Characterization of the microbial acid mine drainage microbial community using culturing and direct sequencing techniques

• Published in: Journal of microbiological methods Vol. 93; no. 2; pp. 108 - 115
• Main Authors: Auld, Ryan R., Myre, Maxine, Mykytczuk, Nadia C.S., Leduc, Leo G., Merritt, Thomas J.S.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2013
• Subjects: 16S rRNA; acid mine drainage; Acidiphilium; Acidithiobacillus; AMD; Bacteria - classification; Bacteria - genetics; Bacteria - growth & development; Bacteria - isolation & purification; bacterial communities; Bacteriological Techniques - methods; biosphere; Biota; Cluster Analysis; community structure; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; economic impact; Environmental Microbiology; genes; genetic markers; Industrial Microbiology; Legionella; Microbial diversity; mine tailings; minerals; mining; Molecular Sequence Data; nucleotide sequences; oxidation; Phylogeny; Rare biosphere; ribosomal RNA; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA; AMD; Microbial diversity; 16S rRNA; Rare biosphere; Legionella
• ISSN: 0167-7012; 1872-8359
• DOI: 10.1016/j.mimet.2013.01.023

We characterized the bacterial community from an AMD tailings pond using both classical culturing and modern direct sequencing techniques and compared the two methods. Acid mine drainage (AMD) is produced by the environmental and microbial oxidation of minerals dissolved from mining waste. Surprisingly, we know little about the microbial communities associated with AMD, despite the fundamental ecological roles of these organisms and large-scale economic impact of these waste sites. AMD microbial communities have classically been characterized by laboratory culturing-based techniques and more recently by direct sequencing of marker gene sequences, primarily the 16S rRNA gene. In our comparison of the techniques, we find that their results are complementary, overall indicating very similar community structure with similar dominant species, but with each method identifying some species that were missed by the other. We were able to culture the majority of species that our direct sequencing results indicated were present, primarily species within the Acidithiobacillus and Acidiphilium genera, although estimates of relative species abundance were only obtained from direct sequencing. Interestingly, our culture-based methods recovered four species that had been overlooked from our sequencing results because of the rarity of the marker gene sequences, likely members of the rare biosphere. Further, direct sequencing indicated that a single genus, completely missed in our culture-based study, Legionella, was a dominant member of the microbial community. Our results suggest that while either method does a reasonable job of identifying the dominant members of the AMD microbial community, together the methods combine to give a more complete picture of the true diversity of this environment. •Characterization of AMD microbial community•A comparison of culturing and direct 16S rRNA sequencing techniques•17 distinct bacterial isolates were cultured and identified.•16S rRNA indicates Acidithiobacillus, Legionella, and Acidiphilium are predominant.•4 direct sequencing “rare” species were confirmed by culturing techniques.