Hydrocarbon Formation and the Charge Field

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Hydrocarbon Formation and the Charge Field Empty Hydrocarbon Formation and the Charge Field

Post by Cr6 on Sun Oct 27, 2019 10:05 pm

Came across this article which followed up assorted research on this over various sources.  Wanted to get a post going similar to that on TB's forum just in case ideas develop around this:

Proc Natl Acad Sci U S A. 2019 Sep 3;116(36):17666-17672. doi: 10.1073/pnas.1907871116. Epub
2019 Aug 19.

Abiotic methane synthesis and serpentinization in olivine-hosted fluid inclusions.

Klein F1, Grozeva NG2, Seewald JS3.

Author information

1 Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543; fklein@whoi.edu.
2 Massachusetts Institute of Technology-Woods Hole Oceanographic Institution Joint Program in Oceanography, Cambridge, MA 02139.
3 Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543.


The conditions of methane (CH4) formation in olivine-hosted secondary fluid inclusions and their prevalence in peridotite and gabbroic rocks from a wide range of geological settings were assessed using confocal Raman spectroscopy, optical and scanning electron microscopy, electron microprobe analysis, and thermodynamic modeling. Detailed examination of 160 samples from ultraslow- to fast-spreading midocean ridges, subduction zones, and ophiolites revealed that hydrogen (H2) and CH4 formation linked to serpentinization within olivine-hosted secondary fluid inclusions is a widespread process. Fluid inclusion contents are dominated by serpentine, brucite, and magnetite, as well as CH4(g) and H2(g) in varying proportions, consistent with serpentinization under strongly reducing, closed-system conditions. Thermodynamic constraints indicate that aqueous fluids entering the upper mantle or lower oceanic crust are trapped in olivine as secondary fluid inclusions at temperatures higher than ∼400 °C. When temperatures decrease below ∼340 °C, serpentinization of olivine lining the walls of the fluid inclusions leads to a near-quantitative consumption of trapped liquid H2O. The generation of molecular H2 through precipitation of Fe(III)-rich daughter minerals results in conditions that are conducive to the reduction of inorganic carbon and the formation of CH4 Once formed, CH4(g) and H2(g) can be stored over geological timescales until extracted by dissolution or fracturing of the olivine host. Fluid inclusions represent a widespread and significant source of abiotic CH4 and H2 in submarine and subaerial vent systems on Earth, and possibly elsewhere in the solar system.

More at link with subscription: https://www.ncbi.nlm.nih.gov/pubmed/31427518


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Post by Cr6 on Tue Oct 29, 2019 11:13 pm

Wikipedia on the Lost City also covered in depth by NOAA:

Geology and Chemistry

Lost City vents release methane and hydrogen into the surrounding water; they do not produce significant amounts of carbon dioxide, hydrogen sulfide or metals, which are the major outputs of volcanic black smoker vents. The temperature and pH of water surrounding the two types of vent is also significantly different.

Geology and Mineralogy

The Mid-Atlantic Ridge spreading center pulls the lithosphere apart, creating normal faults which expose sub-surface rocks to seawater.

Hydrocarbon Formation and the Charge Field 330px-Olivine_%28peridot%29
Olivine, the mineral responsible for Lost City's serpentinization.

The Atlantis Massif is described as an ultramafic oceanic core complex of the Mid-Atlantic Ridge, with upper-mantle rock being exposed to seawater through faulting from tectonic extension associated with ocean spreading centers.[24] The spreading half-rate is approximated to about 12 mm/yr, classifying it as a slow-spreading ridge.[25] Seismic events have been detected at the massif of Richter magnitude 4 and 4.5.[13]

The dominant minerals found at Lost City are ultramafic, composed primarily of olivine and pyroxene with very little silica content. Peridotite (primarily spinel harzburgite) minerals undergo serpentinization and form magnetite and serpentine minerals.[6] Because little to no carbon dioxide or metals are released in the venting fluids, Lost City bears the appearance of a non-smoker, with few particulates to give a smokey appearance.

Once pore waters have permeated the surface and return to the surface, aragonite, brucite, and calcite chimneys as calcium carbonates precipitate out of solution.[26] Younger chimneys are primarily brucite and aragonite, being white and flaky in appearance. As vents mature, porosity decreases as precipitates clog fluid pathways. Mineral compositions change with aragonite succeeded by calcite and brucite being removed through dissolution, and the chimneys darken to a grey or brown color.[27]

On the side of the Atlantis Transform Fault, the Atlantis Massif wall terminates approximately 740 meters below sea level, where rock types deform to various mylonitic rocks with deformation fabric minerals of talc, tremolite, and ribbon serpentine.[6]


Lost City is an exemplary location for the study of abiotic methanogenesis and hydrogenesis, as serpentinization reactions produce methane and hydrogen. Supplementing Fischer-Troph reactions;

   Olivine(Fe,Mg)2SiO4 + Watern·H2O + Carbon dioxideCO2 → SerpentineMg3Si2O5(OH)4 + MagnetiteFe3O4 + MethaneCH4


   Fayalite (Olivine)3 Fe2SiO4 + water2 H2O → Magnetite2 Fe3O4 + Silica (aqueous)3 SiO2 + Hydrogen2 H2

The reactions are exothermic and warm surrounding waters via reaction heating, though fluid temperatures are still relatively low (40° - 90 °C) when compared to other hydrothermal systems.[28] Furthermore, pH is increased to values of over 9 which enables calcium carbonate precipitation. Since serpentinization is particularly extensive, carbon dioxide concentrations are also very low. Low temperature, carbon dioxide concentrations, combined with the low hydrogen sulfide and metal content of the plume make the vents more difficult to identify from CTD measurements or optical backscatter methods.

A visiting shark at the Lost City field.

Lost City and other vent systems support vastly different lifeforms due to Lost City's unique chemistry.

A variety of microorganisms live in, on, and around the vents. Methanosarcinales-like archaea form thick biofilms inside the vents where they subsist on hydrogen and methane; bacteria related to the Firmicutes also live inside the vents. External to the vents archaea, including the newly described ANME-1 and bacteria including proteobacteria oxidise methane and sulfur as their primary source of energy.[citation needed]



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Post by M11S on Sun Dec 15, 2019 11:45 pm

I also came across this topic recently and have started reading "The Deep Hot Biosphere The Myth of Fossil Fuels" by: Thomas Gold. So far it seems like methane genesis is a gateway for the formation of heavier hydrocarbons and a gateway for our understanding of the processes involved since it reaches the surface more often(easily) and is easily detected/measured.

This could also align with Miles recent update (Dec 3) on the solar min. where he mentions "It means you have been like a battery on very low charge" Where these archaea and or bacteria evolved to use heat or decompose hydrocarbons for fuel. This book making the case that these organisms are a likely genesis for life on earth, We may have innate capabilities to harvest energy from the charge field. For example. the extreme energy density of the mitochondria. Comparable to the energy density of a lightning bolt and unexplained by mainstream science.


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Post by Chromium6 on Sat Dec 21, 2019 4:49 am

M11S wrote:I also came across this topic recently and have started reading "The Deep Hot Biosphere  The Myth of Fossil Fuels" by: Thomas Gold. So far it seems like methane genesis is a gateway for the formation of heavier hydrocarbons and a gateway for our understanding of the processes involved since it reaches the surface more often(easily) and is easily detected/measured.

This could also align with Miles recent update (Dec 3) on the solar min. where he mentions "It means you have been like a battery on very low charge" Where these archaea and or bacteria evolved to use heat or decompose hydrocarbons for fuel. This book making the case that these organisms are a likely genesis for life on earth, We may have innate capabilities to harvest energy from the charge field. For example. the extreme energy density of the mitochondria. Comparable to the energy density of a lightning bolt and unexplained by mainstream science.

Thanks MS11 this very interesting. There appears to be both natural biological processes and non-biological processes that create Hydrocarbons. The FTT (Fischer) process happening deep in the Earth as Gold has postulated is in effect. Super Critical Water (SCW) is another avenue with Olivine that needs further research.

The moon Titan with its massive Methane beds needs to be explained. This isn't "old biologically infused lakes-sea beds". Interesting that it is near poles reflecting Mathis' Charge Field channels for planets CF recycling:

"The Cassini mission affirmed the former hypothesis, although not immediately. When the probe arrived in the Saturnian system in 2004, it was hoped that hydrocarbon lakes or oceans might be detectable by reflected sunlight from the surface of any liquid bodies, but no specular reflections were initially observed.[6]

The possibility remained that liquid ethane and methane might be found on Titan's polar regions, where they were expected to be abundant and stable.[7] In Titan's south polar region, an enigmatic dark feature named Ontario Lacus was the first suspected lake identified, possibly created by clouds that are observed to cluster in the area.[8] A possible shoreline was also identified near the pole via radar imagery.[9] Following a flyby on July 22, 2006, in which the Cassini spacecraft's radar imaged the northern latitudes (which were at the time in winter), a number of large, smooth (and thus dark to radar) patches were seen dotting the surface near the pole.[10] Based on the observations, scientists announced "definitive evidence of lakes filled with methane on Saturn's moon Titan" in January 2007.[7][11] The Cassini–Huygens team concluded that the imaged features are almost certainly the long-sought hydrocarbon lakes, the first stable bodies of surface liquid found off Earth. Some appear to have channels associated with liquid and lie in topographical depressions.[7] Channels in some regions have created surprisingly little erosion, suggesting erosion on Titan is extremely slow, or some other recent phenomena may have wiped out older riverbeds and landforms.[12] Overall, the Cassini radar observations have shown that lakes cover only a few percent of the surface and are concentrated near the poles, making Titan much drier than Earth.[13] The high relative humidity of methane in Titan's lower atmosphere could be maintained by evaporation from lakes covering only 0.002–0.02% of the whole surface.[14] "


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Post by Chromium6 on Sun Jan 05, 2020 12:36 am

Hey guys, I'm back after a bit of a hiatus. I plan to blow this thread out with several articles. Hopefully, if Miles can help crack this nut of OG formation -- it could lead to a lot of great things. --Cr6

Magnetite is interesting:


Oil spill cleanup employing magnetite nanoparticles and yeast-based magnetic bionanocomposite

Author links open overlay panelKarina B.DebsaDébora S.CardonaaHeron D.T.da SilvaaNashaat N.NassarbElma N.V.M.CarrilhocPaula S.HaddadaGeórgiaLabutoa
Show more
https://doi.org/10.1016/j.jenvman.2018.09.094Get rights and content

• A new magnetic bionanocomposite was synthetized and removed around  55  and 89% of different oils.
• The temperature is a relevant parameter on oil removal, affecting the 3 oils tested.
• The oils are different from each other, grouping themselves in distinct clusters.
• Oil removal is a physic phenomenon which can not be described as adsorption process.
• The neural networks and D-optimals models well describe the experimental data.


Oil spill is a serious environmental concern, and alternatives to remove oils from water involving biosorbents associated to nanoparticles is an emerging subject. Magnetite nanoparticles (MNP) and yeast magnetic bionanocomposite (YB-MNP) composed by yeast biomass from the ethanol industry were produced, characterized, and tested to remove new motor oil (NMO), mixed used motor oil (MUMO) and Petroleum 28 °API (P28API) from water following the ASTM F726–12 method, which was adapted by insertion of a lyophilization step to ensure the accuracy of the gravimetric approach. Temperature, contact time, the type and the amount of the magnetic material were the parameters evaluated employing a fractional factorial design. It was observed the removal of 89.0 ± 2.6% or 3522 ± 118 g/kg (NMO) employing MNP; 69.1 ± 6.2% or 2841 ± 280 g/kg (MUMO) with YB-MNP; and 55.3 ± 8.2% or 2157 ± 281 g/kg (P28API) using MNP. The temperature was the most significant parameter in accordance with the Pareto's graphics (95% confidence) for all oil samples considered in this study as well as the two magnetic materials. Contact time and the interaction between the materials and temperature were also relevant. The D-Optimals designs showed that the NMO and P28API responded in a similar way for all evaluated parameters, while the uptake of MUMO was favored at higher temperatures. These behaviors demonstrate the influence of oil characteristics and the intermolecular forces between the oil molecules on the mechanism dragging process performed by the attraction between magnetite nanoparticles and a 0.7 T magnet. It was clear that this kind of experiment is predominantly a physic phenomenon which cannot be described as adsorption process.


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Post by Chromium6 on Sun Jan 05, 2020 12:41 am

After looking at various papers...I truly believe Miles' C.F. is involved directly in O&G formation and trapping.
His Salt Paper and Carbon Paper and various papers on Charge Flows through the Earth can point directly to formation characteristics? There are people starting to explore alternative ideas/physics around the formation of hydrocarbons.  Question

http://milesmathis.com/salt.pdf ---Salt in O/G formation with iron, carbon, olivine, heat, pressure and magnetite?
http://milesmathis.com/graphene.pdf -- Indicates Carbon Molecule properties
Seepage-Induced Magnetic Anomalies Associated with Oil and Gas Fields: Onshore and Offshore Examples*

Dietmar (Deet) Schumacher and Robert S. Foote
Search and Discovery Article #80416 (2014)
Posted October 27, 2014

*Adapted from extended abstract prepared for oral presentation at AAPG International Conference and Exhibition, Istanbul, Turkey, September 14-17,
2014, AAPG © 2014

E&P Field Services of Mora, NM (deetschumacher@gmail.com)

Geoscience International Inc., Dallas TX


The presence of magnetic anomalies over oil and gas fields has been noted for several decades, but it is only in recent years that the phenomenon has been critically examined. Studies of geologically and geographically diverse regions document that:

1. Authigenic magnetic minerals occur in near-surface sediments over many petroleum accumulations,
2. This hydrocarbon-induced mineralization is detectable in high resolution, broad bandwidth magnetic data acquired at low altitude and with closely-spaced flight lines, and in ground magnetic surveys,
3. The magnetic susceptibility analysis of drill cuttings and near-surface sediments confirms the existence of the aeromagnetic anomalies,
4. Sediments with anomalous magnetic susceptibility frequently contain ferromagnetic minerals such as greigite, maghemite, magnetite, and pyrrhotite,
5. Approximately 80% of oil and gas discoveries are associated with hydrocarbon-induced magnetic anomalies.

The association between hydrocarbon seepage and the formation of authigenic magnetic minerals in the near-surface has important applications in hydrocarbon exploration. Application of this methodology can quickly identify the areas or prospects with the greatest petroleum potential. Although the discovery of shallow sedimentary magnetic anomalies does not guarantee the discovery of commercial hydrocarbon accumulations, it does identify areas requiring more detailed evaluation, thereby focusing attention and resources on a relatively small number of high potential sites. More significantly, these seep-induced magnetic anomalies have been documented over many deep-water discoveries in the Gulf of Mexico. Proper integration of near-surface magnetic data with geologic and seismic data can improve exploration success and reduce development costs. This presentation is illustrated with examples from North America (including the deep-water Gulf of Mexico) and Africa.


Variation in the measurement of the earth's magnetic field can result from the following causes:

- Lithologic and magnetic changes associated with basement rocks
- Intrusive igneous bodies, volcanic deposits, shallow salt masses
- Cultural contamination from surface and near-surface iron material
- Solar modulation of the earth’s magnetic field
- Authigenic ferromagnetic minerals in near-surface sediments.

Low-terrain-clearance, high- sensitivity cesium vapor aeromagnetic measurements provide a composite of these effects on the magnetic field data. Data reduction techniques that remove the influence of magnetic basement rocks on the total magnetic field and, where possible, the effects of cultural iron contamination allow the identification of sedimentary residual magnetic (SRM) anomalies (Figure 1) as they exist along the flight line. When these SRM anomalies are positioned line-to-line adjacent to one another, they define SRM anomaly clusters. It is these clusters that define the micromagnetic anomaly – also referred to as “Magnetic Bright Spots” (Figure 2) – which provide valuable clues to an underlying oil or gas accumulation.

Applications for Deep-Water Exploration

The association between hydrocarbon seepage and the formation of authigenic magnetic minerals in near-surface sediments has important applications in deep-water hydrocarbon exploration. Sepage-induced sedimentary magnetic anomalies can reliably identify areas and prospects with the highest petroleum potential in water depths as great as 9000 feet (2800 m). The highresolution cesium vapor aeromagnetic data used in this study by Robert Foote and his colleagues were acquired between 1986 and 1992 and extend from East Breaks to Viosca Knoll in the Gulf of Mexico. A comparison of the specially processed and interpreted aeromagnetic data with post-survey drilling results documents that more than 80% of wells drilled on prospects within or adjacent to Magnetic Bright Spots have resulted in commercial discoveries. In contrast, only 40% of wells drilled on prospects located more than 800 m from the MBS have resulted in discoveries. Although the discovery of MBS anomalies does not guarantee the discovery of hydrocarbon accumulations, it does identify areas requiring more detailed evaluation, thereby focusing attention and resources on a relatively small number of high potential sites.

Selected References
Foote, R.S., 1996, Relationship of near-surface magnetic anomalies to oil and gas-producing areas: AAPG Memoir 66, p. 111-126.
Foote, R.S., 2007, Method helps find hydrocarbon areas; aids optimum seismic survey planning: Oil & Gas Journal, 5 Feb 2007,p. 3
(more at link: )

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Post by Chromium6 on Sun Jan 05, 2020 12:48 am

Magnetics for Hydrocarbon Exploration

Christine Fichler, NTNU. Column Editors: Lasse Amundsen and Martin Landrø

How can a tiny mineral called magnetite help to unravel hydrocarbon seepage and subsurface petrology?

It’s not MAGIC – it’s MAGNETICS… in integrated workflows!This article appeared in Vol. 13, No. 6 - 2017

'Magnetism, as you recall from physics class, is a powerful force that causes certain items to be attracted to refrigerators.' Dave Barry


Magnetite from Bolivia. These crystals measure over 1 cm across. (Source: Rob Lavinsky/Wikipedia)
Magnetite is the most important member in the family of magnetic minerals, which are found in varying amounts in crystalline rocks and to a lesser extent in sediments.

Magnetite has the ability to respond to a magnetic field by generating its own field, known as the induced magnetic field.

In oceanic crustal rocks, it is common for magnetic minerals to permanently hold substantial magnetic fields. These remanent fields date back to the moment when the rocks in the hot and just solidified magmas of mid-oceanic ridges cooled through the Curie point (the temperature at which magnetic materials undergo a sharp change in their magnetic properties) and captured and stored the acting magnetic field characteristics.

This can be used to unravel the paleomagnetic history of the rocks.

Magnetic Anomalies

We know the direction of the Earth’s magnetic field from the compass needle pointing north. The Earth’s field looks like that of a magnetic dipole - a huge blueprint of your refrigerator magnet, but which is located in the Earth’s core. All rocks on Earth, as well as you and me, are bathed in this magnetic field and respond with induced magnetic fields. But since we do not have much magnetic material in our bodies, the fields of the rocks will dominate.

Geophysics uses a parameter called magnetic susceptibility, which expresses the strength of the response of a rock to an imposed magnetic field - an easy alternative to estimating the amount of magnetic minerals in a rock sample. High magnetic susceptibility will give a strong induced magnetic field and vice versa. These induced magnetic fields, together with the remanent magnetic fields, cause very small deviations to the Earth’s magnetic field strength, known as magnetic anomalies. They are measured by intricate yet backpack-sized instruments, typically mounted on airplanes for hydrocarbon exploration applications. Onshore and offshore areas are mapped line by line and the results processed to create maps of magnetic anomalies, which present the sum of the induced and remanent magnetic anomalies of every single magnetic mineral in the subsurface; in other words, they reflect the distribution of magnetic susceptibility and remanence.

The Magnetic Choir

In order to understand the recorded anomalies at the surface, imagine that the magnetic minerals form a choir and you are the magnetometer ‘listening’ to the choir from the front. You will easily hear the nearest singers, but listening to those further away gets more and more difficult with increasing distance - only if somebody far away is singing very loudly with a megaphone, will you hear them. The shallowest magnetic rocks in the subsurface are nearest to the magnetometer and will as such generate the strongest anomalies and show a lot of details. With increasing depth, the anomalies become smaller in amplitude and lose details, as illustrated in the left part of Figure 1.

Figure 1: (Left) Magnetic anomalies caused by the same body at different depths; (Right) A synthetic section with calculated magnetic anomalies for magnetic rocks typically found in sedimentary basins. The induced Earth magnetic field (H) is typical for the North Sea. (Generated using GEOSOFT GMSYS2D)

The right-hand image of Figure 1 illustrates magnetic rocks in sediments and crust and their associated magnetic anomalies: in our choir analogy, the large anomalies (grey) from the crystalline rocks are the ‘singers with megaphones’, while the tiny, small scale anomalies (red) from just a very few structures in the sediments are the ‘singers in the front’. The most important thing to understand about sedimentary anomalies is that they are small in amplitude and as such are only detectable if located in the uppermost kilometer of the subsurface. Furthermore, mapping them needs high resolution data, which means acquisition with dense line spacing and high accuracy.

High pass filtering of the magnetic data brings out the shallow sedimentary anomalies of short wavelength. This is illustrated in Figure 2, which compares high pass filtered anomalies of both high resolution magnetic data and global magnetic data; note the difference!

Figure 2: Upper maps: seismically mapped Quaternary channels and high pass filtered, high-resolution magnetic data (modified from Fichler, Henriksen, Rueslåtten and Hovland, 2005; magnetic data: VGVG /TGS-Nopec , 1995). Lowermost map: global magnetic data (EMAG2; www.geomag.org, 2009) of the northern North Sea; the area marked by the larger white box is filtered in the same way as the high resolution data and shown in the second lowest map. The smaller box marks the area shown in Figure 4 and the white line shows the location of the profile in Figure 5.

Magnetic Anomalies as Hydrocarbon Indicators

Magnetic minerals deposited in sedimentary layers reflect the provenance of the sediments. For the continental shelf offshore Norway, Mørk, McEnroe and Olesen (2002) documented that the magnetic susceptibility and remanence are generally small, and few sands and shales were found to have high values. These workers also showed that diagenetic magnetic mineralization in the form of highly magnetic siderite cementation is observed in some dark shales, a phenomenon which can also be seen at outcrops of source rocks. In Venezuela an increased content of magnetic minerals was found in cap rocks of oil-filled reservoirs by Perez-Perez, Onofrio, Bosch and Zapata (2011). These and other effects may cause small magnetic anomalies and it has been suggested that they form indirect hydrocarbon indicators; many case histories can be found if you dig into the literature.

However, the big problem is the inherent ambiguity in the interpretation. Small magnetic anomalies are caused by many shallow sources, not just by chemical changes due to hydrocarbons. Common sources are depositional and erosional patterns, sills and dykes, hydrothermal systems and, looking at onshore environments, the tropical weathering product called laterite. How can you tell the difference? The only way forward is through integrating magnetic anomaly interpretation with other data.

Let’s look at some examples from the North Sea where combining the interpretation of magnetic and 3D seismic data could explain some of the shallow anomalies. One distinct group of sedimentary magnetic anomalies is related to melt-water channels which are eroded and filled by glaciogenic sediments due to repeated glaciations and deglaciations in the Pleistocene. The resulting spaghetti pattern of cross-cutting channels is shown in Figure 2. Some channels generate positive anomalies, others negative ones as a consequence of the susceptibility contrast between infill and host rock, which can vary between negative, zero or positive. These channeled sands may form a reservoir rock, as proven by the small, shallow discovery, Peon, in the northern North Sea.

Figure 3: Gas blowout crater in the Russian Arctic. (Source: Vasily Bogoyavlensky)
Magnetic anomalies have yet further relevance in the search for hydrocarbons.

If hydrocarbon gas seeped into the permafrost during the Pleistocene glaciation periods, gas hydrates will have been precipitated and, in the next warm period, would melt and be released. The melting of gas hydrates below tight cap rocks is known to create blowout craters, as spectacularly observed in the Russian Arctic (see Figure 3 opposite, and Gas Blowouts on the Yamal and Gydan Peninsulas by Vasily Bogoyavlensky), and if such a crater is later filled with magnetic sediments, the result is a magnetic anomaly.

This rather special hydrocarbon seepage indicator is illustrated in Figure 4, showing a circular magnetic anomaly from the eastern shoulder of the Viking Graben.

Figure 4: Depression on seismic section correlating with a circular magnetic anomaly; interpreted as gas hydrate expulsion crater filled with magnetic glaciogenic sediments (modified from Fichler, Henriksen, Rueslåtten & Hovland, 2005); for location see Figure 2. Black line indicates line of section.

Basement Anomalies

Let’s now look at the ‘singers with the megaphone’ - the crystalline basement with wide and large magnetic anomalies as introduced in Figure 1.

Crustal magnetic anomalies rarely mimic the topography of the top basement, whereas gravity anomalies often do. There are several reasons for this. The magnetic susceptibility of crustal rocks varies between 10-4 and 10-1 SI units, i.e., by a factor of 1,000, whereas crustal densities just vary between 2.5 and 3.4 g/cm3, meaning that large magnetic anomalies can be generated by deep as well as by shallow rock units. An example is the deep mafic intrusion in Figure 1, which gives almost the same magnetic amplitude as the shallow basement high. However, the anomaly of the intrusion has a larger wavelength than the basement high. Such differences in shape can be used to find the depth to the top of the structure by various manual or automatic methods.

Another factor affecting induced magnetic anomalies is related to the change of the Earth’s magnetic field direction, from vertical at the poles to horizontal at the equator. This explains why a magnetic body at fixed depth generates different anomaly shapes depending on its location, with a maximum anomaly over its center at the poles, a minimum at the equator, and in between a combination of maximum and minimum. The North Sea shows near-polar characteristics.

Integrating Data

The final example (Figure 5) shows the workflow for crustal rock classification through the integration of different geophysical data. A deep seismic depth section along a 300 km-long transect crossing the northern North Sea was loaded into a gravity and magnetic modeling program. The subsurface was divided into polygons, each representing a different rock type. The divisions reflect the boundaries within sediments and crust as defined by the seismic data. Each polygon was assigned a magnetic susceptibility and density. Well data provided sedimentary densities and magnetic susceptibilities as well as the depth to the top crystalline basement, the latter found to consist of mainly granitic rocks. In the initial model, the parameters for granites were used for the entire crust. The mantle was assigned peridotite parameters and the high velocity body in the lower crust was given eclogite parameters.

Figure 5: Magnetic susceptibilities (Clark, 1999) cross-plotted against densities (Hinze, Frese and Saad, 2013); location of profile see Figure 1. (Modified from Fichler, Odinsen, Rueslåtten, Olesen, Vindstad and Wienecke, 2011)

The calculated gravity and magnetic anomalies of this simple model showed a large mismatch, especially in the long wave length-range, indicating a need for modification in the deep parts of the crust. The gravity and magnetic anomalies governed the crustal modification, which resulted in a model of more complex density and susceptibility distributions. The final model matches observed gravity and magnetic anomalies as well as rock types considered geologically reasonable with respect to the geological history. Modeling in general carries an inherent uncertainty and the interpreter should therefore include alternative models where feasible.

You can apply this workflow to detect granitic rocks, known for their high radiogenic heat production which influences hydrocarbon maturation (Hokstad, Tasarova, Kyrkjebø, Fichler, Wiik and Duffaut, 2016), or to map the boundary between oceanic and continental crust. Furthermore, detection of intrusives, which have brought hot magma into crust or sediments, may also be of importance for unraveling the thermal history of a sedimentary basin.

Summing up, magnetic data contributes to hydrocarbon exploration on a broad scale and in mainly integrated geophysical interpretation tasks. It can address problems from the deep crust to the shallowest sedimentary strata. Magnetic data on a large scale is globally available at low cost or even free. High resolution data is more expensive, but is still only a fraction of the cost of a seismic survey.

About the authors

Guest author, Christine Fichler holds a PhD in geophysics (1985) from the Karlsruhe Institute of Technology (KIT) in Germany.

A post-doc. position at the Dept. of Petroleum Engineering and Applied Geophysics at the Norwegian University of Science and Technology (NTNU) followed (1986-1990) and, in 1990, Christine became a Specialist Geophysicst at Statoil, Norway.

Since 2013 Christine has been Adjunct Professor at the Dept. for Geology and Mineral Resources Engineering, Norwegian University of Science and Technology (NTNU).

Editors Martin Landrø and Lasse Amundsen are regular contributors to Geo ExPro. You can find more articles by these authors by using the search function at the top of this page or by following this link.


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Hydrocarbon Formation and the Charge Field Empty Re: Hydrocarbon Formation and the Charge Field

Post by Chromium6 on Sun Jan 05, 2020 12:56 am

NXT Energy

The Science of SFD®

Hydrocarbon exploration utilizes many different geophysical methods to create models of the earth’s subsurface, with the goal of identifying areas which may be “anomalous” to permit the economic accumulations of oil and natural gas. This accumulation requires the combination of suitable structural or stratigraphic conditions with appropriate hydro-dynamic conditions. Mitigating geological exploration risks associated with factors such as trap configuration, reservoir quality and seal integrity is critical to overall exploration success.

Gravity based tools have long been used in the exploration process, and generally utilize mass-density or field-strength based measurements. The SFD® airborne survey technology also utilizes gravity as a medium, but in a unique manner through exploiting wave attributes of the acquired signal to rapidly identify and rank prospect leads for oil and gas exploration.

The earth’s gravitational field is influenced by many sources, and has a complex three-dimensional shape, resulting in part from the inherent anisotropy within the crust. The basic operating premise of SFD® is that it responds to subtle variations or perturbations in earth’s gravity field, and these can be indicative of anomalies which arise from subsurface changes relating to geologic features of interest, such as faults, fault blocks, anticlines, carbonate bank edges, channel systems, over-pressure of fluids, etc. This family of geologic features are commonly correlated with the potential for occurrence of hydrocarbon trapping conditions. In essence, changes in subsurface homogeneity are the fundamental factor of the physical contrast to which SFD® responds.

In general, porous rocks and the presence of fluid cause a decrease in bulk density, which will produce a gravity low. If more fluid is accumulated in a trap with high porosity, then the reservoir system becomes more homogenous provided there is adequate permeability distribution. This results in greater spatial subsurface homogeneity.

In SFD® exploration, a background condition is characterized by a random distribution of Δ ρ (change in density) with hydrostatic pressure gradients. An anomalous condition is characterized by an isolated homogeneous distribution of ρ due to enhanced porosity and fluid presence bounded by abnormal stress gradients. The anomalous condition is further characterized by a marked reduction in shear stress inside the reservoir and a reorientation of the horizontal principal stresses around it.

In addition to subsurface density changes, the principal stresses also play a significant role in the development of subsurface conditions associated with discontinuities. In general, fluid migration follows the direction of the maximum horizontal stress (SHmax) and fluid expulsion follows the direction of the minimum horizontal stress (Shmin). As fluid moves into reservoirs, SHmax will reduce and Shmin will increase as pore pressure increases. Also, shear stress will be further reduced as fluid accumulates in the reservoir. Reservoir rock permeability distribution is controlled by SHmax and a high value indicates an increase in homogeneity. Investigations of gravity gradients and stress changes have shown that there is a physical relationship between the two at small scale. The gravity field includes local-scale perturbations or distortions which arise from a combination of mass-density and field transmission effects.

To respond to small-scale changes in the gravitational acceleration (Δ g), the SFD® device is designed:

to employ a reduced proof mass assembly for minimizing inertial effects and allow high frequency interaction with the field to allow a mechanical instability for enhancing detection sensitivity to utilize rectilinear motion for dynamic detection and continuously accumulating Δ g necessary to resolve reservoir scale features, and to obtain wave-based signal patterns for analysis as opposed to the standard magnitude measurement employed by standard gravity based tools.

Based on extensive empirical observation and past correlations with other geological and geophysical data, SFD® data has proven highly effective in identifying potential hydrocarbon traps in a wide variety of geological settings, including thrust-fold belts, foreland basins, sub-salt plays, and extensional regimes. Interpretation of SFD® signals involves a pattern recognition process. Based on extensive experience, recognizable SFD® signal patterns (example below) have been empirically correlated to a variety of subsurface geologic fluid trapping conditions and are especially pronounced within regions of fluid-filled porosity bounded by abnormal stress gradients.

A sample SFD® signal from Ladyfern gas field

(Devonian carbonate reef structure), British Columbia, Canada.

This example clearly illustrates amplitude and frequency effects embedded in the SFD® signal.

The end result is that SFD® is capable of detecting subsurface conditions which are favorable for fluid entrapment, using a unique detection system. SFD® yields an independent dataset that is highly complementary to other geophysical methods such as 2D and 3D seismic surveys. In conjunction with other geological data, SFD® can be a fundamental step in assessing whether lead areas are then elevated to prospects, aiding in the goal of focusing exploration efforts and reducing overall risk.


NXT Energy Solutions Inc.
Summary of Technical Reference Materials
(February 2015)


Anderson, B.M., Taylor, J.M. and Galitski, V.M. (2011). “Interferometry with synthetic gauge
fields.” Physical Review A 83, 031602.
Bell, J.S. (1996). “In situ stresses in sedimentary rocks (Part II): Applications of stress
measurements.” Geoscience Canada 23(3), 135–153.

Dake, L.P. (2001). The Practice of Reservoir Engineering, Elsevier.

Finkbeiner, T. (1999). In Situ Stress, Pore Pressure and Hydrocarbon Migration and
Accumulation in Sedimentary Basins, Ph.D. thesis, Stanford University.

Hayes, T.J. (2008). Using Gravity as a Proxy for Stress Accumulation in Complex Fault Systems,
Ph.D. thesis, University of Western Ontario.

Hayes, T.J., Tiampo, K.F., Fernandez, J. and Rundle, J.B. (2008). “A gravity gradient method
for characterizing the post-seismic deformation field for a finite fault.” Geophysical Journal
International 173, 802–805.

Hillis, R.R. (2001). “Coupled changes in pore pressure and stress in oil fields and sedimentary
basins.” Petroleum Geoscience 7, 419–425.

McCulloh, T.H. (1967). Mass Properties of Sedimentary Rocks and Gravimetric Effects of
Petroleum and Natural-Gas Reservoirs, Geological survey professional paper 528-A, U.S.
Department of the Interior.

Prieto, C. (1998). “Gravity/magnetic signatures of various geologic models - An exercise in
pattern recognition.” Geologic Applications of Gravity and Magnetics: Case Histories, AAPG &
SEG, 20–27.
Silva, P. R. (1997). “A new interpretation of the de Broglie frequency.” Physics Essays 10(4),
Street, R.L., Watters, G.Z. and Vennard, J.K. (1996). Elementary Fluid Mechanics, 7th edition,
John Wiley & Sons.

NXT Publications

Cotton J. and Mustaqeem, A. (2010). The Geologic and Geophysical Integration of SFD® Data
Offshore Colombia, Block RC 4 & 5, NXT Internal Report, Calgary, Canada.

Escalera, J.A., García, M.V., Olazarán, J.J.H., Ponce, A., García, O.V., Cardador, M.H. and
Liszicasz, G. (2013). “Application of stress field detection (SFD®) technology for identifying
areas of hydrocarbon potential in the Gulf of Mexico region.” Next Generation Oil & Gas Summit
Latin America, Cartagena, Colombia.

Liszicasz, G., Mustaqeem, A., Khan, M.R., Bhatti, M.A. and Hussain, A. (2013). “SFD®
(Stress Field Detection) and its integration with seismic in Kharan Forearc Basin and its implications for
hydrocarbon exploration in a frontier area.” SPE/PAPG Annual Technical Conference,
Islamabad, Pakistan.


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Post by Chromium6 on Sun Jan 05, 2020 4:51 am

Wikipedia on Magnetite. Has very interesting characteristics. We may need to use the C.F. to describe "color" as well as property. Why "Black"?  What does the C.F. radiate in ambient light to the eye?


Magnetite is a rock mineral and one of the main iron ores, with the chemical formula Fe3O4. It is one of the oxides of iron, and is ferrimagnetic; it is attracted to a magnet and can be magnetized to become a permanent magnet itself.[5][6] It is the most magnetic of all the naturally-occurring minerals on Earth.[5][7] Naturally-magnetized pieces of magnetite, called lodestone, will attract small pieces of iron, which is how ancient peoples first discovered the property of magnetism. Today it is mined as iron ore.

Small grains of magnetite occur in almost all igneous and metamorphic rocks. Magnetite is black or brownish-black with a metallic luster, has a Mohs hardness of 5–6 and leaves a black streak.[5]

The chemical IUPAC name is iron(II,III) oxide and the common chemical name is ferrous-ferric oxide.


In addition to igneous rocks, magnetite also occurs in sedimentary rocks, including banded iron formations and in lake and marine sediments as both detrital grains and as magnetofossils. Magnetite nanoparticles are also thought to form in soils, where they probably oxidize rapidly to maghemite.[8]
Crystal structure

The chemical composition of magnetite is Fe2+Fe23+O42−. The main details of its structure were established in 1915. It was one of the first crystal structures to be obtained using X-ray diffraction. The structure is inverse spinel, with O2− ions forming a face centered cubic lattice and iron cations occupying interstitial sites. Half of the Fe3+ cations occupy tetrahedral sites while the other half, along with Fe2+ cations, occupy octahedral sites. The unit cell consists of 32 O2− ions and unit cell length is a = 0.839 nm.[9]

Magnetite contains both ferrous and ferric iron, requiring environments containing intermediate levels of oxygen availability to form.[10]

Magnetite differs from most other iron oxides in that it contains both divalent and trivalent iron.[9]

As a member of the spinel group, magnetite can form solid solutions with similarly structured minerals, including ulvospinel (Fe2TiO4), hercynite (FeAl2O4) and chromite (FeCr2O4). Titanomagnetite, also known as titaniferous magnetite, is a solid solution between magnetite and ulvospinel that crystallizes in many mafic igneous rocks. Titanomagnetite may undergo oxyexsolution during cooling, resulting in ingrowths of magnetite and ilmenite.

Crystal morphology and size

Natural and synthetic magnetite occurs most commonly as octahedral crystals bounded by {111} planes and as rhombic-dodecahedra.[9] Twinning occurs on the {111} plane.

Hydrothermal synthesis usually produce single octahedral crystals which can be as large as 10mm across.[9] In the presence of mineralizers such as 0.1M HI or 2M NH4Cl and at 0.207 MPa at 416-800 °C, magnetite grew as crystals whose shapes were a combination of rhombic-dodechahedra forms.[9] The crystals were more rounded than usual. The appearance of higher forms was considered as a result from a decrease in the surface energies caused by the lower surface to volume ratio in the rounded crystals.[9]


Magnetite has been important in understanding the conditions under which rocks form. Magnetite reacts with oxygen to produce hematite, and the mineral pair forms a buffer that can control oxygen fugacity. Commonly, igneous rocks contain solid solutions of both titanomagnetite and hemoilmenite or titanohematite. Compositions of the mineral pairs are used to calculate how oxidizing was the magma (i.e., the oxygen fugacity of the magma): a range of oxidizing conditions are found in magmas and the oxidation state helps to determine how the magmas might evolve by fractional crystallization. Magnetite also is produced from peridotites and dunites by serpentinization.

Biological occurrences

Biomagnetism is usually related to the presence of biogenic crystals of magnetite, which occur widely in organisms.[23] These organisms range from bacteria (e.g., Magnetospirillum magnetotacticum) to animals, including humans, where magnetite crystals (and other magnetically-sensitive compounds) are found in different organs, depending on the species.[24][25] Biomagnetites account for the effects of weak magnetic fields on biological systems.[26] There is also a chemical basis for cellular sensitivity to electric and magnetic fields (galvanotaxis).[27]

Magnetite magnetosomes in Gammaproteobacteria

Pure magnetite particles are biomineralized in magnetosomes, which are produced by several species of magnetotactic bacteria. Magnetosomes consist of long chains of oriented magnetite particle that are used by bacteria for navigation. After the death of these bacteria, the magnetite particles in magnetosomes may be preserved in sediments as magnetofossils. Some types of anaerobic bacteria that are not magnetotactic can also create magnetite in oxygen free sediments by reducing amorphic ferric oxide to magnetite.[28]

Several species of birds are known to incorporate magnetite crystals in the upper beak for magnetoreception,[29] which (in conjunction with cryptochromes in the retina) gives them the ability to sense the direction, polarity, and magnitude of the ambient magnetic field.[24][30]

Chitons, a type of mollusk, have a tongue-like structure known as a radula, covered with magnetite-coated teeth, or denticles.[31] The hardness of the magnetite helps in breaking down food, and its magnetic properties may additionally aid in navigation.[dubious – discuss] Biological magnetite may store information about the magnetic fields the organism was exposed to, potentially allowing scientists to learn about the migration of the organism or about changes in the Earth's magnetic field over time.[32]

Human brain Shocked

Living organisms can produce magnetite.[25] In humans, magnetite can be found in various parts of the brain including the frontal, parietal, occipital, and temporal lobes, brainstem, cerebellum and basal ganglia.[25][33] Iron can be found in three forms in the brain – magnetite, hemoglobin (blood) and ferritin (protein), and areas of the brain related to motor function generally contain more iron.[33][34] Magnetite can be found in the hippocampus. The hippocampus is associated with information processing, specifically learning and memory.[33] However, magnetite can have toxic effects due to its charge or magnetic nature and its involvement in oxidative stress or the production of free radicals.[35] Research suggests that beta-amyloid plaques and tau proteins associated with neurodegenerative disease frequently occur after oxidative stress and the build-up of iron.[33]

Some researchers also suggest that humans possess a magnetic sense,[36] proposing that this could allow certain people to use magnetoreception for navigation.[37] The role of magnetite in the brain is still not well understood, and there has been a general lag in applying more modern, interdisciplinary techniques to the study of biomagnetism.[38]

Electron microscope scans of human brain-tissue samples are able to differentiate between magnetite produced by the body's own cells and magnetite absorbed from airborne pollution, the natural forms being jagged and crystalline, while magnetite pollution occurs as rounded nanoparticles. Potentially a human health hazard, airborne magnetite is a result of pollution (specifically combustion). These nanoparticles can travel to the brain via the olfactory nerve, increasing the concentration of magnetite in the brain.[33][35] In some brain samples, the nanoparticle pollution outnumbers the natural particles by as much as 100:1, and such pollution-borne magnetite particles may be linked to abnormal neural deterioration. In one study, the characteristic nanoparticles were found in the brains of 37 people: 29 of these, aged 3 to 85, had lived and died in Mexico City, a significant air pollution hotspot. A further eight, aged 62 to 92, came from Manchester, and some had died with varying severities of neurodegenerative diseases.[39] According to researchers led by Prof. Barbara Maher at Lancaster University and published in the Proceedings of the National Academy of Sciences, such particles could conceivably contribute to diseases like Alzheimer's disease. Though a causal link has not been established, laboratory studies suggest that iron oxides like magnetite are a component of protein plaques in the brain, linked to Alzheimer's disease.[40]

Increased iron levels, specifically magnetic iron, have been found in portions of the brain in Alzheimer's patients.[41] Monitoring changes in iron concentrations may make it possible to detect the loss of neurons and the development of neurodegenerative diseases prior to the onset of symptoms[34][41] due to the relationship between magnetite and ferritin.[33] In tissue, magnetite and ferritin can produce small magnetic fields which will interact with magnetic resonance imaging (MRI) creating contrast.[41] Huntington patients have not shown increased magnetite levels; however, high levels have been found in study mice.[33]

Magnetite nanoparticles

Magnetite micro- and nanoparticles are used in a variety of applications, from biomedical to environmental. One use is in water purification: in high gradient magnetic separation, magnetite nanoparticles introduced into contaminated water will bind to the suspended particles (solids, bacteria, or plankton, for example) and settle to the bottom of the fluid, allowing the contaminants to be removed and the magnetite particles to be recycled and reused.[46] This method works with radioactive and carcinogenic particles as well, making it an important cleanup tool in the case of heavy metals introduced into water systems.[47] These heavy metals can enter watersheds due to a variety of industrial processes that produce them, which are in use across the country. Being able to remove contaminants from potential drinking water for citizens is an important application, as it greatly reduces the health risks associated with drinking contaminated water.

Another application of magnetic nanoparticles is in the creation of ferrofluids. These are used in several ways, in addition to being fun to play with. Ferrofluids can be used for targeted drug delivery in the human body.[46] The magnetization of the particles bound with drug molecules allows “magnetic dragging” of the solution to the desired area of the body. This would allow the treatment of only a small area of the body, rather than the body as a whole, and could be highly useful in cancer treatment, among other things. Ferrofluids are also used in magnetic resonance imaging (MRI) technology.[48]

Coal mining industry

For the separation of coal from waste, dense medium baths were used. This technique employed the difference in densities between coal (1.3-1.4 tonnes per m³) and shales (2.2-2.4 tonnes per m³). In a medium with intermediate density (water with magnetite), stones sank and coal floated.[49]


Nevyn's MBL engine representation of Magnetite:

Hydrocarbon Formation and the Charge Field Magnet10


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Hydrocarbon Formation and the Charge Field Empty Re: Hydrocarbon Formation and the Charge Field

Post by Chromium6 on Mon Jan 06, 2020 1:06 am

Magnetic Bright Spots Can Identify the Most Prospective Deep-Water Areas and Prospects*

(updated from October 27, 2014 paper above --Cr6)

Robert S. Foote1
and Dietmar Schumacher

Search and Discovery Article #41871 (2016)**
Posted September 12, 2016

*Adapted from poster presentation given at AAPG 2016 Annual Convention and Exhibition, Calgary, Alberta, Canada, June 19-22, 2016
**Datapages © 2016 Serial rights given by author. For all other rights contact author directly.

1Geoscience International Inc., Euless, TX, USA

E&P Field Services, Mora, NM, USA (deetschumacher@gmail.com)


The presence of magnetic anomalies over oil and gas fields has been noted for decades, but only in recent years has the phenomenon has been critically examined. Studies of geologically and geographically diverse regions document that:
(1) authigenic magnetic minerals occur in nearsurface sediments over many petroleum accumulations,
(2) this hydrocarbon-induced mineralization is detectable in high resolution, broad bandwidth magnetic data acquired at low altitude and with closely-spaced flight lines,
(3) the magnetic susceptibility analysis of drill cuttings confirms the existence of the aeromagnetic anomalies,
(4) sediments with anomalous magnetic susceptibility frequently contain ferromagnetic minerals such as greigite, maghemite, magnetite, and pyrrhotite, and
(5) 80% or more of offshore deep-water oil and gas discoveries in Gulf of Mexico are associated with these shallow, sedimentary hydrocarbon-induced magnetic anomalies.
The association between hydrocarbon seepage and authigenic magnetic minerals has important applications in deep-water hydrocarbon exploration. Seep-induced sedimentary magnetic anomalies, known as Magnetic Bright Spots (MBS), can reliably identify areas and prospects with the highest petroleum potential in water depths as great as 9000 feet (2800 m). The high-resolution cesium vapor aeromagnetic data used in this study were acquired between 1986 and 1992, and extend from East Breaks to Viosca Knoll in the Gulf of Mexico. A comparison of the processed and interpreted aeromagnetic data with post-survey drilling results documents that 89% of wells drilled on prospects within or adjacent to Magnetic Bright Spots have resulted in commercial discoveries. In contrast, fewer than 30% of wells drilled on prospects located more than 800 m from the MBS have resulted in discoveries. Furthermore, MBS areas account for 65% of production – almost 5 times that from within salt-covered areas where no MBS could be determined, although the areas are roughly similar in size. Although the discovery of MBS anomalies does not guarantee the discovery of commercial oil or gas, it does identify areas requiring more detailed evaluation, thereby focusing attention and resources on a relatively small number of high potential sites.

References Cited

Foote, R.S., 1996, Relationship of near-surface magnetic anomalies to oil and gas producing areas: in D. Schumacher and M.A. Abrams,
Hydrocarbon Migration and its Near-Surface Expression: AAPG Memoir 66, p. 111-126.
Foote, R.S., R. Novak, and J. Sobehrad, 1997, Aeromagnetic near-surface profiling as an exploration tool: in Applications of Emerging
Technologies: Unconventional Methods in Exploration for Petroleum and Natural Gas, V: SMU Press, ISEM, p. 183-193.
Machel, H.G. and E.A. Burton, 1991, Chemical and microbial processes causing anomalous magnetization in environments affected by
hydrocarbon seepage: Geophysics, v. 56, p. 598-605.
Schumacher, D., 1996, Hydrocarbon-induced alteration of soils and sediments: in D. Schumacher and M.A. Abrams, Hydrocarbon Migration
and its Near-Surface Expression, AAPG Memoir 66, p. 111-126.


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Post by Chromium6 on Mon Jan 06, 2020 1:14 am

Interesting links on Magenetic Bacteria from biological and geophysical perspectives.  

Martian Olivine and Magnetite (but not found from living bacteria):

Research Methods in Biomineralization Science
Jinhui Tao, in Methods in Enzymology, 2013

1 Introduction

Biomineralization is the process by which living organism manufactures minerals for different functional purposes, such as mechanical stiffening of tissue, magnetic or gravitational sensing, and element storage (Mann, 1988; Sigel, Sigel, & Sigel, 2008; Weiner & Lowenstam, 1989). From the perspective of taxonomic distribution, the most widespread biominerals are calcium carbonate and calcium phosphate, which are firmly associated with organic matrices such as chitin and collagen to form hybrid structure for shells and bones (Arias & Fernández, 2008; Boskey, 1998; Palmer, Newcomb, Kaltz, Spoerke, & Stupp, 2008; Sarikaya, 1999). The structures of these composites have hierarchical levels from the nano- to microscale. Because of the potential application in guiding new composite material design and controllable synthesis, there has been an increasing interest in deciphering the mechanisms of biomineralization over the past decades.


Magnetotactic bacteria, magnetosomes and their application

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Magnetotactic bacteria (MTB) are a diverse group of microorganisms with the ability to orient and migrate along geomagnetic field lines. This unique feat is based on specific intracellular organelles, the magnetosomes, which, in most MTB, comprise nanometer-sized, membrane bound crystals of magnetic iron minerals and organized into chains via a dedicated cytoskeleton. Because of the special properties of the magnetosomes, MTB are of great interest for paleomagnetism, environmental magnetism, biomarkers in rocks, magnetic materials and biomineralization in organisms, and bacterial magnetites have been exploited for a variety of applications in modern biological and medical sciences. In this paper, we describe general characteristics of MTB and their magnetic mineral inclusions, but focus mainly on the magnetosome formation and the magnetisms of MTB and bacterial magnetosomes, as well as on the significances and applications of MTB and their intracellular magnetic mineral crystals.

1. Introduction

MTB are a group of Gram-negative prokaryotes that passively align and actively swim along the geomagnetic field and other fields (Bazylinski and Williams 2007). This ability is based on specific intracellular structures, the magnetosomes, which, in most MTB, are nanometer-sized, membrane-bound crystals of the magnetic iron minerals magnetite (Fe3O4) or greigite (Fe3S4) (Lefèvre et al. 2011). These intriguing microorganisms were first documented by Salvatore Bellini as early as 1963 (Jogler and Schüler 2009). He microscopically observed a certain group of bacteria swam toward the Earth's North Pole and hence named them “magnetosensitive bacteria”. Eleven years later, Blakemore (1975) independently described these microorganisms and coined the terms magnetotaxis for the phenomena and MTB for the bacteria. The discovery of MTB proved to have a serious impact in a number of diverse research fields including microbiology, geology, mineralogy and biomineralization, crystallography, chemistry, biochemistry, physics, limnology and oceanography, and even astrobiology (Bazylinski and Schübbe 2007).

Despite the ubiquitous occurrence of MTB and their high abundance in the sediments of many freshwater and marine habitats, the isolation and cultivation of MTB are difficult due to their fastidious lifestyle (Postec et al. 2012). Because of this, the research in this area has been slow at times. However, with the development in biotechnology and magneto-technology, some progress has been made in laboratory MTB culture, biomineralization, ecology of MTB, magnetisms of MTB and magnetosomes, and identification of fossil magnetosomes in sediments.

The goal of this review is to give a broad overview over the current knowledge of the physiology, ecology, phylogeny, and molecular biology of MTB. Further, we will summarize new insights into the general feature and formation mechanism of magnetosomes. And what is more, the magnetism, significance, and application of MTB and magnetosomes will be presented. Finally, we will briefly discuss some related perspectives and possible directions for future studies.

2. Magnetotactic bacteria

2.1. Physiology, ecology, and phylogeny of MTB

MTB are commonly distributed in water columns or sediments with vertical chemical stratification (Bazylinski and Williams 2007). They can propel themselves through the water by rotating their helical flagella. One interesting microbiological aspect of MTB is that they can swim at speeds nearly twice that of Escherichia coli cells in spite of being larger in size and in spite of having less flagellar proteins (Sharma et al. 2008). Further, in presence of magnetic fields, different strains of MTB show different morphological properties and adjustments as swimmers, presumably due to intracellular magnetosome arrangements (Sharma et al. 2007). These observations highlight the interesting diversity of microbiological species. Generally, they swim to the magnetic north in the northern hemisphere, to the magnetic south in the southern hemisphere, and both ways on the geomagnetic equator (Lefèvre et al. 2011). Almost all the MTB are microaerophiles or anaerobes or facultatively anaerobic microaerophiles. Therefore, they are generally found in relatively high cell numbers at the oxic–anoxic interface (OAI) and the anoxic regions of the habitat or both (Bazylinski and Williams 2007). MTB have been shown to be the dominant species of the bacterial population in some environments, implying a remarkable ecological significance (Spring et al. 1993). The sulfate concentration in freshwater systems is very low and the OAI is located on the water-sediment interface or several millimeters below it (Bazylinski and Schübbe 2007).

The MTB of various morphological types have been found from the freshwater sediments (Thornhill et al., 1994, Amann et al., 2006), including bacillus, vibrios, spirilla, cocci, and multicellular forms (Fig. 1). MTB are known to produce two types of minerals, i.e., iron oxides and iron sulfides (Bazylinski and Frankel 2004). Those that produce iron oxides only biomineralize magnetite (Fe3O4) (Frankel et al. 1979), those that only produce iron sulfides biomineralize greigite (Fe3S4) (Heywood et al. 1990), and those that both produce iron oxide magnetite (Fe3O4) and iron sulfide greigite (Fe3S4) (Bazylinski et al. 1995). In freshwater systems, only iron oxide-producing MTB have been found (Faivre and Schüler 2008). Recently, MTB were found in freshwater in Lake Miyun, northern China (Lin et al. 2009). Moreover, MTB were also detected in extreme environments. Mono Lake, located in California in the United States, is an alkaline and saline lake which is iron limited due to the low solubility of the metal at high pH. Nevertheless, MTB were still found in this environment (Faivre and Schüler 2008). In addition, various magnetic cocci were discovered in mud sediments which have a high content of organic matter (Flies et al. 2005). The distribution of OAI in marine and freshwater is similar, but in many mostly undisturbed marine coastal habitats, the situation is markedly different (Bazylinski and Williams 2007). MTB which can produce both iron oxide and iron sulfide are present in marine and lake environments (Faivre and Schüler 2008). A wide variety of MTB were found in salt marshes, particularly in the surface layers of sulfidic sediments where they co-occur with sulfide oxidizing bacteria (Simmons and Edwards 2007). Large quantities of marine magnetotactic cocci were found in a seawater pond within an intertidal zone at Huiquan Bay in the China Sea (Pan et al. 2008). A marine magnetotactic spirillum was isolated and characterized from an intertidal zone of the China Sea (Zhu et al. 2010). It is reported that in some harbor with chemical stratification, various chemicals can create vertical concentration gradient with depth in the water, MTB were also found in the aqueous layer in microaerobic zone of this environment (Bazylinski et al. 1995).

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Fig. 1. Various morphology of MTB, vibrios: a; rods: b (Bar = 1.0 μm) and d; coccoid: c (Bar = 200 nm); spirilla: e; multicellular organism: f (Bar = 1.0 μm). Figure a and d reproduced from Scheffel and Schüler (2006), figure b reproduced from Baumgartner and Faivre (2011), figure c reproduced from Lefèvre et al. (2011), with permission from Springer. Figure e and f reproduced from Schüler (2008) and Keim et al. (2004), respectively, with permission from John Wiley and Sons.

Only a limited number of MTB have been isolated in pure culture so far (Arakaki et al. 2008). Among them, Magnetospirillum gryphiswaldense MSR-1, Magnetospirillum magneticum AMB-1, Magnetospirillum magneticum MGT-1, Magnetovibrio MV-1, Magnetococcus sp. MC-1, Marine magnetic spirillum QH-2, Magnetospirillum sp. WM-1 and Magnetospirillum magnetotacticum MS-1 are all affiliated to the α-Proteobacteria; Desulfovibrio magneticus RS-1 is affiliated to the δ-Proteobacteria (Fig. 2). Additionally, the 16S rDNA analysis of uncultured MTB was also reported. Previous studies (Keim et al., 2004, Simmons et al., 2004) suggested that different sources of multicellular magnetotactic prokaryotes are affiliated to the δ-Proteobacteria. It has been reported that the Corynebacterium tentatively named Magnetobacterium bavaricum is affiliated to Nitrospira (Fig. 2). 16S rDNA analysis of MTB MHB-1 was carried out by Flies et al. (2005) and the results showed that the sequence homology of MHB-1 with M. bavaricum was 91.0%.

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Fig. 2. Phylogenetic relationships of MTB. Pure culture MTB are indicated in bold characters.

2.2. Molecular biology of MTB
M. magnetotacticum MS-1 was first used for molecular genetic study (Schüler and Frankel 1999). It was suggested that some genes of this bacterium can be expressed in E. coli, the transcription and translation elements of the two microorganisms are compatible, which is necessary for molecular genetic manipulation (Waleh 1988). The recA gene of this organism was cloned and expressed in E. coli by Berson et al. (2006). They cloned a 2 kb DNA fragment from M. magnetotacticum MS-1 that complemented iron-uptake deficiencies in E. coli and Salmonella typhimurium mutants lacking a functional aroD gene. These indicate that this 2 kb DNA may regulate the uptake of iron (Berson et al. 2006).

Development of MTB culture technology on agar plate provides the possibility of screening nonmagnetic mutants which have no magnetosomes. Non-magnetic mutant of M. magneticum AMB-1 in which Tn5 was shown to be integrated into the chromosome were obtained on agar plate (Matsunaga et al. 1992). Using transposon mutagenesis, Nakamura et al. (1995) identified a gene, designated magA, that encodes for a protein with significant sequence homology to the cation efflux proteins, KefC, a potassium-ion-translocating protein in E. coli. The gene of magA was expressed in E. coli and inverted membrane vesicles prepared from E. coli cells indicated that energy was required for iron transport (Nakamura et al. 1995). The expression of magA was higher when wild-type M. magneticum AMB-1 cells were grown under iron-limited conditions rather than iron-sufficient conditions in which they would produce more magnetosomes (Nakamura et al. 1995). Therefore, the role of the magA gene in magnetosome formation is uncertain. However, recent reports suggested that magA could serve as a candidate for a genetically encoded contrast agent for magnetic resonance imaging (MRI) (Goldhawk et al. 2009). Wahyudi et al. (2003) identified a gene, designated as aor, that encodes for a protein with homology to the tungsten-containing aldehyde ferredoxin oxidoreductase (AOR) from Pyrococcus furiosus, which functions for aldehyde oxidation. The gene of aor was found to be expressed under microaerobic conditions and localized in the cytoplasm of M. magneticum AMB-1 (Wahyudi et al. 2003). Additionally, iron uptake and growth of non-magnetic mutant of M. magneticum AMB-1 were lower than wild type. These indicated that aor gene may contribute to ferric iron reduction during magnetosome formation in M. magneticum AMB-1 under microaerobic respiration. Calugay et al. (2004) inserted Tn5 transposon into an open reading frame (ORF) coding for a periplasmic transport binding protein kinase gene homolog. The growth inhibition imposed by the exogenous non-assimilable iron chelator nitrilotriacetate was relieved in wild type but not in non-magnetic mutant of M. magneticum AMB-1, by the addition of the isolated wild type siderophore (Calugay et al. 2004). These implied that the interruption of periplasmic transport binding protein kinase gene homologue is required for siderophore transport into M. magneticum AMB-1.

Using reverse genetics, the mam22 gene was cloned in M. magnetotacticum MS-1 (Okuda et al. 1996) and a gene encoding for a homologous protein, mamA, was found in M. gryphiswaldense MSR-1, M. magneticum AMB-1, and Magnetococcus sp. MC-1 (Grunberg et al., 2001, Komeili et al., 2004, Amemiya et al., 2005). Okuda et al. (1996) used the N-terminal amino acid sequence from a 22 kDa protein specifically associated with the magnetosome membrane to clone and sequence its gene. On the basis of the amino acid sequence, the protein shows high homology to protein of the tetratricopeptide repeat (TPR) protein family (Okuda et al. 1996). However, the function of the protein in magnetosome formation is still unclear. A deletion of mamA in M. magneticum AMB-1 resulted in shorter magnetosome chains and it was concluded that mamA is required for functional magnetosome vesicle formation (Komeili et al. 2004). Recent study showed that the loss of mamA resulted in the change of the number of crystals produced per cell, while the formation of the magnetosome membrane was not affected (Murat et al. 2010). The majority of the genes essentially participating in magnetosome formation are grouped in four conserved gene clusters present within a large unstable genomic region called the magnetosome island (MAI) (Murat et al. 2010). Although the size and gene content of the MAI vary significantly between species, this region shares common characteristics in all MTB analyzed thus far: it is well conserved; it has a low GC content; it is located between two repetitive sequences; and an integrase is present in the flanking region of the first repetitive sequence (Matsunaga et al., 2007, Lefèvre et al., 2011). Dynamic analysis of MAI in M. magneticum AMB-1 revealed that this region as undergone a lateral gene transfer (Fukuda et al. 2006). Similar genomic regions have been found in the genomes of other MTB (Schübbe et al., 2003, Ullrich et al., 2005, Richter et al., 2007).

(more at link:  https://www.sciencedirect.com/science/article/pii/S094450131200047X )

Last edited by Chromium6 on Mon Jan 06, 2020 2:06 am; edited 2 times in total


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Post by Chromium6 on Mon Jan 06, 2020 1:43 am

JANUARY 3, 2020
(more at link: https://phys.org/news/2020-01-scientists-evidence-venus-volcanoes.html )\

Scientists find evidence that Venus has active volcanoes
by Suraiya Farukhi, Universities Space Research Association

This figure shows the volcanic peak Idunn Mons (at 46 degrees south latitude, 214.5 degrees east longitude) in the Imdr Regio area of Venus.

Dr. Filiberto and his colleagues recreated Venus' hot caustic atmosphere in the laboratory to investigate how the observed Venusian minerals react and change over time. Their experimental results showed that an abundant mineral in basalt—olivine—reacts rapidly with the atmosphere and within weeks becomes coated with the iron oxide minerals—magnetite and hematite. They further found that the Venus Express observations of this change in minerology would only take a few years to occur. Thus, the new results by Filiberto and coauthors suggest that these lava flows on Venus are very young, which in turn would imply that Venus does indeed have active volcanoes.


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Post by Chromium6 on Tue Jan 07, 2020 2:39 am

The Nano-Magnetic Dancing of Bacteria Hand-in-Hand with Oxygen

Ayesha Talib1
Abid Ali Khan1  *
Haroon Ahmed1
Ghulam Jilani2

Braz. arch. biol. technol. vol.60  Curitiba  2017  Epub Aug 17, 2017

1Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Tarlai Kalan, 45550 Islamabad, Pakistan. ;
2University of Arid Agriculture - Department of Soil Sciences Rawalpindi, Punjab.


Magnetotactic bacteria are mostly microaerophilic found at the interface between oxic-anoxic zones. We report a magnetotactic bacterial strain isolated from an oil refinery sludge sample that grows aerobically in simple chemical growth medium, 9K. They open a new window of isolation of magnetic nanoparticles through an easy natural living system.

Key words: Magnetotactic Bacteria; Bacillus; Aerobic; Magnetosomes

Magnetotactic bacteria (MTB) are considered as self-propelled oxygen sensors with overall sizes of only 1 to 2 μm across. The cells contain chains of magnetic nanoparticles that act as magnetic nanocompasses and portray the best example of a nanoscale navigation system in nature (1,2 ). Magnetotaxis directional control can be applied from a weak magnetic field to force the cells towards specific areas where oxygen gradient is present (3).

MTB are widespread, motile, morphologically, phylogenetically, and physiologically diverse group of ubiquitous, gram-negative bacteria with the ability to orientate and migrate along geomagnetic field lines (4,5 ). This ability is based on intracellular magnetic structures, the magnetosomes, which comprise membrane bound nano-sized crystals of magnetic iron minerals, organized into chains via a dedicated cytoskeleton and are responsible for the cell magnetotactic behavior (6).

MTB are a heterogeneous group of aquatic prokaryotes and due to their high abundance in marine and freshwater they play an important role in biogeochemical cycling of iron and other elements (7). They are ubiquitous in sediments of freshwater, brackish, marine, and hypersaline habitats as well as in chemically stratified water columns of these environments. The presence of these bacteria depends on opposing gradient of reducing and oxidizing sulfur species and oxygen. Availability of soluble iron (Fe2+/Fe3+) is also the reason for their abundance in the particular environment (Cool.

MTB provide an interesting example for the biosynthesis of magnetic nanoparticles (MNP) in nature. Intracellular (enveloped) crystals of (magnetite-Fe3O4) magnetic nanoparticles are synthesized through a process known as Biologically Controlled Mineralization (BCM) which results in monodispersed, complex nanostructure with unique magnetic properties useful for a variety of medical and industrial applications (9-11). MTB use biomineralization proteins to produce these magnetic crystals. Fe2+ and Fe3+ are first taken up in an energy-dependent process by a periplasmic binding-protein-dependent iron-transport system, accumulated and then rapidly precipitate in specialized sub cellular compartments, the magnetosome vesicles under chemically defined conditions (12,13 ). These vesicles serve as nanobioreactors by providing controlled redox, pH conditions and supersaturating iron concentrations for biomineralization. The membrane of the magnetosome is formed by the invagination of the cytoplasmic membrane and provides a natural coating to the matured magnetic crystal (14). MTB are microaerophiles or anaerobes which prefer environment with little or no oxygen and are considered as typical example of gradient organisms that are present at oxic/anoxic interface (OAI) (15,16 ). MTB play an important role in bioremediation by digesting heavy metals from toxic compounds in industrial areas.

On the basis of the aforementioned interesting properties of MTB, we have isolated aerobic bacteria from a nearby oil refinery sludge sample. To the best of our knowledge this is the first report of an MTB isolation from Pakistan.

A sludge sample was collected from a nearby oil refinery in a pre-sterilized 15 mL plastic tube and returned to the lab. 2 g of the sample was dissolved in 50 mL sterile distilled water and passed through a filter paper to remove the larger particles. 20 µL of the filtrate was added to 15 mL Luria broth and incubated on a shaker at 30 °C overnight. The medium was also added Clotrimazole (0.025 mg/mL) to avoid fungal growth. 10 µL of bacterial suspension from Luria broth was cultured in the 9K medium (pH 2.0) (17) at 30 °C on continuous shaking (120 rpm). The growth of the bacterial was regularly catered by measuring the Optical Density (OD) of the culture at a wavelength of 600 nm and subsequently plotted against time. Cells were harvested during the exponential phase, washed thrice in 0.9 M saline solution and tested for response (alignment) towards a permanent magnet. The live cells were imaged under a light microscope at 100X magnification. The bacterial cells were also Gram stained as per the standard procedure to classify them. Magnetometry analysis was performed in a MPMS-VSM (Magnetic Property Measurement System-Vibrating Sample Magnetometer) (Quantum Design, US). Specially designed diamagnetic containers were filled with (dried) purified bacterial cell mass and the M-vs-H was performed at room temperature (300 K). The samples were centered using a magnetic field of 1000-2000 Oe.

Most of the reported MTB are microaerophilic (or anaerobic) as per their oxygen requirements (17, 18). This very property of these bacteria makes them difficult candidates for culture under lab conditions (13). However, the reported bacterial strain in this study is totally aerobic and thrives well in simple medium, i.e. 9k. This make them suitable candidates to exploit them for magnetic nanoparticles biosynthesis and isolation in lab conditions.

The isolated strain from an oil refinery sludge was cultured in 9K (medium) a number of times to reproduce and confirm our results. It was found out that the bacterial strain was able to grow in 9K aerobically at 30-32 ºC. Reproduced growth plots of these bacterial cells are given in Fig. 1 which shows that these cells required around 3 hours as their lag phase followed by active cell division and rapid increase in the cell number until 15th hour. This was followed by a 2.5 hours stationary phase embarked by a balance between viable and dead cells. The toxic waste material accumulation and depletion of nutrients (to thrive) led to the decline phase of these cells 22-24 hours. The cell viability was found to be drastically reducing in the following measurements. Gram staining showed that they are gram negative rods (Inset of Fig. 1).

Figure 1.  Reproduced growth plots of bacterial cells cultured in 9K. Inset shows a light microscopy image of the gram (negative) stained bacilli.

The bacterial cells harvested (in exponential phase), washed 2-3 times in 0.9 M saline and a permanent magnet of strength (gradient) approximately 0.2 T was applied to one end of the tube to check if the bacterial cells would respond to it or not? The cultured bacterial cells upon exposure to a permanent magnet externally aligned parallel towards the field gradient (Fig. 2A). It was observed in this experimental test even by naked eye that these cells harboured magnetic content inside them which pushed them to swim towards the magnetic field gradient and aligned towards it. This experiment proved the fact that the bacterial cells isolated in this work are magnetic or to be precise magnetotactic. However, when 9K was treated

the same way, it showed no alignment of any particles towards the magnet. This proves the fact that these bacteria have the capacity to grow in 9K aerobically capable of utilizing iron ions and biosynthesize magnetosomes (magnetic nanoparticles).

As already discussed, these bacterial cells were magnetically responsive towards a permanent magnet, however, it was also noticed that these cells were not strongly magnetic but rather had a weak magnetic response, i.e. it always took them some time to swim towards the applied magnetic gradient. To investigate further the magnetism of these nanomachineries, we performed physical characterization in a VSM, i.e. magnetization was plotted as a function of the applied magnetic field at room temperature. The purified cell mass (as shown in Fig. 2A) was dried and evaluated for their magnetic properties. The aim was to check if the magnetic moment of these particles is good enough to be detected by the magnetometer. The results proved that these dried cells were superparamagnetic at room temperature (300 K). The hysteresis loop resulted (Fig. 2B) clearly indicated the presence of magnetic nanoparticles inside these bacterial cells. This strengthen our previous results that we had obtained with permanent magnet exposure to these cells.



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Post by Chromium6 on Mon Jan 13, 2020 2:47 am

USGS Identifies Largest Continuous Oil and Gas

Resource Potential Ever Assessed

Estimates Include 46.3 Billion Barrels of Oil, 281 Trillion Cubic feet of Natural Gas, and 20 Billion Barrels of Natural Gas Liquids in Texas and New Mexico’s Wolfcamp Shale and Bone Spring

Last edited 12/6/2018
Date: December 6, 2018
Contact: Interior_Press@ios.doi.gov

WASHINGTON - Today, the U.S. Department of the Interior announced the Wolfcamp Shale and overlying Bone Spring Formation in the Delaware Basin portion of Texas and New Mexico’s Permian Basin province contain an estimated mean of 46.3 billion barrels of oil, 281 trillion cubic feet of natural gas, and 20 billion barrels of natural gas liquids, according to an assessment by the U.S. Geological Survey (USGS). This estimate is for continuous (unconventional) oil, and consists of undiscovered, technically recoverable resources.

"Christmas came a few weeks early this year," said U.S. Secretary of the Interior Ryan Zinke. "American strength flows from American energy, and as it turns out, we have a lot of American energy. Before this assessment came down, I was bullish on oil and gas production in the United States. Now, I know for a fact that American energy dominance is within our grasp as a nation."

“In the 1980s, during my time in the petroleum industry, the Permian and similar mature basins were not considered viable for producing large new recoverable resources. Today, thanks to advances in technology, the Permian Basin continues to impress in terms of resource potential. The results of this most recent assessment and that of the Wolfcamp Formation in the Midland Basin in 2016 are our largest continuous oil and gas assessments ever released,” said Dr. Jim Reilly, USGS Director. “Knowing where these resources are located and how much exists is crucial to ensuring both our energy independence and energy dominance.”

Although the USGS has previously assessed conventional oil and gas resources in the Permian Basin province, this is the first assessment of continuous resources in the Wolfcamp shale and Bone Spring Formation in the Delaware Basin portion of the Permian. Oil and gas companies are currently producing oil here using both traditional vertical well technology and horizontal drilling and hydraulic fracturing.

The Wolfcamp shale in the Midland Basin portion of the Permian Basin province was assessed separately in 2016, and at that time it was the largest assessment of continuous oil conducted by the USGS. The Delaware Basin assessment of the Wolfcamp Shale and Bone Spring Formation is more than two times larger than that of the Midland Basin. The Permian Basin province includes a series of basins and other geologic formations in West Texas and southern New Mexico. It is one of the most productive areas for oil and gas in the entire United States.

“The results we’ve released today demonstrate the impact that improved technologies such as hydraulic fracturing and directional drilling have had on increasing the estimates of undiscovered, technically recoverable continuous (i.e., unconventional) resources,” said Walter Guidroz, Program Coordinator of the USGS Energy Resources Program.

Undiscovered resources are those that are estimated to exist based on geologic knowledge and already established production, while technically recoverable resources are those that can be produced using currently available technology and industry practices. Whether or not it is profitable to produce these resources has not been evaluated.

USGS is the only provider of publicly available estimates of undiscovered technically recoverable oil and gas resources of onshore lands and offshore state waters. The USGS Delaware Basin Wolfcamp shale and Bone Spring Formation assessment was undertaken as part of a nationwide project assessing domestic petroleum basins using standardized methodology and protocols.

The new assessment of the Delaware Basin Wolfcamp shale may be found online. To find out more about USGS energy assessments and other energy research, please visit the USGS Energy Resources Program website.



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Post by Chromium6 on Sun Jan 26, 2020 10:18 pm


Naturally occurring bacteria converts CO2 into calcium carbonate

By Darren Quick
February 23, 2009


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Post by Chromium6 on Sun Jan 26, 2020 10:21 pm

Microbiologically induced calcite precipitation

Microbiologically induced calcium carbonate precipitation (MICP) is a bio-geochemical process that induces calcium carbonate precipitation within the soil matrix.[1] Biomineralization in the form of calcium carbonate precipitation can be traced back to the Precambrian period.[2] Calcium carbonate can be precipitated in three polymorphic forms, which in the order of their usual stabilities are calcite, aragonite and vaterite.[3] The main groups of microorganisms that can induce the carbonate precipitation are photosynthetic microorganisms such as cyanobacteria and microalgae; sulfate-reducing bacteria; and some species of microorganisms involved in nitrogen cycle.[4] Several mechanisms have been identified by which bacteria can induce the calcium carbonate precipitation, including urea hydrolysis, denitrification, sulphate production, and iron reduction. Two different pathways, or autotrophic and heterotrophic pathways, through which calcium carbonate is produced have been identified. There are three autotrophic pathways, which all result in depletion of carbon dioxide and favouring calcium carbonate precipitation.[5] In heterotrophic pathway, two metabolic cycles can be involved: the nitrogen cycle and the sulfur cycle [6]. Several applications of this process have been proposed, such as remediation of cracks and corrosion prevention in concrete,[7][8][9][10][11][12][13][14][15] biogrout,[16][17][18][19][20][21][22][23] sequestration of radionuclides and heavy metals.[24][25][26][27][28][29]



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Post by Chromium6 on Sun Jan 26, 2020 10:27 pm

Open Access
Published: 18 February 2019

Carbonate formation in salt dome cap rocks by microbial anaerobic oxidation of methane

K. H. Caesar, J. R. Kyle, […]S. J. Loyd
Nature Communications volume 10, Article number: 808 (2019) Cite this article

1997 Accesses

3 Citations

9 Altmetric

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Major hydrocarbon accumulations occur in traps associated with salt domes. Whereas some of these hydrocarbons remain to be extracted for economic use, significant amounts have degraded in the subsurface, yielding mineral precipitates as byproducts. Salt domes of the Gulf of Mexico Basin typically exhibit extensive deposits of carbonate that form as cap rock atop salt structures. Despite previous efforts to model cap rock formation, the details of subsurface reactions (including the role of microorganisms) remain largely unknown. Here we show that cap rock mineral precipitation occurred via closed-system sulfate reduction, as indicated by new sulfur isotope data. 13C-depleted carbonate carbon isotope compositions and low clumped isotope-derived carbonate formation temperatures indicate that microbial, sulfate-dependent, anaerobic oxidation of methane (AOM) contributed to carbonate formation. These findings suggest that AOM serves as an unrecognized methane sink that reduces methane emissions in salt dome settings perhaps associated with an extensive, deep subsurface biosphere.

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Earth’s climate is modulated by the concentration of atmospheric greenhouse gases. These gases (e.g., CO2 and CH4) are largely generated at depth and subsequently transported to surface environments. These gases may fail to reach the surface due to chemical reaction along the way, resulting in their degradation and the subsequent precipitation of mineral phases. The geochemical compositions of these diagenetic minerals can provide insight into the nature of degradation mechanisms, thus leading to a better understanding of the fate of subsurface gaseous and aqueous chemical species.

Evaporites, elemental sulfur, metal sulfides, and carbonate minerals can co-occur in unique diagenetic settings. Examples of this association include those observed in cap rocks formed atop Jurassic salt in the Gulf of Mexico Basin (GMB)1, Permian salt of Germany and the North Sea Basin2, and Triassic salt in northern Tunisia3. Similar deposits occur in Permian, hydrocarbon-bearing evaporite successions of the Delaware Basin in western Texas and Miocene strata in Carpathian basins of Poland, Ukraine, and Iraq4. These systems have been studied extensively due to their association with economic hydrocarbon and mineral resources5. Such environments provide appropriate conditions for microbial communities to take advantage of mineral-, aqueous-, and hydrocarbon-sourced reactants for metabolic gain. Despite the likelihood of active microbial cycling, little is known about the specific natures and impacts of these interactions.

The GMB subsurface represents one of the world’s best-developed salt dome provinces (Fig. 1), containing hundreds of salt structures associated with post-depositional diapiric movement of the Jurassic Louann Salt6,7,8. The Louann Salt consists primarily of halite with minor (1–5%) anhydrite and gypsum9. Dome structures form when salt mobilizes and intrudes into overlying strata, partially as a result of the preferential subsidence of surrounding sediments. The GMB is also known for its large deposits of oil and natural gas that typically accumulate along the flanks of salt domes as a result of confinement by structural traps10.



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Post by Chromium6 on Sun Jan 26, 2020 10:31 pm

Methane formation by metal-catalyzed hydrogenation of solid calcium carbonate

Noritetsu Yoshida, Takeshi Hattori, […]Takayuki Wada
Catalysis Letters volume 58, pages119–122(1999)Cite this article

238 Accesses

14 Citations


A study of the hydrogenation of solid CaCO3 has shown that the addition of Pd and Ir catalysts causes a change in the gaseous product and, consequently, in the kinetics of the reaction. In the absence of catalyst, CO is formed at higher than 700 K with the activation energy of 236 kJ/mol and a nearly half order with respect to H2 pressure, which is explained by the mechanism consisting of predecomposition and reduction. In the presence of the catalysts, CH4 is exclusively formed even at 573 K at which the equilibrium decomposition pressure of CaCO3 is extremely low, 1.1 × 10−5 Torr. Activation energies found in the range 105–118 kJ/mol and the H2-pressure dependence of the initial rate suggest the direct interaction of CaCO3 with spilt-over hydrogen atoms.



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Post by Chromium6 on Sun Jan 26, 2020 10:34 pm

Thermodynamics and kinetics of methane hydrate formation and dissociation in presence of calcium carbonate

Author links open overlay panelEktaChaturvediAjayMandal
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Dissolution of CaCO3 in water increases with pH of the solution.

Hydrate formation thermodynamics is affected by presence of CaCO3 powder in water.

Nucleation point for the hydrate formation is increased with % carbonate in water.

Hydrate formation rate decreases with increase in concentration of CaCO3.

Phase stability curve shifts with the variation in CaCO3 concentration.


Huge amount of gas hydrate deposits are identified in deep marine sediments, which may be considered as a future source of energy. Since carbonate is one of the major components of marine sediments, in the present study attention has been given to characterize methane hydrate formation and dissociation in presence of calcium carbonate. Experiments were performed with 0%, 2%, 4%, 6% and 10% by weight of calcium carbonate in distilled water. Extensive investigations have been done on pressure-temperature equilibrium behavior of hydrate formation and dissociation at varying concentrations of calcium carbonate. Hydrate formation rate was found to vary with concentration of calcium carbonate as the solubility of calcium carbonate in water is controlled by the presence of simultaneous chemical equilibria involving a high number of species like Ca2+, CO32−, HCO3−, CO2, etc. Induction time for hydrate formation has also been measured at different concentrations of carbonate. Nucleation point for the hydrate formation was observed to be slightly higher at higher concentration of calcium carbonate due to increased heat absorption. Dissociation enthalpy of hydrates was calculated by using Clausius-Clapeyron at different measured conditions. Moles consumption of methane gas during hydrate formation at different concentrations of carbonate was measured using real gas equation and found to be minimum at 10 wt%.



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Post by Chromium6 on Sun Jan 26, 2020 10:39 pm

Deep Diving Scientists Discover Bubbling CO2 Hotspot

Gordz At Soda Springs

A researcher collects gas samples at Soda Springs in the Philippines. Photo: University of Texas Jackson School of Geosciences.

AUSTIN, Texas — Diving 200 feet under the ocean surface to conduct scientific research can lead to some interesting places. For University of Texas at Austin Professor Bayani Cardenas, it placed him in the middle of a champagne-like environment of bubbling carbon dioxide with off-the-chart readings of the greenhouse gas.

Cardenas discovered the region – which he calls “Soda Springs” – while studying how groundwater from a nearby island could affect the ocean environment of the Verde Island Passage in the Philippines. The passage is one of the most diverse marine ecosystems in the world and is home to thriving coral reefs.

The amazing bubbling location, which Cardenas captured on video, is not a climate change nightmare. It is linked to a nearby volcano that vents out the gases through cracks in the ocean floor and has probably been doing so for decades or even millennia. However, Cardenas said that the high CO2 levels could make Soda Springs an ideal spot for studying how coral reefs may cope with climate change. The site also offers a fascinating setting to study corals and marine life that are making a home among high levels of CO2.

“These high CO2 environments that are actually close to thriving reefs, how does it work?” said Cardenas, who is a professor in the Jackson School of Geosciences at UT Austin. “Life is still thriving there, but perhaps not the kind that we are used to. They need to be studied.”

Cardenas and his coauthors from institutions in the Philippines, the Netherlands and UT described Soda Springs along with multiple scientific findings about groundwater in a paper published this month in the journal Geophysical Research Letters.

The scientists measured CO2 concentrations as high as 95,000 parts per million (ppm), more than 200 times the concentration of CO2 found in the atmosphere. The readings range from 60,000 to 95,000 and are potentially the highest ever recorded in nature. The CO2 levels fall quickly away from the seeps as the gas is diluted in the ocean, but the gas still creates an elevated CO2 environment along the rest of the coastline of the Calumpan Peninsula, with levels in the 400 to 600 ppm range.

Cardenas is a hydrologist and not an expert on reef systems. He discovered Soda Springs while researching whether groundwater from the nearby land could be discharging into the submarine ocean environment, which is a phenomenon that is generally ignored by scientists looking at the water cycle, Cardenas said.

“It’s an unseen flux of water from land to the ocean,” he said. “And it’s hard to quantify. It’s not like a river where you have a delta and you can measure it.”

More at link... https://news.utexas.edu/2020/01/22/deep-diving-scientists-discover-bubbling-co2-hotspot/


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Post by Chromium6 on Sat Feb 01, 2020 6:51 pm

Generation of methane in the Earth's mantle: In situ high pressure–temperature measurements of carbonate reduction

Henry P. Scott, Russell J. Hemley, [...], and Sorin Bastea

Additional article information


We present in situ observations of hydrocarbon formation via carbonate reduction at upper mantle pressures and temperatures. Methane was formed from FeO, CaCO3-calcite, and water at pressures between 5 and 11 GPa and temperatures ranging from 500°C to 1,500°C. The results are shown to be consistent with multiphase thermodynamic calculations based on the statistical mechanics of soft particle mixtures. The study demonstrates the existence of abiogenic pathways for the formation of hydrocarbons in the Earth's interior and suggests that the hydrocarbon budget of the bulk Earth may be larger than conventionally assumed.

Understanding the speciation of carbon at the high pressures and temperatures that prevail within the Earth has a long and controversial history. It is well known that terrestrial carbon exists in several forms: native, oxidized, and reduced in a wide variety of hydrocarbons. This complexity is demonstrated by many examples: diamonds in kimberlite formations; graphite in metamorphic rocks; CO2 emission from volcanoes; ubiquitous carbonate minerals in the crust; methane hydrates on and beneath the ocean floor; and petroleum reservoirs in sedimentary basins. Of particular interest are the stability and formation of reduced species such as methane and heavier hydrocarbons. The stability, formation, and occurrence of methane under low-pressure conditions of the Earth's crust are well established. Recently, methane and C2-C4 alkanes have been documented to occur in many locations for which isotopic evidence points to an abiogenic origin (
1, 2). Furthermore, it has been shown that nickel-iron alloys can catalyze the formation of CH4 from bicarbonate
(3), and that a variety of transition metal-bearing minerals can catalyze Fischer–Tropsch-type formation of hydrocarbons at conditions relevant to the upper crust
(4, 5). Yet the evidence is considered to rule out a globally significant abiogenic source of hydrocarbons
(2), and hydrothermal experiments suggest that with the exception of methane a vapor phase is required for the formation of heavier hydrocarbons (5). In contrast, theoretical calculations and experimental data have been presented in support of a persistent assertion that petroleum originates chiefly through abiogenic processes at the high pressures and temperatures found <100 km (6). The experiments, extending to 5 GPa and 1,500°C, involved mass spectroscopic analysis of quenched samples and found methane and smaller amounts of C2-C6 hydrocarbons. We report here in situ high pressure and temperature experiments to show that methane readily forms by reduction of carbonate under conditions typical for the Earth's upper mantle. The results may have significant implications for the hydrocarbon budget at depth in the planet.

Many factors are known to control the stability of carbon-bearing phases in the C-O-H system, including pressure, temperature, C/H ratio, and oxidation state, and it has long been appreciated that the relevant species in this system are C, O2,H2, CO, CO2,CH4, and H2O (7). At low pressures this system is well understood, and available thermodynamic databases can accurately predict phase stability. For example, studies of the C-O-H system in relation to crustal fluids and fluid inclusions have been carried out by using well established techniques (7, Cool. Notably, theoretical modeling is both thermodynamically and observationally consistent at pressures <≈1 GPa (e.g., ref. 9) and can satisfactorily treat organic species (10). Previous experimental and theoretical work has shown that methane may be an important fluid phase at pressures of up to 1 GPa and low oxygen fugacities, and that methane may be the dominant C-bearing fluid phase at substantially reducing conditions (e.g., ref. Cool. Furthermore, it has been shown that meteorite hydrocarbons can be formed by the thermal decomposition of FeCO3-siderite at low pressure (11). Thermodynamic calculations can be performed at higher pressures (12), but the system is poorly constrained by experimental work under the high-pressure conditions of the upper mantle (13). The importance of pressure is straightforward as it increases by ≈1 GPa (10 kbar) for every 30 km of depth in the Earth. Kimberlite eruptions, for example, typically come from depths near 150 km (5 GPa). Higher-pressure work has been completed on the effects of various species in the C-O-H system on the melt characteristics of mantle minerals (14, 15), but these results do not directly assess the stability of carbon-bearing phases.

We have conducted in situ high-pressure and temperature experiments specifically designed to detect methane formation under geologically relevant conditions for the Earth's upper mantle. Starting materials were natural CaCO3-calcite, FeO-wüstite, and distilled H2O. Experiments were conducted by using diamond anvil cell (DAC) techniques: simultaneous high-pressure and high-temperature conditions were produced by both resistive (16) (T < 600°C) and laser heating (T > 1,000°C) methods. We used three different laser heating systems, including both single- and double-sided and both CO2 and Nd-YLF lasers (17, 18). DACs with anvil culets ranging between 350 and 700 μm in diameter were used. Sample chambers were constructed by drilling a hole ≈70% of the culet diameter into an initially 260-μm-thick spring steel foil, which was used as a gasket material; the gaskets were preindented before drilling to a thickness of ≈60 μm. Pressure was measured by use of the ruby fluorescence technique (19). CO2 and double-sided Nd-YLF laser heating experiments and Raman scattering and optical microscopy analyses were performed at the Geophysical Laboratory (17, 18). Pyrometry was used to determine sample temperature in selected runs. The x-ray measurements and double-sided Nd-YLF laser heating were performed at the High Pressure Collaborative Access Team facilities of the Advanced Photon Source, Argonne National Laboratory, Argonne, CA.

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Post by Chromium6 on Sat Feb 01, 2020 7:08 pm

Formation processes of methane-derived authigenic carbonates from the Gulf of Cadiz

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Vitor H.Magalhãesa  LuisSomozaf

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The Gulf of Cadiz, NE Atlantic, represents an area of extensive formation of methane-derived authigenic carbonates (MDAC), indicative of fluid seepage. These MDAC, that reach extraordinary length and thickness, were geophysically mapped and sampled and the recovered carbonate-cemented material has δ13C values as low as − 56.2‰ VPDB, indicating methane as the major carbon source. The MDAC form two main lithologic groups, one mainly comprising dolomite and the second dominated by aragonite. The dolomite-dominated samples were found along fault-controlled diapiric ridges, on some mud volcanoes and mud diapirs, all on the pathway of the Mediterranean Outflow Water, and along fault scarps. Aragonite pavements were found associated with mud volcanoes and along fault scarps, but are otherwise not restricted to the pathways of the Mediterranean Outflow Water. Based on the results from this study, we propose that the two lithologic groups reflect different geochemical formation environments associated with a formation model based on their morphology, mineralogy and geochemistry. The aragonite-dominated samples represent precipitation of authigenic carbonates at the sediment–seawater interface or close to it, in a high alkalinity environment resulting from anaerobic oxidation of methane-rich fluids venting into sulphate-bearing porewaters. In contrast, the dolomite-dominated samples result from cementation along fluid conduits inside the sedimentary column with a somewhat restricted seawater ventilation. The dolomite chimneys form in places presently swept by the strong flow of the Mediterranean undercurrent so that the unconsolidated sediments are eroded and the chimneys are exposed at the seafloor. The widespread and large abundance of MDAC is a direct evidence of extensive methane seepage episodes in the Gulf of Cadiz. The coincidence of the different lithologic types in close spatial and temporal association indicates a persistence of seepage episodes in some structures over large periods of time.

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Post by Chromium6 on Sat Feb 01, 2020 7:14 pm

An Inexhaustible Source of Energy from Methane in Deep Earth

September 15, 2004

Untapped reserves of methane, the main component in natural gas, may be found deep in Earth’s crust, according to a recently released report in the Proceedings of the National Academy of Sciences of the United States of America (PNAS). These reserves could be a virtually inexhaustible source of energy for future generations. The team of researchers from Lawrence Livermore National Laboratory, Carnegie Institution’s Geophysical Laboratory, Harvard University, Argonne National Laboratory and Indiana University, South Bend, through a series of experiments and theoretical calculations, showed that methane forms under conditions that occur in Earth’s upper mantle.

Methane is the most plentiful hydrocarbon in Earth’s crust and is a main component of natural gas. However, oil and gas wells are typically only drilled 5 to 10 kilometers beneath the surface. These depths correspond to pressures of a few thousand atmospheres.

Using a diamond anvil cell, the scientists squeezed materials common at Earth’s surface — iron oxide (FeO), calcite (CaCO3) (the primary component of marble) and water to pressures ranging from 50,000 to 110,000 atmospheres and temperatures more than 2,500 degrees Fahrenheit — to create conditions similar to those found deep within Earth.

Methane (CH4) formed by combining the carbon in calcite with the hydrogen in water. The reaction occurred over a range of temperatures and pressures. Methane production was most favorable at 900 degrees Fahrenheit and 70,000 atmospheres of pressure.

The experiments show that a non-biological source of hydrocarbons may lie in Earth’s mantle and was created from reactions between water and rock — not just from the decomposition of living organisms.

“The results demonstrate that methane readily forms by the reaction of marble with iron-rich minerals and water under conditions typical in Earth’s upper mantle,” said Laurence Fried, of Livermore’s Chemistry and Materials Science Directorate. “This suggests that there may be untapped methane reserves well below Earth’s surface. Our calculations show that methane is thermodynamically stable under conditions typical of Earth’s mantle, indicating that such reserves could potentially exist for millions of years.”

The study is published in the Sept. 13-17 early, online edition of the PNAS.

The mantle is a dense, hot layer of semi-solid rock approximately 2,900 kilometers thick. The mantle, which contains more iron, magnesium and calcium than the crust, is hotter and denser because temperature and pressure inside Earth increase with depth. Because of the firestorm-like temperatures and crushing pressure in Earth’s mantle, molecules behave very differently than they do on the surface.

“When we looked at the samples under these pressures and temperatures, they revealed optical changes indicative of methane formation,” Fried said. “At temperatures above 2,200 degrees Fahrenheit, we found that the carbon in calcite formed carbon dioxide rather than methane. This implies that methane in the interior of Earth might exist at depths between 100 and 200 kilometers. This has broad implications for the hydrocarbon reserves of the planet and could indicate that methane is more prevalent in the mantle than previously thought. Due to the vast size of Earth’s mantle, hydrocarbon reserves in the mantle could be much larger than reserves currently found in Earth’s crust.”



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Post by Chromium6 on Sat Feb 01, 2020 7:22 pm



The search for methane in Earth's mantle


In one experiment, a sample of iron oxide, calcite, and water is heated to 600°C at a pressure of about 2 gigapascals. Raman spectra of the sample show a carbon-hydrogen (C-H) stretching vibration at 2,932 centimeters-1, which is the industry-standard signature for methane.
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Petroleum geologists have long searched beneath Earth's surface for oil and gas, knowing that hydrocarbons form from the decomposition of plants and animals buried over time. However, methane, the most plentiful hydrocarbon in Earth's crust, is also found where biological deposits seem inadequate or improbable--for example, in great ocean rifts, in igneous and metamorphic rocks, and around active volcanoes. Some scientists thus wonder whether untapped reserves of natural gas may exist in Earth's mantle.

A collaboration of researchers from Lawrence Livermore and Argonne national laboratories, Carnegie Institution's Geophysical Laboratory, Harvard University, and Indiana University at South Bend is finding that methane may also be formed from nonbiological processes. Experiments and calculations conducted by the team indicate that Earth's mantle may provide the temperature and pressure conditions necessary to produce methane.

The idea that methane could be formed nonbiogenically came from observing the solar system. In the 1970s, astronomer Thomas Gold proposed that methane must form from nonbiogenic materials as well as from biological decomposition because large amounts of methane and other hydrocarbons could be detected in the atmospheres of Jupiter, Saturn, Uranus, and Neptune. In fact, in studying Titan, Saturn's largest moon, researchers found seven different hydrocarbons. At the time Gold proposed this theory, conventional geochemists argued that hydrocarbons could not possibly reside in Earth's mantle.

They reasoned that at the mantle's depth--which begins between 7 and 70 kilometers below Earth's surface and extends down to 2,850 kilometers deep--hydrocarbons would react with other elements and oxidize into carbon dioxide. (Oil and gas wells are drilled between 5 and 10 kilometers deep.)

However, more recent research using advanced high-pressure thermodynamics has shown that the pressure and temperature conditions of the mantle would allow hydrocarbon molecules to form and survive at depths of 100 to 300 kilometers. Because of the mantle's vast size, its hydrocarbon reserves could be much larger than those in Earth's crust.

Simulating Thermochemical Conditions

Livermore's work on the methane research, led by chemist Larry Fried, uses a thermodynamics code called CHEETAH to simulate chemical reactions using data from the collaboration's experiments. Fried developed CHEETAH in 1993 for the Department of Defense (DoD) to predict the performance of different explosives formulations. Since then, Fried and his colleagues have continued to improve the code. (See S&TR, May 1999, Leveraging Science and Technology in the National Interest; June 1999, Unraveling the Mystery of Detonation; July/August 2003, A New Generation of Munitions; July/August 2004, Going to Extremes.)
Thermochemical calculations for a mixture of iron oxide, calcite, and water heated to 500°C show that methane is produced at pressures up to almost 7 gigapascals.

Click here for a high resolution photograph.
One improvement was to include intermolecular interaction potentials. As a result, CHEETAH can model accurate equations of state, describing the relationship of a material's pressure, volume, and temperature at the molecular level, for a broad range of thermodynamic conditions. Because materials behave differently under extreme pressures than they do at normal atmospheric pressure, the equation-of-state data produced with CHEETAH help improve the precision of other computer codes used to model materials for stockpile stewardship.

With funding from the Laboratory Directed Research and Development Program, Fried's team is using CHEETAH to analyze the data from experiments conducted at the Geophysical Laboratory and at Argonne. "CHEETAH was designed for defense-related efforts," says Fried. "Our current studies for the methane collaboration are validating the code for work in high-pressure chemistry. These results will in turn help us better understand the processes occurring in a high-explosive detonation."

For the methane experiments, researchers at the Geophysical Laboratory used Argonne's diamond anvil cell (DAC)--a small mechanical press that forces together the tips of two diamond anvils and creates extremely high pressures on a sample of a material held within a metal gasket. DACs allow researchers to measure material properties under static pressure and at varying pressures and temperatures over many hours. (See S&TR, December 2004, Putting the Squeeze on Materials.) Diamonds are used because they can withstand these ultrahigh pressures.

More at link: https://www.eurekalert.org/features/doe/2005-08/drnl-tsf082205.php


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