Abstract
Bioremediation is becoming an increasingly popular approach for the remediation of sites contaminated with the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Multiple lines of evidence are often needed to assess the success of such approaches, with molecular studies frequently providing important information on the abundance of key biodegrading species. Towards this goal, the current study utilized shotgun sequencing to determine the abundance and diversity of functional genes (xenA, xenB, xplA, diaA, pnrB, nfsI) and species previously associated with RDX biodegradation in groundwater before and after biostimulation at an RDX-contaminated Navy Site. For this, DNA was extracted from four and seven groundwater wells pre- and post-biostimulation, respectively. From a set of 65 previously identified RDX degraders, 31 were found within the groundwater samples, with the most abundant species being Variovorax sp. JS1663, Pseudomonas fluorescens, Pseudomonas putida, and Stenotrophomonas maltophilia. Further, 9 RDX-degrading species significantly (p<0.05) increased in abundance following biostimulation. Both the sequencing data and qPCR indicated that xenA and xenB exhibited the highest relative abundance among the six genes. Several genes (diaA, nsfI, xenA, and pnrB) exhibited higher relative abundance values in some wells following biostimulation. The study provides a comprehensive approach for assessing biomarkers during RDX bioremediation and provides evidence that biostimulation generated a positive impact on a set of key species and genes.
Key points
• A co-occurrence network indicated diverse RDX degraders.
• >30 RDX-degrading species were detected.
• Nine RDX-degrading species increased following biostimulation.
• Sequencing and high-throughput qPCR indicated that xenA and xenB were most abundant.
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Data availability
MG-RAST ID numbers and sequencing data have been summarized (Table S1), and the datasets are publicly available on MG-RAST.
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Acknowledgements
Thanks to M. M. Michalsen (U.S. Army Engineer Research Development Center) for providing the groundwater and the RDX concentrations.
Funding
Thanks to Malcolm Gander (Naval Facilities Engineering Command) for partially funding this project and thanks to Craig Tobias (University of Connecticut) for facilitating project funding.
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Hongyu Dang: Conceptualization, methodology, programming, validation, formal analysis, writing, and investigation. Alison Cupples: Resources, data curation, writing-review and editing, visualization, supervision, project administration, and funding acquisition.
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Dang, H., Cupples, A.M. Diversity and abundance of the functional genes and bacteria associated with RDX degradation at a contaminated site pre- and post-biostimulation. Appl Microbiol Biotechnol 105, 6463–6475 (2021). https://doi.org/10.1007/s00253-021-11457-x
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DOI: https://doi.org/10.1007/s00253-021-11457-x