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Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design


Next-generation DNA sequencing and metagenomic analysis provide powerful tools for the environmentally friendly design of nanoparticles. Herein we demonstrate this approach using a model community of environmental microbes (that is, wastewater-activated sludge) dosed with gold nanoparticles of varying surface coatings and morphologies. Metagenomic analysis was highly sensitive in detecting the microbial community response to gold nanospheres and nanorods with either cetyltrimethylammonium bromide or polyacrylic acid surface coatings. We observed that the gold-nanoparticle morphology imposes a stronger force in shaping the microbial community structure than does the surface coating. Trends were consistent in terms of the compositions of both taxonomic and functional genes, which include antibiotic resistance genes, metal resistance genes and gene-transfer elements associated with cell stress that are relevant to public health. Given that nanoparticle morphology remained constant, the potential influence of gold dissolution was minimal. Surface coating governed the nanoparticle partitioning between the bioparticulate and aqueous phases.

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Fig. 1: Characterization of gold nanoparticles before and after addition to SBRs.
Fig. 2: Taxonomic shifts in the SBR microbial community structure throughout the nanoparticle-dosing period.
Fig. 3: MDS ordination of Bray–Curtis similarity.
Fig. 4: Relative abundance of ARG classes normalized to 16S rRNA gene abundance.
Fig. 5: Relative abundance of MRG classes (number of MRGs of each class normalized to 16S rRNA gene abundance).


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This research was funded by the National Science Foundation (NSF) PIRE: Halting Environmental Antimicrobial Resistance Dissemination (award no. OISE:1545756) and NSF CBET:1336353, the US Environmental Protection Agency (Star Grant no. 834856), the Center for the Environmental Implications of Nanotechnology (EF-0830093), the Water Environment Research Foundation Paul L. Busch Award and the Virginia Tech Institute for Critical Technology and Applied Science. The authors also thank R. Jones for help in maintaining the SBRs, M. Chan for assisting in the electrophoretic mobility measurements and W. Leng for assistance in the TEM sample preparation.

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J.W.M., P.J.V. and A.P. conceived and designed the study. N.D.B. and C.J.M. synthesized and characterized the nanoparticles. J.W.M. performed the experiments. J.W.M., P.J.V. and A.P. analysed the data. All the authors contributed to the writing of the manuscript.

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Correspondence to Amy Pruden or Peter J. Vikesland.

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The authors declare no competing financial interests.

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Supplementary Figs. 1–10, Supplementary Table 1, Supplementary Discussion

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Metch, J.W., Burrows, N.D., Murphy, C.J. et al. Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design. Nature Nanotech 13, 253–259 (2018).

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