Monthly Archives: April 2016

New Publication: Testing the potential of the ribosomal 16S marker for DNA metabarcoding

Last year we used a freshwater invertebrate mock community to test the standard COI barcoding Folmer primers in a metabarcoding setting and demonstrated that primer bias makes estimation of biomass impossible. Together with our colleagues from France we now tested the same mock samples with a ribosomal marker, which is supposed to show less primer bias due to more conserved primer binding sites. As we show in the new article which was just published in PeerJ, the 16S marker indeed leads to more consistent amplification results than the Folmer primer set when used in DNA metabarcoding.

However, primer bias is still substantial (two orders of magnitude) and thus estimation of biomass still impossible. Furthermore, we are currently lacking comprehensive 16S reference databases for animals, which are available for the COI barcoding marker. First tests show that the COI marker performance can be greatly improved by using metabarcoding optimised primers (we will publish a PrePrint soon). Thus, while the 16S marker might have potential, we focus on using the COI maker for DNA metabarcoding of insects but just not with Folmer primers.

 

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Figure: The tested 16S marker shows less variation in read numbers than the COI Folmer maker, thus allows for better detection of freshwater taxa. However, with improved COI primers better detection rates are possible as well, as first tests demonstrated.

Video Tutorial: How we dry and grind samples for DNA metabarcoding!

The first step for DNA metabarcoding of invertebrate kick samples from stream ecosystems is sample homogenisation. The samples often contain hundreds of organisms which have to be dried and then homogenised, to assure that the DNA of all specimens in mixed. Only then every individual in the sample can be detected, extracting just a small subset of the ground tissue. We are using the IKA ULTRA-TURRAX Tube Drive control system for tissue grinding, as discussed in a previous video. In this new video we are detailing the complete process from sample handling, drying over night and grinding using invertebrate kick samples from Finland.