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

Our plain-English summary of Metagenomic investigation of the microbial diversity in a chrysotile asbestos mine pit pond, Lowell, Vermont, USA, by H.E. Driscoll, J.J. Vincent, E.L. English, et al (Genomics Data, 2016).

The study

• Authors: H.E. Driscoll, J.J. Vincent, E.L. English, E.D. Dolci
• Journal: Genomics Data
• Published: 2016;10:158-164
• Cited by: 3 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

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.

In plain English

This short data report described the microbes living in the flooded open-pit pond of the abandoned Vermont Asbestos Group chrysotile asbestos mine in Lowell, Vermont. It did not study people or health, and it reported no asbestos fiber measurements. On August 6 and 7, 2012, the authors pumped water from three depths (0.5 m, 3.5 m and 25 m) at three sites in the pond. They measured water conditions and sequenced the DNA in eight samples, because one 25 m sample yielded no DNA. The pond was alkaline. Average pH rose from 8.76 at the surface to 9.18 at 25 m, and average conductivity rose from 271.3 to 351.6 uS. The two upper layers had similar bacteria: mostly Actinobacteria (46% and 53% of reads), Proteobacteria (45% and 38%) and Bacteroidetes (7% in both). At 25 m, Proteobacteria made up 60% of reads and Actinobacteria 18%, and more phyla were found. The authors concluded that the microbial mix reflected the pond's physical and chemical layering. They also said that the many unidentified reads suggest novel proteins or organisms.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Environmental metagenomic survey (whole metagenome shotgun DNA sequencing of water samples), published as a data report
• Who was studied: Microbial communities in water from the Lowell mine pit pond at the abandoned Vermont Asbestos Group Mine, Vermont, USA. Samples came from three sites and three depths (0.5 m, 3.5 m, 25 m) on August 6 and 7, 2012. Nine samples were collected, but no DNA was recovered from sample 1-B, so eight were sequenced.
• Exposure: Not a human exposure study. The habitat was a flooded open-pit quarry next to tailings piles at an abandoned chrysotile asbestos mine. Water temperature, pH, dissolved oxygen, conductivity, light and metals were measured; no asbestos fiber measurements were reported.
• Main results:
  • The pond water was alkaline, and pH increased with depth: an average of 8.76 at the surface and 9.18 in the deepest layer (25 m).
  • Average conductivity was 271.3 uS at the surface and 351.6 uS at 25 m. The authors described this as higher ionic concentrations than expected in Vermont waters at this elevation.
  • Water temperature was 23.53 °C at the surface and 6.03 °C in the deepest layer, and there was no light below 10 m.
  • At 0.5 m and 3.5 m, the sequence reads were dominated by Actinobacteria (46% and 53% of reads, respectively), Proteobacteria (45% and 38%, respectively) and Bacteroidetes (7% in both).
  • At 25 m, nine phyla were identified across the two samples. Proteobacteria made up 60% of reads, Actinobacteria 18%, Planctomycetes 10%, Bacteroidetes 5% and Cyanobacteria 2.5%.
  • Compared with the 0.5 m and 3.5 m samples, the 25 m samples had a significantly greater relative abundance of Planctomycetes, Verrucomicrobia and Cyanobacteria (FDR corrected p-values of 7.98 × 10–6, 0.0002 and 0.0010). They had a significantly lower relative abundance of Actinobacteria (FDR corrected p-value of 0.007).
  • The 0.5 m and 3.5 m layers shared 11 taxa, while the 3.5 m and 25 m layers shared two.
  • 48.2% of quality-trimmed reads had no protein match in the reference database, and 27.2% of reads with protein matches could not be classified.
• The authors' conclusion: The authors concluded that the distribution of microbes reflected the pond's physical and chemical layering. They said the large share of unmatched or unclassified reads suggests novel proteins and/or organisms in this community.

Topics

Medical terms in this study, explained in our Lexicon: Chrysotile, Serpentine Group, Belvidere Mountain.

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