Subsurface Sedimentary Environments Research Articles

Preferential degradation of long-chain alkyl substituted hydrocarbons in heavy oil under methanogenic conditions

Methanogenic crude oil degradation is a significant process in subsurface environments and degradation of crude oil n-alkanes has been well documented. However, little is known about the biodegradability of the resulting heavy oil. In this study, a methanogenic consortium enriched from Shengli oilfield generated 1.3–1.9 mmol CH4/g of heavy oil at a rate of 2.9–8.8 μmol CH4/g of oil/day. Four SARA fractions (saturates, aromatics, resins and asphaltenes) of oils experienced a loss in linear aliphatic structures. n-Alkylcyclohexanes, methyl-n-alkylcyclohexanes, n-alkyldecalins, n-alkylbenzenes, n-alkyltoluenes and n-alkylxylenes with alkyl side chains longer than 14 carbons were degraded over 50% compared to the undegraded oil. In addition, the extent of degradation of these hydrocarbons increased with increasing carbon length. Correspondingly, n-fatty acids and naphthenic acids with 1–3 naphthenic rings accumulated over time. 16S rRNA gene analysis revealed that aceticlastic Methanosarcina and Methanothrix dominated in the archaeal domain, and bacterial members related to Dehalococcoidia and Soehngenia were consistently present in the successive transfer cultures. However, neither assA/masD-like genes nor alkyl-substituted succinate metabolites were detected, indicating an alternative degradation pathway, rather than addition to fumarate. This study provides novel insights into methanogenic degradation of long-chain alkyl substituted hydrocarbons in heavy oil, which also extends our understanding of anaerobic degradation of crude oil in subsurface sedimentary environments.

The Sedimentary Cycle on Early Mars

Two decades of intensive research have demonstrated that early Mars ([Formula: see text]2 Gyr) had an active sedimentary cycle, including well-preserved stratigraphic records, understandable within a source-to-sink framework with remarkable fidelity. This early cycle exhibits first-order similarities to (e.g., facies relationships, groundwater diagenesis, recycling) and first-order differences from (e.g., greater aeolian versus subaqueous processes, basaltic versus granitic provenance, absence of plate tectonics) Earth's record. Mars’ sedimentary record preserves evidence for progressive desiccation and oxidation of the surface over time, but simple models for the nature and evolution of paleoenvironments (e.g., acid Mars, early warm and wet versus late cold and dry) have given way to the view that, similar to Earth, different climate regimes on Mars coexisted on regional scales and evolved on variable timescales, and redox chemistry played a pivotal role. A major accomplishment of Mars exploration has been to demonstrate that surface and subsurface sedimentary environments were both habitable and capable of preserving any biological record. ▪ Mars has an ancient sedimentary rock record with many similarities to but also many differences from Earth's sedimentary rock record. ▪ Mars’ ancient sedimentary cycle shows a general evolution toward more desiccated and oxidized surficial conditions. ▪ Climatic regimes of early Mars were relatively clement but with regional variations leading to different sedimentary mineral assemblages. ▪ Surface and subsurface sedimentary environments on early Mars were habitable and capable of preserving any biological record that may have existed.

Arsenic Detoxification by Geobacter Species.

This study examines arsenic transformation mechanisms utilized by Geobacter, a genus of iron-reducing bacteria that are predominant in many anoxic iron-rich subsurface environments. Geobacter species play a major role in microbially mediated arsenic release from metal hydroxides in the subsurface. This release raises arsenic concentrations in drinking water to levels that are high enough to cause major health problems. Therefore, information obtained from studies of Geobacter should shed light on arsenic cycling in iron-rich subsurface sedimentary environments, which may help reduce arsenic-associated illnesses. These studies should also help in the development of biosensors that can be used to detect arsenic contaminants in anoxic subsurface environments. We examined 14 different Geobacter genomes and found that all of these species possess genes coding for an arsenic detoxification system (ars operon), and some also have genes required for arsenic respiration (arr operon) and arsenic methylation (arsM).

Hydrogen Utilization Potential in Subsurface Sediments.

Subsurface microbial communities undertake many terminal electron-accepting processes, often simultaneously. Using a tritium-based assay, we measured the potential hydrogen oxidation catalyzed by hydrogenase enzymes in several subsurface sedimentary environments (Lake Van, Barents Sea, Equatorial Pacific, and Gulf of Mexico) with different predominant electron-acceptors. Hydrogenases constitute a diverse family of enzymes expressed by microorganisms that utilize molecular hydrogen as a metabolic substrate, product, or intermediate. The assay reveals the potential for utilizing molecular hydrogen and allows qualitative detection of microbial activity irrespective of the predominant electron-accepting process. Because the method only requires samples frozen immediately after recovery, the assay can be used for identifying microbial activity in subsurface ecosystems without the need to preserve live material. We measured potential hydrogen oxidation rates in all samples from multiple depths at several sites that collectively span a wide range of environmental conditions and biogeochemical zones. Potential activity normalized to total cell abundance ranges over five orders of magnitude and varies, dependent upon the predominant terminal electron acceptor. Lowest per-cell potential rates characterize the zone of nitrate reduction and highest per-cell potential rates occur in the methanogenic zone. Possible reasons for this relationship to predominant electron acceptor include (i) increasing importance of fermentation in successively deeper biogeochemical zones and (ii) adaptation of H2ases to successively higher concentrations of H2 in successively deeper zones.

Microbial Iron Redox Cycling in a Circumneutral-pH Groundwater Seep

The potential for microbially mediated redox cycling of iron (Fe) in a circumneutral-pH groundwater seep in north central Alabama was studied. Incubation of freshly collected seep material under anoxic conditions with acetate-lactate or H(2) as an electron donor revealed the potential for rapid Fe(III) oxide reduction (ca. 700 to 2,000 micromol liter(-1) day(-1)). Fe(III) reduction at lower but significant rates took place in unamended controls (ca. 300 micromol liter(-1) day(-1)). Culture-based enumerations (most probable numbers [MPNs]) revealed significant numbers (10(2) to 10(6) cells ml(-1)) of organic carbon- and H(2)-oxidizing dissimilatory Fe(III)-reducing microorganisms. Three isolates with the ability to reduce Fe(III) oxides by dissimilatory or fermentative metabolism were obtained (Geobacter sp. strain IST-3, Shewanella sp. strain IST-21, and Bacillus sp. strain IST-38). MPN analysis also revealed the presence of microaerophilic Fe(II)-oxidizing microorganisms (10(3) to 10(5) cells ml(-1)). A 16S rRNA gene library from the iron seep was dominated by representatives of the Betaproteobacteria including Gallionella, Leptothrix, and Comamonas species. Aerobic Fe(II)-oxidizing Comamonas sp. strain IST-3 was isolated. The 16S rRNA gene sequence of this organism is 100% similar to the type strain of the betaproteobacterium Comamonas testosteroni (M11224). Testing of the type strain showed no Fe(II) oxidation. Collectively our results suggest that active microbial Fe redox cycling occurred within this habitat and support previous conceptual models for how microbial Fe oxidation and reduction can be coupled in surface and subsurface sedimentary environments.

Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs

Biodegradation of crude oil in subsurface petroleum reservoirs has adversely affected the majority of the world's oil, making recovery and refining of that oil more costly. The prevalent occurrence of biodegradation in shallow subsurface petroleum reservoirs has been attributed to aerobic bacterial hydrocarbon degradation stimulated by surface recharge of oxygen-bearing meteoric waters. This hypothesis is empirically supported by the likelihood of encountering biodegraded oils at higher levels of degradation in reservoirs near the surface. More recent findings, however, suggest that anaerobic degradation processes dominate subsurface sedimentary environments, despite slow reaction kinetics and uncertainty as to the actual degradation pathways occurring in oil reservoirs. Here we use laboratory experiments in microcosms monitoring the hydrocarbon composition of degraded oils and generated gases, together with the carbon isotopic compositions of gas and oil samples taken at wellheads and a Rayleigh isotope fractionation box model, to elucidate the probable mechanisms of hydrocarbon degradation in reservoirs. We find that crude-oil hydrocarbon degradation under methanogenic conditions in the laboratory mimics the characteristic sequential removal of compound classes seen in reservoir-degraded petroleum. The initial preferential removal of n-alkanes generates close to stoichiometric amounts of methane, principally by hydrogenotrophic methanogenesis. Our data imply a common methanogenic biodegradation mechanism in subsurface degraded oil reservoirs, resulting in consistent patterns of hydrocarbon alteration, and the common association of dry gas with severely degraded oils observed worldwide. Energy recovery from oilfields in the form of methane, based on accelerating natural methanogenic biodegradation, may offer a route to economic production of difficult-to-recover energy from oilfields.

Geochemical constraints on CaCO 3 transport in subsurface sedimentary environments

Simple models for carbonate transport in subsurface sedimentary environments that do not carefully consider solution chemistry are unable to produce even order of magnitude predictions of the volume of water or time needed to transport calcium carbonate into or out of a carbonate rock unit. We feel that the time intervals necessary for creation or destruction of porosity cannot usually be well established, because the solution chemistry (e.g., P CO 2 ) and flow velocities of ancient waters are generally not determinable. Our calculations also indicate that major changes in porosity of medium- to large-sized carbonate rock units cannot take place by transporting a significant fraction of the calcium carbonate into or out of the rock unit. This conclusion is based on both the time needed for sufficient volumes of water to flow through the unit, and the probable reaction kinetics between the solution and rock that will usually result in relatively sharp reaction fronts. Based on these considerations, we suggest that most changes in porosity in carbonate rocks are the result of the redistribution of material within the rocks, rather than massive importation or exportation of calcium carbonate. However, in some sequences, allochthonous cementation of limestones may occur, because of mobilization of CaCO 3 brought about by high effective tectonic stresses and high pore-water fluid pressures.

Hydrogen concentrations as an indicator of the predominant terminal electron-accepting reactions in aquatic sediments

Factors controlling the concentration of dissolved hydrogen gas in anaerobic sedimentary environments were investigated. Results, presented here or previously, demonstrated that, in sediments, only microorganisms catalyze the oxidation of H 2 coupled to the reduction of nitrate, Mn(IV), Fe(III), sulfate, or carbon dioxide. Theoretical considerations suggested that, at steady-state conditions, H 2 concentrations are primarily dependent upon the physiological characteristics of the microorganism(s) consuming the H 2 and that organisms catalyzing H 2 oxidation, with the reduction of a more electrochemically positive electron acceptor, can maintain lower H 2 concentrations than organisms using electron acceptors which yield less energy from H 2 oxidation. The H 2 concentrations associated with the specified predominant terminal electron-accepting reactions in bottom sediments of a variety of surface water environments were: methanogenesis, 7–10 nM; sulfate reduction, 1–1.5 nM; Fe(III) reduction, 0.2 nM; Mn(IV) or nitrate reduction, less than 0.05 nM. Sediments with the same terminal electron acceptor for organic matter oxidation had comparable H 2 concentrations, despite variations in the rate of organic matter decomposition, pH, and salinity. Thus, each terminal electron-accepting reaction had a unique range of steady-state H 2 concentrations associated with it. Preliminary studies in a coastal plain aquifer indicated that H 2 concentrations also vary in response to changes in the predominant terminal electron-accepting process in deep subsurface environments. These studies suggest that H 2 measurements may aid in determining which terminal electron-accepting reactions are taking place in surface and subsurface sedimentary environments.