Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site.

Lesley-Ann Giddings,Holly Peterson,Kevin Kunstman,Kieran Bhave,George Chlipala,Katherine Morillo,Mark Maienschein-Cline,Stefan Green,Heather Driscoll

doi:10.1371/journal.pone.0237599

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.

Highlights

During the 19th and 20th centuries, the mining industry exploited Vermont’s copper belt in Orange County (Fig 1), after which several copper mines were abandoned and left to accumulate acid rock drainage (ARD) [1]
We identified six biosynthetic gene clusters (BGCs) that colocalized with BacMet-annotated Metal resistance genes (MRGs) on contigs (Fig 7) [42]
The present study is the first seasonal characterization of a metagenome and metatranscriptome at the Ely Copper Mine Superfund site, providing insight into the microbial community as well as the genes and metabolites they use to adapt to ARD in Ely Brook

Summary

Introduction

During the 19th and 20th centuries, the mining industry exploited Vermont’s copper belt in Orange County (Fig 1), after which several copper mines were abandoned and left to accumulate acid rock drainage (ARD) [1]. ARD is the outflow of acidic water from mining regions containing metal-sulfide-rich rocks. Resources and Lake Studies Center 104b grant (subaward award G16AP00087 for L.-A.G and K.B; https://www.uvm.edu/rsenr/vtwatercenter); the Institutional Development Award from the National Institute of General Medical Sciences (NIGMS) of the National Institutes of Health (NIH) Nigms.nih.gov/Research/DRCB/IDeA/); and the National Center for Advancing Translational Sciences The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

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Conclusion