Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities

Soil protists, critical components of the soil microbiome and useful bio-indicators for soil quality, are often overlooked in microbial ecology. Here, a long-term field experiment with a cucumber monoculture was adopted to disentangle the influence of Trichoderma-enriched bio-fertilizers (BF) and organic fertilizers (OF) on the soil protists compared with that of chemical fertilizers (CF) without extra microbial inoculation. The results showed CF application was associated with lower protist richness and diversity than applications of and BF in both bulk and rhizosphere soils. Principal coordinate analysis revealed significant differences in the bulk and rhizosphere soil protist community structures, and the structures from CF treatment were obviously distinct from those resulting from OF and BF treatments in both bulk and rhizosphere soils. Moreover, in bulk soils, OF had higher relative abundances of Alveolata, Amoebozoa, Archaeplastida and Opisthokonta than did CF and BF. Compared with rhizosphere soils, Alveolata and Amoebozoa increased in bulk soil with CF, while the latter group decreased with OF. The most abundant OTUs were assigned to functional groups, and it was found that omnivores were on average, but not significantly, more abundant in bulk soil compared to rhizospheres. OTU_144 (Acanthamoebidae arachisporum) increased while OTU_54 (Hypotrichia, belonging to omnivores) decreased from bulk to rhizosphere soils in all treatments. Overall, we conclude that soil management strategies such as organic amendments can greatly alter the bulk soil protist community and that plants can further select protist community in the rhizosphere with potential consequences for plant growth in agricultural systems.