In this study, a protist mock community was created and analysed by DNA metabarcoding.
Our technical manager Antón Vizcaíno has been involved in a project along with Danish, Dutch, and German scientists in which the quantitative implications of DNA metabarcoding were studied using protist samples. The results of this project have just been published in the journal Molecular Ecology.
Protists are the most diverse and one of the most abundant eukaryotes in soils. Despite this, protists are one of the least researched groups because it is difficult to study them using classic approaches. They are usually small and transparent organisms, hard to cultivate, and hard to identify. Therefore, DNA metabarcoding is a good option to circumvent these obstacles.
In this paper, researchers created a mock community (an artificial mixture of previously identified specimens) made up of protist and metazoan individuals. Then, a DNA metabarcoding approach was followed in an attempt to detect the organisms present in the mock community. Researchers wanted to evaluate whether the expected protist community structure was altered by the co-amplification of metazoan-associated protist taxa.
The results of this study revealed a different community composition than expected. This was due to the presence of non-added protist taxa. The presence of these extra taxa can be explained by the occurrence of protists which parasitise soil fauna in the samples analysed.
Finally, this study underlines the pitfalls of using DNA metabarcoding data as quantitative. DNA metabarcoding is not a quantitative method because PCR may cause biases due to differences in primer specificity. However, DNA metabarcoding is an extremely useful method to detect the presence of difficult-to-cultivate organisms (which are hard to detect using classic methods) in environmental samples.
Geisen S, Laros I, Vizcaíno A, Bonkowski M, de Groot GA (2015) Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa. Molecular Ecology DOI: 10.1111/mec.13238.