Metagenome-Assembled Genomes of Novel Taxa from an Acid Mine Drainage Environment

Christen L. Grettenberger, Trinity L. Hamilton

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


Acid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from 16S rRNA gene amplicons, but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome-assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, Kentucky, USA. The genomes span 11 bacterial phyla and one archaeal phylum and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies. IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements such as carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome-assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies, including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.

Original languageEnglish (US)
Pages (from-to)1-17
Number of pages17
JournalApplied and environmental microbiology
Issue number17
StatePublished - Aug 2021

Bibliographical note

Funding Information:
We are grateful to the staff of the National Forest Service and Daniel Boone National Forest, especially Margueritte Wilson and Claudia Cotton, for the advice and insight regarding mine locations. We thank A. Gangidine, M. Berberich, R. Jain, and C. Schuler for assistance in field sampling and processing samples in the laboratory. We thank Eric Kees for assistance with MAG analyses and Clara Chan and Sean McAllister for sharing their alignment and trees for Cyc2 sequences. We acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported within this paper. C.L.G and T.L.H designed the study, completed the analyses, and wrote the paper. We declare no competing financial interests.

Publisher Copyright:
Copyright © 2021 Grettenberger and Hamilton. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.


  • AMD
  • MAG
  • acid mine drainage
  • biogeochemical cycling
  • bioremediation
  • iron
  • metagenome
  • metagenome-assembled genome
  • Biodegradation, Environmental
  • Bacteria/classification
  • Oxidation-Reduction
  • Acids/metabolism
  • Waste Water/analysis
  • Phylogeny
  • Archaea/classification
  • Mining
  • Microbiota
  • Metagenome

PubMed: MeSH publication types

  • Journal Article


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