Metabolome patterns identify active dechlorination in bioaugmentation consortium SDC-9™

Amanda L May; Yongchao Xie; Fadime Kara Murdoch; Mandy M Michalsen; Frank E Löffler; Shawn R Campagna

doi:10.3389/fmicb.2022.981994

Metabolome patterns identify active dechlorination in bioaugmentation consortium SDC-9™

Front Microbiol. 2022 Oct 25:13:981994. doi: 10.3389/fmicb.2022.981994. eCollection 2022.

Authors

Amanda L May¹, Yongchao Xie², Fadime Kara Murdoch¹, Mandy M Michalsen³, Frank E Löffler^{1

2

4

5

6}, Shawn R Campagna^{7

8

9}

Affiliations

¹ Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, United States.
² Department of Civil and Environmental Engineering, Tickle College of Engineering, University of Tennessee, Knoxville, TN, United States.
³ Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, United States.
⁴ Department of Microbiology, College of Arts and Sciences, The University of Tennessee, Knoxville, TN, United States.
⁵ Department of Biosystems Engineering and Soil Science, Herbert College of Agriculture, The University of Tennessee, Knoxville, TN, United States.
⁶ Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, United States.
⁷ Department of Chemistry, College of Arts and Sciences, The University of Tennessee, Knoxville, TN, United States.
⁸ Biological and Small Molecule Mass Spectrometry Core, College of Arts and Sciences, The University of Tennessee, Knoxville, TN, United States.
⁹ University of Tennessee-Oak Ridge Innovation Institute, University of Tennessee, Knoxville, TN, United States.

Abstract

Ultra-high performance liquid chromatography-high-resolution mass spectrometry (UPHLC-HRMS) is used to discover and monitor single or sets of biomarkers informing about metabolic processes of interest. The technique can detect 1000's of molecules (i.e., metabolites) in a single instrument run and provide a measurement of the global metabolome, which could be a fingerprint of activity. Despite the power of this approach, technical challenges have hindered the effective use of metabolomics to interrogate microbial communities implicated in the removal of priority contaminants. Herein, our efforts to circumvent these challenges and apply this emerging systems biology technique to microbiomes relevant for contaminant biodegradation will be discussed. Chlorinated ethenes impact many contaminated sites, and detoxification can be achieved by organohalide-respiring bacteria, a process currently assessed by quantitative gene-centric tools (e.g., quantitative PCR). This laboratory study monitored the metabolome of the SDC-9™ bioaugmentation consortium during cis-1,2-dichloroethene (cDCE) conversion to vinyl chloride (VC) and nontoxic ethene. Untargeted metabolomics using an UHPLC-Orbitrap mass spectrometer and performed on SDC-9™ cultures at different stages of the reductive dechlorination process detected ~10,000 spectral features per sample arising from water-soluble molecules with both known and unknown structures. Multivariate statistical techniques including partial least squares-discriminate analysis (PLSDA) identified patterns of measurable spectral features (peak patterns) that correlated with dechlorination (in)activity, and ANOVA analyses identified 18 potential biomarkers for this process. Statistical clustering of samples with these 18 features identified dechlorination activity more reliably than clustering of samples based only on chlorinated ethene concentration and Dhc 16S rRNA gene abundance data, highlighting the potential value of metabolomic workflows as an innovative site assessment and bioremediation monitoring tool.

Keywords: Dehalococcoidia; biomarkers; bioremediation; consortium SDC-9™; environmental monitoring; metabolomics; reductive dechlorination.