Alav I., Kobylka J., Kuth M.S., Pos K.M., Picard M., Blair J.M.A. et al. (2021). Structure, assembly, and function of tripartite efflux and Type 1 secretion systems in gram-negative bacteria. Chem Rev 121: 5479-5596.
Alcock B.P., Raphenya A.R., Lau T.T.Y., Tsang K.K., Bouchard M., Edalatmand A. et al. (2019). CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48: D517-D525.
Bahram M., Hildebrand F., Forslund S.K., Anderson J.L., Soudzilovskaia N.A., Bodegom P.M. et al. (2018). Structure and function of the global topsoil microbiome. Nature 560: 233-237.
Bengtsson-Palme J., Larsson D.G.J. (2016). Concentrations of antibiotics predicted to select for resistant bacteria: Proposed limits for environmental regulation. Environ Int 86: 140-149.
Berendonk T.U., Manaia C.M., Merlin C., Fatta-Kassinos D., Cytryn E., Walsh F. et al. (2015). Tackling antibiotic resistance: the environmental framework. Nat Rev Microbiol 13: 310-317.
Bolger A.M., Lohse M., Usadel B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
Boolchandani M., D’Souza A.W., Dantas G. (2019). Sequencing-based methods and resources to study antimicrobial resistance. Nat Rev Genet 20: 356-370.
Buchfink B., Xie C., Huson D.H. (2015). Fast and sensitive protein alignment using DIAMOND. Nat Methods 12: 59-60.
Chen Q.-L., Hu H.-W., Yan Z.-Z., Zhu Y.-G., He J.-Z., Delgado-Baquerizo M. (2022). Cross-biome antibiotic resistance decays after millions of years of soil development. ISME J 16: 1864-1867.
Edgar R.C. (2013). UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10: 996-998.
Forsberg K.J., Reyes A., Wang B., Selleck E.M., Sommer M.O.A., Dantas G. (2012). The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens. Science 337: 1107-1111.
Ghoul M., Mitri S. (2016). The ecology and evolution of microbial competition. Trends Microbiol 24: 833-845.
Henderson P.J.F., Maher C., Elbourne L.D.H., Eijkelkamp B.A., Paulsen I.T., Hassan K.A. (2021). Physiological functions of bacterial “multidrug” efflux pumps. Chem Rev 121: 5417-5478.
Hernando-Amado S., Coque T.M., Baquero F., Martínez J.L. (2019). Defining and combating antibiotic resistance from One Health and Global Health perspectives. Nat Microbiol 4: 1432-1442.
Hu J., Zhao Y., Yao X., Wang J., Zheng P., Xi C. et al. (2021). Dominance of comammox Nitrospira in soil nitrification. Sci Total Environ 780: 146558.
Jadeja N.B., Worrich A. (2022). From gut to mud: dissemination of antimicrobial resistance between animal and agricultural niches. Environ Microbiol DOI: doi.org/10.1111/1462-2920.15927.
Jakubczyk D., Dussart F. (2020). Selected Fungal Natural Products with Antimicrobial Properties. Molecules 25: 911.
Jiang X., Ellabaan M.M.H., Charusanti P., Munck C., Blin K., Tong Y. et al. (2017). Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nat Commun 8: 15784.
Kang D.D., Li F., Kirton E., Thomas A., Egan R., An H. et al. (2019). MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7: e7359.
Kim D.-W., Cha C.-J. (2021). Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission. Exp Mol Med 53: 301-309.
Kim H.-S., Nagore D., Nikaido H. (2010). Multidrug efflux pump MdtBC of Escherichia coli is active only as a B2C heterotrimer. J Bacteriol 192: 1377-1386.
Klenotic P.A., Moseng M.A., Morgan C.E., Yu E.W. (2021). Structural and Functional Diversity of Resistance–Nodulation–Cell Division Transporters. Chem Rev 121: 5378-5416.
Larsson D.G.J., Flach C.F. (2022). Antibiotic resistance in the environment. Nat Rev Microbiol 20: 257-269.
Lewis K. (2020). The science of antibiotic discovery. Cell 181: 29-45.
Li D., Liu C.-M., Luo R., Sadakane K., Lam T.-W. (2015). MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31: 1674-1676.
Li W., Liu Z.S., Hu B.L., Zhu L.Z. (2021). Co-occurrence of crAssphage and antibiotic resistance genes in agricultural soils of the Yangtze River Delta, China. Environ Int 156.
Lomovskaya O., Zgurskaya H.I., Totrov M., Watkins W.J. (2007). Waltzing transporters and 'the dance macabre' between humans and bacteria. Nat Rev Drug Discov 6: 56-65.
Murray C.J.L., Ikuta K.S., Sharara F., Swetschinski L., Robles Aguilar G., Gray A. et al. (2022). Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399: 629-655.
Obermeier M.M., Wicaksono W.A., Taffner J., Bergna A., Poehlein A., Cernava T. et al. (2021). Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance. ISME J 15: 921-937.
Palmer J.D., Foster K.R. (2022). Bacterial species rarely work together. Science 376: 581-582.
Parks D.H., Imelfort M., Skennerton C.T., Hugenholtz P., Tyson G.W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25: 1043-1055.
Parks D.H., Chuvochina M., Waite D.W., Rinke C., Skarshewski A., Chaumeil P.-A. et al. (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 36: 996-1004.
Qian X., Gunturu S., Guo J., Chai B., Cole J.R., Gu J. et al. (2021). Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems. Microbiome 9: 108.
Sokol N.W., Slessarev E., Marschmann G.L., Nicolas A., Blazewicz S.J., Brodie E.L. et al. (2022). Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nat Rev Microbiol 10.1038/s41579-022-00695-z.
Staff S.S.D. (2017). Chapter 3: Examination and description of soil profiles. In: Ditzler C, Scheffe K, Monger H (eds). Soil survey manual, USDA Handbook 18. Government Printing Office: Washington, DC. pp 83-233.
Thomas IV J.C., Oladeinde A., Kieran T.J., Finger Jr. J.W., Bayona-Vásquez N.J., Cartee J.C. et al. (2020). Co-occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site. Microb Biotechnol 13: 1179-1200.
Wang F., Fu Y.-H., Sheng H.-J., Topp E., Jiang X., Zhu Y.-G. et al. (2021). Antibiotic resistance in the soil ecosystem: A One Health perspective. Curr Opin Environ Sci Health 20: 100230.
Yang B., Cheng X., Zhang Y., Li W., Wang J., Guo H. (2021a). Insight into the role of binding interaction in the transformation of tetracycline and toxicity distribution. Environ Sci Ecotechnol 8: 100127.
Yang B., Cheng X., Zhang Y., Li W., Wang J., Guo H. (2021b). Probing the roles of pH and ionic strength on electrostatic binding of tetracycline by dissolved organic matters: Reevaluation of modified fitting model. Environ Sci Ecotechnol 8: 100133.
Yi X., Liang J.-L., Su J.-Q., Jia P., Lu J.-l., Zheng J. et al. (2022). Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes. ISME J 10.1038/s41396-022-01258-z.
Yin X., Jiang X.-T., Chai B., Li L., Yang Y., Cole J.R. et al. (2018). ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. Bioinformatics 34: 2263-2270.
Zhu D., Ma J., Li G., Rillig M.C., Zhu Y.-G. (2022). Soil plastispheres as hotspots of antibiotic resistance genes and potential pathogens. ISME J 16: 521-532.
Zhu G., Wang X., Yang T., Su J., Qin Y., Wang S. et al. (2021). Air pollution could drive global dissemination of antibiotic resistance genes. ISME J 15: 270-281.