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Terrestrial ecosystems play a crucial role in the formation of soil resistome and the spread of antibiotic-resistant bacteria. Comprehensive studies of soil microbial communities, their structure, integrity, and level of antibiotic resistance (AR) in various terrestrial ecosystems were conducted. In total, 389 strains of dominant bacteria were isolated from the studied ecosystems, 57 of which were resistant to antibiotics, with levels of antibiotic resistance exceeding 70%. The soil microbiome of primeval forests was characterized by a low content of bacteria resistant to antibiotics; only two species, Bacillus cereus and Pantoea agglomerans, showed a high resistance to antibiotics. In the soil of agroecosystems of medicinal plants, among 106 strains of bacteria, a high level of resistance to antibiotics was found in 13 species. It was established that the number of antibiotic-resistant bacteria is highest in the soil of agroecosystems contaminated by enrofloxacin. Among 190 tested bacterial strains, 42 (22%) were characterized by a high level of antibiotic resistance. Therefore, the soil ecosystem is a key link in the formation and spread of antibiotic-resistant bacteria, which is a potential danger to humans. To reduce the risk of AR for humans, it is necessary to take appropriate measures to manage the soil microbiome and avoid soil contamination with antibiotics.