Community Composition of Nitrite Reductase Gene Sequences in an Acid Mine Drainage Environment

  • Ben R. Wise
  • Timberley M. Roane
  • Annika C. MosierEmail author
Environmental Microbiology


Denitrifying microbial communities play a central role in the nitrogen cycle, contribute to greenhouse gas production, and provide ecosystem services through the mitigation of nitrogen pollution. The impacts of human-induced acid mine drainage (AMD) and naturally occurring acid rock drainage (ARD), both characterized by low pH and high metal concentrations, on denitrifying microbial communities is not well understood. This study examined denitrifying microbes within sediments impacted by acidic and metal-rich AMD or ARD in the Iron Springs Mining District (10 sites across four regions over four time points) located in Southwest Colorado, USA. Denitrification functional gene sequences (nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.5 and metals > 2 mg/L (including aluminum, iron, manganese, strontium, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The overall community structure for nirK and nirS genes was correlated to conductivity and calcium (respectively), which may suggest that conductivity may play an important role in shaping the distribution of nirK- and nirS-type denitrifiers. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD or ARD and provide a foundation for future research to understand the rates and physiology of denitrifying organisms in these systems.


Denitrification Acid mine drainage Nitrite reductase Metals pH 



We thank Joshua Sackett, Bhargavi Ramanathan, and Ashley Joslin for assistance with sample collection and DNA extraction. We thank Robert Edgar, Sladjana Subotic, Adrienne Narrowe, Andrew Boddicker, and Bhargavi Ramanathan for guidance on bioinformatic data analyses. Portions of this manuscript were previously published and copyrighted as a part of the University of Colorado Denver Master’s thesis submission (BW, 2017). This publication was made possible through data from the Iron Springs Project, which was collected and analyzed by the US Environmental Protection Agency, and through funding provided by the US Department of Agriculture, Forest Service (to TR), and by the University of Colorado, Denver (to AM). USDA is an equal opportunity employer, provider, and lender.

Supplementary material

248_2019_1420_MOESM1_ESM.pdf (873 kb)
ESM 1 (PDF 873 kb)
248_2019_1420_MOESM2_ESM.xlsx (587 kb)
ESM 2 (XLSX 587 kb)


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Integrative BiologyUniversity of Colorado DenverDenverUSA

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