scholarly journals Bioinformatics Analysis of Microbial Abundance and Diversity in Acid Mine Drainage from the Solomon Mine Near Creede, Colorado

Fine Focus ◽  
2018 ◽  
Vol 4 (1) ◽  
pp. 41-65
Author(s):  
Ryan K. Miller ◽  
Robert M. Kirkham ◽  
Adam J. Kleinschmit
Keyword(s):  
Acid Mine Drainage ◽  
Microbial Communities ◽  
Constructed Wetland ◽  
Beta Diversity ◽  
Bioinformatics Analysis ◽  
Mine Drainage ◽  
Statistical Testing ◽  
Acid Mine ◽  
Wetland System ◽  
Wetland Cell

This study focused on characterizing the phylotypic composition of acid mine drainage (AMD) communities associated with the Solomon Mine near Creede, Colorado, and its relative diversity compared to microbial communities found in the East Willow Creek (EWC) watershed. AMD from the Solomon Mine adit flows into an existing passive bioremediation wetland system located next to the Solomon Mine adit that currently is ineffective and is under consideration for renovation. We are interested in gaining an understanding of the baseline microbial communities present in AMD/EWC and to monitor them during future wetland renovation. Prokaryotic community profiling was approached using SSU 16S rRNA marker gene amplification coupled with next generation sequencing. Bioinformatics analysis included raw read preprocessing, data visualization, and statistical testing using a combination of USEARCH and QIIME-based scripts. A pH and conductivity gradient were observed for water moving through the currently inefficient wetland system at the Solomon Mine. The EWC microbiomes had statistically significant higher alpha diversity compared to the AMD microbiomes. Beta diversity analysis parsed the sample locations into statistically significant groups including core AMD microbiomes, the wetland Cell 3 microbiome, and EWC microbiomes using multidimensional scaling. Taxa driving beta diversity included the phylum Proteobacteria for the core AMD microbiomes, the phyla Firmicutes and Chloroflexi for the constructed wetland Cell 3, and the phyla Bacteroidetes and Verrucomicrobia for EWC. Our data suggests that the microbial community in constructed wetland Cell 3 is likely where limited sulfate reduction activity is operating at low capacity, which will be further investigated via shotgun metagenomic analysis.

scholarly journals Comparison of Acid Mine Drainage Microbial Communities in Physically and Geochemically Distinct Ecosystems

2000 ◽  
Vol 66 (11) ◽  
pp. 4962-4971 ◽  
Author(s):  
Philip L. Bond ◽  
Greg K. Druschel ◽  
Jillian F. Banfield
Keyword(s):  
Acid Mine Drainage ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Acid Leaching ◽  
Massive Sulfide ◽  
Molecular Data ◽  
Oligonucleotide Probes ◽  
Acid Mine ◽  
Ore Body ◽  
A Site

ABSTRACT This study presents population analyses of microbial communities inhabiting a site of extreme acid mine drainage (AMD) production. The site is the inactive underground Richmond mine at Iron Mountain, Calif., where the weathering of a massive sulfide ore body (mostly pyrite) produces solutions with pHs of ∼0.5 to ∼1.0. Here we used a suite of oligonucleotide probes, designed from molecular data recently acquired from the site, to analyze a number of microbial environments by fluorescent in situ hybridization. Microbial-community analyses were correlated with geochemical and mineralogical data from those environments. The environments investigated were within the ore body and thus at the site of pyrite dissolution, as opposed to environments that occur downstream of the dissolution. Few organism types, as defined by the specificities of the oligonucleotide probes, dominated the microbial communities. The majority of the dominant organisms detected were newly discovered or organisms only recently associated with acid-leaching environments. “Ferroplasma” spp. were detected in many of the communities and were particularly dominant in environments of lowest pH and highest ionic strength.Leptospirillum spp. were also detected in many slime and pyrite-dominated environments. In samples of an unusual subaerial slime, a new uncultured Leptospirillum sp. dominated.Sulfobacillus spp. were detected as a prominent inhabitant in warmer (∼43°C) environments. The information gathered here is critical for determining organisms important to AMD production at Iron Mountain and for directing future studies of this process. The findings presented here also have relevance to the microbiology of industrial bioleaching and to the understanding of geochemical iron and sulfur cycles.

scholarly journals Metagenome assembled genomes of novel taxa from an acid mine drainage environment

2021 ◽  
Author(s):  
Christen L. Grettenberger ◽  
Trinity L. Hamilton
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Biogeochemical Cycling ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Carbon And Nitrogen ◽  
Acid Mine

Acid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from 16S rRNA gene amplicons but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, KY, USA. The genomes span 11 bacterial phyla and one Archaea and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies. IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements like carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.

Comparative Analyses of the Microbial Communities Inhabiting Coal Mining Waste Dump and an Adjacent Acid Mine Drainage Creek

2019 ◽  
Vol 78 (3) ◽  
pp. 651-664 ◽  
Author(s):  
Weimin Sun ◽  
Enzong Xiao ◽  
Valdis Krumins ◽  
Yiran Dong ◽  
Baoqin Li ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Microbial Communities ◽  
Coal Mining ◽  
Mine Drainage ◽  
Mining Waste ◽  
Waste Dump ◽  
Comparative Analyses ◽  
Acid Mine

scholarly journals Efficient Low-pH Iron Removal by a Microbial Iron Oxide Mound Ecosystem at Scalp Level Run

2017 ◽  
Vol 83 (7) ◽  
Author(s):  
Christen L. Grettenberger ◽  
Alexandra R. Pearce ◽  
Kyle J. Bibby ◽  
Daniel S. Jones ◽  
William D. Burgos ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Iron Oxidation ◽  
Cost Effective ◽  
Low Ph ◽  
Content Type ◽  
Oxidation Rates ◽  
Acid Mine

ABSTRACT Acid mine drainage (AMD) is a major environmental problem affecting tens of thousands of kilometers of waterways worldwide. Passive bioremediation of AMD relies on microbial communities to oxidize and remove iron from the system; however, iron oxidation rates in AMD environments are highly variable among sites. At Scalp Level Run (Cambria County, PA), first-order iron oxidation rates are 10 times greater than at other coal-associated iron mounds in the Appalachians. We examined the bacterial community at Scalp Level Run to determine whether a unique community is responsible for the rapid iron oxidation rate. Despite strong geochemical gradients, including a >10-fold change in the concentration of ferrous iron from 57.3 mg/liter at the emergence to 2.5 mg/liter at the base of the coal tailings pile, the bacterial community composition was nearly constant with distance from the spring outflow. Scalp Level Run contains many of the same taxa present in other AMD sites, but the community is dominated by two strains of Ferrovum myxofaciens, a species that is associated with high rates of Fe(II) oxidation in laboratory studies. IMPORTANCE Acid mine drainage pollutes more than 19,300 km of rivers and streams and 72,000 ha of lakes worldwide. Remediation is frequently ineffective and costly, upwards of $100 billion globally and nearly $5 billion in Pennsylvania alone. Microbial Fe(II) oxidation is more efficient than abiotic Fe(II) oxidation at low pH (P. C. Singer and W. Stumm, Science 167:1121–1123, 1970, https://doi.org/10.1126/science.167.3921.1121 ). Therefore, AMD bioremediation could harness microbial Fe(II) oxidation to fuel more-cost-effective treatments. Advances will require a deeper understanding of the ecology of Fe(II)-oxidizing microbial communities and the factors that control their distribution and rates of Fe(II) oxidation. We investigated bacterial communities that inhabit an AMD site with rapid Fe(II) oxidation and found that they were dominated by two operational taxonomic units (OTUs) of Ferrovum myxofaciens, a taxon associated with high laboratory rates of iron oxidation. This research represents a step forward in identifying taxa that can be used to enhance cost-effective AMD bioremediation.

Metal Removal Efficiencies from Acid Mine Drainage in the Big Five Constructed Wetland.

1990 ◽  
Vol 1990 (2) ◽  
pp. 417-424 ◽  
Author(s):  
Thomas R. Wildman ◽  
Steven R Machemer ◽  
Ronald W. Klusman ◽  
Ronald, R. Cohen ◽  
Peter. Lemke
Keyword(s):  
Acid Mine Drainage ◽  
Big Five ◽  
Constructed Wetland ◽  
Mine Drainage ◽  
Metal Removal ◽  
Acid Mine ◽  
Removal Efficiencies
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