Nanopore-based metagenomic analysis of the impact of nanoparticles on soil microbial communities

The current trend of using nanotechnology products in all spheres of human life, including for crop improvement may have a possible impact on soil microorganisms which influence soil and plant health. Nanopore-based metagenomic study reported here used full-length 16S rRNA gene sequences to assess shifts in community composition of soil microorganisms when treated with silver, titanium dioxide and zinc oxide nanoparticles (S-NP, T-NP, Z-NP, respectively). Firmicutes and Proteobacteria were the two dominant phyla in this soil, and there were no significant differences (p < 0.05) observed in these phyla across treatments. However, in the phylum Firmicutes, the abundance of the order Clostridiales showed a significant decrease (p < 0.05) in the presence of S-NP. Similarly, in the phylum Proteobacteria, a significant decrease in the presence of S-NP was seen for two orders, Vibrionales (p < 0.05) and Rhodobacterales (p < 0.01). Analysis at a further depth revealed that abundance of the genus Clostridium (order Clostridiales) decreased in the presence of both S-NP (p < 0.01) and T-NP (p < 0.05). The abundance of the genus Vibrio (order Vibrionales) was likewise impacted in the presence of all the three NPs - S-NP (p < 0.01), T-NP (p < 0.05) and Z-NP (p < 0.05). Analyses at high taxon ranks such as phyla may not give a good representation of the nature of microbial community shifts, and at times may paint an erroneous picture. The use of full-length 16S rRNA gene sequences here yielded a greater taxonomic depth, and some shifts at the lower ranks were discernible.