Biochar applications have an enormous impact on the soil microbial community and functionality. However, the majority of the knowledge on biochar–microbe interaction derives almost exclusively from bacterial and fungal studies, while the vast majority of eukaryotic diversity, protists, are mostly neglected. Protists play important roles in the soil ecosystem as microbial predators, decomposers, photoautotrophs, pathogens, and parasites and they are essential for a healthy soil ecosystem. Toward a comprehensive understanding of the effects of biochar application, we need more studies on protists across the full breadth of eukaryotic diversity. The aim of this article is to highlight the research needs and discuss potential research ideas on biochar–protist interaction, which would advance our knowledge of biochar–microbe interaction. Highlights: Biochar–microbe interaction is almost exclusively studied for bacteria and fungi. Only a few studies are available on how soil protists react to biochar application. More research on biochar–protist is needed for a better understanding of biochar–microbe interaction.

The plant-microbe interactions, which is crucial for plant health and productivity, mainly occur in rhizosphere: a narrow zone of soil surrounding roots of living plants. The rhizosphere hosts one of the most intense habitats for microbial prey–predator interactions, especially between predatory protists and bacteria. Here, based on two key facts, microbial predators modulate rhizobacterial community composition, and the rhizobacterial community is the primary source of root microbiome, endophytes; we hypothesized that predation upon rhizobacteria would modulate the community composition of endophytic bacteria. The effects of three taxonomically distinct axenic protist species (Acanthamoeba castellanii, Vermamoeba vermiformis, and Heteromita globosa) were tested in this study. To examine the robustness of the hypotheses, the experiments were conducted in three soil types characterized by distinct bacterial communities and physicochemical properties. The bacterial community compositions were analyzed with high throughput sequencing. Bacterial gene abundances were estimated with a real-time-PCR method. The results showed that protists modulated endophytic communities, which originated in the rhizosphere soil. The modulation of endophytic communities by protists showed chaotic patterns rather than a deterministic effect under different soil types. The observed chaotic dynamics were further confirmed with an additional experiment, in which chaos was triggered by changes in the dilution rates of soil nutrients. Furthermore, the presence of predators enhanced the root colonization of endophytes. Our findings identify a key mechanism for the modulation of root endophytes and enhance understanding of underground plant-microbe interactions, which can lead to open new avenues for modulating the root microbiome to enhance crop production.