Identifying and Understanding Microbial Methanogenesis in CO2 Storage.

Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO2 can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO2, yet there has been little consideration of the subsurface microbial impact on CO2 storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO2 that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO2 storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H2 generation. We expect that the bioavailability of H2 (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO2 storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO2 storage sites and its potential impact.

Rapid microbial methanogenesis during CO2 storage in hydrocarbon reservoirs.

Carbon capture and storage (CCS) is a key technology to mitigate the environmental impact of carbon dioxide (CO2) emissions. An understanding of the potential trapping and storage mechanisms is required to provide confidence in safe and secure CO2 geological sequestration1,2. Depleted hydrocarbon reservoirs have substantial CO2 storage potential1,3, and numerous hydrocarbon reservoirs have undergone CO2 injection as a means of enhanced oil recovery (CO2-EOR), providing an opportunity to evaluate the (bio)geochemical behaviour of injected carbon. Here we present noble gas, stable isotope, clumped isotope and gene-sequencing analyses from a CO2-EOR project in the Olla Field (Louisiana, USA). We show that microbial methanogenesis converted as much as 13-19% of the injected CO2 to methane (CH4) and up to an additional 74% of CO2 was dissolved in the groundwater. We calculate an in situ microbial methanogenesis rate from within a natural system of 73-109 millimoles of CH4 per cubic metre (standard temperature and pressure) per year for the Olla Field. Similar geochemical trends in both injected and natural CO2 fields suggest that microbial methanogenesis may be an important subsurface sink of CO2 globally. For CO2 sequestration sites within the environmental window for microbial methanogenesis, conversion to CH4 should be considered in site selection.

Hydrothermal 15N15N abundances constrain the origins of mantle nitrogen.

Nitrogen is the main constituent of the Earth's atmosphere, but its provenance in the Earth's mantle remains uncertain. The relative contribution of primordial nitrogen inherited during the Earth's accretion versus that subducted from the Earth's surface is unclear1-6. Here we show that the mantle may have retained remnants of such primordial nitrogen. We use the rare 15N15N isotopologue of N2 as a new tracer of air contamination in volcanic gas effusions. By constraining air contamination in gases from Iceland, Eifel (Germany) and Yellowstone (USA), we derive estimates of mantle δ15N (the fractional difference in 15N/14N from air), N2/36Ar and N2/3He. Our results show that negative δ15N values observed in gases, previously regarded as indicating a mantle origin for nitrogen7-10, in fact represent dominantly air-derived N2 that experienced 15N/14N fractionation in hydrothermal systems. Using two-component mixing models to correct for this effect, the 15N15N data allow extrapolations that characterize mantle endmember δ15N, N2/36Ar and N2/3He values. We show that the Eifel region has slightly increased δ15N and N2/36Ar values relative to estimates for the convective mantle provided by mid-ocean-ridge basalts11, consistent with subducted nitrogen being added to the mantle source. In contrast, we find that whereas the Yellowstone plume has δ15N values substantially greater than that of the convective mantle, resembling surface components12-15, its N2/36Ar and N2/3He ratios are indistinguishable from those of the convective mantle. This observation raises the possibility that the plume hosts a primordial component. We provide a test of the subduction hypothesis with a two-box model, describing the evolution of mantle and surface nitrogen through geological time. We show that the effect of subduction on the deep nitrogen cycle may be less important than has been suggested by previous investigations. We propose instead that high mid-ocean-ridge basalt and plume δ15N values may both be dominantly primordial features.

Author Correction: Forearc carbon sink reduces long-term volatile recycling into the mantle.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

Author Correction: Forearc carbon sink reduces long-term volatile recycling into the mantle.

Change history: In this Article, the original affiliation 2 was not applicable and has been removed. In addition, in the Acknowledgements there was a statement missing and an error in a name. These errors have been corrected online.

Forearc carbon sink reduces long-term volatile recycling into the mantle.

Carbon and other volatiles in the form of gases, fluids or mineral phases are transported from Earth's surface into the mantle at convergent margins, where the oceanic crust subducts beneath the continental crust. The efficiency of this transfer has profound implications for the nature and scale of geochemical heterogeneities in Earth's deep mantle and shallow crustal reservoirs, as well as Earth's oxidation state. However, the proportions of volatiles released from the forearc and backarc are not well constrained compared to fluxes from the volcanic arc front. Here we use helium and carbon isotope data from deeply sourced springs along two cross-arc transects to show that about 91 per cent of carbon released from the slab and mantle beneath the Costa Rican forearc is sequestered within the crust by calcite deposition. Around an additional three per cent is incorporated into the biomass through microbial chemolithoautotrophy, whereby microbes assimilate inorganic carbon into biomass. We estimate that between 1.2 × 108 and 1.3 × 1010 moles of carbon dioxide per year are released from the slab beneath the forearc, and thus up to about 19 per cent less carbon is being transferred into Earth's deep mantle than previously estimated.

IP3-gated channels and their occurrence relative to CNG channels in the soma and dendritic knob of rat olfactory receptor neurons.

Olfactory receptor neurons respond to odorants with G protein-mediated increases in the concentrations of cyclic adenosine 3',5'-monophosphate (cAMP) and/or inositol-1,4,5-trisphosphate (IP3). This study provides evidence that both second messengers can directly activate distinct ion channels in excised inside-out patches from the dendritic knob and soma membrane of rat olfactory receptor neurons (ORNs). The IP3-gated channels in the dendritic knob and soma membranes could be classified into two types, with conductances of 40 +/- 7 pS (n = 5) and 14 +/- 3 pS (n = 4), with the former having longer open dwell times. Estimated values of the densities of both channels from the same inside-out membrane patches were very much smaller for IP3-gated than for CNG channels. For example, in the dendritic knob membrane there were about 1000 CNG channels x microm(-2) compared to about 85 IP3-gated channels x microm(-2). Furthermore, only about 36% of the dendritic knob patches responded to IP3, whereas 83% of the same patches responded to cAMP. In the soma, both channel densities were lower, with the CNG channel density again being larger ( approximately 57 channels x microm(-2)) than that of the IP3-gated channels ( approximately 13 channels x microm(-2)), with again a much smaller fraction of patches responding to IP3 than to cAMP. These results were consistent with other evidence suggesting that the cAMP-pathway dominates the IP3 pathway in mammalian olfactory transduction.

Anomalous mole-fraction effects in recombinant and native cyclic nucleotide-gated channels in rat olfactory receptor neurons.

Anomalous mole-fraction effects (AMFE) were studied, using the inside-out configuration of the patchclamp technique, in both recombinant wild-type alpha-homomeric rat olfactory adenosine 3',5'-cyclic monophosphate (cAMP)-gated channels (rOCNC1) expressed in human embryonic kidney cells (HEK 293) and native cyclic nucleotide-gated (CNG) channels in acutely isolated rat olfactory receptor neurons. Single-channel and macroscopic currents were activated by 200 microM and 500 microM cAMP, respectively. Macroscopic currents, measured with mixtures of Na(+)-NH(4)(+) or Cs(+)-Li(+) in the cytoplasmic bathing solution, displayed AMFE in the rOCNC1 channels at both positive and negative membrane potentials. The rOCNC1 single-channel conductance showed a distinct minimum (or maximum) in an 80% Na(+)-20% NH(4)(+) mixture (or a 60% Cs(+)-40% Li(+) mixture), but only at positive membrane potentials. Macroscopic measurements in native olfactory CNG channels with mixtures of Na(+)-NH(4)(+) indicated similar AMFE. These results suggest that both native CNG channels and recombinant alpha-homomeric channels allow several ions to be present simultaneously within the channel pore. They also further validate the dominant role of the alpha-subunit in permeation through these channels, provide the first evidence to suggest that rOCNC1 channels have multi-ion properties and further justify the use of the rOCNC1 channel as an effective model for structure-function studies of ion permeation and selectivity in olfactory CNG channels.

Numerical analysis of Ca2+ depletion in the transverse tubular system of mammalian muscle.

Calcium currents were recorded in contracting and actively shortening mammalian muscle fibers. In order to characterize the influence of extracellular calcium concentration changes in the small unstirred lumina of the transverse tubular system (TTS) on the time course of the slow L-type calcium current (I(Ca)), we have combined experimental measurements of I(Ca) with quantitative numerical simulations of Ca2+ depletion. I(Ca) was recorded both in calcium-buffered and unbuffered external solutions using the two-microelectrode voltage clamp technique (2-MVC) on short murine toe muscle fibers. A simulation program based on a distributed TTS model was used to calculate the effect of ion depletion in the TTS. The experimental data obtained in a solution where ion depletion is suppressed by a high amount of a calcium buffering agent were used as input data for the simulation. The simulation output was then compared with experimental data from the same fiber obtained in unbuffered solution. Taking this approach, we could quantitatively show that the calculated Ca2+ depletion in the transverse tubular system of contracting mammalian muscle fibers significantly affects the time-dependent decline of Ca2+ currents. From our findings, we conclude that ion depletion in the tubular system may be one of the major effects for the I(Ca) decline measured in isotonic physiological solution under voltage clamp conditions.

Ion permeation and selectivity of wild-type recombinant rat CNG (rOCNC1) channels expressed in HEK293 cells.

The permeation properties of adenosine 3', 5'-cyclic monophosphate (cAMP)-activated recombinant rat olfactory cyclic nucleotide-gated channels (rOCNC1) in human embryonic kidney (HEK 293) cells were investigated using inside-out excised membrane patches. The relative permeability of these rOCNC1 channels to monovalent alkali cations and organic cations was determined from measurements of the changes in reversal potential upon replacing sodium in the bathing solution with different test cations. The permeability ratio of Cl(-) relative to Na(+) (P(Cl)/P(Na)) was about 0.14, confirming that these channels are mainly permeable to cations. The sequence of relative permeabilities of monovalent alkali metal ions in these channels was P(Na) > or = P(K) > P(Li) > P(Cs) > or = P(Rb), which closely corresponds to a high-strength field sequence as previously determined for native rat olfactory receptor neurons (ORNs). The permeability sequence for organic cations relative to sodium was P(NH3OH) > P(NH4) > P(Na) > P(Tris) > P(Choline) > P(TEA), again in good agreement with previous permeability ratios obtained in native rat ORNs. Single-channel conductance sequences agreed surprisingly well with permeability sequences. These conductance measurements also indicated that, even in asymmetric bi-ionic cation solutions, the conductance was somewhat independent of current direction and dependent on the composition of both solutions. These results indicate that the permeability properties of rOCNC1 channels are similar to those of native rat CNG channels, and provide a suitable reference point for exploring the molecular basis of ion selectivity in recombinant rOCNC1 channels using site-directed mutagenesis.

M2 pore mutations convert the glycine receptor channel from being anion- to cation-selective.

Three mutations in the M2 transmembrane domains of the chloride-conducting alpha1 homomeric glycine receptor (P250Delta, A251E, and T265V), which normally mediate fast inhibitory neurotransmission, produced a cation-selective channel with P(Cl)/P(Na), = 0.27 (wild-type P(Cl)/P(Na) = 25), a permeability sequence P(Cs) > P(K) > P(Na) > P(Li), an impermeability to Ca(2+), and a reduced glycine sensitivity. Outside-out patch measurements indicated reversed and accentuated rectification with extremely low mean single channel conductances of 3 pS (inward current) and 11 pS (outward current). The three inverse mutations, to those analyzed in this study, have previously been shown to make the alpha7 acetylcholine receptor channel anion-selective, indicating a common location for determinants of charge selectivity of inhibitory and excitatory ligand-gated ion channels.

Very negative potential for half-inactivation of, and effects of anions on, voltage-dependent sodium currents in acutely isolated rat olfactory receptor neurons.

Previous measurements with CsF pipette solutions using whole-cell patch-clamp techniques in dissociated rat olfactory receptor neurons (ORNs) indicated that the sodium currents had very negative inactivation characteristics with the implication that the cell resting potential must also normally have a very negative value. This study supports the conclusions that such an effect was real and not dependent on either the nature of the pipette anions or the recording situation previously used. For all pipette solutions, sodium currents showed a threshold activation approximately -80 mV and half-maximal activation voltages approximately -55 with half-inactivation potential < or =-100 mV, without being significantly affected by the replacement of F(-) by other pipette anions (H(2)PO(-)(4) and acetate(-)) or the addition of nucleotides and glutathione (which did cause a very slight positive shift). F(-), followed by H(2)PO(-)(4) and to a much lesser extent by acetate(-), was the most favorable pipette anion for obtaining good seals and whole-cell sodium currents in these extremely small ORNs. These results implied that resting potentials, for viable responsive cells, should be more negative than about -90 mV, as supported by the observation that action potentials could only be evoked from holding potentials more negative than -90 mV.

Glycine receptors: what gets in and why?

1. The glycine receptor channel (GlyR), a member of the ligand-gated ion channel superfamily, shares many similar permeation properties with the GABAA receptor channel. 2. The GlyR is anion permeable, with PK/PCl < 0.05, has a 5-6 A minimum pore diameter and a permeation selectivity sequence dominated by hydration energies. 3. The channels, which display multiple subconductance states, can be multiply occupied. 4. Two positive arginine rings at the ends of the pore region may contribute to the anion selectivity of the GlyR. 5. Mutation of the extracellular charged arginine ring can impair channel function by decreasing the sensitivity of glycine activation, reducing channel conductance, shifting the normal multi-subconductance states to lower values and by decoupling the link between ligand binding and channel gating. 6. These and other site-directed mutagenesis studies of recombinant GlyR, together with studies of native GlyR, are providing further insights into what controls gating and ion permeation and selectivity through this channel.

Measurement of the limiting equivalent conductivities and mobilities of the most prevalent ionic species of EGTA (EGTA2- and EGTA3-) for use in electrophysiological experiments.

In many experimental biological situations, chelating agents like EGTA (ethylene glycol-bis-(beta-amino-ethyl ether) N,N,N',N'-tetra-acetic acid) are commonly used to control or suppress the concentration of divalent ions like Ca2+. The evaluation of liquid junction potentials in electrophysiological measurements, and particularly in patch-clamp situations, requires information about the ions within the solution. Where there is a significant concentration of EGTA present, it is necessary to know the values of the relative mobility of at least the most predominant ionic species of EGTA in order to complete these calculations. EGTA, with four negative charges with different pKas, can therefore exist as four differently charged ions in solution (EGTA-, EGTA2-, EGTA3- and EGTA4-) or as uncharged, although between pH 5.5 and 8 it is almost exclusively EGTA2-. We have measured limiting equivalent conductivities of the most common ionic forms of EGTA (EGTA2- and EGTA3-) encountered at physiological pHs. These were 35.9 +/- 0.7 and 56 +/- 2.5 S cm2 equiv(-1) respectively. Their mobilities relative to K+ were 0.24 +/- 0.01 for EGTA2- and 0.25 +/- 0.01 for EGTA3-. Thus for typical electrophysiological solutions, the contribution of EGTA to the liquid junction potential should be small (e.g. approximately 0.4 mV).

The startle disease mutation Q266H, in the second transmembrane domain of the human glycine receptor, impairs channel gating.

Hyperekplexia (startle disease) results from mutations in the glycine receptor chloride channel that disrupt inhibitory synaptic transmission. The Q266H missense mutation is the only hyperekplexia mutation located in the transmembrane domains of the receptor. Using recombinant expression and patch-clamping techniques, we have investigated the functional properties of this mutation. The ability of glycine and taurine to open the channel was reduced in the mutated channel, as shown by a 6-fold shift in the concentration-response curve for both agonists. This was not accompanied by similar changes in agonist displacement of strychnine binding, suggesting that the mutation affects functions subsequent to ligand binding. Taurine was also converted to a weak partial agonist and antagonized the actions of glycine, consistent with changes in its channel gating efficacy. Because the Q266H mutation is within the pore-forming second transmembrane domain, we tested for a direct interaction with permeating ions. No change in either the cation/anion selectivity ratio or in single channel conductance levels was observed. No differential effects of Zn++, pH, and diethylpyrocarbonate were observed, implying that the histidine side chain is not exposed to the channel lumen. Single-channel recordings revealed a significant reduction in open times in the mutant receptors, at both high and low agonist concentrations, consistent with the open state of the channel being less stable. This study demonstrates that residues within the second transmembrane domain of ligand-gated ion channel receptors, even those whose side chains do not directly interact with permeating ions, can affect the kinetics of channel gating.

Morphological and electrical characteristics of postnatal hippocampal neurons in culture: the presence of bicuculline- and strychnine-sensitive IPSPs.

A modified method was developed for tissue-culturing postnatal hippocampal neurons using simple mechanical trituration for cell isolation and not including any hydrolysing enzymes, nerve growth factors or antiproliferating agents. The morphological properties of such neurons were characterized with light and interference polarizing microscopy, which revealed the appearance of growth cones from peripheral neurons and the presence of different types of neurons, including bipolar, stellate and pyramidal-like cells (i.e., pyramidal and dentate gyrus granule cells), which could be related to their putative counterparts in intact brain. The whole-cell configuration of the patch-clamp method was used for electrophysiological recordings of inhibitory synapses between these dissociated cultured neurons from the early postnatal rat hippocampus. This study indicated the presence of tetrodotoxin (TTX)-sensitive and TTX-resistant inhibitory postsynaptic potential (IPSPs) and inhibitory postsynaptic currents (IPSCs) in current-clamp and voltage clamp modes respectively. The coincident reversal potentials for IPSCs and for GABAA and glycine-evoked currents, and the sensitivity of the IPSCs to bicuculline or strychnine, indicated that these IPSCs were Cl-(-)dependent and mediated by either GABAA or glycine receptors. Inhibitory postsynaptic currents recorded under voltage-clamp conditions decayed with a time course that could be fitted by a single exponential with a value of 26 ms. An average quantal content of 2.5 was responsible for a typical GABA and glycine-activated IPSC and a single quantum for GABAergic input was inferred to activate about 160, and for glycinergic, about 200 Cl-, channels.

Derivation of unstirred-layer transport number equations from the Nernst-Planck flux equations.

Since the late 1960s it has been known that the passage of current across a membrane can give rise to local changes in salt concentration in unstirred layers or regions adjacent to that membrane, which in turn give rise to the development of slow transient diffusion potentials and osmotic flows across those membranes. These effects have been successfully explained in terms of transport number discontinuities at the membrane-solution interface, the transport number of an ion reflecting the proportion of current carried by that ion. Using the standard definitions for transport numbers and the regular diffusion equations, these polarization or transport number effects have been analyzed and modeled in a number of papers. Recently, the validity of these equations has been questioned. This paper has demonstrated that, by going back to the Nernst-Planck flux equations, exactly the same resultant equations can be derived and therefore that the equations derived directly from the transport number definitions and standard diffusion equations are indeed valid.

Characterization of calcium-activated chloride channels in patches excised from the dendritic knob of mammalian olfactory receptor neurons.

We investigated the properties of calcium-activated chloride channels in inside-out membrane patches from the dendritic knobs of acutely dissociated rat olfactory receptor neurons. Patches typically contained large calcium-activated currents, with total conductances in the range 30-75 nS. The dose response curve for calcium exhibited an EC50 of about 26 microM. In symmetrical NaCl solutions, the current-voltage relationship reversed at 0 mV and was linear between -80 and +70 mV. When the intracellular NaCl concentration was progressively reduced from 150 to 25 mM, the reversal potential changed in a manner consistent with a chloride-selective conductance. Indeed, modeling these data with the Goldman-Hodgkin-Katz equation revealed a PNa/PCl of 0.034. The halide permeability sequence was PCl > PF > PI > PBr indicating that permeation through the channel was dominated by ion binding sites with a high field strength. The channels were also permeable to the large organic anions, SCN-, acetate-, and gluconate-, with the permeability sequence PCl > PSON > Pacetate > Pgluconate. Significant permeation to gluconate ions suggested that the channel pore had a minimum diameter of at least 5.8 A.

An analysis of odorant-induced currents in on-cell patches on mammalian olfactory receptor neurons.

Because of the difficulty of obtaining odorant-induced currents in mammalian olfactory receptor neurons using whole-cell recording, we have developed a mathematical model of the electrical circuit of the patch and rest-of-cell. This can be used to quantitatively analyze on-cell patch pipette currents in response to perfusion of the cell by solutions containing odorants or other compounds that can alter membrane conductance or cell potential. We have analyzed pipette currents from on-cell patches of olfactory receptor neurons (ORNs) dissociated from adult rats. Initially, we perfused the ORNs with a high (100 mM; control 10 mM) KCl solution, which immediately induced a current flux from cell to pipette of a magnitude to imply a depolarization of approximately 52 mV, close to the value predicted from the Nernst equation (56 mV), and no change in the patch conductance. In contrast, perfusion by a cocktail of five cyclic adenosine-3',5'-monophosphate (cAMP)-stimulating odorants (cineole, n-amyl acetate, methyl salicylate, limonene and alpha-pinene, each at a concentration of 1 mM), after a delay of 4-10 sec, induced a current flux from pipette into the cell. Data in normal [Ca2+] and [Mg2+] implied an average patch conductance increase of approximately 36 pS, a cell depolarization of approximately 13 mV and an odorant-induced single channel conductance of approximately 16 pS. In low [Ca2+] and no Mg2+ approximately 40% of cells responded to odorants, with an induced current flow from cell to pipette implying a patch conductance increase of approximately 115 pS and cell depolarization of approximately 32 mV. The results were consistent with the odorants gating cAMP-gated cation channels. This analytical approach, which enables estimates of odorant-induced voltage and conductance changes to be made from changes in pipette current, should also be of general use for comparing cell responses to different perfusing solutions.

Concentration dependence of sodium permeation and sodium ion interactions in the cyclic AMP-gated channels of mammalian olfactory receptor neurons.

The dependence of currents through the cyclic nucleotide-gated (CNG) channels of mammalian olfactory receptor neurons (ORNs) on the concentration of NaCl was studied in excised inside-out patches from their dendritic knobs using the patch-clamp technique. With a saturating concentration (100 microM) of adenosine 3',5'-cyclic monophosphate (cAMP), the changes in the reversal potential of macroscopic currents were studied at NaCl concentrations from 25 to 300 mM. In symmetrical NaCl solutions without the addition of divalent cations, the current-voltage relations were almost linear, reversing close to 0 mV. When the external NaCl concentration was maintained at 150 mM and the internal concentrations were varied, the reversal potentials of the cAMP-activated currents closely followed the Na+ equilibrium potential indicating that PCl/PNa approximately 0. However, at low external NaCl concentrations (< or = 100 mM) there was some significant chloride permeability. Our results further indicated that Na+ currents through these channels: (i) did not obey the independence principle; (ii) showed saturation kinetics with K(m)s in the range of 100-150 mM and (iii) displayed a lack of voltage dependence of conductance in asymmetric solutions that suggested that ion-binding sites were situated midway along the channel. Together, these characteristics indicate that the permeation properties of the olfactory CNG channels are significantly different from those of photoreceptor CNG channels.