Practical Examples of High-Throughput DNA Sequencing Support Engineering and Policy Decisions
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Background/Objectives. Environmental microbial diagnostics is a rapidly evolving field that enables understanding of causal relationships between the microbial community and their environment that would be too challenging to otherwise investigate.

Although in its infancy, this practice area has a wide range of applications, including the development of predictive models, cleanup and monitoring strategies, and bioremediation and biogeochemistry.  Examples of areas where this technical approach is specifically beneficial to meeting regulatory requirements with greater fidelity than currently practiced include addressing EPA's Surface Water Treatment Rule (SWTR), Total Coliform Rule, and Groundwater Rule.  Microbial diagnostic approaches also function as both leading and lagging indicators of bioprocess stability such as upset waste water treatment processes. This presentation discusses practical examples of where the use of high-throughput DNA sequencing provided diagnostic information to understand factors that influenced the DNA signature of specific environments.

Approach. High-throughput sequencing has been successful in characterizing prokaryotic and eukaryotic populations in a number of habitats intersecting environmental protection, restoration activities, and waste management. Sequencing total sample DNA for 16s and 18s ribosomal RNA genes allows the taxonomic classification of each unique gene sequence to the degree supported by available nucleotide reference databases. Emerging applications of this technology include the investigation of potable groundwater for bioindicators of surface water intrusion; bioreactors for changes in microbial community composition; landfill microbiota for stable methane production and temperature control; and biogeochemical engineering of coal combustion residuals (CCR). 

Conclusions. Observations from high-throughput sequencing of environmental samples illustrate the diagnostic ability of this technology to capture molecular signatures which signify leading or lagging indicators of environmental changes that may affect water quality, remediation performance, or process outputs.  Examples follow.

  • Groundwater potentially directly impacted by surface water was observed to contain certain gene sequences that were of clear surface origin including both eukaryotic and prokaryotic species. 
  • In an unexpected detection, genetically modified yeast DNA was detected in groundwater and provided an opportunity to evaluate the approximate timing of surface water intrusion into groundwater and to trace the DNA source. 
  • Analysis of biomass in a bioreactor revealed that changes in operating conditions dramatically affected microbial population distribution but without any loss of product output and quality.
  • Analysis of CCR detected over 500 different species of bacteria that hold the metabolic capacity to transform the inorganic chemistry of CCR to address associated environmental concerns.

Overall, results from our applications, demonstrate the ability of high-throughput sequencing to define microbial community composition at higher resolution than ever before with the benefit of greater understanding of the fine balance between microbial populations and environmental conditions. These results refine decision-making with information previously unavailable.

Publication Summary

  • Geosyntec Authors: Andrea Rocha, Jacques Smith, Duane Graves
  • All Authors: Andrea Rocha, Jacques Smith, Duane Graves
  • Title: 2018 Battelle Chlorinated Conference
  • Event or Publication: Event
  • Practice Areas: Contaminated Site Assessment and Cleanup
  • Citation: Session: I9. Use of Advanced Molecular Tools for Site Assessment or Remedy Performance
  • Date: April 8-12, 2018
  • Location: Palm Springs Convention Center in Palm Springs, California