Skip to main content

Predicted functional genes for the biodegradation of xenobiotics in groundwater and sediment at two contaminated naval sites


The goals of this study were to predict the genes associated with the biodegradation of organic contaminants and to examine microbial community structure in samples from two contaminated sites. The approach involved a predictive bioinformatics tool (PICRUSt2) targeting genes from twelve KEGG xenobiotic biodegradation pathways (benzoate, chloroalkane and chloroalkene, chlorocyclohexane and chlorobenzene, toluene, xylene, nitrotoluene, ethylbenzene, styrene, dioxin, naphthalene, polycyclic aromatic hydrocarbons, and metabolism of xenobiotics by cytochrome P450). Further, the predicted phylotypes associated with functional genes early in each pathway were determined. Phylogenetic analysis indicated a greater diversity in the sediment compared to the groundwater samples. The most abundant genera for sediments/microcosms included Pseudomonas, Methylotenera, Rhodococcus, Stenotrophomonas, and Brevundimonas, and the most abundant for the groundwater/microcosms included Pseudomonas, Cupriavidus, Azospira, Rhodococcus, and unclassified Burkholderiaceae. Genes from all twelve of the KEGG pathways were predicted to occur. Seven pathways contained less than twenty-five genes. The predicted genes were lowest for xenobiotics metabolism by cytochrome P450 and ethylbenzene biodegradation and highest for benzoate biodegradation. Notable trends include the occurrence of the first genes for trinitrotoluene and 2,4-dinitrotoluene degradation. Also, the complete path from toluene to benzoyl-CoA was predicted. Twenty-two of the dioxin pathway genes were predicted, including genes within the first steps. The following phylotypes were associated with the greatest number of pathways: unclassified Burkholderiaceae, Burkholderia-Caballeronia-Paraburkholderia, Pseudomonas, Rhodococcus, unclassified Betaproteobacteria, and Polaromonas. This work illustrates the value of PICRUSt2 for predicting biodegradation potential and suggests that a subset of phylotypes could be important for the breakdown of organic contaminants or their metabolites.

Key points

• The approach is a low-cost alternative to shotgun sequencing.

• The genes and phylotypes encoding for xenobiotic degradation were predicted.

• A subset of phylotypes were associated with many pathways.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Copyright Permission] 210,692). B Genes present (pink) in all samples and those analyzed for phylotypes (red) for the KEGG toluene degradation pathway (used with permission [KEGG Copyright Permission] 210,692). C Genes present (pink) in all samples and those analyzed for phylotypes (red) for the KEGG dioxin degradation pathway (used with permission [KEGG Copyright Permission] 210,692)

Fig. 10

Availability of data

Illumina sequencing data were deposited in the NCBI Sequence Read Archive under Bioproject Number PRJ302752.


Download references


Thanks to Mark E. Fuller and Paul Hatzinger (CB&I Federal Services) for providing groundwater samples. Thanks to David Liu (Naval Facilities Engineering Command Northwest) and Mandy Michalsen (USACE, Seattle District) for providing the sediment samples.


Strategic Environmental Research and Development Program (SERDP Project ER1606), Michigan State University College of Engineering ENSURE program and NSF (grant number 1902250).

Author information

Authors and Affiliations



AV: Writing, editing, methodology, programming, formal analysis, and investigation. FW: Methodology, investigation, and editing. AC: Conceptualization, resources, data curation, writing (review and editing), visualization, supervision, project administration, and funding acquisition.

Corresponding author

Correspondence to Alison M. Cupples.

Ethics declarations

Ethical statement

This work was supported by the College of Engineering ENSURE program, SERDP, and NSF.

Conflict of interest

The authors declare no competing interests.

Human and animal rights and informed consent

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 6751 KB)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Vera, A., Wilson, F.P. & Cupples, A.M. Predicted functional genes for the biodegradation of xenobiotics in groundwater and sediment at two contaminated naval sites. Appl Microbiol Biotechnol 106, 835–853 (2022).

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:


  • Xenobiotic
  • PICRUSt2
  • Nitrotoluene
  • Toluene
  • RDX