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Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on "Trends and Future Challenges in Sampling The Deep Subsurface" was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty, and sponsored by The Ohio State University and the Sloan Foundation's Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop. [ABSTRACT FROM AUTHOR]

The texture and mineralogy of solid phases resulting from biogeochemical metal reduction of U(VI)-FeOOH slurries was investigated over a period of four years. Solid-phase reaction products were analyzed with EXAFS, TEM, and XRD following fermentative reduction of uranium-loaded ferric hydroxide precursors with 0.01 and 0.05 cation mole fraction (CMF) U by cultures of Thermoanaerobacter sp. strain TOR-39. Only minor changes could be distinguished between 3 and 51 months for most slurries. Magnetite, goethite, uraninite, and minor akaganéite were present after 3 months at both U-CMFs. Akaganéite was not detected by XRD after 3 months, but was still observed by TEM after 50 months. Increasing uranium in the starting slurries led to a greater proportion of oxidized iron in the solid-phase products. Euhedral goethite and subhedral to euhedral magnetite were observed at all times. Uraninite was observed in clusters of <10 nm particles without any particular relationship to the iron minerals. HRTEM imaging indicated that even the smallest uraninite particles were well crystallized, with textures that remained consistent throughout the duration of experiments. X-ray absorption spectra after 3 months indicated 100% and 96.4% U(IV) in 0.01 and 0.05 CMF U slurries, respectively. EXAFS spectra were consistent with uraninite at both uranium levels, plus additional non-uraninite U(IV) for 0.05 CMF U. One 0.05 CMF U culture slurry was found to have a lower pH and a more oxidized final iron mineral assemblage; in this case uraninite was not observed by XRD, but large (101 nm average diameter) rounded uraninite grains were observed by TEM. These grains were observed in chains or aggregates often connected by necks, in textures suggestive of biological influence. HRTEM demonstrated each grain was composed of poorly oriented, primary, 2-5 nm uraninite crystallites. Uraninite crystal growth occurred by nanoparticle aggregation, but ripening was not observed even though incubation temperatures were held at 65 °C for 20 days. Thus, previous studies of biogenic nanoparticulate uraninite short-term reactivity are likely to be representative of systems aged over a period of years. [ABSTRACT FROM AUTHOR]

Abstract: The Southeast Regional Carbon Sequestration Partnership (SECARB) early project in western Mississippi has been testing monitoring tools and approaches to document storage efficiency and storage permanence under conditions of CO2 EOR as well as downdip injection into brine. Denbury Onshore LLC is host for the study and has brought a depleted oil and gas reservoir, Cranfield Field, under CO2 flood. Injection was started in July 2008 and has now achieved injection rates greater than 1.2 million tons/year though 23 wells, with cumulative mass injected as of August, 2010 of 2.2 million metric tons. Injection is into coarse grained fluvial deposits of the Cretaceous lower Tuscaloosa Formation in a gentle anticline at depths of 3300 m. A team of researchers from 10 institutions has collected data from five study areas, each with a different goal and different spatial and temporal scale. The Phase 2 study began at the start of injection and has been using pressure and temperature as a tool for assessing permanence mostly in the oil productive interval. Real-time read-out shows high sensitivity to distant changes in injection rate and confirms the geologic model of reservoir compartmentalization. Above-zone pressure monitoring ∼120 m above the injection interval is used to test the sensitivity of this approach for documentation of integrity of the confining system in an area of numerous well completions as pressure increase is induced in the reservoir by more than 70 bar. Monitoring of the High Volume Injection Test (HiVIT) area includes repeat measurements of aqueous geochemistry in the injection zone. Rock-water- CO2 interactions in the reservoir as CO2 dissolves are minimized by mineral “armoring” by abundant chlorite cement in high permeability reservoir sandstone. Geochemical monitoring of confined freshwater aquifers at depths of 70–100 m is underway. Groundwater analysis focuses on assessment of the sensitivity of this method to detect leakage above background variability. A repeat seismic survey of the HiVIT is planned for late 2010 to assess saturation change especially in downdip brine-only areas. A study focused on feasibility of monitoring the shallow subsurface to separate leakage from normal complex surface fluxes is underway at an monitoring array installed in October 2009 to assess the interactions of recharge, soil gas, and shallow groundwater aquifers. Recent well re-entry and tracer injection will provide further information to interpret observed elevated deep-sourced methane. The Detailed Area Study (DAS) is collecting dense time-lapse data from closely-spaced three well array of an injector and two observation wells. The observation wells were completed with fiberglass casing to facilitate electrical resistance tomography (ERT) measurements, and a diverse array of instrumentation was both cemented behind casing and suspended on tubing. Injection started at the DAS December 1, 2009. We have measured pulsed neutron and resistivity via wireline, downhole and above-zone pressure, distributed temperature, and fluid chemistry including introduced pulses of perfluorocarbons, noble gases, and SF6 as tracers. Between wells, time-lapse crosswell seismic and electrical resistance tomography (ERT) are used to measure saturation change. The goals are to measure changes as fluids evolve from single phase (brine) to two phase (CO2–brine) in order to document linkages between pressure and sweep efficiency. A time-lapse VSP survey bridges the vertical resolution and areal coverage between cross-well and surface seismic. The repeat surveys for many tools are scheduled for September, 2010. Reservoir characterization based on cores, historic and new wireline log data, production history, hydrologic tests, fluid analysis, and a three-D seismic survey have been used in multiple numerical models to predict reservoir response in order to design effective monitoring strategies and optimize deployment. History matching of observed response to predicted response is used to interpret results and improve confidence in conceptual models and numerical approaches. Probabilistic methods have been used to assess the significant uncertainties resulting from reservoir heterogeneity. This study is funded by the US Department of Energy, National Energy Technology Laboratory as part of the Regional Carbon Sequestration Partnerships program. SECARB is led by Southern States Energy Board. [Copyright &y& Elsevier]

Production of both nano-sized particles of crystalline pure phase magnetite and magnetite substituted with Co, Ni, Cr, Mn, Zn or the rare earths for some of the Fe has been demonstrated using microbial processes. This microbial production of magnetic nanoparticles can be achieved in large quantities and at low cost. In these experiments, over 1 kg (wet weight) of Zn-substituted magnetite (nominal composition of ZnFeO) was recovered from 30 l fermentations. Transmission electron microscopy (TEM) was used to confirm that the extracellular magnetites exhibited good mono-dispersity. TEM results also showed a highly reproducible particle size and corroborated average crystallite size (ACS) of 13.1 ± 0.8 nm determined through X-ray diffraction ( N = 7) at a 99% confidence level. Based on scale-up experiments performed using a 35-l reactor, the increase in ACS reproducibility may be attributed to a combination of factors including an increase of electron donor input, availability of divalent substitution metal ions and fewer ferrous ions in the case of substituted magnetite, and increased reactor volume overcoming differences in each batch. Commercial nanometer sized magnetite (25–50 nm) may cost $500/kg. However, microbial processes are potentially capable of producing 5–90 nm pure or substituted magnetites at a fraction of the cost of traditional chemical synthesis. While there are numerous approaches for the synthesis of nanoparticles, bacterial fermentation of magnetite or metal-substituted magnetite may represent an advantageous manufacturing technology with respect to yield, reproducibility and scalable synthesis with low costs at low energy input. [ABSTRACT FROM AUTHOR]

The potentially toxic effects of soluble lanthanide (L) ions, although microbially induced mineralization can facilitate the formation of tractable materials, has been one factor preventing the more widespread use of L-ions in biotechnology. Here, we propose a new mixed-L precursor method as compared to the traditional direct addition technique. L (Nd, Gd, Tb, Ho and Er)-substituted magnetites, L y Fe3 − y O4 were microbially produced using L-mixed precursors, L x Fe1 − x OOH, where x = 0.01–0.2. By combining lanthanides into the akaganeite precursor phase, we were able to mitigate some of the toxicity, enabling the microbial formation of L-substituted magnetites using a metal reducing bacterium, Thermoanaerobacter sp. TOR-39. The employment of L-mixed precursors enabled the microbial formation of L-substituted magnetite, nominal composition up to L0.06Fe2.94O4, with at least tenfold higher L-concentration than could be obtained when the lanthanides were added as soluble salts. This mixed-precursor method can be used to extend the application of microbially produced L-substituted magnetite, while also mitigating their toxicity. [ABSTRACT FROM AUTHOR]

The article reports on the physicochemical and mineralogical characterization of soil from a field research site in Oak Ridge, Tennessee. Site characterization is an essential step in determining the feasibility of remedial alternatives at hazardous waste sites. Physico-chemical and mineralogical characterization of uranium-contaminated soils in deeply weathered saprolite at Area 2 of the Department of Energy Field Research Center, was accomplished to examine the feasibility of bioremediation. The results indicate that concentrations of uranium in saprolite were closely related to low pH.

Advances in our understanding of functional genomics are best addressed by integrative studies that include measurements of mRNA, proteins, and low molecular weight metabolites over time and varied conditions. Bioinformatics can then be used to relate this data to the genome. Current technology allows for comprehensive and rapid mRNA expression profiling and mass spectrophotometric measurement of low molecular weight intermediates and metabolic products. In prokaryotic organisms, this combination provides a potentially powerful tool for identifying gene function and regulatory networks even in the absence of a combined proteomic approach. [Copyright &y& Elsevier]

Abstract: A highly integrated geochemical program was conducted at the Cranfield CO2-enhanced oil recovery (EOR) and sequestration site, Mississippi, U.S.A.. The program included extensive field geochemical monitoring, a detailed petrographic study, and an autoclave experiment under in situ reservoir conditions. Results show that mineral reactions in the Lower Tuscaloosa reservoir were minor during CO2 injection. Brine chemistry remained largely unchanged, which contrasts with significant changes observed in other field tests. Field fluid sampling and laboratory experiments show consistently slow reactions. Carbon isotopic composition and CO2 content in the gas phase reveal simple two-end-member mixing between injected and original formation gas. We conclude that the reservoir rock, which is composed mainly of minerals with low reactivity (average quartz 79.4%, chlorite 11.8%, kaolinite 3.1%, illite 1.3%, concretionary calcite and dolomite 1.5%, and feldspar 0.2%), is relatively unreactive to CO2. The significance of low reactivity is both positive, in that the reservoir is not impacted, and negative, in that mineral trapping is insignificant. [Copyright &y& Elsevier]

The phosphorus composition of banded-iron formations (BIFs) has been used as a proxy for Precambrian seawater composition and the paleoeredox state of Earth's surface environment. However, it is unclear whether the phosphorus in BIFs originally entered the sediment as a sorbed component of the iron oxyhydroxide particles, or whether it was incorporated into the biomass of marine phytoplankton. We conducted high-resolution mineral analyses and report here the first detection of an Fe(III) acetate salt, as well as nanocrystals of apatite in association with magnetite, in the 2.48 Ga Dales Gorge Member of the Brockman Iron Formation (a BIF), Hamersley, Western Australia. The clusters of apatite are similar in size and morphology to biogenic apatite crystals resulting from biomass decay in Phanerozoic marine sediments, while the formation of an Fe(III) acetate salt and magnetite not only implies the original presence of biomass in the BIF sediments, but also that organic carbon likely served as an electron donor during bacterial Fe(III) reduction. This study is important because it suggests that phytoplankton may have played a key role in the transfer of phosphorus (and other trace elements) from the photic zone to the seafloor. [ABSTRACT FROM AUTHOR]

Abstract: Sedimentary basins in general, and deep saline aquifers in particular, are being investigated as possible repositories for large volumes of anthropogenic CO2 that must be sequestered to mitigate global warming and related climate changes. To investigate the potential for the long-term storage of CO2 in such aquifers, 1600t of CO2 were injected at 1500m depth into a 24-m-thick “C” sandstone unit of the Frio Formation, a regional aquifer in the US Gulf Coast. Fluid samples obtained before CO2 injection from the injection well and an observation well 30m updip showed a Na–Ca–Cl type brine with ∼93,000mg/L TDS at saturation with CH4 at reservoir conditions; gas analyses showed that CH4 comprised ∼95% of dissolved gas, but CO2 was low at 0.3%. Following CO2 breakthrough, 51h after injection, samples showed sharp drops in pH (6.5–5.7), pronounced increases in alkalinity (100–3000mg/L as HCO3) and in Fe (30–1100mg/L), a slug of very high DOC values, and significant shifts in the isotopic compositions of H2O, DIC, and CH4. These data, coupled with geochemical modeling, indicate corrosion of pipe and well casing as well as rapid dissolution of minerals, especially calcite and iron oxyhydroxides, both caused by lowered pH (initially ∼3.0 at subsurface conditions) of the brine in contact with supercritical CO2. These geochemical parameters, together with perfluorocarbon tracer gases (PFTs), were used to monitor migration of the injected CO2 into the overlying Frio “B”, composed of a 4-m-thick sandstone and separated from the “C” by ∼15m of shale and siltstone beds. Results obtained from the Frio “B” 6months after injection gave chemical and isotopic markers that show significant CO2 (2.9% compared with 0.3% CO2 in dissolved gas) migration into the “B” sandstone. Results of samples collected 15months after injection, however, are ambiguous, and can be interpreted to show no additional injected CO2 in the “B” sandstone. The presence of injected CO2 may indicate migration from “C” to “B” through the intervening beds or, more likely, a short-term leakage through the remedial cement around the casing of a 50-year old well. Results obtained to date from four shallow monitoring groundwater wells show no brine or CO2 leakage through the Anahuac Formation, the regional cap rock. [Copyright &y& Elsevier]

A marine psychrotolerant, dissimilatory Fe(III)-reducing bacterium, Shewanella sp. strain PV-4, from the microbial mat at a hydrothermal vent of Loihi Seamount in the Pacific Ocean has been further characterized, with emphases on metal reduction and iron biomineralization. The strain is able to reduce metals such as Fe(III), Co(III), Cr(VI), Mn(IV), and U(VI) as electron acceptors while using lactate, formate, pyruvate, or hydrogen as an electron donor. Growth during iron reduction occurred over the pH range of 7.0 to 8.9, a sodium chloride range of 0.05 to 5%, and a temperature range of 0 to 37°C, with an optimum growth temperature of 18°C. Unlike mesophilic dissimilatory Fe(III)-reducing bacteria, which produce mostly superparamagnetic magnetite (<35 nm), this psychrotolerant bacterium produces well-formed single-domain magnetite (>35 nm) at temperatures from 18 to 37°C. The genome size of this strain is about 4.5 Mb. Strain PV-4 is sensitive to a variety of commonly used antibiotics except ampicillin and can acquire exogenous DNA (plasmid pCM157) through conjugation. [ABSTRACT FROM AUTHOR]

Discusses the isolation and characterization of metal-reducing Thermoanaerobacter ethanolicus strains from samples taken from the Piceance Basin in Colorado. Results of the molecular analyses of bacterial isolates; Physiological characteristics of isolates; Mineralogical characteristics.

Arctic permafrost ecosystems store ~50% of global belowground carbon (C) that is vulnerable to increased microbial degradation with warmer active layer temperatures and thawing of the near surface permafrost. We used anoxic laboratory incubations to estimate anaerobic CO2 production and methanogenesis in active layer (organic and mineral soil horizons) and permafrost samples from center, ridge and trough positions of water-saturated low-centered polygon in Barrow Environmental Observatory, Barrow AK, USA. Methane (CH4 ) and CO2 production rates and concentrations were determined at -2, +4, or +8 °C for 60 day incubation period. Temporal dynamics of CO2 production and methanogenesis at -2 °C showed evidence of fundamentally different mechanisms of substrate limitation and inhibited microbial growth at soil water freezing points compared to warmer temperatures. Nonlinear regression better modeled the initial rates and estimates of Q10 values for CO2 that showed higher sensitivity in the organic-rich soils of polygon center and trough than the relatively drier ridge soils. Methanogenesis generally exhibited a lag phase in the mineral soils that was significantly longer at -2 °C in all horizons. Such discontinuity in CH4 production between -2 °C and the elevated temperatures (+4 and +8 °C) indicated the insufficient representation of methanogenesis on the basis of Q10 values estimated from both linear and nonlinear models. Production rates for both CH4 and CO2 were substantially higher in organic horizons (20% to 40% wt. C) at all temperatures relative to mineral horizons (<20% wt. C). Permafrost horizon (~12% wt. C) produced ~5-fold less CO2 than the active layer and negligible CH4 . High concentrations of initial exchangeable Fe(II) and increasing accumulation rates signified the role of iron as terminal electron acceptors for anaerobic C degradation in the mineral horizons., (Published 2014. This article is a U.S. Government work and is in the public domain in the USA.)

A magnetocaloric pump provides a simple means of pumping fluid using only external thermal and magnetic fields. The principle, which can be traced back to the early work of Rosensweig, is straightforward. Magnetic materials tend to lose their magnetization as the temperature approaches the material's Curie point. Exposing a column of magnetic fluid to a uniform magnetic field coincident with a temperature gradient produces a pressure gradient in the magnetic fluid. As the fluid heats up, it loses its attraction to the magnetic field and is displaced by cooler fluid. The impact of such a phenomenon is obvious: fluid propulsion with no moving mechanical parts. Until recently, limitations in the magnetic and thermal properties of conventional materials severely limited practical operating pressure gradients. However, recent advancements in the design of metal substituted magnetite enable fine control over both the magnetic and thermal properties of magnetic nanoparticles, a key element in colloidal-based magnetic fluids (ferrofluids). This paper begins with a basic description of the process and previous limitations due to material properties. This is followed by a review of existing methods of synthesizing magnetic nanoparticles as well as an introduction to a new approach based on thermophilic metal-reducing bacteria. We compare two compounds and show, experimentally, significant variation in specific magnetic and thermal properties. We develop the constitutive thermal, magnetic, and fluid dynamic equations associated with a magnetocaloric pump and validate our finite-element model with a series of experiments. Preliminary results show a good match between the model and experiment as well as approximately an order of magnitude increase in the fluid flow rate over conventional magnetite-based ferrofluids operating below 80 degrees C. Finally, as a practical demonstration, we describe a novel application of this technology: pumping fluids at the "lab-on-a-chip" microfluidic scale.