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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

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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):
culturability; DNA loss; Escherichia coli; filter; Laboratory experiment; liquid impingement; viability
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):
FengChiaUni_bacteria_exp * Latitude: 24.179110 * Longitude: 120.646700 * Date/Time Start: 2021-02-01T08:00:00 * Date/Time End: 2021-08-31T17:00:00 * Method/Device: Experiment (EXP)
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):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1 Type of studyStudy typeLee, Shu-An
2 Sample methodSample methodLee, Shu-AnDI= deionized water, TM=Tween 80 mixtures, PBS= phosphate buffered saline solution, PC= polycarbonate membrane filter, MCE= mixed cellulose ester membrane filter
3 Sampling timeSampling timeminLee, Shu-An#0 = bacterial suspension before addition on the membrane filter
4 ViabilityViab%Lee, Shu-An
5 CulturabilityCulturability%Lee, Shu-An
6 DNA loss rateDNA 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

Data

Download dataset as tab-delimited text — use the following character encoding:

1 
Study type		2 
Sample method		3 
Sampling time [min]		4 
Viab [%]		5 
Culturability [%]		6 
DNA loss rate [%]
Laboratory experimentDI088.4156.180.36
Laboratory experimentDI090.0444.05
Laboratory experimentDI089.2648.130.26
Laboratory experimentDI1587.7745.030.81
Laboratory experimentDI1590.7943.921.85
Laboratory experimentDI1590.3046.770.92
Laboratory experimentDI3086.4842.523.69
Laboratory experimentDI3089.2136.572.95
Laboratory experimentDI3089.1245.243.66
Laboratory experimentDI6084.8330.586.23
Laboratory experimentDI6088.3624.576.04
Laboratory experimentDI6085.1436.6617.26
Laboratory experimentDI12080.3720.9724.58
Laboratory experimentDI12083.2720.0158.75
Laboratory experimentDI12078.8629.9946.66
Laboratory experimentTM097.7273.375.34
Laboratory experimentTM094.6075.213.84
Laboratory experimentTM096.1873.637.99
Laboratory experimentTM6098.2373.8531.28
Laboratory experimentTM6092.1973.3917.54
Laboratory experimentTM6096.7072.2840.75
Laboratory experimentTM12094.5669.9426.50
Laboratory experimentTM12087.4673.2736.10
Laboratory experimentTM12087.7265.7046.21
Laboratory experimentPBS089.4562.4928.01
Laboratory experimentPBS089.0660.1222.59
Laboratory experimentPBS087.3756.0525.39
Laboratory experimentPBS6038.9114.7945.61
Laboratory experimentPBS6032.2312.4848.72
Laboratory experimentPBS6038.2411.4970.48
Laboratory experimentPBS12011.558.7987.98
Laboratory experimentPBS12018.733.0583.19
Laboratory experimentPBS12014.476.0074.20
Laboratory experimentPC#089.9147.641.38
Laboratory experimentPC#088.2845.010.99
Laboratory experimentPC#089.3045.691.57
Laboratory experimentPC052.1333.0564.59
Laboratory experimentPC046.4730.1547.74
Laboratory experimentPC046.4133.3368.96
Laboratory experimentPC1517.840.0161.21
Laboratory experimentPC1510.450.0368.85
Laboratory experimentPC156.810.0149.52
Laboratory experimentPC301.090.0077.91
Laboratory experimentPC300.240.0257.22
Laboratory experimentPC300.020.0048.13
Laboratory experimentPC600.020.0053.82
Laboratory experimentPC600.070.0063.99
Laboratory experimentPC600.020.0071.58
Laboratory experimentPC1200.050.0084.10
Laboratory experimentPC1200.040.0055.84
Laboratory experimentPC1200.040.0047.64
Laboratory experimentMCE#092.3051.860.99
Laboratory experimentMCE#092.0255.030.77
Laboratory experimentMCE#092.7557.131.63
Laboratory experimentMCE091.6551.846.14
Laboratory experimentMCE091.5856.034.62
Laboratory experimentMCE093.8156.363.69
Laboratory experimentMCE1576.651.2330.80
Laboratory experimentMCE1563.961.2724.20
Laboratory experimentMCE1566.971.0813.39
Laboratory experimentMCE3069.491.1028.26
Laboratory experimentMCE3056.410.9628.13
Laboratory experimentMCE3063.310.9740.90
Laboratory experimentMCE6012.540.3144.89
Laboratory experimentMCE6015.770.3132.15
Laboratory experimentMCE6012.330.3013.96
Laboratory experimentMCE1204.160.2659.42
Laboratory experimentMCE1200.530.0860.41
Laboratory experimentMCE1203.540.1163.64