Metagenomics of Tongue River Sediments: Working With Tribal Students to Assess the Impacts of Climate, Season and Resource Extraction on Freshwater Microbial Community Structure and Gene Content

EPA Grant Number: FP917458
Title: Metagenomics of Tongue River Sediments: Working With Tribal Students to Assess the Impacts of Climate, Season and Resource Extraction on Freshwater Microbial Community Structure and Gene Content
Investigators: Gibbons, Sean M
Institution: University of Chicago
EPA Project Officer: Zambrana, Jose
Project Period: September 1, 2012 through August 31, 2015
Project Amount: $126,000
RFA: STAR Graduate Fellowships (2012) RFA Text |  Recipients Lists
Research Category: Academic Fellowships , Fellowship - Environmental Microbiology


These data will enable several hypotheses to be tested. First, “microbial community structure and gene content will shift significantly between fall and spring samples at all sites, with seasonal dynamics having a stronger impact on community diversity and function than any other factor.” Second, “microbial community dynamics in taxonomy represent changes in the relative abundance of community members, rather than fluctuations in community membership.” Thirdly, “community structure will change with proximity to coal bed methane activity and to the Decker Coal Mine, with an increase in genes associated with hydrocarbon metabolism and osmotic stress.”


The study will take sediment samples from six sites along the Tongue River over the course of 2 years (fall and spring samplings). Sample collection, metadata documentation and genomic DNA extractions will be conducted with the help of students at Chief Dull Knife College. Polymerase chain reaction (PCR) and Illumina® Hi-Seq runs will be performed at Argonne National Laboratory. Amplicon and metagenomic data will be processed through the QIIME and MG-RAST workflows, respectively. Multivariate statistical techniques will be used to determine community similarity (principal component analysis and non-metric multidimensional scaling) and to find significant correlations between sequence data and contextual metadata (Resource Description and Access and canonical correspondence analysis). The data will be used to train ecosystem models (microbial assemblage prediction and predictive relative metabolic turnover), which in turn will be used to predict the phylogenetic and functional diversity of the Tongue River across space and time. These models will enable the estimation of carbon and nitrogen cycling in the system, and how these ecosystem services are impacted by human activities (e.g., coal mining and coal-bed methane development) along the Tongue River.

Expected Results:

It is expected to find a strong relationship between season and microbial community structure. Also, it is expected to find an increased prevalence of genes associated with hydrocarbon metabolism and osmotic stress near the Decker Coal Mine and around coal-bed methane extraction sites. The hypothesis is that environmental stressors, like high salt levels or hydrocarbon contamination, will impair key ecosystem services. Based on prior research, it is predicted that microbial communities will harbor a persistent seed bank of low-abundance organisms and that changes in community structure will be due to changes in relative abundance of taxa, rather than presence/absence of particular organisms.

Potential to Further Environmental/Human Health Protection
The results from this study will help elucidate the relationship between environmental conditions and freshwater microbial community structure and function. This information will help the U.S. Environmental Protection Agency to better manage and protect freshwater resources. In addition, tribal authorities can make use of the models to better understand the impacts of human development on their riparian ecosystems. This will lead to better management decisions. Also, several tribal college students are expected to be trained in cutting-edge molecular biology and bioinformatic techniques. These students will be better equipped to pursue a 4-year degree program and then to successful careers in environmental science.

Supplemental Keywords:

metagenomics, microbial ecology, bioinformatics

Progress and Final Reports:

  • 2013
  • 2014
  • Final