Applying Molecular Techniques to Aquatic Bioassessment: The Development of a Robust Biofilm-Based Multimetric Index of Biotic Integrity

EPA Grant Number: FP917813
Title: Applying Molecular Techniques to Aquatic Bioassessment: The Development of a Robust Biofilm-Based Multimetric Index of Biotic Integrity
Investigators: Van Gray, Jonathon Bruce
Institution: Kent State University
EPA Project Officer: Lee, Sonja
Project Period: September 1, 2015 through August 31, 2018
Project Amount: $132,000
RFA: STAR Graduate Fellowships (2015) RFA Text |  Recipients Lists
Research Category: Academic Fellowships


The purpose of this research is to provide a means of overcoming the limitations of current stream bioassessment methods through the use of commonly used high-resolution metagenomic and molecular techniques and the inclusion of multiple taxonomic groups (bacteria and diatoms). Together, these efforts will facilitate the development of a more robust and accessible means of assessing stream ecosystem health.


Biofilm communities from a pristine reference stream will be transplanted to sites along an urbanization gradient within a nearby stream system for 8 weeks before being returned to the reference site for an 8-week recovery period. Samples will be collected from both transplanted and non-transplanted communities over the duration of the study and molecular, metagenomic, and microscopic methods will be used to characterize community composition and functional capabilities. Data comparisons will then be used to determine how compositional and functional characteristics of the community are altered as a function of increasing environmental distress and how these responses are affected as stressors are removed. Analysis of emerging patterns of community response will then be assessed for use in the development of a biofilm-based index of stream health. This index will then be compared to current diatom-based indices and validated using samples from additional sampling sites.

Expected Results:

Due to the high turnover rates of bacterial populations and known specific environmental tolerances of many diatom populations, non-random patterns of bacterial-diatom co-occurrences can potentially be used to identify shifts in overall community response to environmental change. By identifying and then characterizing how these co-occurrence patterns are affected by environmental stress, a robust stream bioassessment tool can be developed that will be responsive at both the taxonomic and temporal resolution necessary to rapidly and accurately detect alterations to stream ecosystem health.

Supplemental Keywords:

Bioindicator, biofilm, metagenomics, microbial ecology, diatoms, ecological restoration

Progress and Final Reports:

  • 2016
  • 2017
  • Final