Top-down effects of protists are greater than bottom-up effects of fertilisers on the formation of bacterial communities in a paddy field soil

Abstract Communities at any trophic level along the food chain are determined by simultaneous top-down (predators) and bottom-up (nutrients) effects; however, we still lack an understanding of this concept in the soil ecosystem. Here, we aimed to reveal the contributions of the top-down and bottom-up factors on the formation of paddy field bacterial communities. The position of an indigenous bacterial community at the trophic level was centred between soil nutrients (chemical and organic fertilisers [CF and OF, respectively], i.e., bottom-up factors) and bacterial predators (phagotrophic protists, i.e., top-down factors) in a paddy field soil. A 16S rRNA gene amplicon sequencing method was used to evaluate the top-down and bottom-up effects on the bacterial community composition. The results showed that the top-down effects of protists were greater than the bottom-up effects of the applied fertilisers on the formation of bacterial communities. The presence of protists caused the formation of a distinct bacterial community by affecting several bacterial species mainly belonging to Proteobacteria and Bacteroidetes. Among the bottom-up factors, OF significantly affected the bacterial beta diversity, while CF did not. The numbers of bioindicator genera that were associated with the top-down factors were 4.4 and 3.7 times higher than those associated with the bottom effects of CF and OF, respectively. Overall, we provided unique information on the importance of protists in regulating bacterial communities in paddy field soil, which is likely to affect bacterial activities and agricultural productivity.