Seasonal Ely Copper Mine Superfund site shotgun metagenomic and metatranscriptomic data analysis.

High throughput sequencing data collected from acid rock drainage (ARD) communities can reveal the active taxonomic and functional diversity of these extreme environments, which can be exploited for bioremediation, pharmaceutical, and industrial applications. Here, we report a seasonal comparison of a microbiome and transcriptome in Ely Brook (EB-90M), a confluence of clean water and upstream tributaries that drains the Ely Copper Mine Superfund site in Vershire, VT, USA. Nucleic acids were extracted from EB-90M water and sediment followed by shotgun sequencing using the Illumina NextSeq platform. Approximately 575,933 contigs with a total length of 1.54 Gbp were generated. Contigs of at least a size of 3264 (N50) or greater represented 50% of the sequences and the longest contig was 488,568 bp in length. Using Centrifuge against the NCBI "nt" database 141 phyla, including candidate phyla, were detected. Roughly 380,000 contigs were assembled and ∼1,000,000 DNA and ∼550,000 cDNA sequences were identified and functionally annotated using the Prokka pipeline. Most expressed KEGG-annotated microbial genes were involved in amino acid metabolism and several KEGG pathways were differentially expressed between seasons. Biosynthetic gene clusters involved in secondary metabolism as well as metal- and antibiotic-resistance genes were annotated, some of which were differentially expressed, colocalized, and coexpressed. These data can be used to show how ecological stimuli, such as seasonal variations and metal concentrations, affect the ARD microbiome and select taxa to produce novel natural products. The data reported herein is supporting information for the research article "Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site" by Giddings et al. [1].

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

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.

Long-term monitoring of waste-rock weathering at the Antamina mine, Peru.

The weathering of mine waste rock can cause release of metal-laden and acidic drainage that requires long-term and costly environmental management. To identify and quantify the geochemical processes and physical transport mechanisms controlling drainage quality, we monitored the weathering of five large-scale (20,000 t) instrumented waste-rock piles of variable and mixed-composition at the Antamina mine, Peru, in a decade-long monitoring program. Fine-grained, sulfidic waste rock with low-carbonate content exhibited high sulfide oxidation rates (>1 g S kg-1 waste rock yr-1) and within 7 years produced acidic (pH < 3) drainage with high Cu and Zn concentrations in the g L-1 range. In contrast, drainage from coarse, carbonate-rich waste rock remained neutral for >10 years and had significantly lower metal loads. Efficient metal retention (>99%) caused by sorption and secondary mineral formation of e.g., gypsum, Fe-(oxy)hydroxides, and Cu/Zn-hydroxysulfates enforced strong (temporary) controls on drainage quality. Furthermore, reactive waste-rock fractions, as small as 10% of total mass, dominated the overall drainage chemistry from the waste-rock piles through internal mixing. This study demonstrates that a reliable prediction of the timing and quality of waste-rock drainage on practice-relevant spatiotemporal scales requires a quantitative understanding of the prevailing in-situ porewater conditions, secondary mineralogy, and spatial distribution of reactive waste-rock fractions in composite piles.