Novel Microbial Assemblages Dominate Weathered Sulfide-Bearing Rock from Copper-Nickel Deposits in the Duluth Complex, Minnesota, USA

Abstract

The Duluth Complex in northeastern Minnesota hosts economically significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfidebearing rock from the Duluth Complex generates moderately acidic leachate (pH 4 to 6). Microorganisms are important catalysts for metal sulfide oxidation and could influence the quality of water from mines in the Duluth Complex. Nevertheless, compared with that of extremely acidic environments, much less is known about the microbial ecology of moderately acidic sulfide-bearing mine waste, and so existing information may have little relevance to those microorganisms catalyzing oxidation reactions in the Duluth Complex. Here, we characterized the microbial communities in decade-long weathering experiments (kinetic tests) conducted on crushed rock and tailings from the Duluth Complex. Analyses of 16S rRNA genes and transcripts showed that differences among microbial communities correspond to pH, rock type, and experimental treatment. Moreover, microbial communities from the weathered Duluth Complex rock were dominated by taxa that are not typically associated with acidic mine waste. The most abundant operational taxonomic units (OTUs) were from the genera Meiothermus and Sulfuriferula, as well as from diverse clades of uncultivated Chloroflexi, Acidobacteria, and Betaproteobacteria. Specific taxa, including putative sulfur-oxidizing Sulfuriferula spp., appeared to be primarily associated with Duluth Complex rock, but not pyrite-bearing rocks subjected to the same experimental treatment. We discuss the implications of these results for the microbial ecology of moderately acidic mine waste with low sulfide content, as well as for kinetic testing of mine waste.IMPORTANCE Economic sulfide mineral deposits in the Duluth Complex may represent the largest undeveloped source of copper and nickel on Earth. Microorganisms are important catalysts for sulfide mineral oxidation, and research on extreme acidophiles has improved our ability to manage and remediate mine wastes. We found that the microbial assemblages associated with weathered rock from the Duluth Complex are dominated by organisms not widely associated with mine waste or mining-impacted environments, and we describe geochemical and experimental influences on community composition. This report will be a useful foundation for understanding the microbial biogeochemistry of moderately acidic mine waste from these and similar deposits.

An Improved hgcAB Primer Set and Direct High-Throughput Sequencing Expand Hg-Methylator Diversity in Nature

“…For environmental samples from the SERC salt marsh and the NH site in EFPC, and for select mock communities ( Supplementary Table S4 ), hgcAB sequence abundance and diversity were also evaluated by high-throughput amplicon-specific sequencing, using Illumina MiSeq 2 × 300 bp chemistry at the University of Minnesota Genomics Facility (UMGC). A two-step PCR amplified hgcAB from environmental and mock community gDNA by adapting published protocols ( Gohl et al, 2016 ; Jones et al, 2017 ). The modified hgcAB -specific primers included 5’ adaptor sequences (adaptor TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG with ORNL-HgcAB-uni-F; adaptor GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA G with ORNL-HgcAB-uni-R and ORNL-HgcAB-uni-32R).…”

An improvedhgcABprimer set and direct high-throughput sequencing expand Hg-methylator diversity in nature

“…For environmental samples from the SERC salt marsh and the NH site in EFPC, and for select mock communities (Table S4), hgcAB sequence abundance and diversity were also evaluated by high-throughput amplicon-specific sequencing, using Illumina MiSeq 2X300 bp chemistry at the University of Minnesota Genomics Facility (UMGC). A two-step PCR amplified hgcAB from environmental and mock community gDNA by adapting published protocols (Gohl et al, 2016;Jones et al, 2017). The modified hgcAB-specific primers included 5' adaptor sequences (adaptor TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG with ORNL-HgcAB-uni-F; adaptor GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA G with ORNL-HgcAB-uni-R and ORNL-HgcAB-uni-32R).…”

“…The modified hgcAB-specific primers included 5' adaptor sequences (adaptor TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG with ORNL-HgcAB-uni-F; adaptor GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA G with ORNL-HgcAB-uni-R and ORNL-HgcAB-uni-32R). Amplicon libraries were created by amplifying hgcAB with the modified primers for 30 or 35 cycles (Table S4) following the PCR protocol for hgcAB cloning described above as in Jones et al (2017). Illumina sequencing adaptors and dual indices were added at UMGC with a second amplification step (10 cycles, after diluting PCR products 1:100) (Gohl et al, 2016).…”

Microbial communities associated with phosphogenic sediments and phosphoclast‐associated DNA of the Benguela upwelling system

“…Data processing was performed using an in-house pipeline (Jones et al, 2017). Sickle (https://github.com/najoshi/sickle) was used to trim and filter raw sequences using a mean quality score of 30.…”