Name: Sediment Core Sectioning and Extraction of Pore Waters under Anoxic Conditions (Video) | JoVE Journal
Uploaded: 2016-03-07T13:00:00.000+00:00
Duration: 9 min 21 s
Description: Learn to section sediment cores and extract pore waters under anoxic conditions using a glove bag technique. This method enables accurate analysis of redox-sensitive species in geochemical and environmental research.

ai_agent_IP

ai_agent

maintenance

instantTrialDurationMinutes

isBiopharma

enableNewMyJoveSectionDesign

educationFeatures

seoMetaApi

ai_copilot_institution_blacklist

ai_chat_institution_blacklist

freeAccessWindow

ssoRoleCapture

scheduledMaintenanceBanner

joveLabsFeatures

disable_autoplay_for_bots

extended_trial_duration

5 minutes

This research was partly supported by the National Science Foundation&#39;s RAPID program (NSF-1048925, 1048919, and 1048914) to Alison Keimowitz, Ming-Kuo Lee, Benedict Okeke, and James Saunders.

1. Preparation of Equipment
<ol>
	<li>Preparation of Core Liners
	<ol>
		<li>Calculate thickness of core slice that will be obtained using Volume = &#960;r2 x thickness; the final volume must be &#60;50 cm3. With a 10 cm core diameter, 2 cm thick slices may be obtained. 
		NOTE: It is not necessary to have the volume be a full 50 ml, but porewater volumes obtained will be proportionately smaller.</li>
		<li>Using a jigsaw (or similar) slice one core liner, or a plastic tube of identical diameter, into 2 cm rings (or other thickness if using a different diameter core). Obtain 3-5 rings.</li>
		<li>Clean all plastic material that will come in contact with sediment, including core liners, core caps, rings, core slicers, centrifuge tubes, syringes, and disposable spoons. (Soak plastic materials in 10% HCl for 24 hr, rinse plastic materials 3x in nanopure (22 M&#937;) water, and allow materials to air dry, preferably in a laminar flow hood, before packing.)</li>
	</ol>
	</li>
	<li>Preparation of Laboratory Jack
	<ol>
		<li>Cut a piece of plywood, using a jigsaw, to cover the 6&#34; x 6&#34; size of the top plate of the laboratory jack and drill a hole in the center of this plywood using a hole saw attachment to a drill. 
		NOTE: This hole should be just slightly larger than the diameter of PVC extender pieces; for the sizes used here, the hole should be 2 &#190;&#34;.</li>
		<li>Drill four small holes in the edges of this plywood to match the holes on the top plate of the laboratory jack using a regular drill bit on a hand drill or drill press. Fasten the plywood to the laboratory jack with zip ties. 
		NOTE: There should be no &#34;wiggle&#34; in this plywood.</li>
	</ol>
	</li>
	<li>Drill a hole in the center of an approximately 2&#39; x 1.5&#39; plywood slightly larger than the outer diameter of the core liners using a hole saw. For 10 cm diameter core liners, a 10.5-11.5 cm hole will be appropriate. This wood is the core guidance plate.</li>
	<li>Preparation of Core Extruder (Plunger)
	<ol>
		<li>Obtain a rubber laboratory stopper that fits snugly inside the core liners. If none is available, shave one to size using a razor. Do not use a too-small stopper.</li>
		<li>Screw the laboratory stopper to an approximately 1&#39;-1.5&#39; long, 1&#34; diameter dowel or broom handle. Cover the screw head on the face of the stopper with waterproof electrical tape. 
		NOTE: The larger side of the stopper should face away from the dowel.</li>
	</ol>
	</li>
	<li>Cut an approximately 1.5&#39; length of PVC pipe into ~6&#34; long sections. 
	NOTE: The internal diameter should be larger than the dowel in step 1.4.2, but smaller than the stopper in step 1.4.1. This protocol assumes using standard 2&#34; PVC with a true outer diameter of 2.375&#34;. These PVC pieces are the core extenders.</li>
	<li>Assemble all other needed equipment listed in the Materials List. 
	NOTE: This should be gathered in the home laboratory and brought to the field laboratory.</li>
</ol>
2. Setting up the Field Laboratory Station
<ol>
	<li>Setting up the Glove Bag
	<ol>
		<li>Clamp the core guidance plate to the work surface (countertop, lab surface, etc.). Ensure that the hole for the core liner is over the work surface, but is open.</li>
		<li>Place the disposable glove bag over the core guidance plate, and run the tubing from the tubing entry of the glove bag to the regulator of the N2 tank. Make sure the tank is safely secured using the cylinder bench clamp.</li>
		<li>Tape the tubing to the glove bag to seal up this entry point by encircling the bag around the exterior of the tubing with electrical tape. Ensure that about 8&#34; of tubing extends into the interior of the glove bag. Slide the tubing clamp onto the tubing inside the glove bag; leave this clamp open.</li>
		<li>Cut an &#34;X&#34; in the bottom of the glove bag over the hole in the core guidance plate using a box cutter or straight razor. This x should be smaller than the core liner diameter.</li>
		<li>Load the glove bag with the items found in Table 1.</li>
	</ol>
	</li>
	<li>Setting up the Core
	<ol>
		<li>Place the laboratory jack on the floor underneath the work area where the glove bag is affixed. Place the core through the &#34;X&#34; cut in the bottom of the glove bag in step 2.1.4, keeping it in an upright position. 
		NOTE: About 4-6&#34; of the core should extend above the core stabilization plate.</li>
		<li>Hold the core steady to allow researcher 2 to perform steps 2.2.3 through 2.2.6.</li>
		<li>Tape the core to the plastic glove bag around the &#34;X&#34;, using plenty of good sealing electrical tape.</li>
		<li>Insert the handle of the core extruder into a 2&#34; diameter, ~6&#34; long PVC spacer, followed by a ~3&#34; long coupling, followed by another spacer. Continue this pattern until the PVC entirely covers the handle; it may extend a short distance past the end of the handle. Place the core extruder (with PVC spacers and couplings) underneath the bottom of the core.</li>
		<li>Support the core extruder with the laboratory jack so that the extruder can support the core. At this time, keep the jack as low as possible and use core spacers wherever possible.</li>
		<li>Use a box cutter to cut carefully around the bottom core cap. This cut should result in a ring of core cap being left around the outside of the core liner and a flat circular portion of the core cap in place against the core materials.</li>
		<li>Insert the hands into the glove bag (researcher 1). Hold the core steady so that it does not move further above the core stabilization plate while researcher 2 begins to turn the laboratory jack slowly to raise the core. The core extruder should enter the core liner and begin to push the sediment upwards like a push pop.</li>
		<li>Wiggle the core extruder side to side slightly if needed to insert it into the core liner (researcher 2). Be prepared for a slight pop when it enters.</li>
		<li>Continue to raise the core until the top of the cored material is at or near the top of the core liner (researchers 1 and 2). Note that the core cap should remain atop the core during this procedure.</li>
	</ol>
	</li>
	<li>Sealing the Glove Bag
	<ol>
		<li>Double check that all necessary supplies are in the glove bag; turn on the portable oxygen meter.</li>
		<li>Open all centrifuge tubes, water bottles, and other items that contain trapped air. If the core has headspace above the standing water, open the top cap to purge this headspace.</li>
		<li>Turn on the regulator so that the flow of nitrogen through the tube into the glove bag is at a moderate rate. Generally a pressure of ~15 psi at the last regulator stage with all valves open is appropriate. 
		NOTE: This should be fast enough to feel like a strong breeze on skin, but not so strong that it scatters glove bag supplies.</li>
		<li>Point the nitrogen into all areas of the glove bag, and push the nitrogen out the main opening to the best of one&#39;s ability. Turn off the nitrogen.</li>
		<li>Purge the glove bag three times by repeating steps 2.3.6 through 2.3.9 three times. 
		NOTE: One person can accomplish this, but it may be easier for two people so that one can keep his or her hands in the gloves that are a part of the glove bag.</li>
		<li>Seal the main opening of the glove bag by wrapping 1-2 bungee cords around it several times. Turn on the nitrogen to a similar flow as in 2.3.3. Place researcher 1&#39;s hands in the built-in gloves of the glove bag.</li>
		<li>Move the nitrogen tube from one area of the bag to another to fill the glove bag with nitrogen. Point the tube into any crevices such as opened centrifuge tube, above the water in a squirt bottle, etc.</li>
		<li>Turn off the nitrogen by closing the tubing clamp. Note that this can be accomplished without removing researcher 1&#39;s hands from the glove bag.</li>
		<li>Open the front of the glove bag and using researcher 1&#39;s body, push as much gas out of the bag as possible. 
		NOTE: The bag should be flat around the supplies inside it at this point.</li>
		<li>Fill the glove bag to a comfortable pressure and turn off the nitrogen using the tubing clamp. Some trial and error may be required to find a comfortable pressure, as too full and it is difficult to move one&#39;s arms, while too empty and it is difficult to see and manipulate objects. Open the nitrogen tubing clamp for short periods to refill the bag if it seems to have a slow leak or is getting emptier for any reason. Open the front of the bag to let out small amounts of nitrogen if it becomes uncomfortably full.</li>
		<li>Check the level of dissolved oxygen on the portable oxygen meter. It should be below 1%.</li>
		<li>Insert the glove bag gloves into disposable gloves. These will improve dexterity. Change them whenever they get dirty or torn; discard in the in-bag waste container.</li>
	</ol>
	</li>
</ol>
3. Sectioning the Core
NOTE: this portion of the procedure is much more easily accomplished with two researchers.
<ol>
	<li>Remove standing water using a syringe. Syringe filter this water and place into 50 ml centrifuge tubes.</li>
	<li>Remove a Core Section
	<ol>
		<li>Place a core sectioning ring above the top of the core liner. Raise the core up (section 3.3) until the top of the sediment is at the top of the ring.</li>
		<li>Insert the core slicer between the top of the core liner and the ring. The sediment section is now sitting atop the core slicer.</li>
		<li>Move the sediment to a 50 ml tube using the disposable spoons. Cap the tube tightly once it is full.</li>
		<li>Rinse the core slicer and core sectioning ring with the nanopure water; squirt the dirty waste into the waste container inside the glove bag. Disposable spoons can also be rinsed, or discarded, depending on the number needed. Dry the core slicer and core sectioning ring with paper towels.</li>
		<li>Repeat step 3.2 until no further core material remains.</li>
	</ol>
	</li>
	<li>Raising the Core
	<ol>
		<li>Throughout 3.2 it is necessary to raise the core. Do this in small increments using the laboratory jack. Perform the following three steps once the laboratory jack is fully extended.</li>
		<li>Hold the core in place in the glove bag (researcher 1).</li>
		<li>Lower the laboratory jack to its lowest setting, when it is fully compressed (researcher 2). Ensure that the core is held in place with researcher 1&#39;s hands within the glove bag and researcher 2&#39;s hands supporting from beneath.</li>
		<li>Fill the space between the bottom end of the core extruder and the jack with PVC spacers and fittings. Ensure that the core is securely supported by the core extender before letting go of the top of the core.</li>
	</ol>
	</li>
</ol>
4. Extracting Porewaters
<ol>
	<li>Open the glove bag and remove the rack of centrifuge tubes.</li>
	<li>Clean up the glove bag as needed by removing any soil, liquid, or condensation by wiping out the inside with paper towels, water, etc. Empty waste container.</li>
	<li>Reseal the glove bag loosely with bungee cords.</li>
	<li>Weigh centrifuge tubes which now contain sectioned sediment (if desired).</li>
	<li>Wrap the tops of the centrifuge tubes with electrical tape to seal the cap/tube junction.</li>
	<li>Balance the tubes for centrifugation by weighing them after taping. Add or remove electrical tape to get weights within 0.5 g. 
	NOTE: Generally, tubes from the top of the core will be lighter than those from the bottom.</li>
	<li>Place tubes in centrifuge and centrifuge at maximum acceleration (1,100 x g is recommended) for 20 min. 
	NOTE: Higher centrifugation rates will permit greater separation of porewaters.</li>
	<li>Remove electrical tape from the centrifuge tubes either by unpeeling or by slicing with a razor prior to returning the tubes to the glove bag. Return centrifuge tubes to rack after centrifugation and return to the glove bag.</li>
	<li>Add another set of centrifuge tubes, syringes, and syringe filters to the glove bag. These new tubes will hold porewaters and can be pre-labeled.</li>
	<li>Purge the glove bag again as in step 2.3.5. If the glove bag was only opened briefly to remove the tubes, and was not cleaned, it will be acceptable to purge it only two times. If an oxygen monitor is being used, ensure that the atmosphere in the glove bag is &#60;1% O2. Do not forget to open the newly added centrifuge tubes and purge them.</li>
	<li>Insert hands to the gloves in the glove bag; as before, cover with disposable gloves.</li>
	<li>Open one tube. Remove the porewaters from above the sediment using a syringe, then attach a syringe filter to the tip of the syringe. If porewaters and sediments are well separated, porewaters may be poured directly into a syringe with the barrel removed and a syringe filter on the tip.</li>
	<li>Push the water through the syringe filter into the appropriate centrifuge tube. 
	NOTE: Some force will be needed; more than one syringe filter per sample may be required.</li>
	<li>Replace the caps on the centrifuge tube containing sediment and the tube containing porewaters.</li>
	<li>Repeat steps 4.13 through 4.15 for each sample.</li>
	<li>Open glove bag and remove samples. Both sediment and porewater tubes can be re-weighed.</li>
	<li>Analyze porewaters immediately if desired. Analyses can include (but are not limited to) ion chromatography for major ions11, ferrozine for iron speciation12, arsenic speciation by voltammetry13, and sulfide speciation14.</li>
	<li>Freeze porewaters and sediments in the dry shipper (approximately -80 &#176;C) to preserve speciation for later analyses if appropriate for the planned analyses. It may also be appropriate to keep samples cool in airtight containers or in nitrogen purged aluminum bags.</li>
	<li>Re-use the glove bag for a second core (starting at 2.2.2) if desired. After two cores, the glove bag usually needs to be changed.</li>
</ol>

<ol><li>Chapman, P. M., Wang, F., Germano, J. D., Batley, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Pore+water+testing+and+analysis%3A+the+good%2C+the+bad%2C+and+the+ugly%5BTitle%5D)+AND+%22Mar+Poll+Bull%22%5BJournal%5D)">Pore water testing and analysis: the good, the bad, and the ugly.</a> Mar Poll Bull. 44, 359-366 (2002).</li>
<li>Teasdale, P. R., Batley, G. E., Apte, S. C., Webster, I. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Pore+water+sampling+with+sediment+peepers%5BTitle%5D)+AND+%22TrAC%22%5BJournal%5D)">Pore water sampling with sediment peepers.</a> TrAC. 14, 250-256 (1995).</li>
<li>Steinmann, P., Shotyk, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Chemical+composition%2C+pH%2C+and+redox+state+of+sulfur+and+iron+in+complete+vertical+porewater+profiles+from+two+Sphagnum+peat+bogs%2C+Jura+Mountains%2C+Switzerland%5BTitle%5D)+AND+%22Geochim+Cosmochim+Acta%22%5BJournal%5D)">Chemical composition, pH, and redox state of sulfur and iron in complete vertical porewater profiles from two Sphagnum peat bogs, Jura Mountains, Switzerland.</a> Geochim Cosmochim Acta. 61, 1143-1163 (1997).</li>
<li>Bufflap, S. E., Allen, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Sediment+pore+water+collection+methods+for+trace+metal+analysis%3A+A+review%5BTitle%5D)+AND+%22Wat+Res%22%5BJournal%5D)">Sediment pore water collection methods for trace metal analysis: A review.</a> Wat Res. 29, 165-177 (1995).</li>
<li>Glew, J., Smol, J., Last, W. Chapter 5, Sediment Core Collection and Extrusion. <a target="_blank" href="http://scholar.google.com/scholar?hl=en&safe=off&q=author%3aGlew%2C+J+%22Developments+in+Paleoenvironmental+Research%22">Developments in Paleoenvironmental Research</a>. Last, W., Smol, J. , Tracking Environmental Change Using Lake Sediments; 1. Springer. Netherlands. 73-105 (2001).</li>
<li>Jahnke, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((A+simple%2C+reliable%2C+and+inexpensive+pore-water+sampler%5BTitle%5D)+AND+%22L%26O%22%5BJournal%5D)">A simple, reliable, and inexpensive pore-water sampler.</a> L&O. 33, 483-487 (1988).</li>
<li>Bufflap, S. E., Allen, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Comparison+of+pore+water+sampling+techniques+for+trace+metals%5BTitle%5D)+AND+%22Wat+Res%22%5BJournal%5D)">Comparison of pore water sampling techniques for trace metals.</a> Wat Res. 29, 2051-2054 (1995).</li>
<li>Zheng, Y., Anderson, R. F., van Geen, A., Kuwabara, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Authigenic+molybdenum+formation+in+marine+sediments%3A+a+link+to+pore+water+sulfide+in+the+Santa+Barbara+Basin%5BTitle%5D)+AND+%22Geochim+Cosmochim+Acta%22%5BJournal%5D)">Authigenic molybdenum formation in marine sediments: a link to pore water sulfide in the Santa Barbara Basin.</a> Geochim Cosmochim Acta. 64, 4165-4178 (2000).</li>
<li>Keimowitz, A. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Arsenic+redistribution+between+sediments+and+water+near+a+highly+contaminated+source%5BTitle%5D)+AND+%22Env+Sci+%26+Tech%22%5BJournal%5D)">Arsenic redistribution between sediments and water near a highly contaminated source.</a> Env Sci & Tech. 39, 8606-8613 (2005).</li>
<li>Natter, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Level+and+Degradation+of+Deepwater+Horizon+Spilled+Oil+in+Coastal+Marsh+Sediments+and+Pore-Water%5BTitle%5D)+AND+%22Env+Sci+%26+Tech%22%5BJournal%5D)">Level and Degradation of Deepwater Horizon Spilled Oil in Coastal Marsh Sediments and Pore-Water.</a> Env Sci & Tech. 46, 5744-5755 (2012).</li>
<li>Jackson, P. E. <a target="_blank" href="http://scholar.google.com/scholar?hl=en&safe=off&q=author%3aJackson%2C+PE+%22Ion+chromatography%22">Ion chromatography</a>. , Journal of Chromatography Library; 46. Elsevier. (1990).</li>
<li>Stookey, L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Ferrozine+-+A+New+Spectrophotometric+Reagent+For+Iron%5BTitle%5D)+AND+%22Anal.+Chem%22%5BJournal%5D)">Ferrozine - A New Spectrophotometric Reagent For Iron.</a> Anal. Chem. 42, 779-781 (1970).</li>
<li>He, Y., Zheng, Y., Ramnaraine, M., Locke, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Differential+pulse+cathodic+stripping+voltammetric+speciation+of+trace+level+inorganic+arsenic+compounds+in+natural+water+samples%5BTitle%5D)+AND+%22Anal.+Chim.+Acta%22%5BJournal%5D)">Differential pulse cathodic stripping voltammetric speciation of trace level inorganic arsenic compounds in natural water samples.</a> Anal. Chim. Acta. 511, 55-61 (2004).</li>
<li>Cline, J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Spectrophotometric+Determination+of+Hydrogen+Sulfide+in+Natural+Waters%5BTitle%5D)+AND+%22L%26O%22%5BJournal%5D)">Spectrophotometric Determination of Hydrogen Sulfide in Natural Waters.</a> L&O. 14, 454-458 (1969).</li>
</ol>

The authors have nothing to disclose.

The technique described herein is a flexible one that can be adjusted for a wide range of locations, core sizes, core section thickness, etc. There are three essential components to this system.
First, prepare a core extrusion system of the right dimensions for the core to be analyzed. Instructions here are given assuming an approximately 30&#34; core; much longer cores may require more PVC extender pieces and PVC fittings to extrude fully. Plan the extrusion system and the packing ca...

Researchers often wish to study the redox state and geomicrobiology of a sediment-water system. This ideally utilizes data from both sediments and pore waters, as pore waters are often sensitive monitors of the system and are a common source, though not the only source, of ecological exposure to redox-sensitive heavy metals1 such as arsenic and uranium. Pore water data may be obtained in situ using diffusion equilibrium filters, also known as &#34;peepers,&#34; installed into the sediment2. Peepers are most commonly used in settings where the field site is known prior to beginning field work and where multiple visits over an extended period of time can be made to the field site, e.g. Shotyk3. Therefore many contexts do not permit the use of peepers, such as sites only accessible for a short time or where multiple exploratory samples are obtained to determine where further investigation should occur4. Additionally peepers do not sample sediment simultaneously to water sampling.
When it is desirable to sample sediment and water together, or in field sites where peeper installation is not feasible, the most common method to obtain sediment and water is sediment coring. Obtaining an unmixed core is a crucial precursor to the procedure described in this work5. Once a core is obtained pore waters may be obtained by squeezing6 or centrifugation; both have advantages and disadvantages. Centrifugation is generally considered the most reliable method for extracting porewaters from sediment cores,7 although care must be taken to prevent oxidation of sediments or pore waters.
In this method we describe core extrusion and centrifugation to extract pore waters with minimal oxidation. The authors have used the method described herein in a variety of contexts including marine8, contaminated lake9, and wetlands10. The representative data shown demonstrates that reducing conditions can be preserved. With the exception of the centrifuge, materials used are inexpensive, and this method can be applied to a wide variety of geochemical and geomicrobiological research questions.

<table><tbody><tr><td>Disposable glove bag(s)</td><td>Sigma-Aldrich</td><td>Z106089-1EA</td><td>One per two cores to be processed is usually sufficient.</td></tr><tr><td>N&lt;sub&gt;2&lt;/sub&gt; tank</td><td>Praxair</td><td></td><td>Often gas supply companies can deliver these directly to the field laboratory.</td></tr><tr><td>Nitrogen gas regulator</td><td>VWR</td><td>55850-478</td><td>Or similar</td></tr><tr><td>Several feet of tubing that fits the regulator</td><td>VWR</td><td>89403-862</td><td>Or similar</td></tr><tr><td>Safety equipment to secure the tank</td><td>VWR</td><td>60142-006</td><td></td></tr><tr><td>Adjustable tubing clamp</td><td>VWR</td><td>62849-112</td><td></td></tr><tr><td>Waterproof, good sealing electrical tape</td><td>Scotch</td><td>Super 33+</td><td>Widely available</td></tr><tr><td>2-4 short bungee cords</td><td></td><td></td><td>Widely available</td></tr><tr><td>Squirt bottles of nanopure water</td><td>VWR</td><td>16650-082</td><td>Any similar bottle is fine; pack an additional supply of nanopure water to refill these.</td></tr><tr><td>Large supply of paper towels and Kimwipes</td><td></td><td></td><td>Widely available</td></tr><tr><td>50 ml centrifuge tubes</td><td>VWR</td><td>21008-951</td><td>Acid cleaned as described in protocol. At least 2/core section needed.</td></tr><tr><td>Several permanent in markers.</td><td></td><td></td><td>Widely available</td></tr><tr><td>Several straight razor blades and box cutters.</td><td></td><td></td><td>Widely available</td></tr><tr><td>Centrifuge</td><td>Beckman-Coulter</td><td>Allegra X-22</td><td>Faster rotor allows greater separation.</td></tr><tr><td>Rotor to accommodate 50 ml tubes</td><td>Beckman-Coulter</td><td>SX-4250</td><td></td></tr><tr><td>50 ml plastic syringes without black rubber tip on the barrel</td><td>VWR</td><td>66064-764&amp;nbsp;</td><td>Acid cleaned as described in protocol. At least 1/core section needed, plus 1 for overlying water.</td></tr><tr><td>Syringe filters compatible with aqueous solutions.</td><td>VWR</td><td>28143-310&amp;nbsp;</td><td>Either 0.45 &amp;mu;m or 0.20&amp;nbsp;&amp;mu;m poresizes may be used. Plan on five filters per core section processed.</td></tr><tr><td>Plastic (disposable) spoons.</td><td></td><td></td><td>Widely available; Acid cleaned as described in protocol.</td></tr><tr><td>Several boxes of disposable gloves.</td><td></td><td></td><td>Widely available</td></tr><tr><td>Large plastic beakers or other waste containers to place in the glove bag.</td><td>VWR</td><td>13890-148</td><td></td></tr><tr><td>Laboratory balance</td><td>VWR</td><td>10205-008</td><td>An available balance will be fine; high precision not required</td></tr><tr><td>Dry shipper, pre-charged with liquid nitrogen</td><td>VWR</td><td>82005-416</td><td>Needed only if samples are being returned to the home laboratory for sensitive analyses.</td></tr><tr><td>Laboratory notebooks</td><td></td><td></td><td>Water repellent can be useful</td></tr><tr><td>Core liners</td><td>Watermark</td><td>77280</td><td>Available from Forrestry Suppliers</td></tr><tr><td>Core caps</td><td>Ben Meadows</td><td>218105</td><td></td></tr><tr><td>Core slicers</td><td>McMaster Carr</td><td>8707K111</td><td>Cut this into 9 3 x 3 squares</td></tr><tr><td>PVC spacers</td><td>McMaster Carr</td><td>48925K96</td><td>Cut this into short lengths</td></tr><tr><td>PVC couplings</td><td>McMaster Carr</td><td>4880K76</td><td>Approximately 12 needed</td></tr><tr><td>Dowel</td><td></td><td></td><td>Widely available</td></tr><tr><td>Lab stopper</td><td>VWR</td><td>59580-400</td><td>Check to ensure the correct size to fit snugly within the core liners</td></tr><tr><td>Plywood for core guidance plate and top of lab jack</td><td></td><td></td><td>Widely available</td></tr><tr><td>Lab jack</td><td>VWR</td><td>89260-826</td><td></td></tr><tr><td>Clamps</td><td></td><td></td><td>Widely available</td></tr><tr><td>Portable oxygen monitor</td><td>RKI instruments</td><td>OX-07</td><td></td></tr></tbody></table>

sediment core sectioning and extraction of pore waters under anoxic conditions

Sediment Core Sectioning and Extraction of Pore Waters under Anoxic Conditions

We demonstrate a method for sectioning sediment cores and extracting pore waters while maintaining oxygen-free conditions. A simple, inexpensive system is built and can be transported to a temporary work space close to field sampling site(s) to facilitate rapid analysis. Cores are extruded into a portable glove bag, where they are sectioned and each 1-3 cm thick section (depending on core diameter) is sealed into 50 ml centrifuge tubes. Pore waters are separated with centrifugation outside of the glove bag and then returned to the glove bag for separation from the sediment. These extracted pore water samples can be analyzed immediately. Immediate analyses of redox sensitive species, such as sulfide, iron speciation, and arsenic speciation indicate that oxidation of pore waters is minimal; some samples show approximately 100% of the reduced species, e.g. 100% Fe(II) with no detectable Fe(III). Both sediment and pore water samples can be preserved to maintain chemical species for further analysis upon return to the laboratory.

The type of results obtained depends on analyses performed and on the geochemical setting from which the core was obtained. Dissolved oxygen may be measured in the extracted porewaters, but in many settings this will be zero below the first few cm of the core. Analyses that usually provide more meaningful information include iron speciation (Fe II/Fe III)12, arsenic speciation (As III/As V)13, and sulfide14. Presence of reduced species such as sulfide indi...

A protocol for sectioning sediment cores and extracting pore waters under anoxic conditions in order to permit analysis of redox sensitive species in both solids and fluids is presented.

We demonstrate a method for sectioning sediment cores and extracting pore waters while maintaining oxygen-free conditions. A simple, inexpensive system is ...

The overall goal of this procedure is to section sediment cores and extract pore waters from these sediment cores while maintaining the original oxidation state. This method can allow researchers in geochemical fields to examine metal speciation in pore waters and sediments from redox-sensitive areas such as lakes and wetlands. The main advantages of this technique are that it's flexible and adaptable, field portable, inexpensive, and does not disrupt sediment layers.Demonstrating the procedure will be Rahul Sinha, an undergraduate from my laboratory. Begin preparing the field laboratory by setting up the glove bag. First, clamp the core guidance plate to a work surface.Position the hole for the core liner extending in front of the counter to ensure it is open. Next, secure the nitrogen tank using a bench clamp. Then, place the glove bag over the plate and run tubing between the bag and the gas regulator.Extend about eight inches of tubing into the bag. Now, seal the tubing connection at the bag with electrical tape and inside the bag slide a clamp onto the tube but leave the clamp open. Next, cut an X into the bottom of the bag over the hole in the plate then load the bag with the listed items.Double check the lists, because forgetting an item is very inconvenient. The next task is to set up the core. First, put a lab jack on the floor under the work surface.The lab jack should have a piece of plywood on it with a hole in the center to stabilize the core. Then, with the core in an upright position, push it through the core guidance plate and through the X in the glove bag. About four to six inches of core should extend above the plate.Now, while one person supports the core, tape the core to the bag around the X with electrical tape. Then, set up the core extruder. First insert the handle into a six-inch long, two-inch diameter PVC spacer followed by a three-inch long coupling and then another space and another coupling and so forth until the handle is completely covered.Now, place the core extruder below the core and support it with the jack. The jack should be cranked as low as possible. Next, with a box cutter carefully cut around the bottom of the core cap.Leave a ring of core cap around the core liner and leave a circular piece of cap against the core materials. Now, one person must reach into the glove bag to secure the core while the other raises the jack. Gradually move the core extruder into the core liner raising the sediment upwards.It may be necessary to wiggle the extruder a little. Continue raising the core until the sediment and overlying water reaches to the top of the core liner. The last task is to seal the bag.First, double check that everything is in there. Then, open all the objects in the bag that contain trapped air. Now, ideally with another person's help, purge the glove three times.First, with the bag as deflated as possible, seal the main opening with a few bungee cords. Then, with an assistant regulating the nitrogen flow at 50 psi, direct the gas around the bag, especially into crevices where air could be trapped. When the bag is highly inflated, turn off the regulator or close the clamp to shut off the gas.Then, open the main opening and push out as much gas from the bag as possible. Repeat the process of filling the bag with nitrogen, including all crevices, and emptying the bag two more times. Once this is completed, the glove bag should contain very low levels of oxygen.Finish with a comfortable amount of gas in the glove bag. This procedure is best performed while working in pairs. For this procedure, put a pair of disposable gloves over the built-in gloves in the bag.Change these gloves whenever they are dirty or torn. First, remove all the standing water from the top of the core using a syringe. Then, filter this water through a 0.45-micron syringe filter.Next, place a core sectioning ring over the top of the core liner. Then, raise the core until the sediment meets the top of the ring. Inside the bag, secure the core liner so when the core moves the liner does not.It may be necessary for the operator working inside the glove bag to push down slightly on the core liner so that the core material is at the top of the ring. Next, push a core slicer between the top of the liner and the ring so that the sediment section is above the slicer. This is the first section of core.With plastic spoons, move the section to a 50-milliliter conical tube and cap it tightly. Wash the tools and repeat the process until the whole core is sectioned and placed into tubes. During the core sectioning process the lab jack may become fully extended.If this occurs, hold the core in place, lower the jack, and position the PVC pieces to extend the core extruder. Then secure the jack back in place. During this process, the bag may get too deflated or inflated.Make adjustments by briefly opening the nitrogen gas valve or by briefly opening the main bag opening to release gas. Once the core is sectioned and all the sediment is in centrifuge tubes, these tubes can be removed from the glove bag and the glove bag closed. Then, prepare the collected tubes for centrifugation as explained in the text protocol.Then, spin them down at 1, 100 g or faster for 20 minutes. After the centrifugation, return the tubes to the oxygen-free environment and introduce some empty tubes for the sample collection. The bag should then be purged again two to three times as before.Now, open a centrifuged tube and remove the porewater using a syringe with tubing on the end. Then, using a 0.45-micron syringe filter, filter the water into a collection tube. The text protocol explains how to further process the samples.Using the described protocol, a core was taken from a wetland near New Orleans nine months after the Deep Water Horizons Bill. This wetland was heavily oiled. Using a Hach DR 2700 portable spectraphotometer, the data showed extremely high sulfide concentrations.Iron concentrations were low and iron in the three plus oxidation state was not detected. So after watching this video you should have a good understanding of how to purge the glove bag of oxygen, extrude the core inside the glove bag to allow sectioning, and separate the porewaters from the sediments. Once mastered, this technique can be done in one to three hours per core, depending on the core length.While attempting this procedure, it's important to remember to purge the glove bag thoroughly and adjust the core height slowly. Following this procedure methods like iron speciation by ferrousing, arsenic speciation by voltammetry or column separation, and mythylmercury separation can be performed in order to answer questions about the redox state of the system. Don't forget that working with compressed gasses can be extremely hazardous and securing the tank is essential while performing this procedure.Some sediment samples may be contaminated with hazardous materials and appropriate cautions should be taken.

sediment-core-sectioning-extraction-pore-waters-under-anoxic

Research

JoVE Journal

Environment

Source:Alessia J. Marchesan1, Guillermo Hernandez Ramirez11Renewable Resources, University of Alberta. This video demonstrates the technique for collecting a soil sample for hydraulic property analysis. The sampling area is cleared, and the top crust is evacuated. The sampling ring is then placed into the soil to collect the sample. The ring with the sample is then cleaned, labeled, packed, and transferred undisturbed for analysis.

Soil Core Sample Collection for Water Retention Property Analysis

Lake eutrophication is a water quality issue worldwide, making the need to identify and control nutrient sources critical. Laboratory determination of phosphorus release rates from sediment cores is a valuable approach for determining the role of internal phosphorus loading and guiding management decisions.

Laboratory-determined Phosphorus Flux from Lake Sediments as a Measure of Internal Phosphorus Loading

We present a methodology for the imaging of multiple fluid phases at reservoir conditions by the use of x-ray microtomography. We show some representative results of capillary trapping in a carbonate rock sample.

Reservoir Condition Pore-scale Imaging of Multiple Fluid Phases Using X-ray Microtomography

Here, we present small core incubations for the measurement of sediment-water gas and solute exchange. These will provide reliable measurements of sediment-water exchange that assess the role of sediment in influencing biological and biogeochemical processes in aquatic ecosystems.

The Benthic Exchange of O2, N2 and Dissolved Nutrients Using Small Core Incubations

An extrusion method using a calibrated threaded-rod is presented, which allows for mm scale subsampling of aquatic sediment cores. Millimeter-scale sampling is necessary to fully characterize recent event stratigraphy in sediment records.

Sediment Core Extrusion Method at Millimeter Resolution Using a Calibrated, Threaded-rod

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.

Soil Lysimeter Excavation for Coupled Hydrological, Geochemical, and Microbiological Investigations

Long-term studies are essential to understanding the process of evolution and the mechanisms of adaptation. Generally, these studies require commitments beyond the life-time of researchers. Here, a powerful method is described that dramatically advances state-of-the-art data collection to generate longitudinal data in natural systems.

Resurrection of Dormant Daphnia magna: Protocol and Applications

This protocol is presented to characterize the complex wetting conditions of an opaque porous medium (hydrocarbon reservoir rock) using three-dimensional images obtained by X-ray microtomography at subsurface conditions.

Pore-scale Imaging and Characterization of Hydrocarbon Reservoir Rock Wettability at Subsurface Conditions Using X-ray Microtomography

This method estimates sediment denitrification rates in sediment cores using the acetylene inhibition technique and microsensor measurements of the accumulated N2O. The protocol describes procedures for collecting the cores, calibrating the sensors, performing the acetylene inhibition, measuring the N2O accumulation, and calculating the denitrification rate.

Estimating Sediment Denitrification Rates Using Cores and N2O Microsensors

This protocol is for the isolation of quartz grains by size for luminescence dating of sediments. Outlined are physical cleansing and chemical digestions by soaking sequentially in H2O2, HCl, HF, and HCl again to isolate quartz grains. The quartz purity is quantified with microscopic assessment, Raman spectroscopy, and IR depletion ratio.

Isolation of Quartz Grains for Optically Stimulated Luminescence (OSL) Dating of Quaternary Sediments for Paleoenvironmental Research

A microdialysis profiler is described to sample dissolved porewater solutes across an oxic-anoxic soil-water interface in situ with minimal disturbance. This device is designed to capture rapid changes in concentration-depth profiles induced by disturbances at the soil-water interface and beyond.

Dissolved Solute Sampling Across an Oxic-Anoxic Soil-Water Interface Using Microdialysis Profilers

Learn to section sediment cores and extract pore waters under anoxic conditions using a glove bag technique. This method enables accurate analysis of redox-sensitive species in geochemical and environmental research.

Sediment Core Sectioning and Extraction of Pore Waters under Anoxic Conditions

Explore More Videos