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Research Fellowships

Data Analysis of Sequences and qPCR for Microbial Communities during Algal Blooms

EPA Office of Research and Development

EPA National Science Foundation Graduate Research Internship Program (GRIP) Opportunity

Opportunity Title:

Data Analysis of Sequences and qPCR for Microbial Communities during Algal Blooms

Research Area:


EPA Lab/Center/Office:

Center for Environmental Measurement & Modeling, Watershed & Ecosystem Characterization, Biological Measurements Branch


Cincinnati, OH


12 months

Brief Summary:

2 training opportunities are open to highly microbial-research-motivated students to conduct experiments and data/modeling analysis, explore novel genes, and metabolic pathways, validate resultant findings using qPCR/RT-qPCR and summarize the findings.

Opportunity Description:

Cyanobacterial harmful algal blooms (HABs) and the toxins produced by the blooms have become a world-wide concern. The shutdown of the Toledo drinking water treatment plant in the summer of 2014 due to elevated toxin concentrations highlighted the need for a better understanding of cyanobacterial HABs. Understanding cyanobacterial HABs production is important because the blooms can be ecologically disruptive, can have economic impacts and produce toxins at relevant health levels. A study that was conducted to evaluate and compare bloom/toxin indicators, toxicity, meta-transcriptomics and detection methodologies in Lake Harsha has provided useful information not only to recreational water users, but also to drinking water treatment plant operators. The analysis on meta-transcriptomics in 2015 revealed novel findings in novel toxic groups and associations of gene expressions with nutrients. Further analysis for the data in 2015-2016 and the future data in 2017 are planned to reveal novel pathways and genes associated with environmental conditions and nutrients. A training opportunity will be provided under this project.

The trainees should be highly motivated by the research project with demonstrated knowledge, expertise and publication records in microbiology or molecular biology or genetics or bioinformatics or statistics, etc. The duties will include to conduct qPCR, RT-qPCR and  data analysis.

Opportunities for Professional Development:

This project aims to examine the relationships between environmental factors and toxin gene quantity and expressions, to elucidate the associations of gene expression with environmental conditions and nutrients, to explore novel genes for develop new assays, and to validate the resultant findings from the analysis using qPCR and RT-qPCR methods.

Point of Contact or Mentor:

Jingrang Lu (

Research Fellowships