Research Project
Extremely acidophilic bacteria are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of microorganisms is not well studied as novel microbe bioremediators for AMD.
The Lee Lab is interested in:
Photo: Red and Bonita Mine
1) identifying and quantifying abundant iron-oxidizing bacteria (FeOB) at two mine drainage sites,
2) investigating the two mine drainage sites by identifying and measuring metal content in sediment and water samples by Microwave Plasma-Atomic Emission Spectroscopy (MP-AES),
3) identifying the influence of physiochemical properties on the bacterial communities between sample locations and concentration of metals.
There should be a shift in the FeOB community structure at AMD sites with increasing pH, from acid- and heavy metal-tolerant to neutrophilic FeOB that might be less metal tolerant.
Original Research Articles at FLC
See Dr. Lee's Google Scholar for previous publications prior to FLC.
‡**Lee, JS, Lowell, JL, Whitewater, K, Roane, TM, Miller, CS, Chan, AP, Sylvester, AW, Jackson, D and Hunter, LE. (2023) Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework. Molecular Ecology Resources.
https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13867
**Hinckley, JL, Bingman, MT, Lee, JS, Bradley, CP, and Cole, CA. (2022) Volatile Profile Survey of Five Apple Varieties Grown in Southwest Colorado from Juice to Finished, Dry-Hopped Cider. Journal of the American Society of Brewing Chemists.
https://www.tandfonline.com/doi/full/10.1080/03610470.2021.2013645
‡Network, T. G. D. S. C., Alcazar, R., Alvarez, M., Arnold, R., Ayalew, M., Best, L. G., ... & Xie, X. (2022). Diversifying the Genomic Data Science Research Community. arXiv preprint arXiv:2201.08443.
PDF: https://arxiv.org/pdf/2201.08443.pdf
‡Network, T. G. D. S. C., Alcazar, R., Alvarez, M., Arnold, R., Ayalew, M., Best, L. G., ... & Xie, X. (2022). Diversifying the Genomic Data Science Research Community. Genome Research. Open-access PDF .
**with FLC undergraduate students
‡ corresponding author
Research Students
- Mentee
- Project/Product
- DB
- 01/23-current Computational Analysis of Carboxyspermidine decarboxylase
- AL*
- 01/23-current GKM microbiome analysis (FLC FYRE funded)
- JD*
- 09/22-current GKM microbiome analysis (Pay it Forward funded)
- KB*
- 01/22-current RNA-Seq project with Dr. David Blake (URISE funded)
- JO
- 01/22-current GKM microbiome analysis (FLC FYRE funded)
- GP
- 05/22-12/22 Upper Animas microbiome analysis (BLaST funded)
- CS
- 05/22-09/22 CZI Scientific computing project (CZI funded)
- CC*
- 01/22-05/22 GKM microbiome analysis (RENAU funded)
- BB
- 01/22-05/22 GKM microbiome analysis (BLaST funded) (FLC graduate)
- JB*
- 09/21--05/22 DD-PCR project with Dr. Christie Chatterley (RENAU funded) (FLC graduate)
- KW*
- 05/21-12//22 GKM microbiome analysis (RENAU funded) (FLC graduate)
- SF*
- 05/21-09/06 GKM microbiome analysis (RENAU funded)
- HS*
- 05/21-09/06 GKM microbiome analysis (RENAU funded) (FLC graduate)
- MAA
- 01/20-05/21 Microbiome bioinformatics pipeline (FLC graduate; current PhD Student)
- EM*
- 01/20-12/20 Title III Research Grant Recipient (FLC graduate)
- KG
- 11/19-05/21 Dual High School-FLC Student (Current undergraduate)
- *Indigenous and/or Alaska Native
Summer 2021
Photo: For the first summer (due to COVID-19) Dr. Lee was able to host three summer research students for a 10-week research experience funded by RENAU. Students went out in the field to collect samples, returned to the lab to culture and isolate microbes, and extracted DNA to send out for 16S amplicon sequencing. Once isolates were grown up, students conducted a whole genome amplification to sequence DNA on the MinION sequencer.
Funding
HHMI’s Inclusive Excellence 3 (IE3) initiative - Program Director 2023-2024
Project Title: Increasing Capacity to Support Equitable and Inclusive Learning Environments for Introductory-level STEM Students across the LCC2 Learning Community
2022 Colorado Outdoor Equity Grant - Principal Investigator 2022-2024
Funding awarded to FLC: $25,000
Project Title: COEG FLC Outdoor Equity group
2021 Chan Zuckerberg Initiative Essential Open Source Software (EOSS) Diversity & Inclusion Grants
Co-wrote grant with Dr. Greg Caporaso (PI) Northern Arizona University
Funding awarded to FLC: $57,000
Project Title: EOSS-DI-0000000019 Engaging Native American Students in Scientific Computing with QIIME 2
2020 Biomedical Learning and Student Training (BLaST) program Equipment Proposal to purchase 24-CORE Mac Pro
Funding awarded: $11,928; written jointly with Dr. Jeff McFarlane