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DNA Sampling: Readying our colonies

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DNA SAMPLING 7 Who is living inside coal mines and AMD sites? image_header 2024-08-05T11:07:52+00:00
Coal mines are not dead-zones. They can harbor communities of endoliths (literally "inside-rocks"). These can include bacteria, archaea, fungi, slime molds, and microscopic eukaryotes. Acid Mine Drainage (AMD) systems are also home to thriving ecologies, even though most macroscopic life has been smothered by the precipitates or harmed by the acid or metals.

To demonstrate the thriving "life-y-ness" of these apparently-barren industrial landscapes, the Summer 2024 STEMLA Fellows conducted DNA analyses of swabs from the No. 9 Coal Mine in Coaldale, PA, and from the Silver Creek AMD site in New Philadelphia, PA. (Huge thanks to Jen Skirkanich for leading these analyses!)

The Fellows took DNA samples inside the mine and AMD site, and swabbed them onto agar plates to encourage any microbes to grow. We put the resulting microbial colonies through PCR analysis and gel electrophoresis to isolate the 16s rRNA gene sequence. We then sent our resulting bits of genetic material for DNA sequencing, and matched the resulting sequences to known organisms in the National Library of Medicine's BLAST database.

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Here is who we found in the No. 9 Coal Mine:
- Pseudomonas: a genus of bacteria with several hundred species. These are widely distributed in soil and water.
- Priestia aryabhattai: a bacterium who doesn't mind growing at low temperatures. Wide distribution in soils, and high tolerance for arsenic (which can be present at high levels in coal mines, due to the presence of arsenopyrite)
- Bacillus mycoides: a bacterium who doesn't mind growing at low temperatures, and has a wide distribution. It tends to grow in colonies that look like little clumps of hair, which is unusual.
- Pantoea agglomerans: another wide-spread bacterium.
Here is who we found at the AMD site:
- Pseudomonas: a genus of bacteria with several hundred species. These are widely distributed in soil and water.
- Bacillus subtilis: a widespread bacterium known to be able to withstand extreme environmental conditions.
- Pantoea ananatis: a bacterium
- Lactobacillus iners: a bacterium that prefers to grow without oxygen
None of these are particularly surprising to find, but their presence demonstrates that these industrially-disturbed areas still have thriving microbial ecologies, even when we can't see them!