Impact of Fertilisation on the Bacterial Core Microbiome of Grassland Soils: Abundance in the Field and Growth In Vitro

Anthropogenic activities may have profound impacts on the soil microbiome with consequences for soil health, agriculture and food production. Here, we investigated the impact of different fertilisation regimes on the composition of the bacterial soil microbiome in grassland ecosystems by 16S rRNA gene amplicon sequencing and in vitro growth experiments with culturable representatives of the bacterial core microbiota. We observed a large proportion of taxa shared across fertilisation regimes without significant differences in their evenness, but shifts in the composition of the bacterial core microbiome by fertilisation. These effects were most pronounced for fertilisation with pig slurry (PS). Analysis of microbiome multivariable association with linear models identified bacterial biomarker taxa for different fertilisation regimes. This enabled the selection of several culturable representatives for in vitro growth experiments. Consistent with the relative abundances of Bradyrhizobium, Nocardioides, and Solirubrobacter in field samples, the growth of Bradyrhizobium japonicum was inhibited by PS, while Nocardioides albus and Solirubrobacter pauli exhibited enhanced growth in its presence. Our results suggest that culturable representatives of the bacterial core soil microbiota can be identified and used to investigate the effects of specific parameters linked to anthropogenic impacts under controlled laboratory conditions.