Lee, Shu-An; Low, Yee-Lynn; Adhikari, Atin; Wang, Wei-Kuang; Liang, Chih-Ming; Chang, Li-Te; Tsai, Chuen-Jinn (2025): Viability, culturability and DNA loss rate obtained for collected bacteria after filter and impingement-based sampling [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.974989
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Published: 2025-07-03 • DOI registered: 2025-07-03
Abstract:
Viability, culturability and DNA loss rate were obtained for collected bacteria after filter and impingement-based sampling. The sample extracts were spread on TSA plates. The inoculated TSA plates were incubated at 37℃ for 1 day, and colony forming units (CFUs) were counted for culturable fungi. Dual-fluorescence method for accurate viability analysis of test samples was performed. With an appropriate mixture of AO/PI, total cells were stained with AO whereas damaged cells were stained with PI. An epifluorescence microscope was used to count the test sample's bacterial cells on the filter at a magnification of 400x. The culturability is determined by percentage of CCFU in CAO while percentage of (CAO-CPI) in CAO is for viability. The qPCR was performed on LightCycler 480 for DNA quantification with universal primers of DG74 (5'-AGGAGGTGATCCAACCGCA-3') and RW01 (5'-AACTGGAGGAAGGTGGGGAT-3') targeting on a conserved 370-bp region of 16S rRNA gene. The DNA loss rate was determined by the ratio of DNA concentrations in the supernatant sample to total DNA concentrations in the entire sample (supernatant sample + pellet sample).
Keyword(s):
Supplement to:
Lee, Shu-An; Low, Yee-Lynn; Adhikari, Atin; Wang, Wei-Kuang; Liang, Chih-Ming; Chang, Li-Te; Tsai, Chuen-Jinn (2025): Effect of Sampling Time and Sampling Media During Filter and Liquid Impingement-Based Sampling on Collected Bacterial Viability, Culturability, and DNA Concentrations. Aerosol and Air Quality Research, 25(6), 28, https://doi.org/10.1007/s44408-025-00021-1
Funding:
National Science and Technology Council, Taiwan, grant/award no. MOST108-2221-E-035-055: Effect of Meteorological and Environmental Factors on DNA Contents and Diversity of Airborne Fungi Collected by Sampler
Coverage:
Latitude: 24.179110 * Longitude: 120.646700
Date/Time Start: 2021-02-01T08:00:00 * Date/Time End: 2021-08-31T17:00:00
Event(s):
Comment:
Microscopic method: (1) Bacterial cells in the samples were counted using a hemocytometer and light microscope. (2) AO/PI-stained cells were counted using an epifluorescence microscope.
Cultivation method: Culturable bacterial cells were cultivated on TSA agar using the standard spread plate technique.
Sampling method: The Button Sampler and BioSampler were employed as filter-based and liquid-impingement-based samplers, respectively.
DNA extraction: DNA in bacterial cells was extracted using QIAmp DNA Mini Kit.
DNA analysis: DNA analysis was performed using qPCR with the LightCycler 480.
Parameter(s):
| # | Name | Short Name | Unit | Principal Investigator | Method/Device | Comment |
|---|---|---|---|---|---|---|
| 1 | Type of study | Study type | Lee, Shu-An | |||
| 2 | Sample method | Sample method | Lee, Shu-An | DI= deionized water, TM=Tween 80 mixtures, PBS= phosphate buffered saline solution, PC= polycarbonate membrane filter, MCE= mixed cellulose ester membrane filter | ||
| 3 | Sampling time | Sampling time | min | Lee, Shu-An | #0 = bacterial suspension before addition on the membrane filter | |
| 4 | Viability | Viab | % | Lee, Shu-An | ||
| 5 | Culturability | Culturability | % | Lee, Shu-An | ||
| 6 | DNA loss rate | DNA loss rate | % | Lee, Shu-An |
License:
Creative Commons Attribution 4.0 International (CC-BY-4.0)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
413 data points