Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in Escherichia coli from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.

There has been little research on the dispersion of carbon nanotubes in dispersions of standard microbiological media. We report that tryptic soy broth (TSB) containing casein digest disperses single-walled carbon nanotubes (SWNT) at concentrations similar to those achieved in lysozyme (LSZ), one of the best known biomolecular SWNT dispersants. Similar to LSZ, the proposed mechanism for SWNT dispersion in TSB is favorable π–π stacking interactions with l-tryptophan. This is supported by similar SWNT concentrations in both LSZ and TSB supernatants, and the absence of appreciable dispersion in TSB that does not contain a source of l-tryptophan. Since l-tryptophan alone is insufficient to enable dispersion, it was previously hypothesized that LSZ’s macromolecular structure created steric hindrance that was critical for SWNT dispersion. These new results show that intermediately sized l-tryptophan containing species can also enable dispersion. In addition, since TSB is a commonly used growth medium for microbiological research, its dispersive ability presents new research avenues for studying the effect of SWNT on prokaryotic cells without the need to oxidize SWNT or add dispersants that may induce microbial stress.

There is significant interest in understanding whether nanomaterials with outstanding mechanical or electrical properties also possess antibacterial properties. However, assessment of antibacterial activity is a complex problem at the interface of chemistry and microbiology. Results can be affected by many factors including nanomaterial size, surface chemistry, concentration, and the dispersion media. The difficulty of dispersing nanomaterials such as single-walled carbon nanotubes (SWNTs) has resulted in many studies being conducted in the presence of dispersion aides which may themselves contribute to bacterial stress. The recent discovery that a standard microbial growth media, tryptic soy broth (TSB), is an effective SWNT dispersant provides a new opportunity to investigate the potential antibacterial activity of SWNTs using dispersants that range from antibacterial to growth-supporting. The five dispersants chosen for this work were Sodium dodecyl sulfate (SDS), pluronic, lysozyme, DNA, and tryptic soy broth. Staphylococcus aureus and Salmonella enterica were used as the model Gram-positive and Gram-negative bacteria. Activity was measured in terms of colony forming unit (CFU) and optical density measurements. None of the systems exhibited activity against Salmonella. SDS was fatal to Staph. aureus regardless of the presence of SWNTs. The activity of pluronic and lysozyme against Staph. aureus was enhanced by the presence of SWNTs. In contrast, the DNA and TSB dispersions did not have any activity regardless of the presence of SWNTs. These results highlight that the purported antibacterial activity of SWNTs may only be effective against bacteria that are sensitized by the dispersant and suggests the need for additional research on the mechanisms by which SWNT-dispersant interactions can result in antibacterial activity.

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