Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, protists, remain poorly understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic protists and increased bacterivorous and omnivorous protists. The addition of individual biocontrol bacteria and fungi further altered the soil protist community composition, and eventually function. Network analysis integrating protist, bacterial and fungal community data, placed protists as a central hub in the soil microbiome, linking diverse bacterial and fungal populations. Given their dynamic response to soil management practices and key position in linking soil microbial networks, protists may provide the leverage between soil management and the enhancement of bacterial and fungal microbiota at the service of improved soil health.

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system.