Assessment of antibiotic resistance in soil and its link to different land use types and intensities

Nowadays, bacterial infections pose a serious risk for human health again, due to multi-resistant pathogens insensitive to antibiotic treatment. Some of the antibiotic resistance genes (ARGs) carried by these pathogens were most likely acquired through horizontal gene transfer (HGT), as this is a more efficient means to adapt to exposition to antibiotics than the invention of protective mechanisms by mutational changes. Many of the ARGs, identified in human pathogens, are believed to originate from microorganisms colonizing soil, where antibiotic synthesis and resistance development have coevolved for millions of years, leading to an inconceivable variety of resistance genes, also termed the soil resistome. Due to knowledge gaps in this field, the soil resistome was investigated in three different work packages within this thesis. First, anthropogenic effectors influencing the distribution of medically relevant ARGs and mobile genetic elements (MGEs) in 300 different soils with divergent land use history were analyzed. In this context, it was determined that, except for the considered beta-lactamase genes, all target ARGs and MGEs were more frequently detected in grassland soils which are in closer proximity to human activities than the investigated forest soils. The macrolide resistance gene mefA and the sulfonamide resistance gene sul2 showed higher abundances in grassland soils that experienced organic fertilization. To potentially reduce the influence of organic fertilizers, which can originate from animals treated with antimicrobial compounds, it was proposed that the frequent veterinary utilization of macrolide preparations with long elimination half-lives should be limited and the prescription range of veterinary utilized sulfonamides reconsidered. However, the input of veterinary antibiotics, ARGs and antibiotic-resistant bacteria into the soil microbial community may be limited best, by reducing factory farming. This would decrease the infection frequency of livestock and thereby the amount of utilized antibiotics. Besides a significant effect of organic fertilization on mefA and sul2, the abundance of the aminoglycoside resistance gene aac(6’)‐lb increased with mowing frequency in grassland soil and a positive correlation between the beta-lactamase gene blaIMP‐12 and fungal diversity was detected in beech forest soil. In the second work package, parts of the so far unexplored variety of resistances against tetracyclines and the synthetic sulfonamides were investigated using function-based screenings of 2 grassland and forest soil metagenomic libraries. Thereby, four major facilitator superfamily (MFS) efflux pumps conferring tetracycline resistance and four dihydropteroate synthases (DHPS) conferring sulfonamide resistance, were identified. The DHPS genes were detected in metagenomic libraries from forest soils without a history of antibiotic exposure. They support the hypothesis that resistance genes against synthetic antibiotics naturally occur in complex microbial communities and are most likely caused by mutational changes which confer resistance as a side effect. This confirms that the soil resistome is a probable source of resistance mechanisms against novel synthetic or semisynthetic antibiotics and underlines the necessity for further screenings with respect to genes conferring resistance against critically important antibiotics. Throughout the third work package, a globally abundant soil verrucomicrobial genus, Candidatus Udaeobacter, was analyzed as the composition of the bacterial community is considered the primary determinant of the composition of the soil resistome. Thereby, it was found that these largely unexplored soil bacteria show multi-resistance and benefit from the release of antibiotics in soil. A metagenome assembled genome (MAG) from a Ca. Udaeobacter representative that showed increased growth upon antibiotics release, was analyzed in terms of features explaining this observed behavior as well as its global distribution in soil. In this context, vitamin and amino acid transporter as well as several vitamin salvage pathways were detected. This indicates that Ca. Udaeobacter efficiently utilizes nutrients which are released by other soil bacteria as a consequence of antibiotic-driven cell lysis. Furthermore, a variety of different ARGs are encoded on the investigated MAG, including several multidrug and macrolide resistance pumps as well as beta-lactam resistance genes. Considering the globally high abundance of Ca. Udaeobacter in soil, its ARG repertoire constitutes a huge fraction of the soil resistome. Components of this repertoire can potentially be mobilized and transferred to clinically relevant strains. These mobilization events may be fostered by environmental antibiotic pollution, especially as Ca. Udaeobacter shows increased growth upon antibiotic exposure which further increases the proportion of the respective ARGs in the resistome. The MAG further indicated that these bacteria are able to perform hydrogen scavenging and are protected against acidic conditions which also may have contributed to the dissemination of Ca. Udaeobacter in soils worldwide