Characterization of an Acid Rock Drainage Microbiome and Transcriptome at the Ely Copper Mine Superfund Site

Authors

Lesley Ann Giddings, Middlebury CollegeFollow
George Chlipala, University of Illinois at Chicago
Kevin Kunstman, University of Illinois at Chicago
Stefan Green, University of Illinois at Chicago
Katherine Morillo, Middlebury College
Kieran Bhave, Middlebury College
Holly Peterson, Guilford College
Heather Driscoll, Norwich University
Mark Maienschein-Cline, University of Illinois at Chicago

Document Type

Article

Publication Date

8-1-2020

Publication Title

PLoS ONE

Abstract

The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI “nt” database, ~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal- (133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.

Volume

15

Issue

8 August

DOI

10.1371/journal.pone.0237599

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Rights

© 2020 Giddings et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Comments

Archived as published.

Recommended Citation

Giddings, Lesley Ann; Chlipala, George; Kunstman, Kevin; Green, Stefan; Morillo, Katherine; Bhave, Kieran; Peterson, Holly; Driscoll, Heather; and Maienschein-Cline, Mark, "Characterization of an Acid Rock Drainage Microbiome and Transcriptome at the Ely Copper Mine Superfund Site" (2020). Chemistry: Faculty Publications, Smith College, Northampton, MA.
https://scholarworks.smith.edu/chm_facpubs/55