Hi all,
I am a soil ecologist interested in soil invertebrates, I have been mainly involved in smaller scale experimental research assessing Collembola and Mite responses to e.g. climate change using traditional species identification (microscope and key... counting hairs, stuff like that ;-) . I have the ambition to spatially upscale my work on soil invertebrates and metabarcoding seems the obvious way forward. I know there have been projects developing such tools (e.g. the ECOFINDERS project), but I have troubles figuring out (in a quick search) how successful these attempts have been. Can anyone update me on this progress? Are there already primers available for e.g. Collembola or soil mites?
Thanks!
Eva
Hello Eva,
During my master prog, I took some course/practical lessons on Collembola/Oribatide Mites given by;
Prof Matty Berg Matty P. Berg
Prof Hans Cornelissen Johannes H C Cornelissen
Prof Nico van Straalen Nico M. van Straalen
You should be able to obtain vital information from them.
Goodluck.
You will be interested in
Article A quantitative protocol for DNA metabarcoding of springtails...
and
Article Metabarcoding and mitochondrial metagenomics of endogean art...
orArticle Biological invasions in soil: DNA barcoding as a monitoring ...
and will find also some additional information especially of the last working group.
Generally metabarcoding and quantification is quite tricky.
Tackling diversity is easier, but all depends on the reference database you use - in Collembola and mites you will have to build up a part on your own.
Greetings
Nikola
Agree with the answers. However, you should be careful with "abundance" as metabarcoding and all other sequencing approaches are at the maximum semi-quantitative. Meaning, you will not be able to avoid at least some counting in addition to your sequencing ;)
and yes, in EcoFINDERS we developed some primers and they have been tested. check with Arjen de Groot for details- but be aware that databases are far from complete and therefore high taxonomic annotation is not that easy. But for some overall diversity analyses sequencing is great and this can be an important part of a particular ecological story...
Good luck with the project!
Hi Eva
In this paper with Noah Fierer, they compare morpho ID and DNA (A DNA metabarcoding approach to characterize soil arthropod communities : https://www.sciencedirect.com/science/article/pii/S0038071718302244)
I think that the team with Decaëns Thibaud are working quite a lot on it as well (a lot on earthworm, but I think collembola as well), and the team with Pierre Taberlet (see paper: Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects).
Hope this help
Mathilde
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