Amplicon dataset of bacteria captured 1 m above the ground in two locations in Miers Valley (Antarctica).
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Bottos E, Woo A, Zawar-Reza P, Pointing S, Cary C (2018): Airborne Bacteria from Miers Valley, Antarctica. v1.2. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=airborne_bacteria_miers_antarctica&v=1.2
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Miers Valley, Antarctica
|Bounding Coordinates||South West [-78.114, 163.786], North East [-78.096, 163.787]|
16S ssu rRNA
|Formation Period||2009-12-11 2010-01-25|
Aerosol samples were collected by filtration onto 0.2-μm-pore-size polycarbonate filters by impaction using solar-powered pumps (SKC, 224-PCXR8, Eighty Four, PA, USA) mounted 1 m above the ground in each location. Filters inserted into cassette apparatus but not exposed to air flow were used as controls. All filters and cassettes were UV-sterilized and rinsed with 70 % alcohol before use. Sampling apparatus was deployed 1 m above the ground surrounded with a 2 mm gauze baffle on the Miers Valley Floor (78°05′.78S, 163°47′.25E, approx. 270 m) and Miers Valley Ridge (78°06′.83S, 163°47′.18E, approx. 550 m).
|Study Extent||Samples were collected from a continuous filtration period December 11, 2009 to January 25, 2010 (55 days), with an estimated sample volume of 75,000 l for each location.|
Method step description:
- Air sampling (see sampling description)
- Filters were stored at −20 °C during transit from Antarctica and until processed.
- Total DNA was extracted directly from the filters using the DNeasy Plant Mini Kit (Qiagen, CA, USA), after first washing with kit lysis buffer for 10 min. The remaining steps of the extraction were carried out according to the manufacturers instructions. Recovered DNA was quantified using NanoDrop™ (Thermo Scientific, Waltham, MA, USA).
- For each sample, PCR targeting the V5–V7 region of the 16S rRNA gene was completed in duplicate. Each 30 μl reaction contained 1× PrimeSTAR buffer, 0.2 mM dNTPs, 0.75 U PrimeSTAR HS DNA Polymerase (Takara Holdings, Kyoto, Japan), 0.4 μM of primers Tx9 (5′-GGATTAGAWACCCBGGTAGTC-3′) and 1391R (5′-GACGGGCRGTGWGTRCA-3′), and 5 μl of template DNA. Thermal cycling conditions consisted of 94 °C for 3 min; 30 cycles of 94 °C for 20 s, 52 °C for 20 s, and 72 °C for 45 s; and 72 °C for 3 min. All thermal cycling was completed on a Bio-Rad DNA Engine Peltier Thermal Cycler 200 (Bio-Rad, Hercules, CA, USA). Duplicate reactions were pooled, and amplicons were size-selected from agarose gels using a MO BIO Gel Extraction Kit (MO BIO Laboratories, Carlsbad, CA, USA). Gel extracted products were cleaned using an Agencourt AMPure XP system (Beckman Coulter, Brea, CA, USA) and quantified using a Qubit dsDNA HS Assay Kit and Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA).
- To prepare the amplicons for sequencing, a second round of PCR was completed in triplicate. PCR reactions were prepared as outlined above, but using 10 ng of purified amplicon as the template and primers MIDX-Tx9F (5′-CCATCTCATCCCTGCGTGTCTCCGACTCAG-MID-GGATTAGAWACCCBGGTAGTC-3′) and BacB_1391R (5′-CCTATCCCCTGTGTGCCTTGGCAGTCTCAG-GACGGGCRGTGWGTRCA-3′), adapted for one-way reads with unique MID identifiers for each sample. Thermal cycling conditions were as outlined above, but reduced to 13 cycles. Triplicate products were pooled, gel-extracted, cleaned, and quantified as outlined above, before quantification of amplifiable molecules using a KAPA Library Quantification Kit for Roche 454 Titanium/Universal (Kapa Biosystems, Woburn, MA, USA) on a Corbett Rotor-Gene 6000 real-time thermal cycler (Life Technologies). Amplicons were sequenced using the GS Junior Titanium emPCR Kit (Lib-L), the GS Junior Titanium Sequencing Kit, PicoTitrePlate Kit, and GS Junior System (Roche 454 Life Sciences, Branford, CT, USA) at The University of Waikato DNA Sequencing Facility.
- Bottos, E. M., Woo, A. C., Zawar-Reza, P., Pointing, S. B., & Cary, S. C. (2014). Airborne bacterial populations above desert soils of the McMurdo Dry Valleys, Antarctica. Microbial ecology, 67(1), 120-128.