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Identifying bioaugmentation candidates for bioremediation of polycyclic aromatic hydrocarbons in contaminated estuarine sediment of the Elizabeth River, VA, USA

  • Environmental Biotechnology
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Abstract

Estuarine sediments near former creosoting facilities along the Elizabeth River (Virginia, USA) are contaminated by polycyclic aromatic hydrocarbons (PAHs). In this study, we interrogated the bacterial community of the Elizabeth River with both culture-based and culture-independent methods to identify potential candidates for bioremediation of these contaminants. DNA-based stable isotope probing (SIP) experiments with phenanthrene and fluoranthene using sediment from the former Republic Creosoting site identified relevant PAH-degrading bacteria within the Azoarcus, Hydrogenophaga, and Croceicoccus genera. Targeted cultivation of PAH-degrading bacteria from the same site recovered 6 PAH-degrading strains, including one strain highly similar to Hydrogenophaga sequences detected in SIP experiments. Other isolates were most similar to organisms within the Novosphingobium, Sphingobium, Stenotrophomonas, and Alcaligenes genera. Lastly, we performed 16S rRNA gene amplicon microbiome analyses of sediment samples from four sites, including Republic Creosoting, with varying concentrations of PAHs. Analysis of these data showed a striking divergence of the microbial community at the highly contaminated Republic Creosoting site from less contaminated sites with the enrichment of several bacterial clades including those affiliated with the Pseudomonas genus. Sequences within the microbiome libraries similar to SIP-derived sequences were generally found at high relative abundance, while the Croceicoccus sequence was present at low to moderate relative abundance. These results suggest that Azoarcus and Hydrogenophaga strains might be good target candidates for biostimulation, while Croceicoccus spp. might be good targets for bioaugmentation in these sediments. Furthermore, this study demonstrates the value of culture-based and culture-independent methods in identifying promising bacterial candidates for use in a precision bioremediation scheme.

Key points

• This study highlights the importance of using multiple strategies to identify promising bacterial candidates for use in a precision bioremediation scheme.

• We used both selective cultivation techniques and DNA-based stable isotope probing to identify bacterial degraders of prominent PAHs at a historically contaminated site in the Elizabeth River, VA, USA.

• Azoarcus and Hydrogenophaga strains might be good target candidates for biostimulation in Elizabeth River sediments, while Croceicoccus spp. might be good targets for bioaugmentation.

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Funding

This work was funded by the NIEHS supported Duke University Superfund Research Center (P42ES010356) and the National Science Foundation (NSF) under grant DGE 1545220.

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Authors and Affiliations

  1. Department of Civil and Environmental Engineering, Pratt School of Engineering, Duke University, 121 Hudson Hall, Durham, NC, 27708, USA

    Savannah J. Volkoff, Daniel L. Rodriguez, David R. Singleton, Alexander W. McCumber & Claudia K. Gunsch

  2. Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27759-7431, USA

    Michael D. Aitken & Jill R. Stewart

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  1. Savannah J. Volkoff
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  2. Daniel L. Rodriguez
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  3. David R. Singleton
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  6. Jill R. Stewart
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  7. Claudia K. Gunsch
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Contributions

Authors SV, CG, DS, DR, and AM contributed to the study conception and design. Material preparation, data collection, and analysis were performed by SV, DR, DS, and AM. The first draft of the manuscript was written by SV, and all authors commented on previous versions of the manuscript. JS and MA contributed equipment and materials. All authors read and approved the manuscript.

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Correspondence to Claudia K. Gunsch.

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Volkoff, S.J., Rodriguez, D.L., Singleton, D.R. et al. Identifying bioaugmentation candidates for bioremediation of polycyclic aromatic hydrocarbons in contaminated estuarine sediment of the Elizabeth River, VA, USA. Appl Microbiol Biotechnol 106, 1715–1727 (2022). https://doi.org/10.1007/s00253-021-11754-5

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