Fertilization impacts microbiomes along the grassland trophic chain

Agricultural grasslands are often managed intensively, influencing soil properties and microbial communities. These changes may, in turn, affect the microbiome of organisms across multiple trophic levels within the same habitat, and significant shifts in these communities can disrupt health and functionality along the entire trophic chain. This study investigates how fertilization affects microbial communities in multiple connected below- and above-ground trophic compartments of grassland ecosystems. We compared control grassland sites to those treated with organic fertilizers-biogas digestate, cow/horse manure, and pig slurry-using 16S rRNA amplicon sequencing and soil nutrient analysis. Shifts in microbial composition occurred in response to fertilization, with compartment-dependent effects. Changes were more pronounced in belowground compartments, with pig slurry fertilization exhibiting the most substantial impact. Overlapping bacterial genera detected among soil, roots, and higher trophic levels show the potential strong interactions across trophic levels shaping microbial communities. Pig slurry-derived microbial taxa were found in all compartments, but their low prevalence suggests an indirect effect of fertilization, primarily due to changes in nutrient availability. Compared to the control sites, pig slurry-fertilized sites showed proliferation of certain taxa, including <i>Clostridium, Ruminococcus</i> or <i>Lachnoclostridium</i>, particularly in the animal compartments. Our study highlights that the effects of fertilization permeate all trophic levels, with potential ecological and health implications aligned with the One Health framework.