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Enrichment of novel Actinomycetales and the detection of monooxygenases during aerobic 1,4-dioxane biodegradation with uncontaminated and contaminated inocula

Abstract

1,4-Dioxane, a co-contaminant at many chlorinated solvent sites, is a problematic groundwater pollutant because of risks to human health and characteristics which make remediation challenging. In situ 1,4-dioxane bioremediation has recently been shown to be an effective remediation strategy. However, the presence/abundance of 1,4-dioxane degrading species across different environmental samples is generally unknown. Here, the objectives were to identify which 1,4-dioxane degrading functional genes are present and which genera may be using 1,4-dioxane and/or metabolites to support growth across different microbial communities. For this, laboratory sample microcosms and abiotic control microcosms (containing media) were inoculated with four uncontaminated soils and sediments from two contaminated sites. Live control microcosms were treated in the same manner, except 1,4-dioxane was not added. 1,4-Dioxane decreased in live microcosms with all six inocula, but not in the abiotic controls, suggesting biodegradation occurred. A comparison of live sample microcosms and live controls (no 1,4-dioxane) indicated nineteen genera were enriched following exposure to 1,4-dioxane, suggesting a growth benefit for 1,4-dioxane biodegradation. The three most enriched were Mycobacterium, Nocardioides, and Kribbella (classifying as Actinomycetales). There was also a higher level of enrichment for Arthrobacter, Nocardia, and Gordonia (all three classifying as Actinomycetales) in one soil, Hyphomicrobium (Rhizobiales) in another soil, Clavibacter (Actinomycetales) and Bartonella (Rhizobiales) in another soil, and Chelativorans (Rhizobiales) in another soil. Although Arthrobacter, Mycobacterium, and Nocardia have previously been linked to 1,4-dioxane degradation, Nocardioides, Gordonia, and Kribbella are potentially novel degraders. The analysis of the functional genes associated with 1,4-dioxane demonstrated three genes were present at higher relative abundance values, including Rhodococcus sp. RR1 prmA, Rhodococcus jostii RHA1 prmA, and Burkholderia cepacia G4 tomA3. Overall, this study provides novel insights into the identity of the multiple genera and functional genes associated with aerobic degradation of 1,4-dioxane in mixed communities.

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Acknowledgements

Thanks to Dr. Dan Jones and Dr. Scott Smith at the Mass Spectrometry Laboratory at the Research Technology Support Facility (MSU) for 1,4-dioxane analytical methods support. Also, our thanks to Dr. Anthony Danko (Naval Facilities Engineering Command) for providing the contaminated site sediments.

Funding

This work is financially supported by a grant awarded to Dr. Cupples from Strategic Environmental Research and Development Program (SERDP). Contract Number: W912HQ-17-C-0006. Financial support for this research was also provided by the NSF Long-term Ecological Research Program (DEB 1832042) at the Kellogg Biological Station and by Michigan State University AgBioResearch.

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Correspondence to Alison M. Cupples.

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Ramalingam, V., Cupples, A.M. Enrichment of novel Actinomycetales and the detection of monooxygenases during aerobic 1,4-dioxane biodegradation with uncontaminated and contaminated inocula. Appl Microbiol Biotechnol 104, 2255–2269 (2020). https://doi.org/10.1007/s00253-020-10376-7

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Keywords

  • 1,4-Dioxane
  • Soluble di-iron monooxygenases
  • Nocardioides
  • Gordonia
  • Kribbella
  • prmA
  • tomA3