Soil protistologists on the road: a snapshot on a global synthesizing effort for a reliable taxonomy of protists (UniEUK)

By Dr. Stefan Geisen, Postdoctoral Reseracher, Netherlands Institute of Ecology


Research into soil protists is developing rapidly.  This is the first in a 4-part blog series highlighting the importance of soil protists and recent developments in the field. 


Research on tiny organisms including bacteria, protists and nematodes is in the midst of a revolution mainly due to developing sequencing technologies. These methods have enabled more reliable characterization of the diversity of those tiny organisms in opaque soils, as complicated classical extraction and cultivation-based efforts can now be circumvented. Of these tiny organisms, protists have been least studied. Only recently it became clear that this group of organisms hosts the vast diversity of eukaryotes. The emergence and diversification of fungi, animals and plants only represent relatively small and recent evolutionary events compared to the huge “background cloud” of protists.


Protists in soils

One gram of soil is suggested to be home for an estimated number of 10,000-100,000 individual protists, including 1,000s of species, many of which are key for ecosystem functioning.  They play a crucial role in food webs as main predators of bacteria and likely also fungi. Protist predation of bacteria and fungi releases nutrients, which can be used by bigger soil animals in the food web and plants, increasing growth. Recently, it has been shown that animal parasites are also abundant and diverse, possibly regulating populations of soil animals.


New possibilities to study soil protists

Recently, protists have become the focus of more research as they can more easily be detected using molecular sequencing technologies. This technique involves taking a small sample of soil, extracting DNA from all organisms present, sequencing the DNA, and identifying what is in the sample by assigning sequences to online databases (e.g. Silva or NCBI). This approach has extensively been applied to study bacteria and fungi, but only recently to target soil protists. One of the key issues to this approach is that online databases are lacking profound information and are full of errors that often lead to unreliable species annotation.


Unifying the taxonomy to enable reliable work with protist AND other soil animal sequences

The field of protistology recently obtained a research fund from the Moore foundation and is currently developing a taxonomy system to enable reliable sequence assignments of not only protists, but a wide range of eukaryotes, called UniEUK. Several soil protistologists are involved in this project that will eventually help scientists to include protists in their research portfolio. This will boost understanding of how diverse soil protists are and eventually allow targeted studies of what these likely important organisms functionally do!


Work on UniEUK just kicked-off at a very productive meeting in Paris.  More to come from Beneath Our Feet on exciting developments in soil protistology!











Protistologists gather in Paris for the UniEUK development kick-off meeting.



Protist ecology

guptavvsr's picture

There is wealth of knowledge on the ecology of protists in soil environments and hopefully this new development / venture would consider this in an integrated approach for the better use of the new information. Also, it is essential to define/describe a standardized methodology that may be used for sequencing (i.e. sample preparation) work esp. in view of the close association of protists with prokaryotoes!