I would like to find a tool (if it exist ...), to predict the porportion of r vs K strategist in samples from a metabarcoding study.
For example, the tool I need (R package or equivalent) could work similarly to functional predictive tools such as Tax4Fun, FAPROTAX or PICRUST, but instead of predicting functions, it investigate ecological strategy such as r vs K as explained by the "r and K selection theory".
Benoît.
Not sure if such tool exists. Yet, I would be careful interpreting results from those extrapolations, as being r/K strategist is not a trait easy to identify.
Moreover, limited resolution from short amplicon sequencing --like 16S rRNA-- rarely identify OTUs/SNVs further than Genus level, so differences in strategy within fine taxonomic level will be totally missed. I wouldn't be surprise if there is two Pseudomonas with different strategies in any environmental sample.
Hi Benoît,
No program that I am aware of. I reckon that differentiate life-strategist from mere amplicon seqs can be, at best, unreliable if considering problems such as uncomplete reference datasets.
A good paper describing this but trying to list taxa that behaves as copio-oligotrophs:
Article Revisiting life strategy concepts in environmental microbial ecology
Please let me know if you come across with a relevant program though
Cheers
Ben
Hi Benjamin,
Thanks a lot for your answers !
Actually I have also come to the conclusion that r/K strategies are not clearly inherent to the genus level, so it would be very difficult to make such predictive tool. I keep you informed if i such tool.
Thanks for the paper, this is exactly the kind of litterature what i was looking for.
Cheers,
B.
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