Name: sediment core sectioning and extraction of pore waters under anoxic conditions
Uploaded: 2016-03-07T13:00:00
Description: Watch this Scientific Journal Video about Sediment Core Sectioning and Extraction of Pore Waters under Anoxic Conditions at JoVE.com

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 identi...

<ol>
	<li>Chapman, P. M., Wang, F., Germano, J. D., Batley, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pore+water+testing+and+analysis:+the+good,+the+bad,+and+the+ugly.">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/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pore+water+sampling+with+sediment+peepers.">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/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemical+composition,+pH,+and+redox+state+of+sulfur+and+iron+in+complete+vertical+porewater+profiles+from+two+Sphagnum+peat+bogs,+Jura+Mountains,+Switzerland.">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/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sediment+pore+water+collection+methods+for+trace+metal+analysis:+A+review.">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., Last, W., Smol, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chapter+5,+Sediment+Core+Collection+and+Extrusion.">Chapter 5, Sediment Core Collection and Extrusion.</a> Developments in Paleoenvironmental Research. , 73-105 (2001).</li><li>Jahnke, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple,+reliable,+and+inexpensive+pore-water+sampler.">A simple, reliable, and inexpensive pore-water sampler.</a> L&amp;O. 33, 483-487 (1988).</li><li>Bufflap, S. E., Allen, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparison+of+pore+water+sampling+techniques+for+trace+metals.">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/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Authigenic+molybdenum+formation+in+marine+sediments:+a+link+to+pore+water+sulfide+in+the+Santa+Barbara+Basin.">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/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Arsenic+redistribution+between+sediments+and+water+near+a+highly+contaminated+source.">Arsenic redistribution between sediments and water near a highly contaminated source.</a> Env Sci &amp; Tech. 39, 8606-8613 (2005).</li><li>Natter, M., 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=Level+and+Degradation+of+Deepwater+Horizon+Spilled+Oil+in+Coastal+Marsh+Sediments+and+Pore-Water.">Level and Degradation of Deepwater Horizon Spilled Oil in Coastal Marsh Sediments and Pore-Water.</a> Env Sci &amp; Tech. 46, 5744-5755 (2012).</li><li>Jackson, P. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Ion chromatography. , (1990).</li><li>Stookey, L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ferrozine+-+A+New+Spectrophotometric+Reagent+For+Iron.">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/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differential+pulse+cathodic+stripping+voltammetric+speciation+of+trace+level+inorganic+arsenic+compounds+in+natural+water+samples.">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/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spectrophotometric+Determination+of+Hydrogen+Sulfide+in+Natural+Waters.">Spectrophotometric Determination of Hydrogen Sulfide in Natural Waters.</a> L&amp;O. 14, 454-458 (1969).</li></ol>

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 border="0" cellpadding="0" cellspacing="0" width="811">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;">&#160;Disposable glove bag(s).&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>Z106089-1EA</td>
			<td>&#160;One per two cores to be processed is usually sufficient.</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;">&#160;N2 tank</td>
			<td>Praxair</td>
			<td></td>
			<td>Often gas supply companies can deliver these directly to the field laboratory.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nitrogen gas regulator</td>
			<td>VWR</td>
			<td>55850-478</td>
			<td>Or similar</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Several feet of tubing that fits the regulator</td>
			<td>VWR</td>
			<td>89403-862</td>
			<td>Or similar</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Safety equipment to secure the tank</td>
			<td>VWR</td>
			<td>60142-006</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Adjustable tubing clamp</td>
			<td>VWR</td>
			<td>62849-112</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Waterproof, good sealing electrical tape</td>
			<td>Scotch</td>
			<td>Super 33+</td>
			<td>Widely available</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">&#160;2-4 short bungee cords</td>
			<td></td>
			<td></td>
			<td>Widely available</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">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 height="21">
			<td height="21" style="height:21px;">Large supply of paper towels and kimwipes.</td>
			<td></td>
			<td></td>
			<td>Widely available</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">50 mL centrifuge tubes</td>
			<td>VWR</td>
			<td>21008-951</td>
			<td>Acid cleaned as described in protocol.&#160; At least 2/core section needed.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Several permanent in markers.</td>
			<td></td>
			<td></td>
			<td>Widely available</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">&#160;Several straight razor blades and box cutters.</td>
			<td></td>
			<td></td>
			<td>Widely available</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Centrifuge</td>
			<td>Beckman-Coulter</td>
			<td>Allegra X-22</td>
			<td>Faster rotor allows greater separation.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Rotor to accommodate 50 mL tubes</td>
			<td>Beckman-Coulter</td>
			<td>SX-4250</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">]50 mL plastic syringes without black rubber tip on the barrel</td>
			<td>VWR</td>
			<td>66064-764&#160;</td>
			<td>Acid cleaned as described in protocol.&#160; At least 1/core section needed, plus 1 for overlying water.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Syringe filters compatible with aqueous solutions.</td>
			<td>VWR</td>
			<td>28143-310&#160;</td>
			<td>Either 0.45 &#956;m or 0.20 &#956;m poresizes may be used.&#160; Plan on five filters per core section processed.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Plastic (disposable) spoons.</td>
			<td></td>
			<td></td>
			<td>Widely available; Acid cleaned as described in protocol.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Several boxes of disposable gloves.</td>
			<td></td>
			<td></td>
			<td>Widely available</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;">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 height="21">
			<td height="21" style="height:21px;">Laboratory balance</td>
			<td>VWR</td>
			<td>10205-008</td>
			<td>An available balance will be fine; high precision not required</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">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 height="21">
			<td height="21" style="height:21px;">Laboratory notebooks</td>
			<td></td>
			<td></td>
			<td>Water repellent can be useful</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Core liners</td>
			<td>Watermark</td>
			<td>77280</td>
			<td>Available from Forrestry Suppliers</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Core caps</td>
			<td>Ben Meadows</td>
			<td>218105</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Core slicers</td>
			<td>McMaster Carr</td>
			<td>8707K111</td>
			<td>Cut this into 9 3x3 squares</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PVC spacers</td>
			<td>McMaster Carr</td>
			<td>48925K96</td>
			<td>Cut this into short lengths</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PVC couplings</td>
			<td>McMaster Carr</td>
			<td>4880K76</td>
			<td>Approximately 12 needed</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dowel</td>
			<td></td>
			<td></td>
			<td>Widely available</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">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 height="21">
			<td height="21" style="height:21px;">Plywood for core guidance plate and top of lab jack</td>
			<td></td>
			<td></td>
			<td>Widely available</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Lab jack</td>
			<td>VWR</td>
			<td>89260-826</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Clamps</td>
			<td></td>
			<td></td>
			<td>Widely available</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">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

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...

Watch this Scientific Journal Video about Sediment Core Sectioning and Extraction of Pore Waters under Anoxic Conditions at JoVE.com

Sediment Core Sectioning and Extraction of Pore Waters under Anoxic Conditions

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 ...

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