Abstract
Protists are mostly unicellular eukaryotes. Some protists are beneficial for plants, while others live as endosymbionts and can cause severe plant diseases. More detailed studies on plant-protist interactions exist only for plant pathogens and parasites. A number of protists live as inconspicuous endophytes and cause no visible disease symptoms, while others appear closely associated with the rhizosphere or phyllosphere of plants, but we still have only a vague understanding on their identities and functions. Here, we provide a protocol on how to assess the plant-associated protist community via Illumina-sequencing of ribosomal marker-amplicons and describe how to assign taxonomic affiliation to the obtained sequences.
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