Responses of Soil Bacterial Community and Its Resistome to Short-term Exposure to Macrolide Antibiotic Macrolactin A: Metagenomic analysis

Abstract

An important aspect of studying potential antibacterial biopreparations for crop protection is determining their potential negative impacts on the environment. Plant-associated Bacillus velezensis produce macrolactin A (McA), which determine effectiveness of this bacterial species against numerous human and plant pathogens. However, the effects of McA on the soil microbiome and the selection of specific antibiotic resistance genes (ARGs) among soil bacteria remain unknown. In this study, we use high-throughput sequencing-based metagenomic methods to investigate the differences in structure of the soil bacterial community and the abundance and diversity of ARGs in both McA-treated and untreated samples. The presence of high (10 mg per kg soil) and low (1 mg per kg soil) concentrations of McA induced changes in soil bacterial populations as shown by taxonomic analysis. The relative abundance of Alphaproteobacteria and Betaproteobacteria significantly increased under the McA treatments, while the relative abundance of Thermoleophilia, Rubrobacteria, Planctomycetia and Acidimicrobiia decreased. The ARG profiling results showed that both low and high doses of McA affected ARGs representation in the community. At the same time, a low dose of McA altered the representation of a larger number of ARGs (7 genes) compared to a high dose (3 genes). Overall, exposure to McA consistently altered the abundance of genes associated with resistance to elfamycin, glycopeptide, fluoroquinolone, rifampicin, and macrolide. Correlation analysis identified 185 relationships between 52 antibiotic resistance genes (ARGs) and 34 bacterial genera. Among these bacteria, Streptomyces, Baekduia, and Capillimicrobium were predicted to carry the most diverse ARGs. By assembling and annotating bacterial genomes, we identified the true hosts of ARGs. Chloroflexota were the most prevalent phylum harboring ARGs. Furthermore, profiling the soil microbiomes metabolic potential under low-dose McA revealed increased abundance of genes associated with signaling, chemotaxis, and broad-substrate drug efflux. The collectively obtained data significantly expands the understanding of the functional role of McA in the ecology of Bacillus velezensis, and at the same time provides an assessment of environmental risks associated with the use of biopreparations containing metabolites or living cells of this species bacteria.