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Seasonal change is a major driver of soil resistomes at a watershed scale

  • 1.

    D’Costa, V. M. et al. Antibiotic resistance is ancient. Nature. 477, 457–461 (2011).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 2.

    Allen, H. K. et al. Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259 (2010).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 3.

    Udikovic-Kolic, N., Wichmann, F., Broderick, N. A. & Handelsman, J. Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. Proc. Natl Acad. Sci. USA. 111, 15202–15207 (2014).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 4.

    Chen, Q. L. et al. Long-term field application of sewage sludge increases the abundance of antibiotic resistance genes in soil. Environ. Int. 92–93, 1–10 (2016).

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • 5.

    Gillings, M. R. & Stokes, H. W. Are humans increasing bacterial evolvability? Trends Ecol. Evol. 27, 346–352 (2012).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 6.

    Zhu, Y. G. et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc. Natl Acad. Sci. USA. 110, 3435–3440 (2013).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 7.

    Woods, L. C. et al. Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation. Proc. Natl Acad. Sci. USA117, 26868–26875 (2020).

  • 8.

    World Health Organization. Antimicrobial resistance: global report on surveillance. World Health Organization. (2014).

  • 9.

    Forsberg, K. J. et al. The shared antibiotic resistome of soil bacteria and human pathogens. Science. 337, 1107–1111 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 10.

    Zhu, G. et al. Air pollution could drive global dissemination of antibiotic resistance genes. ISME J. 15, 270–281 (2021).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 11.

    Xiang, Q. et al. Agricultural activities affect the pattern of the resistome within the phyllosphere microbiome in peri-urban environments. J. Hazard Mater. 382, 121068 (2020).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 12.

    Wang, F. H. et al. High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation. Environ. Sci. Technol. 48, 9079–9085 (2014).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 13.

    Ding, J. et al. Long-term application of organic fertilization causes the accumulation of antibiotic resistome in earthworm gut microbiota. Environ. Int. 124, 145–152 (2019).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 14.

    Zhou, S. Y. et al. Phyllosphere of staple crops under pig manure fertilization, a reservoir of antibiotic resistance genes. Environ. Pollut. 252, 227–235 (2019).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 15.

    Wang, F. H., Qiao, M., Chen, Z., Su, J. Q. & Zhu, Y. G. Antibiotic resistance genes in manure-amended soil and vegetables at harvest. J. Hazard Mater. 299, 215–221 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 16.

    Marti, R. et al. Impact of manure fertilization on the abundance of antibiotic-resistant bacteria and frequency of detection of antibiotic resistance genes in soil and on vegetables at harvest. Appl. Environ. Microb. 79, 5701–5709 (2013).

    CAS 
    Article 

    Google Scholar 

  • 17.

    Zhu, Y. G. et al. Continental-scale pollution of estuaries with antibiotic resistance genes. Nat. Microbiol. 2, 16270 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 18.

    Du, S. et al. Large-scale patterns of soil antibiotic resistome in Chinese croplands. Sci. Total Environ. 712, 136418 (2020).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 19.

    Pruden, A., Pei, R. T., Storteboom, H. & Carlson, K. H. Antibiotic resistance genes as emerging contaminants: studies in northern Colorado. Environ. Sci. Technol. 40, 7445–7450 (2006).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 20.

    Bahram, M. et al. Structure and function of the global topsoil microbiome. Nature. 560, 233–237 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 21.

    Hu, H. W. et al. Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes. Environ. Microbiol. 20, 3186–3200 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 22.

    Han, X. M. et al. Antibiotic resistance genes and associated bacterial communities in agricultural soils amended with different sources of animal manures. Soil Biol. Biochem. 126, 91–102 (2018).

    CAS 
    Article 

    Google Scholar 

  • 23.

    Hu, H. W. et al. Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure. FEMS Microbiol. Ecol. 92, fiv169 (2016).

  • 24.

    Zhang, Y. J. et al. Temporal succession of soil antibiotic resistance genes following application of swine, cattle and poultry manures spiked with or without antibiotics. Environ. Pollut. 231, 1621–1632 (2017).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 25.

    Zhou, J. et al. Reproducibility and quantitation of amplicon sequencing-based detection. ISME J. 5, 1303–1313 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 26.

    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods. 7, 335–336 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 27.

    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26, 2460–2461 (2010).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 28.

    Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microb. 73, 5261–5267 (2007).

    CAS 
    Article 

    Google Scholar 

  • 29.

    Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 30.

    Su, J. Q. et al. Antibiotic resistome and its association with bacterial communities during sewage sludge composting. Environ. Sci. Technol. 49, 7356–7363 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 31.

    Ouyang, W. Y., Huang, F. Y., Zhao, Y., Li, H. & Su, J. Q. Increased levels of antibiotic resistance in urban stream of Jiulongjiang River, China. Appl. Microbiol. Biotechnol. 99, 5697–5707 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 32.

    Roberts D. W. labdsv: ordination and multivariate analysis for ecology. R package version 1.8-0. 2016. https://CRAN.R-project.org/package=labdsv.

  • 33.

    Oksanen J. et al. Vegan: community ecology package. R package version 2.2-0. 2014. http://CRAN.R-project.org/package=vegan.

  • 34.

    Jiao, S. et al. Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems. Microbiome. 6, 1–13 (2018).

  • 35.

    Sloan, W. T. et al. Quantifying the roles of immigration and chance in shaping prokaryote community structure. Environ Microbiol. 8, 732–740 (2006).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 36.

    Ning, D., Deng, Y., Tiedje, J. M. & Zhou, J. A general framework for quantitatively assessing ecological stochasticity. Proc. Natl Acad. Sci. USA. 116, 16892–16898 (2019).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 37.

    De Caceres, M. & Legendre, P. Associations between species and groups of sites: indices and statistical inference. Ecology. 90, 3566–3574 (2009).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • 38.

    Doerks, T., Copley, R. R., Schultz, J., Ponting, C. P. & Bork, P. Systematic identification of novel protein domain families associated with nuclear functions. Genome Res. 12, 47–56 (2002).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 39.

    Wickham H. ggplot2: elegant graphics for data analysis. (Springer-Verlag, 2009).

  • 40.

    Kassambara A. ggpubr: ‘ggplot2’ based publication ready plots. R package version 0.2. 2018. https://CRAN.R-project.org/package=ggpubr.

  • 41.

    Ahlmann-Eltze C. ggsignif: significance brackets for ‘ggplot2’. R package version 0.4. 0. 2018. https://CRAN.R-project.org/package=ggsignif.

  • 42.

    Zhao, F. K. et al. Soil contamination with antibiotics in a typical peri-urban area in eastern China: seasonal variation, risk assessment, and microbial responses. J. Environ. Sci. (China). 79, 200–212 (2019).

    Article 

    Google Scholar 

  • 43.

    Zhang, Y., Snow, D. D., Parker, D., Zhou, Z. & Li, X. Intracellular and extracellular antimicrobial resistance genes in the sludge of livestock waste management structures. Environ. Sci. Technol. 47, 10206–10213 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 44.

    Mao, D. et al. Persistence of extracellular DNA in river sediment facilitates antibiotic resistance gene propagation. Environ. Sci. Technol. 48, 71–78 (2014).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 45.

    Xiang, Q. et al. Spatial and temporal distribution of antibiotic resistomes in a peri-urban area is associated significantly with anthropogenic activities. Environ. Pollut. 235, 525–533 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 46.

    Forsberg, K. J. et al. Bacterial phylogeny structures soil resistomes across habitats. Nature. 509, 612–616 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 47.

    Li, B. et al. Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes. ISME J. 9, 2490–2502 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • 48.

    Hu, H. W. et al. Field-based evidence for copper contamination induced changes of antibiotic resistance in agricultural soils. Environ. Microbiol. 18, 3896–3909 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • 49.

    Birgander, J., Rousk, J. & Olsson, P. A. Comparison of fertility and seasonal effects on grassland microbial communities. Soil Biol. Biochem. 76, 80–89 (2014).

    CAS 
    Article 

    Google Scholar 

  • 50.

    Fournier, B. et al. Higher spatial than seasonal variation in floodplain soil eukaryotic microbial communities. Soil Biol. Biochem. 147, 107842 (2020).

    CAS 
    Article 

    Google Scholar 

  • 51.

    Zhang, K., Delgado-Baquerizo, M., Zhu, Y. G. & Chu, H. Space is more important than season when shaping soil microbial communities at a large spatial scale. Msystems. 5, e00783–19 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 52.

    Ladau, J. & Eloe-Fadrosh, E. A. Spatial, temporal, and phylogenetic scales of microbial ecology. Trends Microbiol. 27, 662–669 (2019).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 


  • Source: Ecology - nature.com

    Susan Solomon, scholar of atmospheric chemistry and environmental policy, delivers Killian Lecture

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