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eDNA Filter Options: The Choices Can Be Overwhelming!

Advances in filtration techniques and material options are changing the eDNA world

August 19, 2021

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In part 1 of the eDNA blog series we delved into the environmental DNA world, where eDNA is detected in aquatic or soil samples weeks or months after the organism has passed through. eDNA is thus so diluted in the environmental sample, a concentration step is needed. We discussed why filtration is chosen rather than precipitation as the preferred method in the sample prep stage prior to eDNA extraction. In part 2 of this blog series, we turn our attention to the importance of filtration material type and pore size. Advances in filtration techniques and material options are making sample filtration easier and quicker, leading to improved eDNA extraction. But how to choose? Which filter material is best? What pore size? All valid questions researchers in the eDNA space are asking.

 

In fact, there are currently so many choices for scientists it can often feel overwhelming, so read on to find out the latest developments in the field.

 

Does the choice of filter material really matter?

 

Many factors influence the success of the filtration method. Both the filter material and pore size in the selected filter can affect the particle retention and flow rate. The following materials are most commonly used in the filtering step of eDNA studies: mixed cellulose ester (e.g., Metricel® MCE membrane filter), and polyethersulfone (e.g., Supor® PES membrane filter) and polycarbonate (e.g., MicroFunnel™ with polycarbonate membrane). Materials such as cellulose acetate, glass fiber, cellulose nitrate, and nylon are also used.

 

Current thinking is that DNA binds to each filter paper differently and this has been supported by research carried out by Liang and Keeley who investigated the effect of filter paper type on the recovery of spiked DNA plasmid and showed that DNA had different binding affinities to different filter papers (1). Recent eDNA studies have shown that filtration using mixed cellulose ester or cellulose nitrate are some of the most effective filters that deliver the highest eDNA yield (2, 3)  when compared with other filters such as PES and PC filters. Researchers postulate that this might be because eDNA is trapped within the matrix itself and not only on the surface (2). Whilst further investigation is underway to determine which factors allow eDNA to bind to some filter types more than others, Pall continues to supply the full spectrum of filter material types to eDNA researchers.

 

What else is important to consider in eDNA filtration?

 

eDNA capture from aqueous environments is complicated by factors such as pH, organic and inorganic particles, and filter pore size, all which are thought to influence the final eDNA yield. 

 

In general, small pore size filters yield the most eDNA, but they may clog easily in turbid waters, which causes slow filtering speeds and increases sampling time. Thus, larger pore-size filters may be preferable, however, the target water volume needs to be increased to ensure the yield is equivalent to the eDNA captured using smaller pore-sized filters. 

 

Figure 1: Pore size is specific to application. In general,> 0.8 µm is pre-filtration, 0.45 - 0.8 µm is to clarify and < 0.2 µm is sterile filtration. eDNA researchers tend to rely on filter pore sizes anywhere from 0.2 – 5 µm, with 0.45 µm being the most common.

 

Last year, the Alliance for Coastal Technologies held a workshop on the future of eDNA sampling to focus on addressing the challenges and needs during eDNA collection and processing.  It was reported that most participants relied on filtration to concentrate samples, with filter pore sizes ranging from 0.2 µm-5 µm (4). While there is no consensus on the exact pore size that should be used, a pore size of 0.45 µm appears to be the most commonly used, according to the published literature. It is always worth remembering that wide pores may make it easier to filter higher volumes of water but are likely to involve a trade-off in amount/diversity of eDNA molecules captured.

 

To learn more about how additional Pall products have been integrated into eDNA workflows by the scientific community, please read the Scientific Brief: The Importance of Filtration in the Environmental DNA (eDNA) World or contact us and one of our specialists will discuss which filter and pore size might work best for your studies. In order to accelerate research in the eDNA space, we also work with end users on custom solutions for their needs.

 

Stay tuned for part 3 of this blog series, where we will look at eDNA, the evolution of eRNA, sterile conditions, and re-usable filtration options.

 

References

 

  • Liang Z, Keeley A. (2013) Filtration Recovery of Extracellular DNA from Environmental Water Samples. Environmental Science & Technology: 47(16):9324–31.
  • Hinlo R, Gleeson D, Lintermans M, Furlan E. (2017) Methods to maximise recovery of environmental DNA from water samples. PLoS ONE 12(6): e0179251. 
  • Majaneva, M., Diserud, O.H., Eagle, S.H.C. et al. (2018) Environmental DNA filtration techniques affect recovered biodiversity. Sci Rep 8, 4682
  • The Alliance for Coastal Technologies: Envisioning the Future of eDNA Sampling and Sample Processing Virtual Workshop Preliminary Report 23 June 2020
 
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