Protists, abundant but enigmatic single-celled eukaryotes, are important soil microbiota providing numerous ecosystem functions. We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene, to characterize changes in their abundance, species richness, and community structure with conversion of lowland rainforest into rubber agroforest (jungle rubber), and rubber and oil palm plantations; typical agricultural systems in Sumatra, Indonesia. We identified 5,204 operational taxonomic units (OTUs) at 97% identity threshold of protists from 32 sites. Protists species richness was similar in rainforest, jungle rubber and oil palm plantations but significantly lower in rubber plantations. After standardization, 4,219 OTUs were assigned to five trophic groups, and inspected for effects of land-use change, and potential biotic and abiotic driving factors. The most abundant trophic group was phagotrophs (52%), followed by animal parasites (29%), photoautotrophs (12%), plant parasites (1%), and symbionts (<1%). However, the relative abundance and OTU richness of phagotrophs and photoautotrophs increased significantly with increasing land-use intensity. This was similar, but less pronounced, for the relative abundance of symbionts. Animal and plant parasites decreased significantly in abundance and species richness with increasing land-use intensity. Community compositions and factors affecting the structure of individual trophic groups differed between land-use systems. Parasites were presumably mainly driven by the abundance and species richness of their hosts, while phagotrophs by changes in soil pH and increase in Gram-positive bacteria, and photoautotrophs by light availability. Overall, the results show that relative species richness, relative abundance, and community composition of individual trophic groups of protists in tropical lowland rainforest significantly differ from that in converted ecosystems. This is likely associated with changes in ecosystem functioning. The study provides novel insight into protist communities and their changes with land-use intensity in tropical lowland ecosystems. We show, that trophic groups of protists are powerful indicators reflecting changes in the functioning of ecosystems with conversion of rainforest into monoculture plantations.
Keywords: Indonesia; V4 region of 18S rRNA; community composition; high-throughput sequencing; rainforest transformation; soil protist diversity.