10 to 1.16 R A (relative to air) indicating that a significant component of the deeply derived fluid is from the mantle (mean of 5% asthenospheric or 10% subcontinental lithospheric mantle source). Measured CO 2 / 3 He ratios of 2 × 10 9 to 1.4 × 10 13 are adjusted by removing the proportion of CO 2 from C carb and C organic to give values 10 for all but four samples. Various mixing models using CO 2 / 3 He suggest that the mantle-derived components of the CO 2 load are highly variable from spring to spring and may make up an average of ~10% of the total CO 2 load of the regional springs. Fluid-rock interactions involving endogenic fluids are suggested by 87 Sr/ 86 Sr, δ 18 O, and other tracers. The endogenic CO 2 component, multiplied by discharge for each spring, yields an integrated annual flux of deeply derived CO 2 to the groundwater system of ~1.4 × 10 9 mol/yr. This CO 2 emission from the Colorado Plateau region reflects a complex tectonic evolution involving Laramide hydration of the lithosphere above the Farallon slab, addition of fluids from mid-Tertiary mantle tectonism during slab removal, and ongoing fluid movement induced by neotectonic small-scale asthenospheric convection.

Thermal degradation of aqueous oxalate species

Abstract The aqueous thermal degradation of oxalic acid (a naturally occurring dicarboxylic acid) and its anions has been examined experimentally under variable conditions of temperature (160–230°C), time (24–96 h), buffered pH (4–7), and ionic strength (0.2–0.5 M). Decomposition of oxalate species follows a first-order rate law. Degradation rate increases with decreasing pH; the effects of ionic strength are not significant. Changes in reaction rate over the temperature range studied give activation energies that range from 29–50 kcal/mol over a starting solution pH range of 5–7. Extrapolation of these data to sedimentary basin temperatures suggests that oxalate species may be long-lived in formation waters. At 80°C, half-lives range from 2500 to 28,000 years at pH values of 5 and 7, respectively. Formate species are relatively stable degradation products over the range of conditions studied. Comparison of these data with results of other thermal degradation studies of carboxylic acids and their anions indicate that acetate stability > formate stability > oxalate stability > gallate and malonate stability. These results are consistent with the high concentrations of acetate relative to oxalate and malonate observed in formation waters.

Geomicrobiology of Cave Ferromanganese Deposits: A Field and Laboratory Investigation

Abstract Unusual ferromanganese deposits are found in several caves in New Mexico. The deposits are enriched in iron and manganese by as much as three orders of magnitude over the bedrock, differing significantly in mineralogy and chemistry from bedrock-derived insoluble residue. The deposits contain metabolically active microbial communities. Enrichment cultures inoculated from the ferromanganese deposits produced manganese oxides that were initially amorphous but developed into crystalline minerals over an 8-month period and beyond; no such progression occurred in killed controls. Phylogenetic analyses of sequences from clone libraries constructed from culture DNA identified two genera known to oxidize manganese, but most clones represent previously unknown manganese oxidizers. We suggest that this community is breaking down the bedrock and accumulating iron and manganese oxides in an oligotrophic environment.