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Comparative Genomics Analysis of the Aromatic and Xenobiotic Degradation Capacities and Heavy Metal Resistance in Seven Environmentally Derived Bacterial Isolates

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Abstract

This work is a comparative genomics investigation of the aromatic and xenobiotic compound degradation capabilities and heavy metal resistance of environmental bacterial isolates previously identified by our lab, Achromobacter xylosoxidans ADAF13, Exiguobacterium sp. KKBO11, Ochrobactrum anthropi FRAF13, Pseudomonas putida CBF10-2, Pseudomonas stutzeri ODKF13, Rhizobium radiobacter GHKF11, and Stenotrophomonas maltophilia CBF10-1. This work sought to assess the potential of these isolates as bioremediation tools. We found a variety of aromatic degradation pathways though none directly acts on industrial compounds such as polycyclic aromatic compounds, benzene, phthalate, or xylene. Achromobacter xylosoxidans ADAF13, P. putida CBF10-2, and P. stutzeri ODKF13 showed the most complete pathways for aromatic compound degradation and halobenzoate degradation. All isolates contained heavy metal resistance genes for arsenic, cadmium, copper, chromium, lead, mercury, and zinc. Arsenic resistance genes were the most common among isolates and were organized into structurally diverse ars operons. Collectively, our data indicated that A. xylosoxidans ADAF13, P. putida CBF10-2, and P. stutzeri ODKF13 are strong candidates for further enhancement and development as bioremediation tools.

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Data and Code Availability

This work made use of genome sequences already available on NCBI (see text for GenBank accessions). Data that would be necessary to replicate this study (annotations and intermediate files generated by this study) are available in the Zenodo repository under https://doi.org/10.5281/zenodo.7804129. The code used in this study is indicated in the “Methods” section.

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Acknowledgements

The authors would like to the thank Brian N. Iken for his help drafting the manuscript.

Funding

This work was supported by the National Institute of Standards and Technology (NIST) (G110008 58106) and by the National Science Foundation (NSF) (award no. 1726968).

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  1. Houston, USA

    Alexander R. Kneubehl

  2. Research, Innovation and Economic Development, Tarleton State University, Stephenville, TX, USA

    Rupa Iyer

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RI was the principal investigator of this research, acquired the funding, submitted compiled sequence data to NCBI for annotation, and supplied the sequence data for analysis. ARK carried out the annotation and comparative genomics analyses and wrote the manuscript. Both authors read and approved the final text.

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Correspondence to Rupa Iyer.

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ARK was employed as an independent contractor to conduct the analysis and write the manuscript. RI declares no financial interests.

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Kneubehl, A.R., Iyer, R. Comparative Genomics Analysis of the Aromatic and Xenobiotic Degradation Capacities and Heavy Metal Resistance in Seven Environmentally Derived Bacterial Isolates. Water Air Soil Pollut 234, 482 (2023). https://doi.org/10.1007/s11270-023-06495-2

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