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Metagenomic investigation of the microbial diversity in a chrysotile asbestos mine pit pond, Lowell, Vermont, USA

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ABSTRACT

Here we report on a metagenomics investigation of the microbial diversity in a serpentine-hosted aquatic habitat created by chrysotile asbestos mining activity at the Vermont Asbestos Group (VAG) Mine in northern Vermont, USA. The now-abandoned VAG Mine on Belvidere Mountain in the towns of Eden and Lowell includes three open-pit quarries, a flooded pit, mill buildings, roads, and > 26 million metric tons of eroding mine waste that contribute alkaline mine drainage to the surrounding watershed. Metagenomes and water chemistry originated from aquatic samples taken at three depths (0.5 m, 3.5 m, and 25 m) along the water column at three distinct, offshore sites within the mine's flooded pit (near 44°46′00.7673″, − 72°31′36.2699″; UTM NAD 83 Zone 18 T 0695720 E, 4960030 N). Whole metagenome shotgun Illumina paired-end sequences were quality trimmed and analyzed based on a translated nucleotide search of NCBI-NR protein database and lowest common ancestor taxonomic assignments. Our results show strata within the pit pond water column can be distinguished by taxonomic composition and distribution, pH, temperature, conductivity, light intensity, and concentrations of dissolved oxygen. At the phylum level, metagenomes from 0.5 m and 3.5 m contained a similar distribution of taxa and were dominated by Actinobacteria (46% and 53% of reads, respectively), Proteobacteria (45% and 38%, respectively), and Bacteroidetes (7% in both). The metagenomes from 25 m showed a greater diversity of phyla and a different distribution of reads than the two upper strata: Proteobacteria (60%), Actinobacteria (18%), Planctomycetes, (10%), Bacteroidetes (5%) and Cyanobacteria (2.5%), Armatimonadetes (< 1%), Verrucomicrobia (< 1%), Firmicutes (< 1%), and Nitrospirae (< 1%). Raw metagenome sequence data from each sample reside in NCBI's Short Read Archive (SRA ID: SRP056095) and are accessible through NCBI BioProject PRJNA277916.

No MeSH data available.


Environmental parameters: A) average temperature, dissolved oxygen, and conductivity B) average pH (Abbreviations: m = meters, oC = degrees Celsius, μS = microsiemens, D.O. = dissolved oxygen).
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f0010: Environmental parameters: A) average temperature, dissolved oxygen, and conductivity B) average pH (Abbreviations: m = meters, oC = degrees Celsius, μS = microsiemens, D.O. = dissolved oxygen).

Mentions: Metagenomes were generated from samples taken at three depths along the water column at three distinct sites within the mine's pit pond. Environmental parameters of the epilimnion and metalimnion were notably different from the parameters of the hypolimnion. Marked differences were observed in pH, temperature, conductivity, light intensity, and concentrations of D.O. (Fig. 2, Supplementary Table ST1). The pit pond is alkaline, and in contrast to most freshwater lakes, pH increased with depth steadily rising from an average of 8.76 at the surface to 9.18 in the hypolimnion. Conductivity was high throughout the water table and increased with depth at all three sites. Average conductivity at the surface measured 271.3 uS increasing to 351.6 uS at 25 m indicating significantly higher ionic concentrations than expected in Vermont waters at this elevation (Vermont Department of Conservation, personal communication). The hypolimnion also presented greater extremes in temperature and light. Water temperature was nearly fourfold higher at the surface (23.53 °C) than in the hypolimnion (6.03 °C), and light was absent below 10 m. The steep thermocline revealed a narrow metalimnion. Oxygen levels remained near saturation throughout the water column and supersaturated in the thermocline. Heavy metal analysis of the water column revealed significant concentrations of Ni (26 5 μg/L), Fe (563 5 μg/L), and Mn (950 5 μg/L) in sample 1-B only. Levels of Ca, Mg, K, Na, Al, Fe, Mn, Cu, Zn and As were below 5 μg/L in all water samples (not shown).


Metagenomic investigation of the microbial diversity in a chrysotile asbestos mine pit pond, Lowell, Vermont, USA
Environmental parameters: A) average temperature, dissolved oxygen, and conductivity B) average pH (Abbreviations: m = meters, oC = degrees Celsius, μS = microsiemens, D.O. = dissolved oxygen).
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC5121135&req=5

f0010: Environmental parameters: A) average temperature, dissolved oxygen, and conductivity B) average pH (Abbreviations: m = meters, oC = degrees Celsius, μS = microsiemens, D.O. = dissolved oxygen).
Mentions: Metagenomes were generated from samples taken at three depths along the water column at three distinct sites within the mine's pit pond. Environmental parameters of the epilimnion and metalimnion were notably different from the parameters of the hypolimnion. Marked differences were observed in pH, temperature, conductivity, light intensity, and concentrations of D.O. (Fig. 2, Supplementary Table ST1). The pit pond is alkaline, and in contrast to most freshwater lakes, pH increased with depth steadily rising from an average of 8.76 at the surface to 9.18 in the hypolimnion. Conductivity was high throughout the water table and increased with depth at all three sites. Average conductivity at the surface measured 271.3 uS increasing to 351.6 uS at 25 m indicating significantly higher ionic concentrations than expected in Vermont waters at this elevation (Vermont Department of Conservation, personal communication). The hypolimnion also presented greater extremes in temperature and light. Water temperature was nearly fourfold higher at the surface (23.53 °C) than in the hypolimnion (6.03 °C), and light was absent below 10 m. The steep thermocline revealed a narrow metalimnion. Oxygen levels remained near saturation throughout the water column and supersaturated in the thermocline. Heavy metal analysis of the water column revealed significant concentrations of Ni (26 5 μg/L), Fe (563 5 μg/L), and Mn (950 5 μg/L) in sample 1-B only. Levels of Ca, Mg, K, Na, Al, Fe, Mn, Cu, Zn and As were below 5 μg/L in all water samples (not shown).

View Article: PubMed Central - PubMed

ABSTRACT

Here we report on a metagenomics investigation of the microbial diversity in a serpentine-hosted aquatic habitat created by chrysotile asbestos mining activity at the Vermont Asbestos Group (VAG) Mine in northern Vermont, USA. The now-abandoned VAG Mine on Belvidere Mountain in the towns of Eden and Lowell includes three open-pit quarries, a flooded pit, mill buildings, roads, and > 26 million metric tons of eroding mine waste that contribute alkaline mine drainage to the surrounding watershed. Metagenomes and water chemistry originated from aquatic samples taken at three depths (0.5 m, 3.5 m, and 25 m) along the water column at three distinct, offshore sites within the mine's flooded pit (near 44°46′00.7673″, − 72°31′36.2699″; UTM NAD 83 Zone 18 T 0695720 E, 4960030 N). Whole metagenome shotgun Illumina paired-end sequences were quality trimmed and analyzed based on a translated nucleotide search of NCBI-NR protein database and lowest common ancestor taxonomic assignments. Our results show strata within the pit pond water column can be distinguished by taxonomic composition and distribution, pH, temperature, conductivity, light intensity, and concentrations of dissolved oxygen. At the phylum level, metagenomes from 0.5 m and 3.5 m contained a similar distribution of taxa and were dominated by Actinobacteria (46% and 53% of reads, respectively), Proteobacteria (45% and 38%, respectively), and Bacteroidetes (7% in both). The metagenomes from 25 m showed a greater diversity of phyla and a different distribution of reads than the two upper strata: Proteobacteria (60%), Actinobacteria (18%), Planctomycetes, (10%), Bacteroidetes (5%) and Cyanobacteria (2.5%), Armatimonadetes (< 1%), Verrucomicrobia (< 1%), Firmicutes (< 1%), and Nitrospirae (< 1%). Raw metagenome sequence data from each sample reside in NCBI's Short Read Archive (SRA ID: SRP056095) and are accessible through NCBI BioProject PRJNA277916.

No MeSH data available.