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Environmental Science and Pollution Research

, Volume 25, Issue 14, pp 13660–13675 | Cite as

Whole genome analysis of six organophosphate-degrading rhizobacteria reveals putative agrochemical degradation enzymes with broad substrate specificity

  • Rupa IyerEmail author
  • Brian Iken
  • Ashish Damania
  • Jerry Krieger
Research Article

Abstract

Six organophosphate-degrading bacterial strains collected from farm and ranch soil rhizospheres across the Houston-metropolitan area were identified as strains of Pseudomonas putida (CBF10-2), Pseudomonas stutzeri (ODKF13), Ochrobactrum anthropi (FRAF13), Stenotrophomonas maltophilia (CBF10-1), Achromobacter xylosoxidans (ADAF13), and Rhizobium radiobacter (GHKF11). Whole genome sequencing data was assessed for relevant genes, proteins, and pathways involved in the breakdown of agrochemicals. For comparative purposes, this analysis was expanded to also include data from deposited strains in the National Center for Biotechnology Information’s (NCBI) database. This study revealed Zn-dependent metallo-β-lactamase (MBL)-fold proteins similar to OPHC2 first identified in P. pseudoalcaligenes as the likely agents of organophosphate (OP) hydrolysis in A. xylosoxidans ADAF13, S. maltophilia CBF10-1, O. anthropi FRAF13, and R. radiobacter GHKF11. A search of similar proteins within NCBI identified over 200 hits for bacterial genera and species with a similar OPHC2 domain. Taken together, we conclude from this data that intrinsic low-level OP hydrolytic activity is likely prevalent across the rhizosphere stemming from widespread OPHC2-like metalloenzymes. In addition, P. stutzeri ODKF13, P. putida CBF10-2, O. anthropi FRAF13, and R. radiobacter GHKF11 were found to harbor glycine oxidase (GO) enzymes that putatively possess low-level activity against the herbicide glyphosate. These bacterial GOs are reported to catalyze the degradation of glyphosate to α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) and suggest a possible link to AMPA that can be found in glyphosate-contaminated agricultural soil. The presence of aromatic degradation proteins were also detected in five of six study strains, but are attributed primarily to components of the widely distributed β-ketoadipate pathway found in many soil bacteria.

Keywords

Agrochemicals Bioremediation Organophosphates Rhizosphere 

Abbreviations

AMPA

α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid

GO

Glycine oxidase

GOX

Glyphosate oxidoreductase

MBL

Metallo-β-lactamase

MPH

Methyl parathion hydrolase

NCBI

National Center for Biotechnology Information

OP

Organophosphate

opd

Organophosphorus degradation

OPAA

Organophosphorus acid Anhydrolase

OPH

Organophosphorus hydrolase

PTE

Phosphotriesterase

PLL

Phosphotriesterase-like lactonase

WHO

World Health Organization

Notes

Acknowledgements

The authors wish to thank Annette Frenk, a graduate student at the University of Houston, for her help in compiling background information on relevant agrochemical pathways for this project.

Funding for whole genome sequencing of study strains was provided by the National Science Foundation (NSF) (award no. 1505403). The NSF had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Authors’ contributions

RI was the principal investigator of this research and all research work was conducted in her laboratory space. RI designed the project parameters, directed research activity inside the laboratory, submitted compiled sequence data to NCBI, and proofread the manuscript. BI helped with drafting the manuscript and with sequence alignment. JK participated in sample preparation for whole genome sequencing and construction of the phylogenetic trees from compiled sequence data. AD assembled DNA sequence data into contigs for submission to NCBI and helped contribute to bioinformatics analysis of sample strains for aromatic biodegradation.

Compliance with ethical standards

This study did involve animals or human participants.

Competing interests

The authors declare that they have no conflict of interest.

Supplementary material

11356_2018_1435_MOESM1_ESM.docx (20 kb)
ESM 1 (DOCX 20 kb)
11356_2018_1435_MOESM2_ESM.docx (18 kb)
ESM 2 (DOCX 17 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Rupa Iyer
    • 1
    Email author
  • Brian Iken
    • 1
  • Ashish Damania
    • 2
  • Jerry Krieger
    • 1
  1. 1.Center for Life Sciences Technology, Engineering TechnologyUniversity of HoustonHoustonUSA
  2. 2.Department of Pediatrics-Tropical MedicineBaylor College of MedicineHoustonUSA

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