We thank the H.O.G. group at Arizona State University for developing the initial methodology of these hydrothermal experiments, and in particular, we thank I. Gould, E. Shock, L. Williams, C. Glein, H. Hartnett, K. Fecteau, K. Robinson, and C. Bockisch, for their guidance and helpful assistance. Z. Yang and X. Fu were funded by startup funds from Oakland University to Z. Yang.

1. Prepare the Sample for Hydrothermal Experiment
<ol>
	<li>Choose the size of the quartz or silica glass tubes, e.g., 2 mm inner diameter (ID) x 6 mm outer diameter (OD) or 6 mm ID x 12 mm OD, and determine the amounts of organic compounds and minerals to use. In this work, the amounts of nitrobenzene and magnetite (Fe3O4) to load into the silica tube (e.g., 2 mm ID x 6 mm OD) are 3.0 &#181;L and 13.9 mg, respectively. 
	NOTE: The large diameter tubes allow easier loading of the materials but require more efforts of tube sealing.</li>
	<li>Cut the clean silica glass tubing into small pieces with ~30 cm in length using a tube cutter. Seal one end of the tube closed using an oxyhydrogen torch with an appropriate flame head. 
	CAUTION: Follow the safety procedures for using the oxyhydrogen torch.</li>
	<li>Weigh the predetermined amount of the starting organic compound on a 0.1 mg-scale balance (if it is solid) and transfer it into the silica glass tube using a weighing paper. If the compound is liquid (e.g., nitrobenzene in this case), use a microliter syringe (e.g., 10 &#181;L) to transfer it into the small silica tube. Add the weighed minerals into the silica tube through a Pasteur pipette, and then add deionized and deoxygenated water (e.g., 0.3 mL). Use 18.2 M&#937;&#183;cm deionized water and deoxygenate it by sonication.</li>
	<li>Connect the silica tube to a vacuum line (~1 cm ID) with a closed valve. Immerse the tube in a Dewar flask filled with liquid nitrogen for ~3 min until the organics and water are completely frozen. 
	CAUTION: Follow the safety procedures for transferring and using liquid nitrogen.</li>
	<li>When the tube remains immersed in liquid nitrogen, open the vacuum valve and remove the air from the headspace of the tube. 
	NOTE: This process should last until the pressure drops below 100 mtorr on the pressure gauge of the vacuum pump.</li>
	<li>Switch off the valve, remove the tube from the liquid nitrogen, and let the tube warm up to room temperature. Gently tap the bottom of the tube to release the remaining air bubbles from solution to headspace.</li>
	<li>Repeat the above freeze-pump-thaw cycle for two more times and keep the tube in liquid nitrogen before sealing the other end of the tube. Close the vacuum line and use the oxyhydrogen flame to make the entire tube closed. 
	NOTE: When the tube undergoes hydrothermal experiments, the headspace volume of the tube will decrease due to liquid water expansion. For example, the density of water reduces about 30% from room temperature to 300 &#176;C. Calculate and leave enough headspace volume when sealing the tube.</li>
</ol>
2. Set Up the Hydrothermal Experiment
<ol>
	<li>After the sealing steps, put the silica tube into a small steel pipe (~30 cm in length and 1.5 cm in diameter) with loose screw caps, in order to prevent damage from any pressure building or tube failure inside the pipe.</li>
	<li>Place the pipe in a well temperature-controlled furnace or oven and heat it up to the desired temperature (e.g., 150 &#176;C in this work). Use a thermocouple inside the oven to monitor the temperature through the hydrothermal reaction.</li>
	<li>As soon as the reaction time is reached (e.g., 2 h in this work), quench the silica tube by quickly putting the pipe into an ice water bath. 
	NOTE: The quenching process takes less than 1 min to cool down to room temperature, which avoids potential retrograde reactions.</li>
</ol>
3. Analyze the Sample after the Experiment
<ol>
	<li>Open the silica tube using a tube cutter, and quickly transfer all the products (e.g., ~0.3 mL in small silica tube) into a 10 mL glass vial using a Pasteur pipette.</li>
	<li>Extract the organic products with 3 mL dichloromethane (DCM) solution that contains 8.8 mM dodecane as an internal standard for gas chromatography (GC). Cap the vial and shake it by hands for 2 min and vortex it for 1 min. 
	NOTE: This helps to facilitate the extraction of organic products into the organic phase. Also, rinse the transferring pipet and inside walls of the silica tube with DCM to ensure products recovery. For samples with high mineral contents, sonicate them in the DCM solution for better extraction.</li>
	<li>Allow the mineral particles to settle down in the extraction solution (i.e., DCM with dodecane) for 5 min. Use a Pasteur pipette to carefully transfer ~1 mL of the sample from the DCM layer (i.e., the bottom layer) into a GC vial.</li>
	<li>Analyze the organic product distribution using GC with a poly-capillary column (e.g., 5% diphenyl/95% dimethylsiloxane) and a flame ionization detector. Set up the GC oven with a program to start at 50 &#176;C and hold for 8 min, increase at 10 &#176;C/min to 220 &#176;C and hold for 10 min, increase at 20 &#176;C /min to 300 &#176;C and hold for 5 min. Set the injector temperature to 300 &#176;C. 
	NOTE: The GC program needed to be changed based on the type of organic compounds being analyzed.</li>
	<li>Build the GC calibration curves by plotting the peak area ratio of the analyte to the internal standard versus the concentration of the analyte.</li>
	<li>Calculate the reaction conversion based on the concentrations of the starting organic material before and after the reaction, i.e., conversion%&#160;=&#160;([initial]&#160;&#8211;&#160;[final])&#160;&#160;&#8260;&#160;&#160;[initial]&#160;&#215;100%. Use the conversions to determine if the mineral facilitates or slows down the hydrothermal organic transformations.</li>
</ol>

<ol>
	<li>Yang, Z., Gould, I. R., Williams, L. B., Hartnett, H. E., Shock, E. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+iron-containing+minerals+on+hydrothermal+reactions+of+ketones.">Effects of iron-containing minerals on hydrothermal reactions of ketones.</a> Geochimica et Cosmochimica Acta. 223, 107-126 (2018).</li><li>Seewald, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organic-inorganic+interactions+in+petroleum-producing+sedimentary+basins.">Organic-inorganic interactions in petroleum-producing sedimentary basins.</a> Nature. 426 (6964), 327-333 (2003).</li><li>Sogin, M. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microbial+diversity+in+the+deep+sea+and+the+underexplored+"rare+biosphere".">Microbial diversity in the deep sea and the underexplored "rare biosphere".</a> Proceedings of the National Academy of Sciences. 103 (32), 12115 (2006).</li><li>McCollom, T. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laboratory+Simulations+of+Abiotic+Hydrocarbon+Formation+in+Earth's+Deep+Subsurface.">Laboratory Simulations of Abiotic Hydrocarbon Formation in Earth's Deep Subsurface.</a> Reviews in Mineralogy and Geochemistry. 75 (1), 467-494 (2013).</li><li>Foustoukos, D. I., Seyfried, W. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hydrocarbons+in+Hydrothermal+Vent+Fluids:+The+Role+of+Chromium-Bearing+Catalysts.">Hydrocarbons in Hydrothermal Vent Fluids: The Role of Chromium-Bearing Catalysts.</a> Science. 304 (5673), 1002 (2004).</li><li>Bell, J. L. S., Palmer, D. A., Pittman, E. D., Lewan, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=10.1007/978-3-642-78356-2_9.">10.1007/978-3-642-78356-2_9.</a> Organic Acids in Geological Processes. , 226-269 (1994).</li><li>Palmer, D. A., Drummond, S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermal+decarboxylation+of+acetate.+Part+I.+The+kinetics+and+mechanism+of+reaction+in+aqueous+solution.">Thermal decarboxylation of acetate. Part I. The kinetics and mechanism of reaction in aqueous solution.</a> Geochimica et Cosmochimica Acta. 50 (5), 813-823 (1986).</li><li>Yang, Z., Gould, I. R., Williams, L. B., Hartnett, H. E., Shock, E. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+central+role+of+ketones+in+reversible+and+irreversible+hydrothermal+organic+functional+group+transformations.">The central role of ketones in reversible and irreversible hydrothermal organic functional group transformations.</a> Geochimica et Cosmochimica Acta. 98, 48-65 (2012).</li><li>McCollom, T. M., Ritter, G., Simoneit, B. R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lipid+Synthesis+Under+Hydrothermal+Conditions+by+Fischer-+Tropsch-Type+Reactions.">Lipid Synthesis Under Hydrothermal Conditions by Fischer- Tropsch-Type Reactions.</a> Origins of life and evolution of the biosphere. 29 (2), 153-166 (1999).</li><li>Bell, J. L. S., Palmer, D. A., Barnes, H. L., Drummond, S. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thermal+decomposition+of+acetate:+III.+Catalysis+by+mineral+surfaces.">Thermal decomposition of acetate: III. Catalysis by mineral surfaces.</a> Geochimica et Cosmochimica Acta. 58 (19), 4155-4177 (1994).</li><li>Yang, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hydrothermal+Photochemistry+as+a+Mechanistic+Tool+in+Organic+Geochemistry:+The+Chemistry+of+Dibenzyl+Ketone.">Hydrothermal Photochemistry as a Mechanistic Tool in Organic Geochemistry: The Chemistry of Dibenzyl Ketone.</a> The Journal of Organic Chemistry. 79 (17), 7861-7871 (2014).</li><li>Yang, Z., Hartnett, H. E., Shock, E. L., Gould, I. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Organic+Oxidations+Using+Geomimicry.">Organic Oxidations Using Geomimicry.</a> The Journal of Organic Chemistry. 80 (24), 12159-12165 (2015).</li><li>Venturi, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mineral-assisted+production+of+benzene+under+hydrothermal+conditions:+Insights+from+experimental+studies+on+C6+cyclic+hydrocarbons.">Mineral-assisted production of benzene under hydrothermal conditions: Insights from experimental studies on C6 cyclic hydrocarbons.</a> Journal of Volcanology and Geothermal Research. 346, 21-27 (2017).</li><li>Lemke, K. H., Rosenbauer, R. J., Bird, D. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Peptide+Synthesis+in+Early+Earth+Hydrothermal+Systems.">Peptide Synthesis in Early Earth Hydrothermal Systems.</a> Astrobiology. 9 (2), 141-146 (2009).</li><li>Byrappa, K., Yoshimura, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Handbook of Hydrothermal Technology. , (2001).</li><li>Johnson, J. W., Oelkers, E. H., Helgeson, H. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SUPCRT92:+A+software+package+for+calculating+the+standard+molal+thermodynamic+properties+of+minerals,+gases,+aqueous+species,+and+reactions+from+1+to+5000+bar+and+0+to+1000&#176;C.">SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000&#176;C.</a> Computers &amp; Geosciences. 18 (7), 899-947 (1992).</li></ol>

The authors have nothing to disclose.

In this study, we used nitrobenzene with mineral magnetite as an example to demonstrate how to evaluate mineral effects on hydrothermal organic reactions. Although the experiments are carried out in small silica glass tubes, highly reproducible results are observed in the magnetite experiments, i.e., 30.3 &#177; 1.4% in nitrobenzene conversion, which suggests the effectiveness and the reliability of this hydrothermal protocol. In the no-mineral experiments, the conversion of nitrobenzene is 5.2 &#177; 2.1%, which shows a lower reproducibility than the mineral experiment. The relatively high uncertainty in the no-mineral experiment could be due to the low conversion of the starting material, considering the &#181;L (or mg) of samples used in the small tube. To improve reproducibility for low-conversion reactions, silica tubes with larger internal volume are suggested. This protocol could be particularly useful for small-scale experiments when the amount of sample is limited, or the cost of chemical is high. Both mineral and non-mineral hydrothermal experiments can be conducted by this protocol.
As described earlier, this hydrothermal protocol has certain advantages over other traditional methods, such as low cost of reaction tubes, facile operation procedures, and low or negligible catalytic effect11,14. However, due to the limited mineral strength and stability, quartz tubes may cause failure at temperatures above 450 &#176;C or pressures above 400 bar15, which may not be suitable for long-duration hydrothermal experiments near or above the critical point of water. Another limitation of this method is that, at high temperature (e.g., &#62; 400 &#176;C), quartz may also be subject to dissolution, which could produce dissolved silica species that interfere organic hydrothermal reactions. Since the dissolution of silica may also be influenced by the solution pH, the presence of salts, acids or bases, the tube survival temperature could be lower than that in the pure water system, and these factors should also be considered in high-temperature experiments. In addition, compared to flexible reactor materials such as gold, silica tubes are usually associated with a headspace volume that cannot be reduced by applying external pressure, which could allow some gas-phase reactions to occur.
Furthermore, the volume of liquid inside the silica tube could be critical in determining the success of the experiment. Based on the thermodynamics calculation using SUPCRT9216, for example, the saturation pressure of water (Psat) can reach more than 85 bar at 300 &#176;C, and the volume of liquid water inside the silica tube can expand by 30%. To survive at high temperatures and pressures, thicker silica glass tubes (i.e., ID/OD ratio &#60;0.3) with larger headspace should be used. Even with the same diameter, silica tubes from different manufacturers may cause failure at different temperatures. Therefore, the temperature and pressure restrain for each type of the silica tubes should be thoroughly tested before use. Note that borosilicate glass is excluded from this hydrothermal protocol because it is reactive and typically cannot handle temperatures above 300 &#176;C. In addition, loading the organic compounds that are &#34;sticky&#34; or viscous into narrow silica tubes may be challenging, in which case large diameter tubes (e.g., 6 mm ID x 12 mm OD) would be recommended.

Hydrothermal environments (i.e., aqueous media at elevated temperatures and pressures) are ubiquitous on Earth. The hydrothermal chemistry of organic compounds plays an essential role in a wide range of geochemical settings, such as organic sedimentary basins, petroleum reservoirs, and the deep biosphere1,2,3. Organic carbon transformations in hydrothermal systems occur not only in pure aqueous medium but also with dissolved or solid inorganic materials, such as Earth-abundant minerals. Minerals have been found to dramatically and selectively influence the hydrothermal reactivity of various organic compounds,1,4,5 but how to identify the mineral effects in complex hydrothermal systems still remains as a challenge. The goal of this study is to provide a relatively simple experimental protocol for studying mineral effects on hydrothermal organic reactions.
The laboratory studies of hydrothermal reactions traditionally use robust reactors that are made of gold, titanium, or stainless steel6,7,8,9. For example, gold bags or capsules have been favorably used, because gold is flexible, and it allows the sample pressure to be controlled by pressurizing water externally, which avoids generating a vapor phase inside the sample. However, these reactors are expensive and could be associated with potential metal catalytic effects10. Hence, it is imperative to find an alternative method with low cost but high reliability for these hydrothermal experiments.
In recent years, reaction tubes made of quartz or fused silica glass have been more frequently applied to hydrothermal experiments11,12,13. Compared to precious gold or titanium, quartz or silica glass is considerably cheaper but also the strong material. More importantly, quartz tubes have shown little catalytic effects and can be as inert as gold for the hydrothermal reactions11,14. In this protocol, we describe a general method for conducting small-scale hydrothermal organic-mineral experiments in thick-walled silica tubes. We present an example experiment using a model compound (i.e., nitrobenzene) in the presence/absence of an iron-oxide mineral (i.e., magnetite) in a 150 &#176;C hydrothermal solution, in order to show the mineral effect, as well as to demonstrate the effectiveness of this method.

<table><tbody><tr><td>&lt;strong&gt;Chemicals:&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Dichloromethane</td><td>VWR</td><td>BDH23373.400</td><td></td></tr><tr><td>Dodecane</td><td>Sigma-Aldrich</td><td>297879</td><td></td></tr><tr><td>Nitrobenzene</td><td>Sigma-Aldrich</td><td>252379</td><td></td></tr><tr><td>Fe&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt;</td><td>Sigma-Aldrich</td><td>310050</td><td></td></tr><tr><td>Fe&lt;sub&gt;3&lt;/sub&gt;O&lt;sub&gt;4&lt;/sub&gt;</td><td>Sigma-Aldrich</td><td>637106</td><td></td></tr><tr><td>&lt;strong&gt;Supplies:&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Silica tube</td><td></td><td></td><td></td></tr><tr><td>Vacuum pump</td><td>WELCH</td><td>2546B-01</td><td></td></tr><tr><td>Vacuum line</td><td></td><td></td><td></td></tr><tr><td>Oven</td><td>Hewlett Packard</td><td>5890</td><td></td></tr><tr><td>Thermocouple</td><td>BENETECH</td><td>GM1312</td><td></td></tr><tr><td>Gas chromatography</td><td>Agilent</td><td>7820A</td><td></td></tr></tbody></table>

an experimental protocol for studying mineral effects on organic hydrothermal transformations

Organic-mineral interactions are widely occurring in hydrothermal environments, such as hot springs, geysers on land, and the hydrothermal vents in the deep ocean. Roles of minerals are critical in many hydrothermal organic geochemical processes. Traditional hydrothermal methodology, which includes using reactors made of gold, titanium, platinum, or stainless-steel, is usually associated with the high cost or undesired metal catalytic effects. Recently, there is a growing tendency for using the cost-effective and inert quartz or fused silica glass tubes in hydrothermal experiments. Here, we provide a protocol for carrying out organic-mineral hydrothermal experiments in silica tubes, and we describe the essential steps in the sample preparation, experimental setup, products separation, and quantitative analysis. We also demonstrate an experiment using a model organic compound, nitrobenzene, to show the effect of an iron-containing mineral, magnetite, on its degradation under a specific hydrothermal condition. This technique can be applied to study complex organic-mineral hydrothermal interactions in a relatively simple laboratory system.

To demonstrate how to use this approach to study hydrothermal organic-mineral interactions, a simple experiment using a model compound, nitrobenzene, was conducted with mineral magnetite (Fe3O4) at a hydrothermal condition of 150 &#176;C and 5 bars for 2 h. To show the mineral effect, an experiment of nitrobenzene without mineral was also performed under the same hydrothermal condition. As shown in Figure 1a, two silica tubes were made following the protocols prior to the hydrothermal experiment. The sealed tube with no mineral was clear, and the tube with magnetite exhibited a black mineral color inside. The starting concentrations of nitrobenzene were both 0.1 M (in 0.3 mL deionized and deoxygenated water) and the added magnetite was 13.9 mg. After the hydrothermal process, the tube with no mineral showed no color change, whereas the tube with magnetite turned into a brown color (Figure 1b), which implies an oxidation reaction from magnetite to hematite (Fe2O3). Based on gas chromatography analysis, the effect of magnetite was revealed by the nitrobenzene conversions between the experiments (Figure 2). In the no-mineral experiment, the calculated conversion for nitrobenzene was 5.2%; however, in the presence of magnetite, the nitrobenzene conversion was 30.3%, which increased by a factor of 6. Additionally, duplicate but independent experiments were conducted, in which one standard deviation was calculated to be 2.1% and 1.4% for the no-mineral and magnetite experiments, respectively (Figure 2). These results suggest that magnetite, probably through redox reactions, can significantly promote the reaction of nitrobenzene at given hydrothermal conditions. This protocol was found to be successful with relatively high reproducibility in quantifying hydrothermal organic degradation under the influence of minerals.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/58230/58230fig1.jpg" /> 
Figure 1: Example experiment with nitrobenzene in the presence or absence of magnetite. (a) Silica glass tubes before the hydrothermal experiment; (b) silica glass tubes after the hydrothermal experiment. Note that there is a color change in the silica tube with magnetite. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/58230/58230fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/58230/58230fig2.jpg" /> 
Figure 2: Experimental results of nitrobenzene conversion after 2 h under hydrothermal conditions at 150 &#176;C and 5 bar. The reaction conversions are calculated by the amount of nitrobenzene reacted after the reaction. Error bars are one standard deviation of the mean of duplicate experiments. The difference between the no-mineral and magnetite experiments clearly shows the mineral effect on hydrothermal degradation of nitrobenzene. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/58230/58230fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

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An Experimental Protocol for Studying Mineral Effects on Organic Hydrothermal Transformations

Earth-abundant minerals play important roles in the natural hydrothermal systems. Here, we describe a reliable and cost-effective method for the experimental investigation of organic-mineral interactions under hydrothermal conditions.

Organic-mineral interactions are widely occurring in hydrothermal environments, such as hot springs, geysers on land, and the hydrothermal vents in the ...

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5.6K Views.  Oakland University. Earth-abundant minerals play important roles in the natural hydrothermal systems. Here, we describe a reliable and cost-effective method for the experimental investigation of organic-mineral interactions under hydrothermal conditions.

Video: An Experimental Protocol for Studying Mineral Effects on Organic Hydrothermal Transformations

Experimental Protocol for Manipulating Plant-induced Soil Heterogeneity

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Understanding the role of environmental heterogeneity in species coexistence has typically focused on types of heterogeneity that are extrinsic to the community&#8217;s species composition. We provide novel detailed methods for creating soil heterogeneity treatments using soils subject to plant-soil feedback conditioning, or heterogeneity intrinsic to the community composition.

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Laboratory Simulation of an IronII-rich Precambrian Marine Upwelling System to Explore the Growth of Photosynthetic Bacteria

We simulated a Precambrian ferruginous marine upwelling system in a lab-scale vertical flow-through column. The goal was to understand how geochemical profiles of O2 and Fe(II) evolve as cyanobacteria produce O2. The results show the establishment of a chemocline due to Fe(II) oxidation by photosynthetically produced O2.

A conventional concept for the deposition of some Precambrian Banded Iron Formations (BIF) proceeds on the assumption that ferrous iron [Fe(II)] upwelling ...

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This study presents an excavation method for investigating subsurface hydrological, geochemical, and microbiological heterogeneity of a soil lysimeter. The lysimeter simulates an artificial hillslope which was initially under homogeneous condition and had been subjected to approximately 5,000 mm of water over eight cycles of irrigation in an 18-month period.

Studying co-evolution of hydrological and biogeochemical processes in the subsurface of natural landscapes can enhance the understanding of coupled ...

Chemical Gardens as Flow-through Reactors Simulating Natural Hydrothermal Systems

Here we report experimental simulations of hydrothermal chimney growth using injection chemical garden methods. The versatility of this type of experiment allows for testing of various proposed ocean / hydrothermal fluid chemistries that could have driven reactions toward the origin of life in environments on the early Earth, early Mars, or even other worlds such as the icy moons of the outer planets. We show experiments that include growth of chemical garden structures under anoxic conditions simulating the early Earth, inclusion of trace components of phosphates / organics in the injection solution to incorporate them into the structure, a switch of the injection solution to introduce a secondary precipitating anion, and the measurement of membrane potentials generated by chemical gardens. Using this method, self-assembling chemical garden structures were formed that mimic the natural chimneys precipitated at submarine hydrothermal springs, and these precipitates can be used successfully as flow-through reactors by feeding through multiple successive &#8220;hydrothermal&#8221; injections.

We describe chemical garden formation via injection experiments that allow for laboratory simulations of natural chemical garden systems that form at submarine hydrothermal vents.

Here we report experimental simulations of hydrothermal chimney growth using injection chemical garden methods. The versatility of this type of experiment ...

Chemistry

Experimental Column Setup for Studying Anaerobic Biogeochemical Interactions Between Iron (Oxy)Hydroxides, Trace Elements, and Bacteria

Fate and speciation of trace elements (TEs), such as arsenic (As) and mercury (Hg), in aquifers are closely related to physio-chemical conditions, such as redox potential (Eh) and pH, but also to microbial activities that can play a direct or indirect role on speciation and/or mobility. Indeed, some bacteria can directly oxidize As(III) to As(V) or reduce As(V) to As(III). Likewise, bacteria are strongly involved in Hg cycling, either through its methylation, forming the neurotoxin monomethyl mercury, or through its reduction to elemental Hg&#176;. The fates of both As and Hg are also strongly linked to soil or aquifer composition; indeed, As and Hg can bind to organic compounds or (oxy)hydroxides, which will influence their mobility. In turn, bacterial activities such as iron (oxy)hydroxide reduction or organic matter mineralization can indirectly influence As and Hg sequestration. The presence of sulfate/sulfide can also strongly impact these particular elements through the formation of complexes such as thio-arsenates with As or metacinnabar with Hg.
Consequently, many important questions have been raised on the fate and speciation of As and Hg in the environment and how to limit their toxicity. However, due to their reactivity towards aquifer components, it is difficult to clearly dissociate the biogeochemical processes that occur and their different impacts on the fate of these TE.
To do so, we developed an original, experimental, column setup that mimics an aquifer with As- or Hg-iron-oxide rich areas versus iron depleted areas, enabling a better understanding of TE biogeochemistry in anoxic conditions. The following protocol gives step by step instructions for the column set-up either for As or Hg, as well as an example with As under iron and sulfate reducing conditions.

Experimental Column Setup for Studying Anaerobic Biogeochemical Interactions Between Iron OxyHydroxides, Trace Elements, and Bacteria

Fate and speciation of arsenic and mercury in aquifers are closely related to physio-chemical conditions and microbial activity. Here, we present an original experimental column setup that mimics an aquifer and enables a better understanding of trace element biogeochemistry in anoxic conditions. Two examples are presented, combining geochemical and microbiological approaches.

Fate and speciation of trace elements (TEs), such as arsenic (As) and mercury (Hg), in aquifers are closely related to physio-chemical conditions, such as ...

Simulation of Early Earth Hydrothermal Chimneys in a Thermal Gradient Environment

Deep sea hydrothermal vents are self-organizing precipitates generated from geochemical disequilibria and have been proposed as a possible setting for the emergence of life. The growth of hydrothermal chimneys in a thermal gradient environment within an early Earth vent system was successfully simulated by using different hydrothermal simulants, such as sodium sulfide, which were injected into an early Earth ocean simulant containing dissolved ferrous iron. Moreover, an apparatus was developed to sufficiently cool the ocean simulant to near 0 &#176;C in a condenser vessel immersed in a cold water bath while injecting a sulfide solution at hot to room temperatures, effectively creating an artificial chimney structure in a temperature gradient environment over a period of a few hours. Such experiments with different chemistries and variable temperature&#160;gradients resulted in a variety of morphologies in the chimney structure. The use of ocean and hydrothermal fluid simulants at room temperature resulted in vertical chimneys, whereas the combination of a hot hydrothermal fluid and cold ocean simulant inhibited the formation of robust chimney structures. The customizable 3D printed condenser created for this study acts as a jacketed reaction vessel that can be easily modified and used by different researchers. It will allow the careful control of injection rate and chemical composition of vent and ocean simulants, which should help accurately simulate prebiotic reactions in chimney systems with thermal gradients similar to those of natural systems.

The goal of this protocol is to form simulated hydrothermal chimneys via chemical garden injection experiments and introduce a thermal gradient across the inorganic precipitate membrane, using a 3D printable condenser that can be reproduced for educational purposes.

Deep sea hydrothermal vents are self-organizing precipitates generated from geochemical disequilibria and have been proposed as a possible setting for the ...

Bioprospecting of Extremophilic Microorganisms to Address Environmental Pollution

Geothermal springs are rich in various metal ions due to the interaction between rock and water that takes place in the deep aquifer. Moreover, due to seasonality variation in pH and temperature, fluctuation in element composition is periodically observed within these extreme environments, influencing the environmental microbial communities. Extremophilic microorganisms that thrive in volcanic thermal vents have developed resistance mechanisms to handle several metal ions present in the environment, thus taking part to complex metal biogeochemical cycles. Moreover, extremophiles and their products have found an extensive foothold in the market, and this holds true especially for their enzymes. In this context, their characterization is functional to the development of biosystems and bioprocesses for environmental monitoring and bioremediation. To date, the isolation and cultivation under laboratory conditions of extremophilic microorganisms still represent a bottleneck for fully exploiting their biotechnological potential. This work describes a streamlined protocol for the isolation of thermophilic microorganisms from hot springs as well as their genotypical and phenotypical identification through the following steps: (1) Sampling of microorganisms from geothermal sites ("Pisciarelli", a volcanic area of Campi Flegrei in Naples, Italy); (2) Isolation of heavy metal resistant microorganisms; (3) Identification of microbial isolates; (4) Phenotypical characterization of the isolates. The methodologies described in this work might be generally applied also for the isolation of microorganisms from other extreme environments.

The isolation of heavy metal-resistant microbes from geothermal springs is a hot topic for the development of bioremediation and environmental monitoring biosystems. This study provides a methodological approach for isolating and identifying heavy metal tolerant bacteria from hot springs.

Geothermal springs are rich in various metal ions due to the interaction between rock and water that takes place in the deep aquifer. Moreover, due to ...

Transformation of Organic Household Leftovers into a Peat Substitute

A two-step procedure is described for the synthesis of a carbon material with a similar composition and properties as peat. The produced hydrochar is made suitable for agricultural applications by removing plant growing inhibitory substances. Wet household waste such as fruit peel, coffee grounds, inedible vegetable parts, or wet lignocellulosic material in general, are treated in presence of water at 215 &#x00B0;C and 21 bar in an autoclave, i.e., by hydrothermal carbonization. All these leftovers have a considerable water content of up to 90 weight % (wt%). Adding water extends the procedure to drier materials such as nutshells or even garden prunings and compostable polymers, i.e., the plastic bag for collection of the leftovers.
Usually, the resulting carbon material, called hydrochar, produces a negative effect on plant growth when added to soil. It is supposed that this effect is caused by adsorbed phytotoxic compounds. A simple post-treatment under inert atmosphere (absence of oxygen) at 275 &#x00B0;C removes these substances. Therefore, the raw hydrochar is placed on a glass frit of a vertical tubular quartz reactor. A nitrogen gas flow is applied in down-flow direction. The tube is heated to the desired temperature by means of a heating mantle for up to one hour.
The success of the thermal treatment is easily quantified by thermogravimetry (TG), carried out in air. A weight loss is determined when the temperature of 275 &#x00B0;C is reached, since volatile content is desorbed. Its amount is reduced in the final material, in comparison to the untreated hydrochar.
The two-step treatment converts household leftovers, including compostable bags employed for their collection, into a carbon material that may serve as plant growth promoter and, at the same time, as a carbon sink for climate change mitigation.

A protocol for hydrothermal carbonization of vegetable food waste in an autoclave is presented, with subsequent dry thermal treatment at 275 &#x00B0;C in a continuous flow reactor desorbing volatile organic substances. The aim is to produce a carbon material suitable as soil amendment product or substrate component.

A two-step procedure is described for the synthesis of a carbon material with a similar composition and properties as peat. The produced hydrochar is made ...

Using Flexible Gold-Titanium Reaction Cells to Simulate Pressure-Dependent Microbial Activity in the Context of Subsurface Biomining

Laboratory studies investigating subsurface microbial processes, such as metal leaching in deep ore deposits (biomining), share common and challenging obstacles, including the special environmental conditions that need to be replicated, e.g., high pressure and in some cases acidic solutions. The former requires an experimental setup suitable for pressurization up to 100 bar, while the latter demands a fluid container with high chemical resistance against corrosion and unwanted chemical reactions with the container wall. To meet these conditions for an application in the field of in situ biomining, a special flexible gold-titanium reaction cell inside a rocking high-pressure reactor was used in this study. The described system allowed simulation of in situ biomining through sulfur-driven microbial iron reduction in an anoxic, pressure-controlled, highly chemically inert experimental environment. The flexible gold-titanium reaction cell can accommodate up to 100 mL of sample solution, which can be sampled at any given time point while the system maintains the desired pressure. Experiments can be performed on timescales ranging from hours to months. Assembling the high-pressure reactor system is fairly time consuming. Nevertheless, when complex and challenging (microbiological) processes occurring in the earth&#39;s deep subsurface in chemically aggressive fluids have to be investigated in the laboratory, the advantages of this system outweigh the disadvantages. The results found that even at high pressure the microbial consortium is active, but at significantly lower metabolic rates.

This protocol describes microbial experiments under elevated pressures to study in situ biomining processes. The experimental approach employs a rocking high-pressure reactor equipped with a gold-titanium reaction cell containing a microbial culture in an acidic, iron-rich medium.

Laboratory studies investigating subsurface microbial processes, such as metal leaching in deep ore deposits (biomining), share common and challenging ...

Engineering

Synthesis and Discovery of Phosphonate-Based MOFs: A Solvothermal Approach

Discovery and Synthesis Optimization of Isoreticular Al(III) Phosphonate-Based Metal-Organic Framework Compounds Using High-Throughput Methods

High-throughput (HT) methods are an important tool for the fast and efficient screening of synthesis parameters and the discovery of new materials. This manuscript describes the synthesis of metal-organic frameworks (MOFs) from solution using an HT reactor system, resulting in the discovery of various phosphonate-based MOFs of the composition [Al2H12-x(PMP)3]Clx&#8729;6H2O (H4PMP = N,N &#39;-piperazine bis(methylenephosphonic acid)) for x = 4, 6, denoted as Al-CAU-60-xHCl, containing trivalent aluminum ions. This was accomplished under solvothermal reaction conditions by systematically screening the impact of the molar ratio of the linker to the metal and the pH of the reaction mixture on the product formation. The protocol for the HT investigation includes six steps: a) synthesis planning (DOE = design of&#160;experiment) within the HT methodology, b) dosing and working with in-house developed HT reactors, c) solvothermal synthesis, d) synthesis workup using in-house developed filtration blocks, e) characterization by HT powder X-ray diffraction, and f) evaluation of the data. The HT methodology was first used to study the influence of acidity on the product formation, leading to the discovery of Al-CAU-60&#8729;xHCl (x = 4 or 6).

Author Spotlight: Accelerating Discovery in Microporous Material Chemistry 

The targeted synthesis of new metal-organic frameworks (MOFs) is difficult, and their discovery depends on the knowledge and creativity of the chemist. High-throughput methods allow complex synthetic parameter fields to be explored quickly and efficiently, accelerating the process of finding crystalline compounds and identifying synthetic and structural trends.

High-throughput (HT) methods are an important tool for the fast and efficient screening of synthesis parameters and the discovery of new materials. This ...