Name: Small Volume (1-3L) Filtration of Coastal Seawater Samples (Video) | JoVE Journal
Uploaded: 2009-06-19T00:00:00.000+00:00
Duration: 4 min 21 s
Description: Learn small volume seawater filtration to collect microbial biomass for marine microbiology research. This method enables effective isolation of microorganisms to study diversity and ecosystem health.

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5 minutes

We would like to thank the Canadian Foundation for Innovation, the British Columbia Knowledge Development Fund and the National Sciences and Engineering Research Council (NSERC) of Canada for supporting ongoing studies on low oxygen regions of coastal and open ocean waters. D.A.W. was supported by fellowships from NSERC, Killam and the TULA foundation funded Centre for Microbial Diversity and Evolution.

<ol>
<li>Set up of filtration apparatus<ol>
<li>Before filtering, first wipe away any condensation from the full bottles and weigh them </li>
<li>Place an autoclave bin on one side of the pump, and the waste flask on the other.</li>
<li>Then place a full sample bottle in the autoclave bin; however, do not remove the cap of the bottle yet.</li>
<li>Pass the tubing through the peristaltic pump so that the luer end of the tubing is in the flask. </li>
<li>Using tweezers, remove the cotton from a sterile 25 ml pipette, and attach the pipette to the other end of the tubing.</li>
</ol></li>
<li>Filtration of seawater <ol>
<li>To begin filtering seawater, open the bottle and insert the pipette. Turn on the pump and set the flow speed to 1. Watch to ensure that water is being pumped in the proper direction. </li>
<li>Allow ~100 ml of water to pass through the entire tubing. </li>
<li>Turn off the pump and attach a Sterivex filter to the male luer fitting at the free end of the tubing. </li>
<li>Continue filtering until no water is left in the bottles.</li>
</ol></li>
<li>Storage of filters<ol>
<li>To store the filters, first expel any remaining water with a 30-60 ml syringe.</li>
<li>Seal the bottom of the Sterivex filter with Parafilm. Using a pipette, add 1.8ml lysis buffer to the filter, keeping ~ 200 ul of space in the filter for later addition of reagents.</li>
<li>Then, seal the top of the Sterivex filter with a small piece of Parafilm, and label the filters with the date and sample identification.</li>
<li>Store the filters in pre-labelled 50 ml falcon tubes at -80&deg;C</li>
</ol></li>
<li>Clean up<ol>
<li>Insert the 25 ml pipette into a flask containing 0.1% HCl, and switch on the pump.</li>
<li>After the HCl wash, rinse the tubing with autoclaved water. Finally, measure and record the mass of the now empty 1L bottles in order to calculate the volume of water passed through the filter. </li>
</ol></li>
</ol>
Representative Results: Each 1 L water sample yields one Sterivix filter, which contains biomass greater than 0.22 &micro;m. This is stored in lysis buffer for subsequent DNA extraction and analysis. The final result consists of one Sterivix filter per 1-liter bottle stored in lysis buffer and ready for DNA extraction. The filter contains biomass greater than 0.22 &micro;m. Filters can be stored at -80&deg;C prior to eDNA extraction.

The authors have nothing to disclose.

It is imperative to wipe down benches and pumps with a damp towel after use to remove any lingering traces of salt water that would otherwise corrode equipment. Although the procedure is simple, the time requirement can be extensive depending on the concentration of biomass or debris in the sample being filtered.

<table><tbody><tr><td>Peristaltic pump</td><td>Masterflex (Cole Palmer)</td><td>77913-20, 77200-62, 77200-04</td><td></td></tr><tr><td>Tygon LFL tubing</td><td>Masterflex (Cole Palmer)</td><td>06429-24</td><td>For filtration apparatus</td></tr><tr><td>Hose clamps</td><td>Cole-Parmer</td><td>0683204</td><td>For filtration apparatus</td></tr><tr><td>1/4&amp;#8221; x 3/16&amp;#8221; pipe adaptors</td><td>Cole-Parmer</td><td>31702-20</td><td>For filtration apparatus</td></tr><tr><td>Polypropylene prefilter housing</td><td>ADVANTEC</td><td>501200</td><td>For filtration apparatus</td></tr><tr><td>Metal luer fitting (Hose end to Male luer lock)</td><td>Cole-Parmer</td><td>31507-27</td><td>For filtration apparatus</td></tr><tr><td>2&amp;#8220; Magnets</td><td></td><td></td><td>For filtration apparatus</td></tr><tr><td>3 port carboy caps</td><td></td><td></td><td>For filtration apparatus</td></tr><tr><td>GV 0.22 &amp;mu;m STERIVIX filters</td><td>EMD Millipore</td><td>SVGV01R5</td><td></td></tr><tr><td>47 mm diameter 2.7 &amp;mu;m GF/D filters</td><td>Whatman, GE Healthcare</td><td>1823047</td><td></td></tr><tr><td>Lysis buffer</td><td></td><td></td><td>0.75 M sucrose, 40 mM EDTA, 50 mM Tris (pH 8.3)</td></tr><tr><td>0.1 % HCl</td><td></td><td></td><td>For post-filtration rinse</td></tr><tr><td>Autoclaved water</td><td></td><td></td><td>For post-filtration rinse</td></tr></tbody></table>

small volume (1-3l) filtration of coastal seawater samples

Small Volume (1-3L) Filtration of Coastal Seawater Samples

The workflow begins with the collection of coastal marine waters for downstream microbial community, nutrient and trace gas analyses. For today s demonstration samples were collected from the deck of the HMS John Strickland operating in Saanich Inlet. This video documents small volume (~1 L) filtration of microbial biomass from the water column. The protocol is an extension of the large volume sampling protocol described earlier, with one major difference: here, there is no pre-filtration step, so all size classes of biomass are collected down to the 0.22 &mu;m filter cut-off. Samples collected this way are ideal for nucleic acid analysis. The set-up, filtration, and clean-up steps each take about 20-30 minutes. If using two peristaltic pumps simultaneously, up to 8 samples may be filtered at the same time. To prevent biofilm formation between sampling trips, all filtration equipment must be rinsed with dilute HCl and deionized water and autoclaved immediately after use.

This video documents small volume (~1 L) filtration of microbial biomass from the water column.

The workflow begins with the collection of coastal marine waters for downstream microbial community, nutrient and trace gas analyses. For today s ...

Hi, I'm David Walsh from the Laboratory of Steven Hallam in the Department of Microbiology and Immunology at the University of British Columbia. Today we'll show you a procedure for filtering small volumes of seawater for microbial biomass. We use this procedure in our laboratory to study microbial diversity in the marine environment.So let's get started. Before filtering first, wipe away any condensation from the full bottles and weigh them. Place an autoclave bin on one side of the pump and the waste flask in an autoclave bin on the other.Then place a full sample bottle in the autoclave bin. However, do not remove the cap of the bottle yet. Pass the tubing through the peristaltic pump so that the lure end of the tubing is in the beaker.Using tweezers, remove the cotton from a sterile 25 milliliter pipette and attach the pipette to the other end of the tubing. To begin filtering sea water, open the bottle and insert the pipette. Turn on the pump and set the flow speed to one watch to ensure that water is being pumped in the proper direction.Allow about 100 milliliters of water to pass through the entire tubing. Turn off the pump and attach a stev X filter to the male lure fitting at the free end of the tubing, insert filter into waste flask. Turn on the pump and set the flow speed to one.Continue filtering until no water is left in the bottles. To store the filters. First expel any remaining water with a 30 to 60 milliliter syringe.Using a pipette add 1.8 milliliters of lysis buffer to the filter, keeping about 200 microliters of space in the filter. For later edition of reagents, seal the bottom and top of the stair of x filter with a small piece of perfil and label the filters with the date and sample identification. Store the filters in a pre-labeled 50 milliliter Falcon tube at minus 80 degrees Celsius.Insert the 25 milliliter pipette into a flask containing 0.1%hydrochloric acid and switch on the pump. After the hydrochloric acid wash, rinse the tubing with autoclaved water. Finally, measure and record the mass of the now empty one liter bottles in order to calculate the volume of water passed through the filter.Each one liter water sample yields one ster of X filter, which contains biomass greater than 0.2 microns. This is stored in lysis buffer for subsequent DNA. Extraction and analysis filters can be stored at minus 80 degrees Celsius prior to EDNA extraction.We've just demonstrated a small volume filtration protocol for collecting seawater biomass. When doing this procedure, it's important to wipe down benches and pumps with a damp towel after use in order to remove any lingering salt water. They may otherwise corrode the equipment.Although the procedure is simple, the time requirement can be extensive depending on the concentration of biomass or debris in the sample being filtered. So that's it. Thanks for watching and good luck with your experiments.

small-volume-1-3l-filtration-of-coastal-seawater-samples

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